From owner-biophysics@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!news.uoregon.edu!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Verification of the second law (reply to Bryant Fujimoto) Date: 2 Dec 1997 06:58:29 GMT Organization: University of Washington Lines: 141 Distribution: bionet Message-ID: <660bil$8ul$1@nntp3.u.washington.edu> References: <65p1ju$7ke@mserv1.dl.ac.uk> NNTP-Posting-Host: homer22.u.washington.edu X-Trace: nntp3.u.washington.edu 881045909 9173 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant, > I read very carefully your last post and found it quite self-consistent, >so I see no reason to comment on each item. Yes I agree that thermodynamics >works, but only within a certain paradigm. In the same way the concept that >heat is a substance (caloric) did work for quite a lot of time until the >new paradigm (the law of conservation of energy) emerged. > Let us accept for the moment that delta G is the right measure of the >work a chemical system does, under certain conditions, on another system. >But let us also consider an alternative, and compare eventually the two >interpretations. > Let the reaction > ATP = ADP + P /1/ >drive another reaction, e.g. B = C, isothermally and isobarically: > ATP + B = ADP + P + C /2/ >As one mole ATP is used up in the reaction, the energy of the system >ATP-ADP-P dereases by 20 KJ/mole (since the enthalpy of ATP hydrolysis >is -20 KJ/mole). Let us also assume that the enthalpy of /2/ is shown >experimentally to be -10 KJ/mole. This leads to the following quite >simple conclusion.If one mole ATP had been just hydrolysed (without >coupling), 20 KJ heat would have been released. Now, in the coupled >reaction /2/, only 10 KJ heat are released. Therefore, the other 10 KJ >energy coming from the ATP-ADP-P system have been transfered to the >B-C system and have increased its energy. We may call this "energy accepted >by the B-C system" (not "work done on the B-C system" since this last concept >is reserved for delta G): > E = (delta H)o - (delta H)c /3/ >where (delta H)o is the enthalpy of the driving reaction (ATP = ADP + P) >and (delta H)c is the enthalpy of the coupled reaction /2/. > Note how useful the relation /3/ is. First, it defines a valuable >quantity - the energy accepted and stored by a chemical system. If, for >instance, B = C is some biosynthesis, /3/ gives the energy content of >the respective structure acquired during the process. Second, /3/ is >concentration-independent so far as both enthalpies are independent. >Third, the experimental determination of /3/ is extremely easy. >Let us now see what the delta G concept says about the same coupled >reaction /2/. It says that, when /2/ is close to equilibrium, the work >done by the ATP-ADP-P system on the B-C system is > W = -(delta Go + RTln((ADP)(P)/(ATP))) /4/ >where delta Go is the standard free energy of the reaction ATP = ADP + P. >Note that E and W are independent. I spent a lot of effort in trying to >show that they are incompatible, but failed. They are just independent - >two different worlds - we are to choose the more cosy one. So let me >describe three possible cases. In all of them the reactions /2/ are CLOSE >TO EQUILIBRIUM, THE ENTHALPIES ARE THE SAME AND ONLY THE DELTA G VALUES >OF THE ATP-ADP-P SYSTEM DIFFER. >1. E = 10 KJ/mole, i.e. the system B-C accepts 10 KJ/mole energy. However >delta G for the ATP system is -15 KJ/mole, i.e. the ATP system does >15 KJ/mole work on the B-C system (W = 15 KJ/mole). >2. E = 10 KJ/mole, i.e. the system B-C accepts 10 KJ/mole energy. However >delta G for the ATP system is -5 KJ/mole, i.e. the ATP system does >5 KJ/mole work on the B-C system (W = 5 KJ/mole). >3. E = 10 KJ/mole, i.e. the system B-C accepts 10 KJ/mole energy. However >delta G for the ATP system is 5 KJ/mole, i.e. the ATP system GETS >5 KJ/mole work FROM the B-C system (W = -5 KJ/mole). >All three cases are real (in the sense that the combinations of delta H and >delta G values can exist) and, within the definitions, all statements in >them are correct. However common sense tells us that it would be better >to define "the energy the system B-C accepts" as "the work done on the B-C >system"; i.e. to reject the physically meaningless delta G definition of >work and adopt one whose usefulness seems obvious. In other words, I >propose to adopt /3/ as a natural definition of chemical work. > Now I am waiting for your comments. Pentcho First of all, since /3/ is not a definition of work within the framework of thermodynamics, any problems you may see with it will be the result of your definition, not any problems with thermodynamics. And what do you propose to do for a reaction where the volume does change? It seems odd that a definition for chemical work should only be applicable if the reaction occurs in an incompressible fluid. Since reaction /2/ contains the ATP->ADP+P system, what you want to do is not so simple to arrange. You need to adjust all the concentrations (ATP, ADP, P, B and C). Possible of course, but in order to have /2/ at equilibrium in case 3. requires a larger concentration of B (relative to C) than for case 1. More about this point later. I get the impression that you are bothered by the idea that the amount of work which a reaction can do is dependent on the concentration of the reactants and products. I am not bothered, it seems perfectly reasonable to me. Consider your three cases, you say that all three are near equilibrium. If we assume they are all at equilibrium, then no further net reaction occurs in any of the three cases, and no work occurs at all. For every set of molecules which react in the forward direction, a set reacts in the backwards direction. i.e. Delta G = 0, seems the appropriate measure for the amount of work that can be done, not E = 10 kJ/mole. Consider just the ATP hydrolysis for the moment. With or without an enzyme, both the forward and back reactions are present. For the type of systems we are discussing now, the back reaction is so slow that we can neglect it. However, that is because most of the time when we study these systems the reaction is far from equilibrium (lots of ATP, little ADP). Consider the case where the hydrolysis is close to equilibrium, which means a lot of ADP and P, and very little ATP. Since at equilibrium, the forward and back reactions are equal, does it really seem so odd that the reaction cannot perform any useful work? (Delta G = 0). Now consider B -> C. If the concentration of B is so much larger than that of C, that (Delta G) for the B -> C reaction is negative, then a net forward reaction will be observed. (Of course, it may not be proceeding fast enough to be biologically useful, so the enzyme may still be necessary for the organism to survive.) Your case 3 would seem to be such a case. In order for (Delta G) for the ATP hydrolysis to be positive, it would require that there be so little ATP present (relative to the amount of ADP and P) that the back reaction was faster than the forward reaction. Inorder for the overall reaction (/2/) to be at equilibrium, the (Delta G) for the B->C reaction alone, must be negative, so that the forward B->C reaction was favored. If (Delta G) for the total reaction was slightly negative, reaction /2/ would proceed in the direction shown, and in that case the B->C reaction does indeed do work on the ATP -> ADP+P reaction. The B->C reaction goes towards equilbrium, while the ATP hydrolysis is pushed farther away from equilibrium. This should not be surprising. If the concentrations are such that the back reaction of ATP -> ADP + P, was favored, you wouldn't expect the forward reaction to be able to do any work would you? Finally, it appears that you would be happier with a chemical work which was the same for all three of your cases. However, I would not. The further away you are from equilibrium, the more out of balance the forward and backward rates will be. It should take more work to push the reaction still further out of equilibrium, because the system has to overcome a greater tendency for the reaction to go the other way. Regards, Bryant From owner-biophysics@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Chemical work (reply to Bryant Fujimoto) Date: 2 Dec 1997 09:41:03 -0000 Lines: 42 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <660l3f$35h@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant, you wrote:>>>>>>>>> Consider just the ATP hydrolysis for the moment. With or without an enzyme, both the forward and back reactions are present. For the type of systems we are discussing now, the back reaction is so slow that we can neglect it. However, that is because most of the time when we study these systems the reaction is far from equilibrium (lots of ATP, little ADP). Consider the case where the hydrolysis is close to equilibrium, which means a lot of ADP and P, and very little ATP. Since at equilibrium, the forward and back reactions are equal, does it really seem so odd that the reaction cannot perform any useful work? (Delta G = 0).<<<<<<<< It does seem odd to me. Let us assume that the equilibrium of ATP hydrolysis ATP <-> ADP + P /1/ were a bit more "normal", i.e. the back reaction were not so slow and the equilibrium ATP concentration not so low. I hope you would agree that both assumptions are realistic and have nothing to do with the second law. However, as the ATP system drives the reaction B -> C: ATP + B -> ADP + P + C /2/ the equilibrium of the ATP system would be restored by the not-so-slow back reaction. Since this back reaction is endothermic, the whole process amounts to a cycle in which heat is absorbed from the environment and converted into.....? Two questions arise here. 1. Is this quantity into which the equilibrium ATP system converts the heat valuable (potentially, of course - nobody has analysed it yet)? If yes, I will show later that we can call it H-work (H denotes enthalpy) as opposed to G-work (G is free energy) which is also very important for living systems. 2. If the equilibrium of the ATP system is not "normal" and living systems cannot build the above heat engine, can we suspect that they may have made amendments so that some perfectioned reaction is much more suitable for an isothermal heat engine? I believe we can - I need to think a bit more and will present the case. Best regards, Pentcho From owner-biophysics@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!synbio.tpgnet.net!saudekv From: saudekv@synbio.tpgnet.net (Vladimir Saudek) Newsgroups: bionet.biophysics Subject: Protein Modeller Date: 3 Dec 1997 11:22:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <19971203172241566.AAA151@[195.10.9.147]> NNTP-Posting-Host: net.bio.net Synthelabo Biomoleculaire has an immediate opening in the Group of Structural Biology for Protein Modeller The successful candidate will have PhD in structural biology, physical chemistry, theoretical chemistry or chemistry and several years of postdoctoral experience in a well-established protein modelling group. His/her skills will include Analysis of amino and nucleic acid sequences and sequence - function assignment Homology and threading modelling Molecular mechanics and dynamics Docking techniques Use of www modelling and sequence analysis resources Good knowledge of structural biology, familiarity with X-ray crystallography and NMR spectroscopy Ability to collaborate within a specialised protein structure team (X-ray crystallography, NMR and optical spectroscopy) as well as interact with scientists in a multidisciplinary institute (molecular biology, biochemistry, chemistry, genomics, bioinformatics) Excellent communication Integrate in an international team Synthelabo Biomoleculaire, a research institute located in Strasbourg and a subsidiary of the French pharmaceutical company Synthelabo, performs research towards the rapid generation of leads for new therapeutic targets emerging from the human genome. The Group of Structural Biology is equipped with 600, 500 and 360 MHz NMR spectrometers, X-ray diffractometer and a range of optical spectrometers (UV, IR, Raman, CD, fluorescence). The computing environment is based on Silicon Graphics servers and workstations. The group collaborates closely with molecular biology, genomics, bioinformatics, and medicinal and combinatorial chemistry. If you are interested, please send your CV and a letter of interest (preferably by email) to the address below. Vladimir Saudek Structural Biology Synthelabo Biomoleculaire 16, rue d'Ankara Strasbourg 67080 CEDEX, France email: saudekv@synbio.tpgnet.net tel: +33 (0)3 8860 8893 fax: +33 (0)3 8845 9070 ********************************************* Vladimir Saudek Structural Biology Synthelabo Biomoleculaire 16, rue d'Ankara Strasbourg 67080 CEDEX, France email: saudekv@synbio.tpgnet.net tel: +33 (0)3 8860 8893 fax: +33 (0)3 8845 9070 PLEASE NOTE THE NEW TELEPHONE NUMBER ********************************************* From owner-biophysics@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!news.new-york.net!news.columbia.edu!news-not-for-mail From: Justin Lee Newsgroups: bionet.biophysics Subject: Mini Analysis Program Date: Wed, 03 Dec 1997 13:31:50 -0500 Organization: Columbia University Lines: 26 Message-ID: <3485A596.10E7526D@columbia.edu> Reply-To: cjl2@columbia.edu NNTP-Posting-Host: bb110101.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; U) Hi, I have written a mini analysis program to analyse spontaneous miniature EPSCs or IPSCs under Windows environment. It can detect 3pA peaks with 5pA noise. It can also be used for any spontaneous activities, such as spontaneous action potential firing, current recordings for electochemical measurements, etc.. Please visit at http://128.59.170.42 to download the program and try it out. I also have several other programs useful for electophysiology and immunocytochemistry. Justin Lee -- Columbia University Department of Physiology 630 W. 168th Street BB1106 New York, NY 10032 Phone (212) 305-3817 Fax (212) 305-5775 e-mail cjl2@columbia.edu http://128.59.170.42 ftp://128.59.170.42 From owner-biophysics@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!eerie.fr!newsfeed.eerie.fr!newsfeed.nacamar.de!newscore.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!spaniel From: smith@umes07.avl.co.at (Search Spaniel) Newsgroups: bionet.biophysics Subject: Biophysics-search the web quickly with Search Spaniel Date: Wed, 03 Dec 97 17:35:21 GMT Organization: Search Spaniel Lines: 4 Message-ID: <250108648@searchspaniel.com> NNTP-Posting-Host: isdn024.tu-graz.ac.at To Biophysics-search the most search engines in the shortest time, use the internet's newest search engine - Search Spaniel at: http://www.searchspaniel.com/ From owner-biophysics@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!rutgers!gatech!205.252.116.205.MISMATCH!howland.erols.net!newsfeed.internetmci.com!130.132.143.65!news.ycc.yale.edu!not-for-mail From: "Miguel A. Talavera" Newsgroups: bionet.biophysics Subject: General information about Centrifugation Date: Thu, 04 Dec 1997 04:37:50 -0500 Organization: Yale University Lines: 7 Message-ID: <348679EE.AFFB65F6@yale.edu> NNTP-Posting-Host: net186-114.its.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) I would like to know what type of information can you get from a velocity sedimentation experiment, and from an equilibrium sedimentation experiment. Also, what other alternate methods might give the each type of information. From owner-biophysics@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!news.uoregon.edu!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Chemical work (reply to Bryant Fujimoto) Date: 4 Dec 1997 09:04:52 GMT Organization: University of Washington Lines: 76 Distribution: bionet Message-ID: <665rnk$4mo$1@nntp3.u.washington.edu> References: <660l3f$35h@mserv1.dl.ac.uk> NNTP-Posting-Host: homer28.u.washington.edu X-Trace: nntp3.u.washington.edu 881226292 4824 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant, you wrote:>>>>>>>>> >Consider just the ATP hydrolysis for the moment. With or without an >enzyme, both the forward and back reactions are present. For the type of >systems we are discussing now, the back reaction is so slow that we can >neglect it. However, that is because most of the time when we study >these systems the reaction is far from equilibrium (lots of ATP, little >ADP). Consider the case where the hydrolysis is close to equilibrium, >which means a lot of ADP and P, and very little ATP. Since at equilibrium, >the forward and back reactions are equal, does it really seem so odd that >the reaction cannot perform any useful work? (Delta G = 0).<<<<<<<< >It does seem odd to me. Let us assume that the equilibrium of ATP >hydrolysis > ATP <-> ADP + P /1/ >were a bit more "normal", i.e. the back reaction were not so slow and >the equilibrium ATP concentration not so low. I hope you would agree that >both assumptions are realistic and have nothing to do with the second law. >However, as the ATP system drives the reaction B -> C: > ATP + B -> ADP + P + C /2/ >the equilibrium of the ATP system would be restored by the not-so-slow >back reaction. Since this back reaction is endothermic, the whole process >amounts to a cycle in which heat is absorbed from the environment and >converted into.....? In your example there are two pathways /1/ and /2/. If the concentrations of ATP, ADP and P are such that the hydrolysis of ATP will in fact drive reaction /2/ forward, then pathway /1/ will show a net flow in the forward direction as well. That is under these conditions pathway /1/ will produce a net hydrolysis of ATP, not a net production of ATP. As for it being odd that a chemical reaction at equilibrium can't do any work - consider an electric battery, when the chemical reaction inside is at equilibrium, the battery is dead. > Two questions arise here. 1. Is this quantity into which the equilibrium >ATP system converts the heat valuable (potentially, of course - nobody has >analysed it yet)? If yes, I will show later that we can call it H-work >(H denotes enthalpy) as opposed to G-work (G is free energy) which is also >very important for living systems. I hope I didn't give you the impression that I didn't think the enthalpy was important. I only noted that it isn't a good representation of the work being done. Note that at constant P, if the system does only displacement work (i.e. no chemical work), then (Delta H) is the heat absorbed by the system. >2. If the equilibrium of the ATP system is not "normal" and living systems >cannot build the above heat engine, can we suspect that they may have made >amendments so that some perfectioned reaction is much more suitable for >an isothermal heat engine? I believe we can - I need to think a bit more >and will present the case. Pentcho I'm sure you are already aware that your proposed heat engine violates the laws of thermodynamics, and that you are not going to be deterred by that. So as you think about this, remember that all of the reactions in your cycle will have both a forward and back rate. As noted above for your ATP cycle, if you keep track of all the rates, you will see that the heat engine will not work. A mechanical analog of this is the osmotic pressure perpetual motion machine you tried to build. If you remember, you were hoping to create a system where solvent would flow from the left chamber to the right chamber at the upper membrane, and from the right chamber to the left chamber at the lower membrane. As you reported, this didn't work. You had left the reverse flow of solvent at the two membranes (R->L at the upper membrane, and L->R at the lower membrane) out of your considerations and you discovered that they have to be considered when describing the system. Regards, Bryant From owner-biophysics@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Work done by a reaction at equilibrium Date: 4 Dec 1997 16:29:14 -0000 Lines: 46 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <666loq$o54@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote:>>>>>>>>>>>>>> >It does seem odd to me. Let us assume that the equilibrium of ATP >hydrolysis > ATP <-> ADP + P /1/ >were a bit more "normal", i.e. the back reaction were not so slow and >the equilibrium ATP concentration not so low. I hope you would agree that >both assumptions are realistic and have nothing to do with the second law. >However, as the ATP system drives the reaction B -> C: > ATP + B -> ADP + P + C /2/ >the equilibrium of the ATP system would be restored by the not-so-slow >back reaction. Since this back reaction is endothermic, the whole process >amounts to a cycle in which heat is absorbed from the environment and >converted into.....?<<<<<<<<<<<<<<<<<<<<<< Bryant Fujimoto replied:>>>>>>>>>>> In your example there are two pathways /1/ and /2/. If the concentrations of ATP, ADP and P are such that the hydrolysis of ATP will in fact drive reaction /2/ forward, then pathway /1/ will show a net flow in the forward direction as well. That is under these conditions pathway /1/ will produce a net hydrolysis of ATP, not a net production of ATP.<<<<<<<<<<<<< I did not claim that there would be a net production of ATP. Let there be, initially, a great amount of B and no C. Also, let the reaction /1/ be at equilibrium. At the end of the process, both reactions /1/ and /2/ would be at equilirium. All along the back reaction in /1/ has absorbed heat from the environment whereas the forward reaction has transfered, in /2/, this energy to the B-C system. If B -> C is some biosynthesis, this energy can be thought of as stored in the respective synthesized structure. In fact, if the reaction B -> C is a biosynthesis, the reaction /2/ never goes backwards, so the only problem biosystems face is the abnormal equilibrium of /1/. They have solved this problem by replacing /1/ with a reaction in which the equilibrium concentration of ATP is not so low and the back reaction not so slow. However the price to pay was that one of the reagents in this new reaction - H+, had to be constantly transfered through the membrane. So H+ translocation is not an energy storage - rather, it is a regulatory process. Of course, the story is much longer than that. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.syd.connect.com.au!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Chemical work and delta G Date: 4 Dec 1997 09:58:23 -0000 Lines: 52 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <665urv$t3r@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>> Finally, it appears that you would be happier with a chemical work which was the same for all three of your cases. However, I would not. The further away you are from equilibrium, the more out of balance the forward and backward rates will be. It should take more work to push the reaction still further out of equilibrium, because the system has to overcome a greater tendency for the reaction to go the other way.<<<<<< I believe that your last sentence is based on wrong intuition - you just feel that something should be done against a greater tendency and call it work, but then refuse to consider the real energy transfer in the system - after all, work production is always energy transfer - otherwise things would become too mystical. We can easily solve the problem by comparing the work done by the ATP system with other works which do obey the dellta G definition. Let us consider a simplest galvanic system: Zn2+ (high conc.), Zn II Zn, Zn2+ (low conc.) The useful (electric) work done by this system does obey the delta G definition, but note that the energy transfer is specific and definite: HEAT IS ABSORBED FROM THE ENVIRONMENT AND CONVERTED INTO USEFUL WORK. Now let us consider a simplest osmotic system: H+ (high conc.) M H+ (low conc.) As H+ crosses the membrane (M) down the concentration gradient, it can do osmotic work which also obeys the delta G definition. However, again, HEAT IS ABSORBED FROM THE ENVIRONMENT AND CONVERTED INTO WORK. In other words, we know the origin of the energy and can imagine the physical picture of energy transfer to the system on which work is done. In fact, my analysis of the work done by the ATP system was based on the same principle. I defined the origin of the energy (it is the internal energy of ATP molecules) and described quantitatively the transfer of this energy to the system on wich work is done (it was the B-C system). Unfortunately, this energy transfer does not obey the delta G definition - it obeys another one based on the enthalpy concept, so it seems suitable to name this kind of work "H-work", as opposed to "G-work" done in galvanic and osmotic systems. Of course, you may insist that, in the last case, delta G accounts for something (e.g the distance from equilibrium or the tendency to move towards equilibrium), but this something has nothing to do with the ENERGY TRANSFERED FROM THE "WORKING" SYSTEM TO THE SYSTEM ON WHICH WORK IS DONE. In other words, you would insist upon a definition of work not based on the first law of thermodynamics. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Dec 04 22:00:00 1997 Newsgroups: bionet.biophysics Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!newspump.sol.net!sol.net!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!news-peer.bt.net!btnet!newsfeed.cableol.net!server4.netnews.ja.net!bris.ac.uk!usenet From: "Ulrich T. Riedel" Subject: 0.002 mm Droplets: How to produce them? X-Nntp-Posting-Host: dig1.enm.bris.ac.uk Content-Type: text/plain; charset=us-ascii Message-ID: <34884538.5A1C2D6B@Bristol.ac.uk> Sender: usenet@fsa.bris.ac.uk (Usenet) Content-Transfer-Encoding: 7bit Organization: University of Bristol, Dept. of Mech. Eng. Mime-Version: 1.0 Date: Fri, 5 Dec 1997 18:17:28 GMT X-Mailer: Mozilla 4.04 [en] (Win16; I) Lines: 26 For my research I have to apply droplets (1000-2000 nanometer (0.001-0.002 mm) in diameter and about 100 nm in height) to a surface to protect the volume below the droplet during successive treatments. Therefore the material of the droplets has to have the following properties: - the substance should be a fluid which turns into a solid with the mentioned properties in a couple of minutes after application; - it has to stick very well on an inorganic, polar surface (hydroxyapatite with intercalated organic substance and water), which may be uneven; - it has to be chemically stable (meaning: it should not swell in water and should not react in any way with acids); - the surface of the substance should be completely dry and solid (meaning no liquid layer apart from the always existing water layer should be around). - it should be possible to create little droplets of the above mentioned size. The size can be slightly arbitrary, since it can be measured after application. Any ideas, what substance and which application technique could be used, would be _HIGHLY_ appreciated. Thanks and Regards, Ulrich Riedel From owner-biophysics@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!199.0.65.142!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: jamesl@healthtech.com (James W. Larkin) Newsgroups: bionet.biophysics,bionet.molbio.proteins.fluorescent,sci.chem.electrochem Subject: Call for Papers Advances in MOLECULAR LABELS, SIGNALING & DETECTION Date: 5 Dec 1997 16:20:33 GMT Organization: Cambridge Healthtech Institute Lines: 42 Message-ID: <6699kh$t5j@news-central.tiac.net> NNTP-Posting-Host: 207.60.238.8 Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.9 Beta 1 (x86 32bit) Xref: biosci bionet.biophysics:3776 bionet.molbio.proteins.fluorescent:1768 First Announcement and Call for Papers Cambridge Healthtech Institute’s Second Annual Advances in MOLECULAR LABELS, SIGNALING & DETECTION: Enhancing Sensitivity, Accuracy and Speed May 4-5, 1998 San Diego Hilton Extending the limits of assay sensitivity and accuracy, at the same time meeting the demand for greater speed, requires the application of innovative techniques and systems. The development of new probes and labels, homogeneous assay designs, and approaches which allow for the direct detection of compounds or specific binding events are having an impact in basic research, diagnostic and drug development segments. Novel fluorescent and luminescent technology are also critical for the implementation of greater speed and automation. These advances are being applied to the detection, quantification and localization of gene sequences, proteins, infectious organisms and a variety of other targets. Researchers are encouraged to submit a proposal for presentation of their own work. Recommendations for other speakers to be considered are also welcomed. Among the topics to be covered are: Novel Probes and Labels New Homogeneous Assays Methods for Direct (Non-amplified) Quantitation Methods for Ultra-Sensitive Detection Novel Fluorescent Assay Systems New Luminescent Approaches Please submit proposal or suggestions by e-mail or fax to: Mary Chitty Conference Director e-mail: mchitty@healthtech.com fax: 617-630-1325 telephone: 617-630-1316 For full consideration and to allow time for followup, please submit proposal or suggestions by December 12, 1997. From owner-biophysics@net.bio.net Fri Dec 05 22:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.biophysics Subject: Re: General information about Centrifugation Date: Fri, 05 Dec 1997 14:45:40 -0800 Organization: University of Leicester (PCFS User) Lines: 12 Message-ID: <34888413.2AB7@le.ac.uk> References: <348679EE.AFFB65F6@yale.edu> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Miguel A. Talavera wrote: > > I would like to know what type of information can you get from a > velocity sedimentation experiment, and from an equilibrium sedimentation > experiment. Also, what other alternate methods might give the each type > of information. Still a good source of introductory information is "The Ultracentrifuges" by Svedberg, despite being 50 years old. "Ultracentrifugation - A Practical Approach" is also usefull and somewhat more modern. Have a look at your library what they have, there are quite a few good books out there. From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsm.ibm.net!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.biophysics Subject: Re: Verification of the second law (reply to Bryant Fujimoto) Date: Sun, 7 Dec 1997 09:15:45 +0200 Organization: Hebrew University Lines: 60 Message-ID: <66dif4$4p5$1@news.huji.ac.il> References: <65p1ju$7ke@mserv1.dl.ac.uk> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Pentcho Valev wrote in message +ADw-65p1ju+ACQ-7ke+AEA-mserv1.dl.ac.uk+AD4-... ... +AD4- Let the reaction +AD4- +AD4- ATP +AD0- ADP P /1/ +AD4- +AD4-drive another reaction, e.g. B +AD0- C, isothermally and isobarically: +AD4- +AD4- ATP B +AD0- ADP P C /2/ +AD4- +AD4-As one mole ATP is used up in the reaction, the energy of the system +AD4-ATP-ADP-P dereases by 20 KJ/mole (since the enthalpy of ATP hydrolysis +AD4-is -20 KJ/mole). Let us also assume that the enthalpy of /2/ is shown +AD4-experimentally to be -10 KJ/mole. ... Pentcho, Free energy (deltaG) is a much more useful concept than enthalpy for looking at this. You can easily split up the reaction into its component parts: 1. deltaG+AHs-ATP+AH0- +AD0- deltaG'+AHs-ATP+AH0- +- RT ln +AFs-ATP+AF0-/+AFs-ADP+AF0- 2. deltaG+AHs-B+AD0-C+AH0- +AD0- deltaG'+AHs-B+AD0-C+AH0- +- RT ln +AFs-B+AF0-/+AFs-C+AF0- The overall deltaG for the coupled reaction is the total. Thus deltaG+AHs-ATP+AH0- can be negative and deltaG+AHs-B+AD0-C+AH0- positive, but it is the overall total which defines the equilibrium of the coupled reaction. This approach is straightforward and adequate even for very complicated systems where you may have to (additively) include many subsystems. In contrast, using enthalpy changes is less useful since it doesn't easily take account of reactant concentrations. Furthermore, you forget that overall deltaG' can be easily measured simply by looking at the equilibrium concentrations under standard conditions. Pentcho, I really think that you are beating a dead horse. I suggest that you go back to your original perpetual motion example (the semipermeable membrane) and do a full +ACI-deltaG+ACI- analysis taking account of ALL the steps in the cycle. I think that you will find that your subsequent ion-movement models are simply a variant on the same idea. In each case, I think you will find that the system will arrive at equilibrium+ACE- I hope that my comments are useful, but in any case, I do not intend to pursue this until Pentcho or someone else can come up with something more substantive. Jonathan B. Marder +ADw-MARDER+AEA-agri.huji.ac.il+AD4- Department of Agricultural Botany, The Hebrew University of Jerusalem Faculty of Agriculture, P.O.Box 12, Rehovot 76100, ISRAEL Phone: +-972 8 9481918 Fax: +-972 8 9467763 Web page: http://www.agri.huji.ac.il/+AH4-marder From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Work done by a reaction at equilibrium Date: 7 Dec 1997 09:59:06 GMT Organization: University of Washington Lines: 74 Distribution: bionet Message-ID: <66ds1a$r60$1@nntp3.u.washington.edu> References: <666loq$o54@mserv1.dl.ac.uk> NNTP-Posting-Host: homer09.u.washington.edu X-Trace: nntp3.u.washington.edu 881488746 27840 (None) 140.142.64.2 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Pentcho wrote:>>>>>>>>>>>>>> >>It does seem odd to me. Let us assume that the equilibrium of ATP >>hydrolysis >> ATP <-> ADP + P /1/ >>were a bit more "normal", i.e. the back reaction were not so slow and >>the equilibrium ATP concentration not so low. I hope you would agree that >>both assumptions are realistic and have nothing to do with the second law. >>However, as the ATP system drives the reaction B -> C: >> ATP + B -> ADP + P + C /2/ >>the equilibrium of the ATP system would be restored by the not-so-slow >>back reaction. Since this back reaction is endothermic, the whole process >>amounts to a cycle in which heat is absorbed from the environment and >>converted into.....?<<<<<<<<<<<<<<<<<<<<<< >Bryant Fujimoto replied:>>>>>>>>>>> >In your example there are two pathways /1/ and /2/. If the concentrations >of ATP, ADP and P are such that the hydrolysis of ATP will in fact drive >reaction /2/ forward, then pathway /1/ will show a net flow in the forward >direction as well. That is under these conditions pathway /1/ will produce >a net hydrolysis of ATP, not a net production of ATP.<<<<<<<<<<<<< >Pentcho wrote:>>>>>>>>>>>>>> >I did not claim that there would be a net production of ATP. Let there be, >initially, a great amount of B and no C. Also, let the reaction /1/ be at >equilibrium. At the end of the process, both reactions /1/ and /2/ would >be at equilirium. All along the back reaction in /1/ has absorbed heat >from the environment whereas the forward reaction has transfered, in /2/, this >energy to the B-C system. If B -> C is some biosynthesis, this energy can >be thought of as stored in the respective synthesized structure. Pentcho You initially stated that the ATP hydrolysis was driving the B->C reaction. This means that /1/ cannot be at equilibrium. When reading your post, I missed the fact that you wanted /1/ to be at equilibrium. That is, I missed the fact that you made two contradictory statements about your system. If /1/ is at equilibrium and there is no C, then the hydrolysis of ATP does not drive the B->C reaction. For the particular initial conditions which you specify (which probably do not occur naturally), the B->C reaction drives the hydrolysis of ATP. >In fact, if the reaction B -> C is a biosynthesis, the reaction /2/ never >goes backwards, so the only problem biosystems face is the abnormal >equilibrium of /1/. Never say never. What if the organism decides it doesn't need any more C and shuts the biosynthesis down? In any event, while the biosynthesis is running reaction /2/ will never exhibit a _net_ backwards reaction. However, there will be some back reaction, it will just be much smaller than the forward reaction. What do you mean by an abnormal equilibrium? Reaction /1/ is not at equilibrium in a living organism. Its out of equilibrium, and the organism uses that fact to drive other reactions. Regards Bryant >They have solved this problem by replacing /1/ with >a reaction in which the equilibrium concentration of ATP is not so low and >the back reaction not so slow. However the price to pay was that one of >the reagents in this new reaction - H+, had to be constantly transfered >through the membrane. So H+ translocation is not an energy storage - >rather, it is a regulatory process. Of course, the story is much longer >than that. From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Chemical work and delta G Date: 7 Dec 1997 10:40:06 GMT Organization: University of Washington Lines: 108 Distribution: bionet Message-ID: <66due6$srq$1@nntp3.u.washington.edu> References: <665urv$t3r@mserv1.dl.ac.uk> NNTP-Posting-Host: homer09.u.washington.edu X-Trace: nntp3.u.washington.edu 881491206 29562 (None) 140.142.64.2 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant Fujimoto wrote:>>>>>>>>>>> >Finally, it appears that you would be happier with a chemical work which >was the same for all three of your cases. However, I would not. The >further away you are from equilibrium, the more out of balance the >forward and backward rates will be. It should take more work to push >the reaction still further out of equilibrium, because the system has >to overcome a greater tendency for the reaction to go the other way.<<<<<< >I believe that your last sentence is based on wrong intuition - you just >feel that something should be done against a greater tendency and call it >work, but then refuse to consider the real energy transfer in the system - >after all, work production is always energy transfer - otherwise things >would become too mystical. >We can easily solve the problem by comparing the work done by the ATP >system with other works which do obey the dellta G definition. Let us >consider a simplest galvanic system: > Zn2+ (high conc.), Zn II Zn, Zn2+ (low conc.) >The useful (electric) work done by this system does obey the delta G >definition, but note that the energy transfer is specific and definite: >HEAT IS ABSORBED FROM THE ENVIRONMENT AND CONVERTED INTO USEFUL WORK. >Now let us consider a simplest osmotic system: > H+ (high conc.) M H+ (low conc.) >As H+ crosses the membrane (M) down the concentration gradient, it can >do osmotic work which also obeys the delta G definition. However, again, >HEAT IS ABSORBED FROM THE ENVIRONMENT AND CONVERTED INTO WORK. In other >words, we know the origin of the energy and can imagine the physical >picture of energy transfer to the system on which work is done. Pentcho I think we went through this once before, and I didn't give a very good response, so lets try again. Particularly, since it demonstrates why you can't use the enthalpy for work. Consider your simple osmotic system. The enthalpy for the transfer of H+ from the left to the right at constant pressure is zero. This is true regardless of whether any work is done during this process or not. Now, to understand why this is so, you need to understand the physical interpretation of the enthalpy. Starting from the first law of thermodynamics and H=U+pV, we can derive that at constant pressure (Delta H) is equal to the heat absorbed by the system plus any non-displacement work done on the system. At constant P, Wu = (non-displacement work) = (Total work) - (-p(Delta V)) (-p(Delta V) is the displacement work done on the system). So at constant P (Delta H) = q + Wu Wu contains any chemical work which might be done. Up to this point, we need only the first law of thermodynamics, so if you don't like this, you will have to discard the first law as well. This is why using the enthalpy for the work is problematic, since it contains both heat and work, and as we shall see, it can be distributed between q and Wu in many different ways for the same value of Delta H. Now, if the diffusion of H+ across the membrane is not coupled to any reaction, then net diffusion of H+ does no chemical work and Wu=0. Since (Delta H = 0), we get q = 0. That is, no heat absorption. So far so good. What if the diffusion of H+ is coupled to a chemical reaction? In that case Wu < 0 (the diffusion is doing work on something else), and so since Delta H is still zero, we get q > 0, and q = |Wu|. That is the heat absorbed equals the work done. The more work done, the larger q is. >In fact, my analysis of the work done by the ATP system was based on the >same principle. I defined the origin of the energy (it is the internal >energy of ATP molecules) and described quantitatively the transfer of >this energy to the system on wich work is done (it was the B-C system). >Unfortunately, this energy transfer does not obey the delta G definition - >it obeys another one based on the enthalpy concept, so it seems suitable >to name this kind of work "H-work", as opposed to "G-work" done in >galvanic and osmotic systems. As I point out, it doesn't obey your concept of H-work. I don't recall your giving a good reason why this doesn't obey "G-work" as you call it. After all, Delta G for the diffusion of H+ from left to right in your system is negative, which means it can do work on another system. Delta G would be maximum available, how much is actually done depends on the details of the system. On the other hand, (Delta H) is zero regardless of how much work is done, which it makes it difficult to see how you would use it for the work. >Of course, you may insist that, in the last case, delta G accounts for >something (e.g the distance from equilibrium or the tendency to move >towards equilibrium), but this something has nothing to do with the >ENERGY TRANSFERED FROM THE "WORKING" SYSTEM TO THE SYSTEM ON WHICH >WORK IS DONE. In other words, you would insist upon a definition of >work not based on the first law of thermodynamics. Pentcho I pointed out before that Delta G is maximun amount of non-displacement work which a reaction can perform on its surroundings (at constant T and P). How much work is actually done depends on the efficiency of the transfer. There is no contradiction between this and the first law. Notice that my description of Delta G does not claim it represents all the energy in the system, only that which is available to do Wu. Regards Bryant From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uunetukout!newsfeed.ecrc.net!news-feed1.eu.concert.net!newsfeed.skynet.be!poster.skynet.be!not-for-mail From: Marcel Hofman Newsgroups: bionet.biophysics Subject: ECB9 ninth European congress on Biotechnology has a website you might visit Date: Sun, 07 Dec 1997 19:24:18 +0100 Organization: ECB9 Organising Committee Lines: 45 Message-ID: <348AE9D1.378D72CB@skynet.be> Reply-To: ECB9.ORCOM@skynet.be NNTP-Posting-Host: dialup104.mechelen.skynet.be Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------E8EBC1EAE8995DADD036D8AE" X-Trace: news0.skynet.be 881518401 30047 (None) 195.238.30.104 X-Complaints-To: usenet@news0.skynet.be X-Mailer: Mozilla 4.02 [en] (Win95; I) This is a multi-part message in MIME format. --------------E8EBC1EAE8995DADD036D8AE Content-Type: multipart/alternative; boundary="------------502A4B54E15E949F60112EE0" --------------502A4B54E15E949F60112EE0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ECB9 ninth European congress on Biotechnology has a website you might visit http://:www.ecb9.be --------------502A4B54E15E949F60112EE0 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit ECB9 ninth European congress on Biotechnology has a  website you might visit http://:www.ecb9.be --------------502A4B54E15E949F60112EE0-- --------------E8EBC1EAE8995DADD036D8AE Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Marcel Hofman Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Marcel Hofman n: Hofman;Marcel org: ECB9 Organising Committee adr: Hondsbergen 2;;;Tervuren;;3080;Belgium email;internet: ecb9.orcom@skynet.be title: Chairman tel;work: 32 2 767 5301 tel;fax: 32 2 767 2191 x-mozilla-cpt: ;0 x-mozilla-html: TRUE version: 2.1 end: vcard --------------E8EBC1EAE8995DADD036D8AE-- From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: What delta G cannot explain (reply to Bryant). Date: 7 Dec 1997 12:01:56 -0000 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66e37k$l36@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Lines: 42 Bryant, when I wrote my previous message, I had not received your last one, so mine was nervous and ultimative - sorry about that. Now I see that the discussion still makes sense. You are right that, for the osmotic system, the delta G concept is better than the one based on the enthalpy. You are also right that the enthalpy concept does not distinguish between Q and Wu. Still I insist that, except for galvanic and osmotic systems, what I call H-work is the only meaningful concept describing chemical work. Let the reaction A -> B drive the reaction C -> D : A + C -> B + D /1/ The only question we ask for the moment is: How much energy is accumulated by the C-D system for one stoichiometric unit of reaction? It is not diffucult to see that this quantity is E = (delta H)c - (delta H)o /2/ where (delta H)o is the enthalpy change of the reaction A -> B and (delta H)c is the enthalpy change of the coupled reaction /2/. Now what is this E? Part of it may indeed come from the reaction A -> B, but the other part is simply due to the fact that the reaction C -> D is itself endo(exo)thermic. So E cannot be called true work. In the osmotic system, the true work is delta G whereas the thermal component in E makes it "contaminated" work. However, for ATP driven reactions, E is the ONLY quantity reflecting the real energy flow in the system. It is again "contaminated" - we can never know what part of E comes from ATP (i.e. is "true" work) and what part is just absorbed from the environment. Still it is valuable in itself - it is a direct measure of energy accumulation in living systems. In this sense it does not reject the delta G concept of work - it just explains something that delta G cannot explain. The whole problem is whether this something makes sense. I still believe that the adequate interpretation of energy accumulation in living systems makes a lot of sense. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: What thermodynamics cannot explain (reply to Bryant). Date: 7 Dec 1997 11:00:20 -0000 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66dvk4$jah@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant, unfortunately there is too much misunderstanding again - I am again to blaim for imprecise statements and earlier mistakes. So I would like to state the problem clearly and briefly - if nobody finds it important, the discussion would be really pointless. Let there be an energy-consumming reaction: B -> C /1/ It could be a biosynthesis - B are the building blocks and C is some biopolimer structure. We do not know where the equilibrium of the reaction lies, but in any event it must be driven by some energy-transfering reaction. The energy transfered is accumulated in the synthesized structure and is expressed by the concept of H-work that I am trying in vain to introduce. Now please tell me: do you find the energy accumulated during biosynthesis an important quantity? If yes, we will have to go beyond the thermodynamic restrictions. But maybe this quantity is unimportant or just does not exist? Then I see no reason to obtrude any more. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!204.156.128.20!news1.best.com!news.nacamar.de!news.netwave.de!195.52.218.68 From: "Schuricht S.I.N.N." Newsgroups: bionet.biophysics Subject: TESTING DEVICES FOR ENVIRONMENTAL MEASURING TECHNOLOGY Date: Thu, 11 Dec 1997 10:40:29 +0100 Organization: S.I.N.N. Schuricht Interactive New Network Lines: 5 Message-ID: <348FB50D.3247@schuricht.de> Reply-To: cs@schuricht.de NNTP-Posting-Host: bombadil.netwave.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 [de] (Win95; I) TESTING DEVICES FOR ENVIRONMENTAL MEASURING TECHNOLOGY http://www.schuricht.de/schudynae/schuhome?pStockNo=17.463.30 prices are DM(DeutschMark) From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!usenet From: villowan@earthlink.net (Charlsie Patterson) Newsgroups: bionet.biophysics Subject: ]][[ Sr/Principal R & D Scientist B9710 Date: Thu, 11 Dec 1997 18:03:26 GMT Organization: EarthLink Network, Inc. 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Please refer to Job Listing B9710b in all correspondence To submit your CV or have any questions answered, please contact: Ms. Charlsie Patterson Technical and Bio-Science Recruiter Global Staffing and Recruiting (919) 871-0070 Fax: (919) 871-0030 email: techsearch@globals-r.com and/or villowan@earthlink.net Sr. Associate Research Scientist/Principal Associate Research Scientist-R & D Brief Description of the Position: This position is for a research scientist who will stabilize therapeutic plasma proteins using formulation and lypholization techniques. The incumbent will be a team member to develop new freeze dryer cycles and will have the opportunity to work with various other site projects. Position Requirements: MS in Life Sciences or Engineering with 2+ years or more of relevant pharmaceutical experience or equivalent combination of education and experience. The successful candidate must have extensive experience with protein biochemistry and methods of protein stabilization, be proficient with analytical equipment (DSC, FTIR, HPLC, nIR) and be able to interpret results. The ability to analyze data independently, as well as present the data within a team environment is a must. Computer experience and familiarity with various databases helpful. PLEASE NOTE: Hepatitis B immunization is required. From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Delta G vs. Delta H Date: 11 Dec 1997 13:47:36 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66oqto$33t@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to Bryant Fujimoto Bryant, my choice of delta H as a measure of chemical work is based on the following simple physical picture: The ATP system interacts with another system. As one mole ATP is used up, the energy of the other system increases by 10 KJ. These 10 KJ are the only real physical quantity showing the changed energetics of the second system, so I am inclined to think of it as "work done on the second system". Of course, I am ready to consider other definitions of "work done on the second system", but expect them to be in harmony with the first law - if work is done on the second system, its energy content should change accordingly. (Of course, we neglect particular cases - work resulting in a motion for instance is not accumulated but dissipated as heat). As I find that these 10 KJ are the only reliable physical quantity, I analyse them and find that they obey a delta H, not delta G definition: W = (delta H)c - (delta H)o = 10 KJ/mole /1/ where (delta H)c is the enthalpy of the coupled reaction, whereas (delta H)o id the enthalpy of ATP hydrolysis. As you can see, I started from a simple idea - I was interested in the energy the second system had received, not in delta G, delta H, the second law etc. I called this energy "work done on the second system", and only then I started expressing it in terms of thermodynamic functions - it proved a function of delta H, not of delta G. What wrong do you find in my approach? Can you offer an analogous approach leading to delta G - first you give some reasonable physical definition of chemical work based on the first law, and then prove that this work SO DEFINED is expressed by delta G? I am sure you can't. This is the whole problem - delta G only formaly describes chemical work - it does not correspond to any real energy transfer (except for galvanic and osmotic reactions). Best regards, Pentcho From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: What delta G cannot explain (reply to Bryant). Date: 11 Dec 1997 11:48:01 GMT Organization: University of Washington Lines: 92 Distribution: bionet Message-ID: <66ojth$5n1$1@nntp3.u.washington.edu> References: <66e37k$l36@mserv1.dl.ac.uk> NNTP-Posting-Host: homer22.u.washington.edu X-Trace: nntp3.u.washington.edu 881840881 5857 (None) 140.142.64.2 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant, when I wrote my previous message, I had not received your last one, >so mine was nervous and ultimative - sorry about that. Now I see that >the discussion still makes sense. >You are right that, for the osmotic system, the delta G concept is better >than the one based on the enthalpy. You are also right that the enthalpy >concept does not distinguish between Q and Wu. Still I insist that, except >for galvanic and osmotic systems, what I call H-work is the only >meaningful concept describing chemical work. >Let the reaction A -> B drive the reaction C -> D : > A + C -> B + D /1/ >The only question we ask for the moment is: How much energy is accumulated >by the C-D system for one stoichiometric unit of reaction? It is not >diffucult to see that this quantity is > E = (delta H)c - (delta H)o /2/ >where (delta H)o is the enthalpy change of the reaction A -> B and >(delta H)c is the enthalpy change of the coupled reaction /2/. >Now what is this E? Part of it may indeed come from the reaction A -> B, >but the other part is simply due to the fact that the reaction C -> D >is itself endo(exo)thermic. So E cannot be called true work. In the >osmotic system, the true work is delta G whereas the thermal component >in E makes it "contaminated" work. Its not the true work due to an additional complication. See below. > However, for ATP driven reactions, E is the ONLY quantity reflecting >the real energy flow in the system. It is again "contaminated" - we >can never know what part of E comes from ATP (i.e. is "true" work) and >what part is just absorbed from the environment. Still it is valuable >in itself I never said it wasn't important, I said it wasn't the work. >- it is a direct measure of energy accumulation in living >systems. In this sense it does not reject the delta G concept of work - >it just explains something that delta G cannot explain. The whole problem >is whether this something makes sense. I still believe that the adequate >interpretation of energy accumulation in living systems makes a lot >of sense. Pentcho I certainly hope you didn't get the impression that I thought the enthalpy was not important. It certainly is. I was making the point that Delta G is a more appropriate quantity for thinking about the work than Delta H. In addition to the problem of separating q from Wu, an additional complication with trying to use Delta H as a measure of the work involved stems from the fact that H (and G, A, U, and S) are state functions, while work and heat are not. What this means is that if you want to know what (Delta H) is for a process which takes a system from state 1 to state 2, all you need to know is what those two states are, you don't need to know how the system got from state 1 to state 2. However, if you want to know how much work was involved, or how much heat was absorbed, you have to know the path. That is, the amount of work involved (or heat absorbed) depends on how the system got from state 1 to state 2. This dependence is exploited to make refrigerators, steam engines, etc. Delta G doesn't have the problem of distinguishing between q and Wu. For a reversible reaction Delta G is Wu. Second, for a non-reversible reaction Delta G is maximum amount maximun amount of non-displacement work which the driving reaction can perform. This doesn't mean that it will perform that much, if the coupling is inefficient, less will be done. For the reaction being driven, Delta G is the minimum amount of work which needs to be done to cause the reaction to proceed. If the coupling is inefficient, more will be needed. So you can at least think about the limits of how much chemical work can be provided by a driving reaction, or how much is needed by the reaction being driven. The reason that Delta G will depend on the concentration (a fact that seems to bother you) is that we are considering the net reaction, not just the result of a single collision. If the concentrations are such that the back reaction is favored, then it will take more work to get a net forward reaction, than if the reaction is initially at equilibrium. This is what Delta G is about, and it is more in keeping with our concepts of work. You should not be able to get any work out of a reaction at equilibrium. Now Delta H is something else. It has its own uses, and people do measure and think about it. It shows up in the temperature dependence of equilibrium and rate constants, and in bond enthapies, etc. It just isn't thought of as a kind of work. If you want to use it as a measure of accumulated energy, then you are trying to define an enthalpy of formation for an organism. This is can be done in principle. In practice the measurements might not be possible. Regards, Bryant From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!news-hh.maz.net!unlisys!news.snafu.de!fu-berlin.de!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!usenet From: villowan@earthlink.net (Charlsie Patterson) Newsgroups: bionet.biophysics Subject: [Sr/Assoc. Research Scientist] Date: Wed, 10 Dec 1997 18:47:53 GMT Organization: EarthLink Network, Inc. Lines: 52 Message-ID: <66mo66$8jb@ecuador.earthlink.net> NNTP-Posting-Host: 38.30.41.154 X-Newsreader: Forte Free Agent 1.0.82 My client company is a large established pharmaceutical company aggressively seeking to fill this position at the first of the year. It is in the area of research and development. They offer excellent compensation and benefit, as well as great growth potential. The client company will pay all fees associated with recruiting and placement of candidates. The position is located in North Carolina. Please refer to Job Listing B-9785 in all correspondence To submit your CV or have any questions answered, please contact: Ms. Charlsie Patterson Technical and Bio-Science Recruiter Global Staffing and Recruiting (919) 871-0070 Fax: (919) 871-0030 email: techsearch@globals-r.com and/or villowan@earthlink.net Sr./Assoc. Research Scientist Brief Description of the Position: Conduct assays to support the development and characterization of new biological products. The incumbent will also be part of a team that will interact closely with early stages of process scale up and with the QA development and establishment of numerous new assays. (i.e. robotics immunological and real time on-line assays) and advanced characterization of protein products. The incumbent will collaborate closely with projects in New Product Biochemistry, Pathogen Safety and Process Research Sections. The incumbent will work at the laboratory bench and have good oral and written communication skills to keep accurate experimental records, communicate research goals and results on a frequent schedule. Position Requirements: BS in Biochemistry, Analytical chemistry, or closely related field with at least 2 years of relevant job experience. Experience with operating and maintaining Hewlett Package HPLCs, BioSepara ProSys HPLCs and Beckman BioMek Robotics systems is desired. A demonstrated ability to keep clear records, recognize and implement needed experimental controls, communicate with team members, and meet time lines is required. A background with HPLC, enzymatic, and/or immunological assays is required. Experience with mass spectrometry, amino acid analysis, sequence analysis, peptide mapping, disulfide assignment and/or glycoprotien analysis is needed. GLP/GMP experience, analytical methods validation, experience in automation, robotics, on-line assays, a familiarity with the well-characterized biological concept will contribute to the success of a candidate. From owner-biophysics@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!usenet From: villowan@earthlink.net (Charlsie Patterson) Newsgroups: bionet.biophysics Subject: ]][[ Research Scientist/Senior Research Scientist B-9785 Date: Thu, 11 Dec 1997 00:15:00 GMT Organization: EarthLink Network, Inc. Lines: 43 Message-ID: <66nbbg$apj@argentina.earthlink.net> NNTP-Posting-Host: 38.30.41.73 X-Newsreader: Forte Free Agent 1.0.82 My client company is a large, well established pharmaceutical company, who is aggressively seeking to fill this position at the first of the year. It is in the area of research and development. They offer excellent compensation and benefit, as well as great growth potential. The client company will pay all fees associated with recruiting and placement of candidates. The position is located in North Carolina. Please refer to Job Listing B-9817 in all correspondence To submit your CV or have any questions answered, please contact: Ms. Charlsie Patterson Technical and Bio-Science Recruiter Global Staffing and Recruiting (919) 871-0070 Fax: (919) 871-0030 email: techsearch@globals-r.com and/or villowan@earthlink.net Brief Description of the Position: The incumbent will be a member of the Process Engineering Group of the Technology Department and will contribute to the development of new purification processes for plasma proteins. The process optimization work will center around unit operations as chromatography, membrane separation, and filtration. Major focuses will be the scale-up from macro-bench to pilot-scale and beyond. The incumbent will particularly interface with project engineering and play a major role in the realization projects of the new processes. Position Requirements: Requires a Ph.D./MS degree in Chemical Engineering: minimum experience of four plus years in process development or manufacturing, preferably in the pharmaceutical or biotechnology industries. Must be familiar with GLP/GMP rules and conditions. Experience in project engineering as well as working knowledge in protein chemistry is preferred PLEASE NOTE: A Hepatitis B immunization is required From owner-biophysics@net.bio.net Fri Dec 12 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!206.250.118.17!nntp.earthlink.net!usenet From: prismx@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: Headlines (12 Dec 97) Content Increased Date: Sat, 13 Dec 1997 01:22:57 GMT Organization: SCIENCE-WEEK Lines: 54 Message-ID: <66skmp$1q4@suriname.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.166.171 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20972 bionet.biophysics:3795 bionet.cellbiol:8565 bionet.general:28899 SCIENCE-WEEK is a free weekly Email digest of the news of science read each week by 40,000+ people in the scientific community in more than 30 countries. Beginning a few weeks ago, the number of news digests has been substantially increased, and a Book Notes section has been added. News briefs from the major journals are amplified with enough background material to make them intelligible to nonspecialists: the biology is detailed for physicists and chemists, and the physics and chemistry is detailed for biologists. The result is a unique summary of the news of science. 15 to 20 news reports a week, plus annotated listings of new books in the sciences -- and it's absolutely free. Headlines for the current SCIENCE-WEEK (December 12, 1997) (The SW complete weekly news reports are available free via Email. To subscribe, send SUB SW to Reported in This Issue: 1. On Fashions in Science and Technology 2. On the Foundation of the Silicon Age 3. Analysis of Dust Remnants of the Solar Nebula 4. An Analysis of the Cosmic Infrared Background 5. Evidence for Common X-Ray Emission of Comets 6. Macroscale Fluctuations in a Free Diffusion Process 7. New Evidence of Reactivity of Fullerene Segments 8. Organic Molecules and Prebiotic Earth 9. A New Technique for Molecular Analysis of Tissue 10. Persistence of the DNA Form of an RNA Virus 11. An Apparent Involvement of Prion Protein in Copper Binding 12. CD4(+) T-Cell Responses and Control of HIV 13. Engineered Viral Targeting of HIV- and SIV-Infected Cells 14. A New Drug Against Osteoporosis and High Cholesterol 15. A Simple Test to Detect Cardiac Emergencies 16. Ambiguities in the Diagnosis of Dementia 17. The Thyrotropin Receptor in Thyroid Disease SCIENCE-WEEK is a free retransmission educational resource, which means this headline notice and each issue of SCIENCE-WEEK itself can be retransmitted if intact by any installation. All back issues of SCIENCE-WEEK are available at the URL below. Current issues are posted at the URL 2 to 5 days after first publication. The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Sat Dec 13 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eecs-usenet-02.mit.edu!nntprelay.mathworks.com!howland.erols.net!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!news-fra1.dfn.de!news.kfa-juelich.de!aix.zam.kfa-juelich.de!med050 From: med050@aix.zam.kfa-juelich.de (d.gembris) Newsgroups: bionet.neuroscience,bionet.biophysics,de.sci.biologie,sci.med.physics,sci.techniques.mag-resonance,sci.med.informatics Subject: Announcement: new brain-research WWW site Date: 14 Dec 1997 21:28:20 GMT Organization: Forschungszentrum Juelich GmbH (KFA) Lines: 59 Distribution: world Message-ID: <671j1k$llk@zam201.zam.kfa-juelich.de> NNTP-Posting-Host: aix.zam.kfa-juelich.de Keywords: fMRI, BOLD, MR, MRI, functional MR, modelling, Bloch equations, brain, neural activation, non-invasive Xref: biosci bionet.neuroscience:20979 bionet.biophysics:3796 We want to announce that the Institute of Medicine in the Research Center Juelich (Germany) is now online. The WWW address (URL) is: English page: http://ime-web.ime.kfa-juelich.de/index_e.html German page: http://ime-web.ime.kfa-juelich.de The focus of the institute is non-invasive brain imaging with four modalities: MR, PET, MEG, SPECT. The web pages of the MR group can either be accessed via the IME homepage or directly: http://ime-web.ime.kfa-juelich.de/ime_www/nmr/nmr_eng.html Roughly the research of the MR group can be classified into three categories: 1. Signal physiology (including mathematical modelling) 2. Metabolic (Spectroscopic) Imaging 3. Methodology (Hard- und software development) On our site you will find useful information, e.g. a small MR dictionary explaining some of the acronyms used in our field (and there are many!) and information about free positions (positions for PhD students or postdocs). Please tell your colleagues about our site. Thank you. Regards, Daniel Gembris ************************************************************ ********** research center Juelich GmbH , Germany ********** ************************************************************ ****** ****** ****** II MMMM MMMM EEEEE ****** ****** II MM MM MM MM EE ****** ****** II MM MM MM MM EEEEE ****** ****** II MM MM MM MM EE ****** ****** II MM MMMM MM EEEEE ****** ****** ****** ************************************************************ **************** (I)nstitute for (ME)dicine **************** ************************************************************ ****** ****** ****** Daniel Gembris, MR-group ****** ****** ****** ****** email : d.gembris@fz-juelich.de ****** ****** WWW : http://ime-web.ime.kfa-juelich.de ****** ****** tel : ++49 - 2461 - 61 - 2107 ****** ****** FAX : ++49 - 2461 - 61 - 2820 ****** ****** ****** ************************************************************ ************************************************************ From owner-biophysics@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: What is chemical work? Date: 15 Dec 1997 15:02:43 -0000 Lines: 86 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <673gqj$8g@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>>>>>>>>>>>>>> Now for a discussion about chemical work. If the total work is W, as in dU = Q + W then, the "useful" work is Wu = W -(displacement work) At constant pressure the displacement work is -P(Delta V). (If the system is not a constant pressure, then you have to integrate -PdV over the volume change.) So Wu = W + P(Delta V) If there is only chemical and displacement work being done, then Wu is the chemical work. Now the definition of H is H = U + PV /1/ so dH = dU + PdV + VdP = Q + W + PdV + VdP = Q + Wu +VdP At constant pressure dP = 0 and dH = Q + Wu /2/ Which as we can see, is not the work. The definition of G is G = H - TS /3/ so (at constant pressure) dG = dH - TdS - SdT = Q + Wu - TdS - SdT >From the definition of the entropy we have Q = TdS for a reversible reaction, so dG = Wu - SdT So at constant temperature (dT = 0) and pressure, for a reversible process dG = Wu /4/ The only things I have used are the first law, and the definitions of H, G, and S.<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< No, Bryant, something is missing in your analysis. /3/ only formally defines chemical work - the "operative" definition is different - it is ad hoc definition - it defines chemical work so as to satisfy the second law, and in so doing it can produce the absurd result that the work production is a process opposite to the real energy flow. Let the reaction A -> B drive the reaction C -> D: A + C -> B + D /5/ Let us also make the realistic assumption that, as the reaction proceeds, the energy of the system A-B decreases whereas that of the system C-D increases. On the other hand, if /5/ is close to equilibrium, THE WORK DONE BY THE SYSTEM A-B ON THE SYSTEM C-D is given by delta G = delta Go + RTln((B)/(A)) /6/ where delta Go is the standard free energy of the reaction A -> B. Now the concentrations in /6/ can be such that, as the reaction /5/ is still close to equilibrium, delta G is positive - e.g. 5 KJ/mole. Now please try to understand the absurdity of the situation. The value of delta G shows that the work done by the system A-B on the system C-D is NEGATIVE, i.e. it is the system C-D that does work on the system A-B. On the other hand, the energy flow is in the opposite direction - from the system A-B to the system C-D. Please forget for a while about chemistry and see how this sounds in most general terms: THE SYSTEM X DOES WORK ON THE SYSTEM Y. IN THE PROCESS, THE ENERGY OF X INCREASES AND THAT OF Y DECREASES. I simply do not understand how science has tolerated such an absurdity for so many years. What is even more deplorable is that this does not bother anybody. Best regards, Pentcho From owner-biophysics@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.alt.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Delta G vs. Delta H Date: 15 Dec 1997 10:52:12 GMT Organization: University of Washington Lines: 119 Distribution: bionet Message-ID: <67324s$skg$1@nntp3.u.washington.edu> References: <66oqto$33t@mserv1.dl.ac.uk> NNTP-Posting-Host: homer05.u.washington.edu X-Trace: nntp3.u.washington.edu 882183132 29328 (None) 140.142.64.1 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >In reply to Bryant Fujimoto >Bryant, my choice of delta H as a measure of chemical work is based on the >following simple physical picture: >The ATP system interacts with another system. As one mole ATP is used up, >the energy of the other system increases by 10 KJ. These 10 KJ are the >only real physical quantity showing the changed energetics of the second >system, so I am inclined to think of it as "work done on the second system". >Of course, I am ready to consider other definitions of "work done on the >second system", but expect them to be in harmony with the first law - if >work is done on the second system, its energy content should change >accordingly. (Of course, we neglect particular cases - work resulting in a >motion for instance is not accumulated but dissipated as heat). If you think about what happens when two chemical reactions are coupled, there are not two systems, but three. The third one is the environment in which the reaction takes place (the solvents and any other solutes for a liquid phase reaction). Your analysis ignores energy flows to or from the surroundings. >As I find that these 10 KJ are the only reliable physical quantity, I >analyse them and find that they obey a delta H, not delta G definition: > W = (delta H)c - (delta H)o = 10 KJ/mole /1/ >where (delta H)c is the enthalpy of the coupled reaction, whereas (delta H)o >id the enthalpy of ATP hydrolysis. >As you can see, I started from a simple idea - I was interested in the >energy the second system had received, not in delta G, delta H, the second >law etc. I called this energy "work done on the second system", and only >then I started expressing it in terms of thermodynamic functions - it >proved a function of delta H, not of delta G. But the energy received is not the work and furthermore, not all of Delta H is received. For an exothermic reaction, some of Delta H can represent heat given off by the reaction, not energy received. Also, the amount of energy received depends on the efficiency of the coupling between the driving and receiving reactions, and this simply isn't reflected in Delta H. >What wrong do you find in my approach? Can you offer an analogous approach >leading to delta G - first you give some reasonable physical definition of >chemical work based on the first law, and then prove that this work SO >DEFINED is expressed by delta G? I am sure you can't. This is the whole >problem - delta G only formaly describes chemical work - it does not >correspond to any real energy transfer (except for galvanic and osmotic >reactions). Pentcho In addition to my above comments, what I find wrong with your approach is that equating Delta H to any type of work contradicts the first law of thermodynamics. The energy transferred is not the work. The energy transferred is independent of the process used to go from the initial to the final state. The work does depend on it. Therefore Delta H cannot be a work. As I stated before, if Delta G is negative, then Delta G is the maximum useful work the system can perform on its environment. Now for a discussion about chemical work. If the total work is W, as in dU = Q + W then, the "useful" work is Wu = W -(displacement work) At constant pressure the displacement work is -P(Delta V). (If the system is not a constant pressure, then you have to integrate -PdV over the volume change.) So Wu = W + P(Delta V) If there is only chemical and displacement work being done, then Wu is the chemical work. Now the definition of H is H = U + PV so dH = dU + PdV + VdP = Q + W + PdV + VdP = Q + Wu +VdP At constant pressure dP = 0 and dH = Q + Wu Which as we can see, is not the work. The definition of G is G = H - TS so (at constant pressure) dG = dH - TdS - SdT = Q + Wu - TdS - SdT From the definition of the entropy we have Q = TdS for a reversible reaction, so dG = Wu - SdT So at constant temperature (dT = 0) and pressure, for a reversible process dG = Wu The only things I have used are the first law, and the definitions of H, G, and S. Finally, what don't you like about the enthalpy, that you keep trying to redefine it as something else? Its not the work (though it is related to it), and its not the energy (though for reactions in solution it is close). Why can't you just let the enthalpy be the enthalpy? Its a perfectly good, well defined quantity and lots of people study it. Regards, Bryant From owner-biophysics@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!agate!spool.mu.edu!newsspool.sol.net!newspump.sol.net!sol.net!newsfeed.direct.ca!news.uoregon.edu!news.ycc.yale.edu!not-for-mail From: Mike Croning Newsgroups: bionet.biophysics Subject: In vitro chambers - custom fabrication facilities Date: Mon, 15 Dec 1997 10:54:43 -0500 Organization: Yale University School of Medicine Lines: 75 Message-ID: <349552C3.4F67@yale.edu> NNTP-Posting-Host: donnelly.med.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0 (Win95; I) For a number of years R. Felix Garcia has been designing and manufacturing in vitro chambers for neuroscience research in collaboration with researchers at Yale University Medical School and elsewhere. Our speciality is in chamber designs constructed from plexiglass, stainless steel and aluminium. Many designs are available 'off the shelf', with custom designs for your application being produced at little extra cost. Current production chambers include:- **Cell dissociation chamber** For dissociation of neurons from mammalian CNS tissue for patch clamp and optical recordings according to the method of Kay and Wong (Kay AR. Wong RK. Isolation of neurons suitable for patch-clamping from adult mammalian central nervous systems. J Neurosci Methods. (1986). 16(3):227-38. The chamber incorporates a plexiglass jacket (for circulation of heated water), and a glass inner chamber where the nervous tissue is incubated with digestive enzymes. Publications arising from neurons dissociated in this chamber:- Patch clamp recording Jiang C. Haddad GG. A direct mechanism for sensing low oxygen levels by central neurons. Proc Natl Acad Sci U S A. (1994), 91(15):7198-201. Single cell microfluorimetry Friedman JE. Haddad GG. Major differences in Ca2+i response to anoxia between neonatal and adult rat CA1 neurons: role of Ca2+o and Na+o. J Neurosci. (1993), 13(1):63-72. **Superfusion ('fully-submerged') brain slice recording chamber** For electrophysiological recordings. The design is two part, consisting of the chamber proper and a separate water jacket for preheating the aqueous perfusate. The recording chamber volume is small (<0.5 ml), enabling very rapid solution exchange (» 20 s). The design is very similar to that reported by Roger Nicolls lab (Nicoll RA. Alger BE. A simple chamber for recording from submerged brain slices. J Neurosci Methods. (1981) 4(2):153-6). **Interface brain-slice chamber** For electrophysiological recordings. When it is desired to maintain brain slices at a gas-liquid interface on a flat plate plexiglass surface. The design is very similar to the original report of this chamber type (Haas HL. Schaerer B. Vosmansky M. A simple perfusion chamber for the study of nervous tissue slices in vitro. J Neurosci Methods. (1979) 1(4):323-5). The chamber consists of a plexiglass plate which sits on a heated humidfying chamber that both heats the perfusate and the gas flowing over the slices. The chamber can incorporate either a heating wire for electrical heating via a thermostatic heating controller, or a stainless-steel tubular coil for circulation of warmed water to heat the chamber. **Enviromental chamber** For exposure of rodents to controlled breathing mixtures. Chamber includes all hardware to maintain a gas-regulated and air-tight envioment including provisions for connection of an internal oxygen probe, and gas flow tubes for mixing of gases. Enquiries can be passed via email sent to michael.croning@yale.edu or directly to:- R. Felix Garcia 745 Orange Apt. 1 New Haven, CT 06511, USA From owner-biophysics@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!206.172.150.11!news1.bellglobal.com!tor-nx1.netcom.ca!news.uunet.ca!not-for-mail From: "jmouse" Newsgroups: bionet.biophysics Subject: Career related to biology Date: Mon, 15 Dec 1997 16:58:05 -0400 Organization: UUNET Canada News Transport Lines: 4 Message-ID: <6749ji$rs8$1@nntp2.uunet.ca> NNTP-Posting-Host: 209.47.93.178 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 i'm doing a project on careers related to biology, can somebody give me some information? (as detail as possible) Thanks. From owner-biophysics@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!www.nntp.primenet.com!globalcenter0!news.primenet.com!nntp.primenet.com!huron.eel.ufl.edu!usenet.eel.ufl.edu!nntp1.jpl.nasa.gov!nntp.earthlink.net!usenet From: prismx@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: This Week's Headlines (5 Dec 97) Date: Thu, 04 Dec 1997 21:45:09 GMT Organization: SCIENCE-WEEK Lines: 45 Message-ID: <6674u6$5gr@suriname.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.166.28 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20985 bionet.biophysics:3801 bionet.cellbiol:8572 bionet.general:28921 Headlines for the current SCIENCE-WEEK (December 5, 1997) (The SW complete weekly news reports are available free via Email. To subscribe, send SUB SW to Reported in This Issue: 1. On the Swiss Constitutional Prohibition of Gene Manipulation 2. U.S. Congressman Advocates Mind Over Body Medicine. 3. A Funding Crisis in Paleontology 4. Mini-Comet Impact Spots May Be Instrumental Artifacts 5. On the Mysteries of the Star Eta Carinae 6. New Evidence Concerning Gamma Ray Blazars 7. On the Lives of Binary Stars 8. A Cloud Scattering Model for the Warming of Early Mars 9. Rotation Differences of Earth's Inner Core and Mantle 10. Discovery of a New Link in the Evolution of Mammals 11. HIV Replication Recovery After Prolonged Repression 12. Total Synthesis of Important New Cytotoxic Agents 13. A Model for Beta-Hairpin Folding in Proteins 14. Complete Sequencing of Genome of Bacillus Subtilis 15. A Receptor Identified as a Key in Cholesterol Transport 16. A Non-Syndromic Deafness Gene and its Function 17. On the Management of Multiple Sclerosis by Drug Therapy 18. Genetic Testing for Cancer Risk 19. Nucleic Acids and the Detection of Cancer 20. Molecular Biology of Human Acute Leukemias 21. Genetic Approaches to the Design of Anti-Cancer Drugs 22. Environmental Risks and Cancer 23. Chemoprevention of Cancer SCIENCE-WEEK is a free retransmission educational resource, which means this headline notice and each issue of SCIENCE-WEEK itself can be retransmitted if intact by any installation. All back issues of SCIENCE-WEEK are available at the URL below. Current issues are posted at the URL 2 to 5 days after first publication. The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uunetukout!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Elaboration on chemical work Date: 16 Dec 1997 09:59:52 -0000 Lines: 55 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <675jeo$hq9@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to Bryant Fujimoto Bryant, my previous message was negative - I tried to show that delta G gives a description of chemical work incompatible with the real energy flow. Let me develop the positive aspect of the concept of chemical work. The example: The reactions A -> B and C -> D are coupled in A + C -> B + D /1/ For one stoichiometric unit of reaction, the energy increase of the C-D system is 10 KJ/mole. On the other hand, as /1/ is close to equilibrium, delta G for the C-D system is -5 KJ/mole. Now we have to choose between two interpretations: 1. According to the second law, the A-B system receives 5 KJ/mole work. 2. In contradiction to the second law, the C-D system receives 10 KJ/mole work. I hope you would agree that the former interpretaion is absurd. There could be no reason in the belief that the energy of the A-B system DECREASES, the energy of the C-D system INCREASES, and yet the A-B system RECEIVES 5 KJ/mole work. This contradicts directly the first law of thermodynamics. As for the latter interpretation, these 10 KJ/mole are REAL energy the C-D system has received. The only problem is whether we can call them WORK. In fact, these 10 KJ are the enthalpy of the reaction C-D, i.e. delta H(C-D) = Q + Wu /2/ You are absolutely right that /2/ is not exactly the work obtained - it includes also Q. On the other hand, physically, this is the only interesting quantity as far as the energy flow is concerned. Let us forget for a while about second law problems and try to sketch the general methodology of bioenergetics. Aren't we to divide the system into subsystems and describe how much energy each subsystem gains or loses? Then of course we may concentrate on mechanisms, but still this general approach seems essential. If so, why should we deal with a definition of chemical work having nothing to do with the energy flow? Just to defend a principle wrongly attributed to living systems? Why don't we just use /2/ as a REAL quantity - we may not call it WORK - let it be "ENERGY INCREASE". As this new methodology develops, we would be able to answer an important question - how energy flows and accumulates in living systems, to juxtapose energy movement with different concepts of order etc. Also, there would be no need at all to refute the second law - it would be clear that to speak of work production occuring in a direction opposite to the real energy flow is just nonsense. However, until this new approach develops, we will continue the unproductive argument about the formal definition of chemical work - whether it is energy of "tendency" etc. Best regards, Pentcho From owner-biophysics@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!TURING.CS.UCY.AC.CY!csfranks From: csfranks@TURING.CS.UCY.AC.CY (Frank Schnorrenberg) Newsgroups: bionet.biophysics Subject: MEDICON'98 - Conference Announcement Date: 16 Dec 1997 09:16:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 260 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net VIII MEDITERRANEAN CONFERENCE ON MEDICAL AND BIOLOGICAL ENGINEERING AND COMPUTING Medicon'98 June 14-17, 1998, Lemesos, Cyprus Organized and Sponsored by: Department of Computer Science, University of Cyprus The Cyprus Association of Medical Physics and Biomedical Engineering Co-Sponsored by: IEEE Engineering in Medicine and Biology Society European Society for Engineering and Medicine In cooperation with: International Federation for Medical and Biological Engineering (IFMBE) Associazione Italiana di Ingegneria Medica e Biologica Croatian Medical & Biological Engineering Society Greek Society for Biomedical Engineering Israel Society for Medical & Biological Engineering Slovene Society for Medical & Biological Engineering Societe des Electriciens et des Electroniciens (Club Francais des Technologies Biomedicales) Spanish Society of Biomedical Engineering Institute of Electrical and Electronics Engineers (IEEE Cyprus Section) Institution of Electrical Engineers (IEE Cyprus Centre) In association with: Cyprus Institute of Neurology and Genetics Higher Technical Institute United Kingdom Liaison Committee for Sciences Allied to Medicine & Biology (S.A.M.B.) PROGRAMME COMMITTEE D Adam (Israel) J P Morucci (France) K Athanasiou (USA) A Nicolaides (UK) T Bajd (Slovenia) M Nyssen (Belgium) M Bracale (Italy) N Ouzounoglou (Greece) J E W Beneken (Netherlands) N Pallikarakis (Greece) S Cerutti (Italy) P Rabichong (France) A G Constantinides (UK) L M Roa (Spain) K Copeland (UK) V C Roberts (UK) G Dimitrov (Bulgaria) M Sawan (Canada) N Dimitrova (Bulgaria) S Sideman (Israel) U. Faust (Germany) J A E Spaan (The Netherlands) H Hutten (Austria) V A Spasic (Yugoslavia) G Inbar (Israel) N Sphiris (Greece) F Kajiya (Japan) U Stanic (Slovenia) Z Kollitsi (Greece) Y Istefanopoulos (Turkey) K Kouris (Cyprus) D Tsaptsinos (UK) D Koutsouris (Greece) K Turker (Australia) I Krekule (Czech Republic) E M Tzanakou (USA) S Laxminarayan (USA) N Zamboglou (Germany) R Magjarevic (Croatia) ORGANIZING COMMITTEE Conference Co-Chairs: Stelios Christofides (CAMPBE, Cyprus), : Constantinos S Pattichis (University of Cyprus, Cyprus) Program Chair : Christos N Schizas (University of Cyprus, Cyprus) International Chair : Elpida Keravnou-Papailiou (University of Cyprus, Cyprus) Exhibits Chair : Yiannis Theodoulou (CAMPBE, Cyprus) Treasurer : Prodromos Kaplanis (CAMPBE, Cyprus) Publications : Spyros Spyrou (Higher Technical Institute, Cyprus) Social Program : George Christodoulides (CAMPBE, Cyprus) Medicon'98 is the 8th in the series of regional meetings in the Mediterranean of the International Federation for Medical and Biological Engineering (IFMBE). The goal of Medicon'98 is to provide updated information on the state of the art on Medical and Biological Engineering and Computing. The program will consist of both invited and submitted papers on new developments in these fields. Medicon'98 will focus primarily on the following topics: TOPICS OF INTEREST * Biomechanics/Implants * Biosignal Processing and Analysis * Cardiovascular Systems * Cellular Engineering * Clinical Engineering * Health Care Technology Assessment * High Performance Computing in Medicine * Instrumentation * Intelligent Systems in Medicine * Medical Imaging * Medical Multimedia Workstations and Databases * Models of Physiological Systems * Neuromuscular Systems * Patient Monitoring * Radiation Protection * Radiotherapy * Rehabilitation Engineering * Telemedicine * Virtual Reality in Medicine SPECIAL SESSIONS Proposals for plenary and special sessions are invited. For further details please contact Constantinos Pattichis, by January 30, 1998. KEYNOTE LECTURES * Information Technology in Biomedicine Leaping into 2000, Swamy Laxminarayan (USA) * Integrated Telemedicine Networks and Added Value Services, Stelios Orphanoudakis (Greece) * Computational Intelligence: Status and Trends in Medical Diagnostic Systems, Evangelia Micheli-Tzanakou (USA) BEST STUDENT PAPER AWARDS In memory of Dick Poortvliet, dinstinguished biomedical engineer and active member of IEEE Region 8, the IEEE Cyprus Section will organize during Medicon'98 a student paper contest. To qualify, a student or group of students must contribute a significant part of the paper and be the primary author(s). The submission should clearly indicate that the paper is to be considered for the best student paper award, the amount of contribution made by the student, the current level of study, and the address including fax or e-mail. INTERNATIONAL EXHIBITION The conference will provide the attendees with the opportunity of examining state-of-the-art technology (in biomedical and medical physics instrumentation, computer hardware and software) and establishing useful interactions with representatives of manufacturers, vendors, and publishers. PAPER SUBMISSION Papers are invited, but not limited, to theabove topics of interest. Authors are stongly encouraged to submit a PostScript version of their full paper by anonymous ftp to zeus.cc.ucy.ac.cy, and put the paper in the directory /incoming/medicon98. Files should be uniquely named: .ps. In addition, authors should notify by e-mail to med98@turing.cs.ucy.ac.cy the title of the paper, the corresponding author and address, and the first two choices for the topics of interest as given above, under which the paper can be classified. Alternatively, papers can be submitted in paper format (one original and two copies). These submissions should be accompanied with a diskette with the paper in MS Word format, or TEX on IBM PC or MAC, including all figures. In an accompanying letter, authors should specify the title of the paper, the corresponding author and address, and the first two choices from the topics of interest as given above, under which the paper can be classified. The papers must be completed within 6 pages, including figures, tables and references, and should be written in English. An A4 size format with 2,5 cm margin on all four sides should be used. They should be prepared in one-column format, single spaced, in Arial or similar type style of 10 points. Centered at the top of the first page should be the complete title, author name(s), affiliation(s) and mailing address(es), including electronic mailing(s) address(es). This is followed by a blank space and then the abstract, up to 15 lines, followed by the main text. Submission of a proposed paper implies a commitment from one of the authors to present the paper if accepted. ADDRESS FOR PAPER SUBMISSIONS Medicon'98, Department of Computer Science, University of Cyprus, 75 Kallipoleos Str, P.O. Box 537, CY-1678 Nicosia, CYPRUS. CONFERENCE PROCEEDINGS Submitted papers will be reviewed by at least two referees and all accepted papers will be published on CD-ROM. A copy of the proceedings will be given to each participant at the conference. After the conference, the proceedings will be available from the publisher. A few selected authors will be invited to publish extended versions of their papers in a special issue of the IEEE Transactions on Information Technology in Biomedicine (T-ITB). All papers submitted for publication in the Transactions will be subject to a further peer-review process prior to publication in the T-ITB. AUTHORS SCHEDULE * Paper submission January 30, 1998 (Receival acknowledgment will follow) * Notification of acceptance March 30, 1998 (List of all accepted papers will be posted at the WWW page of the conference) REGISTRATION Full conference registration fee includes admission to all sessions, welcome reception, and a copy of the proceedings. Early registration is highly recommended in order to save both time and money. Early registration (before April 30, 1998) Cyp.Pounds 140 Late registration (after April 30, 1998) Cyp.Pounds 160 Students Cyp.Pounds 70 Note: Cyp.Pound 1 ~= US$2 Make all cheques payable to CYDEM TOURS Ltd or charge your Credit card. Mail or fax your payment to the address of the official travel agent. OFFICIAL TRAVEL AGENT Aristos C Demetriou, CYDEM TOURS Ltd, P.O. Box 4134, Nicosia, CYPRUS. Tel: +357-2-773865/451300, Fax: +357-2-457297, Email: cydem@spidernet.com.cy. ABOUT CYPRUS Cyprus is an island situated at the north-east corner of the Mediterranean Sea at the cross-roads of three continents, Europe, Asia and Africa. Its geographically significant position both for trade and military purposes has been one of the main reasons for Cyprus' turbulent history. The passing from the island of different conquerors has helped to blend the character of the Cypriots. Here the visitor may enjoy magnificent pottery and sculpture, ancient ruins all over the island, Byzantine monasteries, churches and medieval monuments of great architectural value. The people of Cyprus are traditionally warm and welcoming. Their language is Greek but English is spoken in all shops, restaurants, hotels, banks and government offices. Life on the island is leisurely and safe. Greek food should be tried. Greek Meze, consisting of as many as thirty dishes, starting with salads, dips, tasty local dishes and kebabs is something the visitor should not miss. CLIMATE Cyprus has what is called a Mediterranean climate, that is hot summers but moderate winters. July and August are the hottest months. Temperatures during the day vary from 32 - 38 deg. C, so bring light clothes, sandals and sunglasses. Temperature falls during the evening but remains warm. Sea water is warm and inviting so don't forget your swimsuits. TRANSPORT Cyprus is easily accessible by air. Larnaca airport is forty-five minutes drive from the Hawaii Beach Hotel at Lemesos. A taxi ride from the airport costs around Cyp.Pounds 20. Pafos airport on the other hand is one hour and twenty minutes drive from the Hotel at Lemesos and costs around Cyp.Pounds 30 by taxi. MORE INFORMATION Constantinos S Pattichis Department of Computer Science University of Cyprus 75 Kallipoleos Street, CY-1678 Nicosia CYPRUS Tel no : +357-2-338705/06 Fax no : +357-2-339062 Email : pattichi@turing.cs.ucy.ac.cy Stelios Christofides Medical Physics Department Nicosia General Hospital P.O. Box 4039 CY-1450 Nicosia CYPRUS Tel no : +357-2-301306 Fax no : +357-2-369170 Email : g.h.library@cytanet.com.cy INFORMATION ON WWW Please refer to this WWW page. It contains the latest information for Medicon'98. URL : http://www.ucy.ac.cy/ucy/cs/med98/med98.htm From owner-biophysics@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!newsfeed2.uk.ibm.net!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.biophysics Subject: Definition of work (for Pentcho) Date: Tue, 16 Dec 1997 15:39:02 +0200 Organization: Hebrew University Lines: 19 Message-ID: <67609n$mgj$1@news.huji.ac.il> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Pentcho raised the difficulty of defining chemical work. Perhaps the following general definition of work will be useful:- "Work performed on a system is the act of moving that system away from equilibrium". In a sense, this simply restates an aspect of the second law of thermodynamics, so Pentcho will object. On the other hand this definition appears applicable to work in all its forms. -- Jonathan B. Marder Department of Agricultural Botany, The Hebrew University of Jerusalem Faculty of Agriculture, P.O.Box 12, Rehovot 76100, ISRAEL Phone: +972 8 9481918 Fax: +972 8 9467763 Web page: http://www.agri.huji.ac.il/~marder From owner-biophysics@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed2.uk.ibm.net!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.biophysics Subject: Re: Elaboration on chemical work Date: Tue, 16 Dec 1997 15:29:25 +0200 Organization: Hebrew University Lines: 21 Message-ID: <675vnn$lth$1@news.huji.ac.il> References: <675jeo$hq9@mserv1.dl.ac.uk> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Pentcho Valev wrote in message +ADw-675jeo+ACQ-hq9+AEA-mserv1.dl.ac.uk+AD4-... ... +AD4-Let me develop the positive aspect of the concept of chemical work. +AD4- +AD4-The example: The reactions A -+AD4- B and C -+AD4- D are coupled in +AD4- +AD4- A C -+AD4- B D /1/ +AD4- +AD4-For one stoichiometric unit of reaction, the energy increase of the C-D +AD4-system is 10 KJ/mole. On the other hand, as /1/ is close to equilibrium, +AD4-delta G for the C-D system is -5 KJ/mole. ... Pentcho, you've lost me already. What is the +ACI-energy increase+ACI- of C-D and how can it be different to deltaG? This is a blatant contradiction. If /1/ is at equilibrium, and deltaG or C-+AD4-D is -5 kJ/mol, then this means that deltaG for A-+AD4-B is +-5 kJ/mol. Anything else is incorrect. From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!MARA.FI.UBA.AR!icie96 From: icie96@MARA.FI.UBA.AR (1995 Congress) Newsgroups: bionet.biophysics Subject: ICIE 98 Date: 16 Dec 1997 16:53:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 83 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net =09=09=09LLAMADO A LA PRESENTACION DE TRABAJOS =09=09IV CONGRESO INTERNACIONAL EN INGENIERIA INFORMATICA =09=09=09=09=09ICIE'98 =09=09=09=09 16 y 17 de Abril de 1998 =09=09=09=09Departamento de Computacion. =09=09=09=09 Facultad de Ingenier=A1a =09=09=09=09Universidad de Buenos Aires. =09=09=09=09=09ARGENTINA Por cuarto an^o consecutivo se desarrolla el CONGRESO INTERNACIONAL EN=20 INGENIERIA INFORMATICA, organizado por el Departamento de Computacion de la Facultad de Ingenier=A1a de la Universidad de Buenos Aires.=20 El mismo se llevara a cabo los d=A1as 16 y 17 de abril de 1998. Pueden ser presentados trabajos de todas las =A0reas de aplicacion que se= =20 encuadren dentro de las siguientes caracter=A1sticas: 1) Resultados de trab= ajos=20 de investigacion en el area de aplicacion, 2) Soluciones a problemas en la industria, los negocios el gobierno o areas relacionadas o 3) Propuestas Acadamicas o Tecnologicas innovadoras. Los temas del congreso abarcan: Sistemas Basados en Conocimiento, Redes Neuronales, Sistema Difusos,=20 Inteligencia Artificial, Bases de Datos, Algebra Computacional, Lenguajes d= e Computacion, Tecnolog=A1a Orientada a Objetos, Multimedia, Vision por=20 Computadora, Robotica, Networking, Ingenier=A1a de Software, Investigaci=A2= n=20 Operativa, Sistemas Distribuidos y Redes, Sistemas de Tiempo Real,=20 Educacion en Informatica y otras =A0reas relacionadas. Las personas o grupos de investigacion y desarrollo interesadas en presentar su trabajos deben enviar un resumen (500 palabras) por e-mail=20 a: icie@mara.fi.uba.ar o cuatro (4) copias escritas en espan^ol, portugues o ingles a: Comite de Programa ICIE '98. Departamento de Computacion. Facultad de Ingenier=A1a. Universidad de Buenos Aires. Paseo Colon 850. 4to Piso. (1063) Capital Federal. ARGENTINA. En caso de hacerlo por correo normal se agradecer=A0 la inclusion de un=20 disquete con el archivo correspondiente, el cual debe estar escrito en=20 letra Arial o Times New Roman, de un taman^o de 12 puntos, espaciado sencillo y un maximo de 15 paginas en tama=A4o A4. Los margenes deben ser de 2,5 cm por lado. Las paginas deben ser numeradas en lapiz en la parte posterior y en la primer hoja se debe indicar tambien el area de aplicacion al que pertenece el trabajo. FECHAS IMPORTANTES Presentacion de resumenes:=0906/02/98 Comunicacion de Aceptacion:=0906/03/98 Presentacion de la version definitiva:=0913/03/98 Tanto la version de evaluaci=A2n como la version definitiva puede ser enviada por e-mail a icie@mara.fi.uba.ar en formato RTF. La presentacion de un trabajo facultara al Departamento de Computacion de la Facultad de Ingenier=A1a de la Universidad de Buenos Aires a publicarlo = en=20 los Anales del ICIE' 98. No obstante es conveniente adjuntar una autorizacion con la firma de sus autores. Los trabajos recibidos despues de los plazos establecidos no seran incluidos en los Anales. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Comite de Programa ICIE '98. Departamento de Computaci=A2n. Facultad de Ingenier=A1a. Universidad de Buenos Aires. Paseo Col=A2n 850. 4to Piso. (1063) Capital Federal. ARGENTINA. e-mail: icie96@mara.fi.uba.ar =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!207.97.14.174!europa.clark.net!152.158.16.55!newsfeed2.uk.ibm.net!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.biophysics Subject: Re: Definition of chemical work Date: Wed, 17 Dec 1997 11:49:56 +0200 Organization: Hebrew University Lines: 61 Message-ID: <678787$31a$1@news.huji.ac.il> References: <677u9l$hlc@mserv1.dl.ac.uk> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Pentcho Valev wrote in message +ADw-677u9l+ACQ-hlc+AEA-mserv1.dl.ac.uk+AD4-... +AD4- +AD4-Jonathan Marder wrote:+AD4- ... +AD4- +ACI-Work performed on a system is the act of moving that system away from +AD4-equilibrium+ACI-. ... +AD4- +AD4-Yes Jonathan I object but not simply because you redefine delta G as a +AD4-measure of chemical work. This definition contradicts our basic +AD4-understanding of physical reality. If this contradicts your understanding of physical reality, then we obviously understand physical reality differently. +AD4-Please consider a most general picture: +AD4- +AD4-A system does work, isothermally, on the surroundings. How? First problem, once you say +ACI-isothermally+ACI- it is already unclear where your system begins and ends. Are the heat sources/sinks part of the system? +AD4-There are two possibilities: +AD4- +AD4-1. The system uses its internal energy for doing work. Obviously in this +AD4-case its internal energy decreases in the process. Yes, the system moves TOWARDS equilibrium, so is able to DO work. This is my definition applied in the opposite direction. +AD4- +AD4-2. The system, like an ideal gas, uses external energy for doing work. +AD4-In this case its internal energy remains the same. +AD4- Now you have a different system which includes the external energy source. Entry of energy from the external source moves the combined system towards equilibrium - same applies as above. +AD4-Please note that in both cases the internal energy of the system CANNOT +AD4-INCREASE. Now your definition allows the system, in principle, to +AD4-INCREASE its internal energy while doing work. If, in the second case, the system is extended to include the external energy source, your statement becomes invalid. Regards, Jonathan B. Marder +ADw-MARDER+AEA-agri.huji.ac.il+AD4- Department of Agricultural Botany, The Hebrew University of Jerusalem Faculty of Agriculture, P.O.Box 12, Rehovot 76100, ISRAEL Phone: +-972 8 9481918 Fax: +-972 8 9467763 Web page: http://www.agri.huji.ac.il/+AH4-marder From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.biophysics Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Dec 1997 02:00:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712171000.CAA14853@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Definition of chemical work Date: 17 Dec 1997 07:17:09 -0000 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <677u9l$hlc@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Jonathan Marder wrote:>>>>>>>>>>>>>>>>>>> Pentcho raised the difficulty of defining chemical work. Perhaps the following general definition of work will be useful:- "Work performed on a system is the act of moving that system away from equilibrium". In a sense, this simply restates an aspect of the second law of thermodynamics, so Pentcho will object. On the other hand this definition appears applicable to work in all its forms.<<<<<<<<<<<<<<<<<<<< Yes Jonathan I object but not simply because you redefine delta G as a measure of chemical work. This definition contradicts our basic understanding of physical reality. Please consider a most general picture: A system does work, isothermally, on the surroundings. How? There are two possibilities: 1. The system uses its internal energy for doing work. Obviously in this case its internal energy decreases in the process. 2. The system, like an ideal gas, uses external energy for doing work. In this case its internal energy remains the same. Please note that in both cases the internal energy of the system CANNOT INCREASE. Now your definition allows the system, in principle, to INCREASE its internal energy while doing work. Here is the crux of the problem. The second law is a principle forbiding an alleged absurdity in physical reality - e.g. cyclical isothermal conversion of heat into work. However its extension in the chemical world leads to another absurdity - a system which does work on the surroundings and increases its internal energy in the process. We are to choose - if one is absurdity, the other is not, and vice versa. Best regards, Pentcho From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news.kfa-juelich.de!aix.zam.kfa-juelich.de!med050 From: med050@aix.zam.kfa-juelich.de (d.gembris) Newsgroups: bionet.neuroscience,bionet.biophysics,de.sci.biologie,sci.med.physics,sci.techniques.mag-resonance,sci.med.informatics Subject: Re: Announcement: new brain-research WWW site Date: 17 Dec 1997 15:51:06 GMT Organization: Forschungszentrum Juelich GmbH (KFA) Lines: 12 Distribution: world Message-ID: <678sda$cr6@zam201.zam.kfa-juelich.de> References: <671j1k$llk@zam201.zam.kfa-juelich.de> NNTP-Posting-Host: aix.zam.kfa-juelich.de Keywords: fMRI, BOLD, MR, MRI, functional MR, modelling, Xref: biosci bionet.neuroscience:20993 bionet.biophysics:3811 To all webmasters of MR-sites: Could you please set a link to our pages? We have already set links to several other MRI-Sites. If you do so please notify me with a short eMail: d.gembris@fz-juelich.de Thanks a lot. Daniel Gembris Research Center Juelich From owner-biophysics@net.bio.net Tue Dec 16 22:00:00 1997 Path: biosci!agate!logbr