From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!news1.chicago.iagnet.net!iagnet.net!nntp.earthlink.net!usenet From: prismx@scienceweek.com (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: Headlines (2 Jan 98) Date: Fri, 02 Jan 1998 20:28:00 GMT Organization: SCIENCE-WEEK Lines: 54 Message-ID: <68jf90$10m@bolivia.earthlink.net> Reply-To: prismx@scienceweek.com NNTP-Posting-Host: 153.36.139.25 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:21057 bionet.biophysics:3864 bionet.cellbiol:8610 bionet.general:29044 SCIENCE-WEEK is a free weekly Email digest of the news of science read each week by 40,000+ people in the scientific community in more than 30 countries. 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All back issues of SCIENCE-WEEK are available at the URL below. Current issues are posted at the URL 2 to 5 days after first publication. The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@scienceweek.com http://scienceweek.com From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: What is a reversible chemical reaction? Date: 2 Jan 1998 14:21:28 -0000 Lines: 83 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68it58$ap0@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>>>>>> What does thermodynamics mean by a reversible process? How do you get a chemical reaction to proceed revesibly?<<<<<<<<<<<<<<<<<<<< Bryant, your question is important. Thermodynamics has given NO general answer to that question - there are only particular examples - e.g. galvanic reactions can be carried our reversibly. As for some standard solute reaction, e.g. A <-> B /1/ it is only implicitly assumed that small shifts of /1/ near equilibrium can be regarded as reversible. Do you accept this? Please note that this time it would not be enough just to hint at my ignorance - it is not my but rather your duty to show how one gets /1/ to proceed reversibly. Otherwise dS = dQ/T may prove to be a fiction. As I suspect that any reversible shifts of /1/ can only occur as /1/ is at equilibrium, let me develop a statement of yours repeated in your last postings. You said that a reaction can be shifted from equilibrium by doing work. In fact, this is a reformulation of the second law which I accept: (I) "If a chemical system is at equilibrium, ONLY WORK can shift it under isothermal conditions" An equivalent formulation reads: (II) "Entropy CANNOT be a function of the state for a chemical system". The proof that the two formulations are equivalent is elementary. By doing work, a small isothermal shift of the system at equilibrium is performed, but then the system returns to its initial state spontaneously. On its way back, the system only exchanges heat with the surroundings. On its way forward, it undergoes the same change in internal energy, but this time work is added to the heat: delta U = Qforward + Wforward = -Qback /2/ Obviously Wforward = -(Qforward + Qback) =/= 0 /3/ The last equation suggests a third formulation of the same principle: (III) "The maximum work that can be extracted from a chemical reaction isothermally and isobarically is equal to the enthalpy of reaction. This work is independent of both the concentrations and the distance from equilibrium." Under isothermal and isobaric conditions, Qback is equal to the enthalpy of reaction. If Qforward is zero, /3/ gives the third formulation. The enthalpy is indeed independent of both the concentrations and the distance from equilibrium. There is a fourth equivalent formulation of the same principle: (IV) "If the reactions A -> B and C -> D are coupled in A + C -> B + D /4/ the product of their equilibrium constants K1 and K2 is (K1)(K2) = Kc /5/ where Kc is the equilibrium constant of the coupled reaction /4/." Indeed, if /5/ were not true, both A -> B and C -> D would be shifted and kept away from their own equilibriums, what would contradict the first formulation of the principle. As you can see, the problem is rather serious - some of the formulations are already in use in chemical thermodynamics (e.g. many delta G interpretations can be derived from /5/), but there are also contradictions with the classical formulations of the second law. I hope you would agree that resolving the problems is much more important than just demonstrating someone's competence or incompetence. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 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: Verification of the second law Date: 2 Jan 1998 04:36:23 GMT Organization: University of Washington Lines: 125 Distribution: bionet Message-ID: <68hqs7$bdm$1@nntp3.u.washington.edu> References: <68gcs1$hkh@mserv1.dl.ac.uk> NNTP-Posting-Host: homer04.u.washington.edu X-Trace: nntp3.u.washington.edu 883715783 11702 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Happy New Year to Everybody| >In reply to Bryant Fujimoto >Bryant, you seem to believe that supportive calorimetric or statistical >mechanical evidence is enough - no further verification of the second law >is needed. I am not competent in these matters, but some time ago I was >interested in enthalpy determination by using van't Hoff's equation. Both >the equation and the method are exact (there are no empirical >assumptions) and yet the ambiguity is enormous - there are direct >recognitions that the method rarely gives reliable results. As far as I >remember, this enthalpy is even given a special name - van't Hoff enthalpy, >as opposed to calorimetric enthalpy with which it rarely coincides. The reason for this is well known. When you determine enthalpies via the van't Hoff formula, you have to assume that Delta H for the reaction is independent of temperature. It isn't. If you do the necessary calorimetric measurements, you can obtain the experimentally measured equilibrium constants as a function of temperature from the calorimetric measurements, and from that you can obtain the van't Hoff enthalpy. >If measurements of this kind are not very reliable for purely practical >purposes, how do you expect that they could tell us something about a >principle as subtle as the second law? Moreover, the second law can only >be disproved in terms of counterexamples - any amount of supportive evidence >is insufficient to compensate for a single counterexample. It is certainly true that you need only a single counterexample to disprove the second law. So where is it? >So I find your >refering to supportive evidence not quite correct - on one hand, it is >irrelevant to the problem of disprovability of the second law; on the other, >you are not concrete - you do not present for discussion any example showing >how a particular result proves (or at least supports) the second law. Your criticism of calorimetry isn't valid and it is not the only evidence I cited. So you still need to explain why the ability to predict the relationships between a wide variety of measured macroscopic parameters does not constitute a test. You also need to demonstrate that you understand what thermodynamics says. I'm waiting for you to demonstrate thay you know what thermodynamics means when it says a process is reversible. I'm also waiting some evidence that you understand the first law. I saw a recent post of yours on another newsgroup where you repeat the contention that work is equal to the energy transfered. Since this contradicts the first law, you should tell us why you don't like the first law. However, what we really are waiting for is an experiment for which thermodynamics will make the wrong prediction. Since you seem certain that such an experiment does exist, why should I spend time looking up references for you? You wouldn't pay any attention to them anyway, you seem to think them irrelevant. >Now it is your turn to tell me why you refuse to take a definition of the >second law and verify the law in terms of this definition. As I was dealing >with the definition "Heat cannot, cyclically and isothermally, be converted >into work" you did not like the presence of "work" in it and seemed to choose >"Entropy is a function of the state". But this definition presupposes >analysing chemical cycles - a function of the state is only compatible with >the idea of a system undergoing a cycle and returning to the initial state. The predictions that thermodynamics makes about calorimetry, equilibrium constants, etc. are derived from the statements of the laws of thermodynamics. If the second law isn't right, then these predictions will fail. To date, they haven't failed. You need to come up with some reason why the predictions will all be satisfied even if the second law is incorrect. If you cannot, then they qualify as a test of the second law. In that case I have taken a definition of the second law and described how to test it. (Incidently, your attempt to restate the definition of the second law which I'm using is incomplete.) >If we came to an agreement that any statement, even the second law, should >be verified, we would easily reach a surprising conclusion: "The entropy >is NEVER a state function for chemical systems", i.e. if a chemical system >undergoes an isothermal reversible cycle, the heat absorbed is never zero >except for degenerate cycles (for which the forward and backward paths >coincide). Maybe we shall still be arguing for a while about insignificant >matters, >but then do what should have been done 100 years ago - analyse an isothermal >reversible chemical cycle and see whether the heat absorbed is zero or not. Pentcho In your argument that the entropy is not a state function for chemical systems, you stated that you needed to find a way to move a particular reaction reversibly. You have previously described performing processes reversibly which I don't think can be performed reversibly. This is why I have asked if you know what thermodynamics means by the reversible (I'm still waiting). Also, though you acknowledged in that earlier post that it was your responsibility to show that the cycle was possible, you now seem to be claiming that the cycle is possible with out presenting any evidence that it is, and that the heat absorbed will not be zero. You need to provide some evidence for your claims. Furthermore, I did respond to your original discussion of your chemical cycle. I pointed out that your claim that on the second part of your chemical cycle that only heat is being transfered is incorrect. Work is being done and some heat may or may not have been transfered. This is also true in the first part of your cycle. You need to figure out how to perform your cycle reversibly, and then to how to measure and describe the heat transfer in _both_ parts of your cycle. You haven't done so. I pointed this out earlier, you haven't responded to my comment. One final complication you will have to deal with, the definition of the entropy in terms of the heat transfer for a reversible process assumes that the system is closed with respect to the transfer of matter. If you want to take the reactant and product molecules as your system, then this will only be true for a purely intramolecular rearrangement reaction. So to sum up, 1) What does thermodynamics mean by a reversible process? How do you get a chemical reaction to proceed reversibly? 2) What does the first law of thermodynamics say? And why do you claim that the energy transfered equals the work, since that contradicts the first law? 3) Why is testing the predictions made by the laws of thermodynamics not a valid test of those laws? 4) Where is your counter example? Regards, Bryant From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!TUNA.NET!amiller From: amiller@TUNA.NET ("Andrew Miller") Newsgroups: bionet.biophysics Subject: free medical image 3D visualization software for indows95/NT Date: 1 Jan 1998 16:56:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980102005522823.AAA178@Meldar> NNTP-Posting-Host: net.bio.net Hello, Just to let you know there's free medical image 3D visualization software (called NeuroModeller) for the Wintel environment available at: http://www.freeyellow.com/members2/amiller/index.html (version 1.07) http://users.infohouse.com/amiller/home.htm (version 1.06) .... download file size is 640 KB. NeuroModeller is a research effort of Cornell Medical Center, Division of Neurosurgery. Sincerely, Andrew Miller, MD amiller@infohouse.com From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!newsfeed.eerie.fr!news-feed.inet.tele.dk!bofh.vszbr.cz!news.dknet.dk!not-for-mail From: Dan Pedersen Newsgroups: bionet.biophysics Subject: Spreadsheet invention Date: Fri, 02 Jan 1998 01:06:41 +0100 Organization: ProFunda Lines: 20 Message-ID: <34AC2F6A.7E1E@pip.dknet.dk> Reply-To: profunda@pip.dknet.dk NNTP-Posting-Host: cph252.ppp.dknet.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Dear Scientist, My partner Henrik Kjaer and I have developed a new spreadsheet in which - from the top-level you can copy/paste/fill text/values/formulas from/into the layers. >From interviews with scientists in biology/chemical/economical/math areas we learned that the new flexibility is an advantage when working with layers of data in these branches. To further discuss and develop the invention we need input from the users working in your areas. Therefore we should be glad if those interested would go to http://isa.dknet.dk/~profunda to view our invention and give us your opinion. There is a demo of the first version too - that Mac-users can download for free (soon also Windows), and you can register to receive info in future too. Thanks in advance - and have a nice day, Dan Pedersen From owner-biophysics@net.bio.net Thu Jan 01 22:00:00 1998 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 is a reversible chemical reaction? Date: 2 Jan 1998 21:30:30 GMT Organization: University of Washington Lines: 139 Distribution: bionet Message-ID: <68jm9m$rrm$1@nntp3.u.washington.edu> References: <68it58$ap0@mserv1.dl.ac.uk> NNTP-Posting-Host: homer30.u.washington.edu X-Trace: nntp3.u.washington.edu 883776630 28534 (None) 140.142.64.6 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant Fujimoto wrote:>>>>>>>>>>>>>>> >What does thermodynamics mean by a reversible process? How do you get >a chemical reaction to proceed revesibly?<<<<<<<<<<<<<<<<<<<< >Bryant, your question is important. Thermodynamics has given NO general >answer to that question - there are only particular examples - e.g. Wrong. Thermodynamics does define what it means by reversible. There may be more than one way of defining it, but definitions exist. >galvanic reactions can be carried our reversibly. As for some standard >solute reaction, e.g. > A <-> B /1/ >it is only implicitly assumed that small shifts of /1/ near equilibrium >can be regarded as reversible. Do you accept this? Please note that this >time it would not be enough just to hint at my ignorance - it is not my >but rather your duty to show how one gets /1/ to proceed reversibly. >Otherwise dS = dQ/T may prove to be a fiction. >As I suspect that any reversible shifts of /1/ can only occur as >/1/ is at equilibrium, let me develop a >statement of yours repeated in your last postings. You said that a reaction >can be shifted from equilibrium by doing work. In fact, this is a >reformulation of the second law which I accept: >(I) >"If a chemical system is at equilibrium, ONLY WORK can shift it under >isothermal conditions" >An equivalent formulation reads: >(II) >"Entropy CANNOT be a function of the state for a chemical system". >The proof that the two formulations are equivalent is elementary. By doing >work, a small isothermal shift of the system at equilibrium is performed, >but then the system returns to its initial state spontaneously. Are you really sure the spontaneous part is reversible? If its not, your proof fails. This is why its important that you understand what themodynamics means by reversible. And you have completely ignored the question of how you get a reaction to proceed reversibly. >On its way >back, the system only exchanges heat with the surroundings. On its way >forward, it undergoes the same change in internal energy, but this time >work is added to the heat: > delta U = Qforward + Wforward = -Qback /2/ What makes you so sure there is no Wback? Maybe the back reaction does work on the solvent. This is certainly true if there is any interchange of atoms between the molecules of the reaction and the solvent. (e.g. a water molecule involved in a hydrolysis reaction.) >Obviously > Wforward = -(Qforward + Qback) =/= 0 /3/ >The last equation suggests a third formulation of the same principle: >(III) >"The maximum work that can be extracted from a chemical reaction isothermally >and isobarically is equal to the enthalpy of reaction. This work is >independent of both the concentrations and the distance from equilibrium." Since (Delta H) = Q + Wu, (III) is clearly wrong. A very good example is when Q is positive and Wu is negative. In that case the magnitude of Wu is larger than (Delta H). >Under isothermal and isobaric conditions, Qback is equal to the enthalpy of >reaction. Only if Wback is zero. >If Qforward is zero, /3/ gives the third formulation. The enthalpy >is indeed independent of both the concentrations and the distance from >equilibrium. Only if Wforward is independent of concentration, what reason is there for believing it is? >There is a fourth equivalent formulation of the same principle: >(IV) >"If the reactions A -> B and C -> D are coupled in > A + C -> B + D /4/ >the product of their equilibrium constants K1 and K2 is > (K1)(K2) = Kc /5/ >where Kc is the equilibrium constant of the coupled reaction /4/." >Indeed, if /5/ were not true, both A -> B and C -> D would be shifted and >kept away from their own equilibriums, what would contradict the first >formulation of the principle. You haven't explained why (IV) is equivalent to the other statements, or why it is a problem for thermodynamics. >As you can see, the problem is rather serious No it isn't. >- some of the formulations are >already in use in chemical thermodynamics (e.g. many delta G >interpretations can be derived from /5/), but there are also contradictions >with the classical formulations of the second law. I hope you would agree >that resolving the problems is much more important than just demonstrating >someone's competence or incompetence. Pentcho I believe you once expressed a desire to rexamine thermodynamics critically to see if it really was a viable theory (or words to that effect). How do you expect to do that if you don't understand how the theory is formulated or what it predicts? This is why I keep asking about the definition of reversiblity. I don't see how you intend to resolve anything if you present arguments which use a particular term when it appears that you don't understand what it means. And the definition of reversibility is just one example. You have ignored my other questions, all of which I feel involve the issues you are trying to resolve. 1) What does thermodynamics mean by a reversible process? How do you get a chemical reaction to proceed reversibly? 2) What does the first law of thermodynamics say? And why do you claim that the energy transfered equals the work, since that contradicts the first law? 3) Why is testing the predictions made by the laws of thermodynamics not a valid test of those laws? 4) Where is your counter example? Regards, Bryant From owner-biophysics@net.bio.net Fri Jan 02 22:00:00 1998 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!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Reversibility of chemical reactions Date: 3 Jan 1998 11:53:04 -0000 Lines: 48 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68l8r0$scl@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>>>>> And you have completely ignored the question of how you get a reaction to proceed reversibly.<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Bryant, I do not think your question is fair enough. Years ago that was my central argument against chemical thermodynamics - the second law is defined in terms of reversible processes (dS = dQ/T), ant yet there is no way to get a (standard solute) reaction to proceed reversibly. For instance, for the reaction A -> B /1/ it is said that the maximum work that can be extracted is delta G = delta Go + RTln((B)/(A)) /2/ but then it is often forgotten that this maximum work done on another reaction, e.g. C -> D, presupposes that the coupled reaction A + C -> B + D /3/ is carried out REVERSIBLY. When is /3/ carried out reversibly, Bryant? So that the maximum work /2/ is done? You and others have agreed many times that it is when /3/ is CLOSE TO EQUILIBRIUM, i.e. if a chemical reaction is close to equilibrium, we can regard any shifts in that region as REVERSIBLE and, accordingly, apply what thermodynamics says about reversible processes - dS is dQ/T, chemical work is maximal etc. I would agree that, if the reaction is close to equilibrium, the movements in the region are not exactly "carried out" in the sense in which a galvanic reaction is carried out reversibly. But this is a problem of chemical thermodynamics - if these processes are not reversible, which ones are? Bryant, I will anwer all your questions, but for the moment I see this particular problem of reversibility as much more important than anything else. I believe I have found a new, "chemical" version of the second law which is in fact in use in chemical thermodynamics but which is wrongly related to the classical definition ("Entropy is a function of the state"). So I would be very grateful if you just help me in the following two possible ways: 1) If you agree that processes close to equilibrium can be regarded as reversible, please state it clearly so that I can present the new theory much better (things have been quite confused so far). 2) If you disagree, please explain how a chemical reaction can proceed reversibly so that dS = dQ/T, the chemical work extracted is maximal etc. Best regards, Pentcho From owner-biophysics@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: An alternative version of the second law for chemical systems Date: 3 Jan 1998 14:05:21 -0000 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68lgj1$3mm@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In a posting of 2 January named "What is a reversible chemical reaction" I tried to develop an alternative version of the second law for chemical systems which is in fact used in practice but which contradicts the classical version. I forgot to add that, on 16 December 1997, Jonathan Marder presented an equivalent formulation in a posting named "Definition of work (for Pentcho)". 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.<<<<<<<<<<<<<<<< This definition has extremely interesting implications - I still believe that alternative developments deserve attention, even if they question the validity of what seem to be unquestionable truths. Best regards, Pentcho From owner-biophysics@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!news-peer-west.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.wli.net!feed.nntp.acc.ca!204.92.54.104.MISMATCH!news.ican.net!not-for-mail From: Academic Assistance Access Newsgroups: bionet.biophysics Subject: Tutors Needed for PHYSICS Mailing List Date: 03 Jan 98 12:32:14 -0500 Organization: Academic Assistance Access Lines: 11 Message-ID: <8bd6.b04e.208@sylvainl> Reply-To: aaa.no.span@N0.SPAM1.tutoraid.org NNTP-Posting-Host: ppp-182.m4-1.ssm.ican.net X-Trace: news.ican.net 883847970 29849 (None) 206.248.78.182 X-Complaints-To: usenet@news.ican.net X-Newsposter: AtomicPost/32 (http://204.57.78.110) Registered content-length: 423 Academic Assistance Access is a free tutoring service on the Web designed to offer assistance in the PHYSICS field for students at post secondary level. If you are interested in sharing your knowledge with today's youth why not join our tutor team. Help make a major contribution towards excellence in higher education. For more information: http://www.tutoraid.org/ Sylvain Lapointe Academic Assistance Access From owner-biophysics@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!wnfeed!204.127.130.5!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Reversibility of chemical reactions Date: 4 Jan 1998 05:28:33 GMT Organization: University of Washington Lines: 78 Distribution: bionet Message-ID: <68n6m1$m97$1@nntp3.u.washington.edu> References: <68l8r0$scl@mserv1.dl.ac.uk> NNTP-Posting-Host: homer03.u.washington.edu X-Trace: nntp3.u.washington.edu 883891713 22823 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant Fujimoto wrote:>>>>>>>>>>>>>> >And you have completely ignored the question of how you get a reaction to >proceed reversibly.<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< >Bryant, I do not think your question is fair enough. Since you wish to talk about a reaction proceeding reversibly it is certainly fair to ask how you intend to go about it. >Years ago that was my >central argument against chemical thermodynamics - the second law is defined >in terms of reversible processes (dS = dQ/T), ant yet there is no way to get >a (standard solute) reaction to proceed reversibly. For instance, for the >reaction > A -> B /1/ >it is said that the maximum work that can be extracted is > delta G = delta Go + RTln((B)/(A)) /2/ >but then it is often forgotten that this maximum work done on >another reaction, e.g. C -> D, presupposes that the coupled reaction > A + C -> B + D /3/ >is carried out REVERSIBLY. When is /3/ carried out reversibly, Bryant? So >that the maximum work /2/ is done? You and others have agreed many times >that it is when /3/ is CLOSE TO EQUILIBRIUM, i.e. if a chemical reaction is >close to equilibrium, we can regard any shifts in that region as REVERSIBLE I don't recall agreeing to this. Its not correct. >and, accordingly, apply what thermodynamics says about reversible processes - >dS is dQ/T, chemical work is maximal etc. >I would agree that, if the reaction is close to equilibrium, the movements >in the region are not exactly "carried out" in the sense in which a >galvanic reaction is carried out reversibly. But this is a problem of >chemical thermodynamics - if these processes are not reversible, which ones >are? Not very many of course. Something for you think about - why is it necessary that any chemical reaction be capable of being carried out reversibly? You appear to think that its necessary to test thermodynamics, but you haven't dealt with the various predictions that thermodynamics. If the entropy is not a state function, then neither is G. If G isn't a state function, then why can it be used to predict the direction of reactions, why does it agree with calorimetric measurements, why does it agree with spectroscopic measurements (using statistical mechanics) and so on. So you don't need to be able to perform any reaction reversibly to be able to test whether the entropy is a state function for chemical reactions. >Bryant, I will anwer all your questions, but for the moment I see this >particular problem of reversibility as much more important than anything >else. I believe I have found a new, "chemical" version of the second law >which is in fact in use in chemical thermodynamics but which is wrongly >related to the classical definition ("Entropy is a function of the state"). >So I would be very grateful if you just help me in the following two >possible ways: 1) If you agree that processes close to equilibrium can be >regarded as reversible, please state it clearly so that I can present the >new theory much better (things have been quite confused so far). No. >2) If you >disagree, please explain how a chemical reaction can proceed reversibly so >that dS = dQ/T, the chemical work extracted is maximal etc. Pentcho I don't really know how to do this. Please read what I wrote above and then please explain why it is necessary. Regards, Bryant From owner-biophysics@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Validity of thermodynamics Date: 4 Jan 1998 13:04:36 -0000 Lines: 100 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68o1d4$tj@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>>>>>>>>>>>> So, before I spend much time trying to fugure out whether any new test has anything to say about the validity of thermodynamics, I want an explanation about why the tests that have already been done are inadequate.<<<<<<<<<<< Bryant, the tests may be adequate and yet there may be problems with the theory. Adequate tests had for a long time proved the existence of a substance called caloric before new tests, within a new paradigm, disproved the concept. This is always the case in science - any developed theory is developed just because it is supported by adequate tests. Still sooner or later internal contradictions appear which initially look insignificant against the great number of supportive tests and lack of any reasonable alternative. However, as soon as a new paradigm emerges, the old one is unavoidably replaced - sometimes we owe this to martyrs (Julius Robert Mayer for instance). So my recent efforts have been directed towards creating the new paradigm - only then can any criticism of the old one be convincing. Otherwise I would continue to repeat endlessly that it is absurd to claim that the system X does work on the system Y whereas Y transfers energy to X, that we cannot define dS = dQ/T for a solute reaction without having any idea about the respective reversible process, and you would continue to believe that all this does not matter as long as supportive tests exist. Still let me describe one such test (although I have already described it many times). The derivation of the osmotic equation can be regarded as a successful test for thermodynamics - it is based on the free energy (chemical potential) concept. However, somewhere in the middle of the derivation, we should integrate dG = VdP /1/ in order to obtain delta G = V(Posm) /2/ The integration presupposes that V, the volume of the system, is constant - otherwise /2/ cannot be obtained at all. Since V is constant, both /1/ and /2/ correspond to a process in which no work of expansion is done. However there are other restrictions imposed on /1/ which reduce the respective physical process to absurdity. /1/ is obtained from dG = dQ + dW + PdV + VdP - TdS - SdT /3/ on the assumption that the process is REVERSIBLE (dQ = TdS), isothermal (dT = 0) and that ONLY WORK OF EXPANSION CAN BE DONE (dW = -PdV). However the integration is possible only if NO WORK OF EXPANSION IS DONE (dV = 0). Therefore, /1/ and /2/ in the derivation of the osmotic equation refer to a REVERSIBLE PROCESS IN WHICH NO WORK AT ALL IS DONE. In my opinion, this is a flagrant absurdity. The example is very typical. The osmotic equation is analogous to the ideal gas law - the analogy is straightforward both formally and physically, so an elegant derivation is possible based on simple thought experiments. However thermodynamics looks for "supportive" tests - here is the opportunity. The solute should no more be analogous to a gas - there should be no bombardment of any wall. Rather, it is the solvent that should move from a high to a low chemical potential. The derivation should be complicated and contain an obligatory for any delta G interpretation absurdity - this time it is a reversible process in which no work at all is done. Students should learn this and ask no respectless questions. Bryant, I would not be sorry if you neglect this example - I believe that a verification of a theory makes more sense if an alternative exists. So please revise your ultimatum "First the old tests, then new ones". I am not devising new tests - rather, I am trying to create a new paradigm allowing us to see all tests in a new light. This new paraigm includes defining what has not been defined so far, so even if it is wrong or you disagree, the discussion may prove useful. Let me start in the simplest possible way. The reaction A <-> B /4/ is at equilibrium. According to thermodynamics, no work can be extracted from it - it is like a massless object - no work is required to push it and, vice versa, it can push nothing. However /1/ can be coupled to another rection, e.g. C -> D: A + C -> B + D /5/ At the molecular level, as A and C react, we can expect either that A transfers energy to C or that C transfers energy to A. In both cases we can speak of MOLECULAR work, and in both cases this work moves /4/ away from equilibrium. So I see no reason to ignore a principle formulated suitably by Jonathan Marder: "WORK IS WHAT MOVES A CHEMICAL SYSTEM AWAY FROM EQUILIBRIUM". I see nothing wrong in an alternative thermodynamic theory based on this principle. It will just confirm some of the results of the old one, but at the same time will resolve some internal contradictions the old one possesses. This is a normal process, Bryant. No theory can be absolutely right, even thermodynamics. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!europa.clark.net!206.229.87.25!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: Reversibility of chemical reactions Date: 4 Jan 1998 06:11:04 GMT Organization: University of Washington Lines: 34 Distribution: bionet Message-ID: <68n95o$o3c$1@nntp3.u.washington.edu> References: <68l8r0$scl@mserv1.dl.ac.uk> NNTP-Posting-Host: homer03.u.washington.edu X-Trace: nntp3.u.washington.edu 883894264 24684 (None) 140.142.64.6 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >2) If you >disagree, please explain how a chemical reaction can proceed reversibly so >that dS = dQ/T, the chemical work extracted is maximal etc. Pentcho I'm not sure if this will work, but it is usually possible to at least talk about changing the volume or temperature of a system reversibly. For a gas phase reaction, changing the volume will change the concentrations of reactants and products. Depending on the stoichiometry, this may shift the reaction one way or the other. Changing the temperature can change the equilibrium constant and in so doing shift the reaction. Before you run off and try to do something with this, you need to (1) figure out what it means for a process to be reversible, (2) verify that my suggestions or any other ideas you may have can be carried out reversibly, and (3) you need to pick a reaction (no more A+B->C+D, the exact properties of the reactants and products are important). One final thing, before I will be willing to do anything more than take a cursory look at what you come up with, you need to explain why this is necessary. That is, what is wrong with using the other predictions to test thermodynamics? Why do you believe it is possible that the entropy not be a state function, and yet all the other predictions still be satisfied? Quite simply, I think thermodynamics has been tested quite thoroughly. So, before I spend much time trying to figure out whether any new test has anything to say about the validity of thermodynamics, I want an explanation about why the tests that have already been done are inadequate. Regards, Bryant From owner-biophysics@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Validity of thermodynamics Date: Sun, 4 Jan 1998 15:40:58 +0200 Organization: Hebrew University Lines: 27 Message-ID: <68o3hc$rjh$1@news.huji.ac.il> References: <68o1d4$tj@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-68o1d4+ACQ-tj+AEA-mserv1.dl.ac.uk+AD4-... ... +AD4-So my recent efforts have been directed towards creating the new paradigm - +AD4-only then can any criticism of the old one be convincing. ... +AD4- So I see no reason to ignore a principle formulated suitably +AD4-by Jonathan Marder: +AD4- +AD4AIg-WORK IS WHAT MOVES A CHEMICAL SYSTEM AWAY FROM EQUILIBRIUM+ACI-. +AD4- Pentcho, I am very pleased that you like my definition. However, whereas you are looking for a new paradigm/theory, I regard my definition as a restatement of classical thermodynamics. In the unlikely event that you find a contradiction, I may have to withdraw my statement. Best 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 Sun Jan 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!206.229.87.25!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: Validity of thermodynamics Date: 5 Jan 1998 01:26:17 GMT Organization: University of Washington Lines: 186 Distribution: bionet Message-ID: <68pcrp$e4o$1@nntp3.u.washington.edu> References: <68o1d4$tj@mserv1.dl.ac.uk> NNTP-Posting-Host: homer22.u.washington.edu X-Trace: nntp3.u.washington.edu 883963577 14488 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Bryant, the tests may be adequate and yet there may be problems with the >theory. Adequate tests had for a long time proved the existence of a >substance called caloric before new tests, within a new paradigm, disproved >the concept. This is always the case in science - any developed theory is >developed just because it is supported by adequate tests. Still sooner or >later internal contradictions appear which initially look >insignificant against the great number of supportive tests and lack of any >reasonable alternative. However, as soon as a new paradigm emerges, the >old one is unavoidably replaced - sometimes we owe this to martyrs (Julius >Robert Mayer for instance). If the theory is inadequate, then there will be a counter example. Until there is a counter example, there is no reason to say there is a problem with the theory. So where is your counter example? >So my recent efforts have been directed towards creating the new paradigm - >only then can any criticism of the old one be convincing. Otherwise I would >continue to repeat endlessly that it is absurd to claim that the system X >does work on the system Y whereas Y transfers energy to X, Then you are continuing to repeat a statement which disagrees with the first law of thermodynamics, and I will continue to ask what you don't like about the first law. >that we cannot >define dS = dQ/T for a solute reaction without having any idea about the >respective reversible process, and you would continue to believe that all >this does not matter as long as supportive tests exist. I didn't say that scientists had no ideas about what a reversible process was, or that I didn't know what it was. I keep asking you what a reversible process is because I want you to deal with the fact that your posts misuse the term. From this I infer that you don't know how thermodynamics is formulated, or what it predicts. All your previous criticisms which include the concept of thermodynamic reversiblity are erroneous because the term is not used correctly. Similar problems afflict your other criticisms. So, what does thermodynamics mean by a reversibly process? >Still let me describe one such test (although I have already described it >many times). The derivation of the osmotic equation can be regarded as >a successful test for thermodynamics - it is based on the free energy >(chemical potential) concept. However, somewhere in the middle of the >derivation, we should integrate > dG = VdP /1/ >in order to obtain > delta G = V(Posm) /2/ >The integration presupposes that V, the volume of the system, is constant - >otherwise /2/ cannot be obtained at all. Since V is constant, both /1/ and >/2/ correspond to a process in which no work of expansion is done. However >there are other restrictions imposed on /1/ which reduce the respective >physical process to absurdity. >/1/ is obtained from > dG = dQ + dW + PdV + VdP - TdS - SdT /3/ >on the assumption that the process is REVERSIBLE (dQ = TdS), isothermal >(dT = 0) and that ONLY WORK OF EXPANSION CAN BE DONE (dW = -PdV). >However the integration is possible only if NO WORK OF EXPANSION IS DONE >(dV = 0). Therefore, /1/ and /2/ in the derivation of the osmotic equation >refer to a REVERSIBLE PROCESS IN WHICH NO WORK AT ALL IS DONE. In my >opinion, this is a flagrant absurdity. Pentcho, you really need to learn how thermodynamics is formulated and what it predicts _before_ you attempt to criticize it. The derivation of the osmotic pressure asks how does G changed when the pressure is changed. Why is it not possible for G to depend on the pressure even if the volume is constant? Its not the energy after all, its the free energy, they are not the same. (Actually, in all the derivations of the osmotic pressure I have seen the relevant quantity is not G, but the partial molar gibbs free energy, mu.) U, H, A, and G are not interchangable. The fact that they all have the same units does not mean they are the same thing. If you continue to confuse them, you will continue to say things which don't make any sense. The fact that G is a state function means that you can calculate what (Delta G) would be for a reversible process. That (Delta G) would equal the (Delta G) for _any_ irreversible process between the same initial and final states. [The preceding is a better, more correct response to this issue than my original one.] >The example is very typical. Regrettably, it is typical of the errors you have been making. >The osmotic equation is analogous to the ideal >gas law - the analogy is straightforward both formally and physically, so >an elegant derivation is possible based on simple thought experiments. >However thermodynamics looks for "supportive" tests - here is the >opportunity. The solute should no more be analogous to a gas - there should >be no bombardment of any wall. Rather, it is the solvent that should move >from a high to a low chemical potential. The derivation should be complicated >and contain an obligatory for any delta G interpretation absurdity - this >time it is a reversible process in which no work at all is done. Students >should learn this and ask no respectless questions. >Bryant, I would not be sorry if you neglect this example - I believe that >a verification of a theory makes more sense if an alternative exists. So >please revise your ultimatum "First the old tests, then new ones". Pentcho, I am perfectly well aware that the laws of thermodynamics are assumed, not proven and that they are accepted because they work, not because they have been proved. One could, therefore, go on devising new tests forever. But why should I pay any attention? If you could point out some defect in the tests already done whereby the second law of thermodynamics could be wrong and yet all the predictions still satisfied, then I would be interested. If you cannot, then I don't see why I should spend a significant amount of time thinking about a new test or pardigm, when you haven't presented any reason why it might be worthwhile. Furthermore, the correct approach is to look for your counter example first. Only when a counter example is found will we have any idea how to modify the original theory, or know if it has to be scrapped altogether. So, where is your counter example? >I am not >devising new tests - rather, I am trying to create a new paradigm allowing >us to see all tests in a new light. This new paraigm includes defining what >has not been defined so far, so even if it is wrong or you disagree, the >discussion may prove useful. I suggest that before you start devising your new paradigm, that you make a more thorough effort to understand thermodynamics first. >Let me start in the simplest possible way. The reaction > A <-> B /4/ >is at equilibrium. According to thermodynamics, no work can be extracted from >it - it is like a massless object - no work is required to push it The last part of this statement isn't true. >and, vice >versa, it can push nothing. However /1/ can be coupled to another rection, >e.g. C -> D: > A + C -> B + D /5/ >At the molecular level, as A and C react, we can expect either that A >transfers energy to C or that C transfers energy to A. In both cases we can >speak of MOLECULAR work, Pentcho, before you speak of it, please define it, and be sure your definition doesn't contradict the first law of thermodynamics. >and in both cases this work moves /4/ away from >equilibrium. So I see no reason to ignore a principle formulated suitably >by Jonathan Marder: >"WORK IS WHAT MOVES A CHEMICAL SYSTEM AWAY FROM EQUILIBRIUM". >I see nothing wrong in an alternative thermodynamic theory based on this >principle. It will just confirm some of the results of the old one, but >at the same time will resolve some internal contradictions the old one >possesses. This is a normal process, Bryant. No theory can be absolutely >right, even thermodynamics. Pentcho I am not claiming that thermodynamics is absolutely correct, or even proven. What I will claim is that it works, and has no known counter examples. I also believe that what you have described in your posts as internal contradictions are just misunderstandings about how thermodynamics is formulated or what it predicts. Incidently, I don't mind debating these things with you. I gives me a chance to think about issues I haven't thought about in a while. However, the amount of time I have to spend on this is limited. Regards, Bryant From owner-biophysics@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Counterexample against thermodynamics Date: 5 Jan 1998 10:46:46 -0000 Lines: 41 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68qdmm$er7@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to Bryant Fujimoto Bryant, I find my activity more and more meaningless - I also suspect that the group is already bored to tears. Still let me give the counterexample you so much insist upon. The maximum work that can be extracted from the reaction ATP -> ADP + P /1/ is, according to thermodynamics, the negative if delta G = delta Go + RTln((ADP)(P)/(ATP)) /2/ This work is a fiction. Never, under any conditions, can this work be extracted. However, in this discussion, you have deliberately made the verification impossible. For quite a long time I have been trying, in accordance with textbooks and other people's opinions, to specify the conditions under which the work /2/ is done - the ATP system does the maximum work on another system, e.g. B -> C, when the coupled reaction ATP + B -> ADP + P + C /3/ is CLOSE TO EQUILIBRIUM - only then can the work production be regarded as (almost) REVERSIBLE. Imitating Lucasz Salwinski, you gave in one of your previous postings a simple and unambiguous answer - "No". Moreover, you explicitly recognized that you have no idea how a solute reaction can be carried out REVERSIBLY. In fact, this is tantamout to recognizing that you see no conditions under which the work /2/ can be done. This is exactly what I claim - one cannot even imagine, let alone create, conditions under which the work /2/ is done - this work is just fiction. I realize with horror that I am the only one interested in REAL work done under REAL conditions. If so, you are right - I am just ignorant - I simply do not know what thermodynamics is interested in. So please tell me - do you really believe that specifying the conditions makes no sense? That we should speak about the work done by the ATP system only in abstract terms, without caring of any energy transfer in any real reaction? If this is true science, I should obviously give up everything. Best regards, Pentcho From owner-biophysics@net.bio.net Mon Jan 05 22:00:00 1998 Message-ID: <34B1ADBC.25BC@richnet.net> Date: Mon, 05 Jan 1998 23:06:20 -0500 From: Sam Sgambellone Organization: Star Interprises X-Mailer: Mozilla 2.02E-KIT (Win95; U) MIME-Version: 1.0 Newsgroups: bionet.biophysics Subject: Quit Smoking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: ppp-s34-162-f.richnet.net Lines: 5 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!205.242.10.4!ns2.richnet.net!ppp-s34-162-f.richnet.net Quit smoking in 7 days or your money back. FREE BROCHURE E-Mail me your address samsable@richnet.net From owner-biophysics@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!205.252.116.205!howland.erols.net!portc02.blue.aol.com!prodigy.com!nntp.earthlink.net!usenet From: villowan@earthlink.net (Charlsie Patterson) Newsgroups: bionet.biophysics Subject: QA Biology Supervisor B97-107 Date: Tue, 06 Jan 1998 16:18:02 GMT Organization: EarthLink Network, Inc. Lines: 60 Message-ID: <68tlgo$b2q@bolivia.earthlink.net> NNTP-Posting-Host: 38.30.41.37 X-Newsreader: Forte Free Agent 1.0.82 I represent a large multi-national client company who is aggressively seeking to fill the following position. They pay all fees associated with filling the position. They offer competitive benefits and salary as well as excellent opportunities for career advancement. The position is located in North Carolina. VERY IMPORTANT: Please refer to job number 97-107 in all correspondence. 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Please send your CV to: Ms. Charlsie Patterson Technical and Bio-Science Recruiting Specialist Global Staffing and Recruiting Email: villowan@earthlink.net or: techsearch@globals-r.com or fax to: (919) 871-0030 QA Biology Supervisor Brief Description of the Position: The QA biology Supervisor will supervise 1) Biologists in the gathering, testing, and reporting of environmental samples throughout the plant; 2) species identification of those isolates; 3) validation activities of the EM group pertaining to environmental concerns throughout the site; 4) the sterility testing of in process and final container products; and media preparation/testing. In addition the supervisor will review test results to assure conformance to specification, review data for trend identification, troubleshoot problems, assist production achieve conformance to environmental specification, and maintain the workplace in compliance with all safety and regulatory requirements. The supervisor will train new employees in all aspects of their job function, audit performance, and monitor results to assure conformance with department guidelines. Position Requirements: Requires a degree in microbiology or equivalent--either a MS with 2 or more years or a BS with 4 or more years of leadership experience in a pharmaceutical facility. Experience should include problem solving in the testing appropriate laboratories to be supervised. (microbiology--including species identification, environmental monitoring, and facility validation in respect to environmental monitoring, and product contamination and sterility issues). The applicant should have strong statistical skills, organizational ability a keen sense of urgency, and excellent written and verbal communication skills. Please Note: Hepatitis B immunization is required. From owner-biophysics@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!SCF-FS.USC.EDU!gera From: gera@SCF-FS.USC.EDU ("S. Gera") Newsgroups: bionet.biophysics Subject: Roommate needed for the Biophyiscs Meeting at Kansas City Date: 6 Jan 1998 12:01:58 -0800 Organization: University of Southern California Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <34B2C523.634C@scf.usc.edu> NNTP-Posting-Host: net.bio.net I am not sure this is an appropriate forum for such a request. I am looking for a roommate (preferably, though not necessarily female) to share a room with during the Biophysical Society annual meeting in Kansas City later this year. I will be in Kansas City from 22 Feb, 1998 (Sunday) till 25th Feb (Wednesday). I may be able to extend my stay by a day, if required. Please respond as soon as possible to gera@scf.usc.edu Thanks sg From owner-biophysics@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!news.sprintisp.com!sprintisp!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!194.22.194.4!masternews.telia.net!News.Amsterdam.UnisourceCS!newsfeed.mad.ibernet.es!news.mad.ibernet.es!not-for-mail From: "José Capel" Newsgroups: bionet.biophysics Subject: I Want to know more about the neural nets Date: 6 Jan 1998 22:44:26 GMT Organization: Unisource Espana NEWS SERVER Lines: 7 Message-ID: <01bd1af3$c5c5eda0$6e0a4cc3@default> NNTP-Posting-Host: 195.76.10.110 X-Newsreader: Microsoft Internet News 4.70.1155 I am a Spanish student of Physiscs and i am very interested in neural nets, can anybody just mail me some information or just tell me where can i find it. Thank you My e-mail is: pepo@maptel.es From owner-biophysics@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!TTUHSC.EDU!phyan From: phyan@TTUHSC.EDU (Alan Neely) Newsgroups: bionet.biophysics Subject: discrete exponential distribution-help Date: 7 Jan 1998 16:04:45 -0800 Organization: TTUHSC Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <34B417EB.B4C00406@ttuhsc.edu> Reply-To: phyan@ttuhsc.edu NNTP-Posting-Host: net.bio.net Recording of single channel activity often reveal slow fluctuations in the probability of being open (Po). These fluctuations are thougth to underly swicth in the "gating mode". Voltage activated calcium channels is a typical example in which membrane depolatization often fail to activate the channels. Repetitive stimulation by square pulse reveal that sweeps without activity tend to cluster. The probality distribution of consecutive sweeps is described by P (n) = L^(n-1) (called a discrete exponential function) with 0 =< L =<1. I have problem with the physical interpretation of L (lambda). Intuitively I see L as the probability that the channel will exit the inactive mode. Alan Neely From owner-biophysics@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!xfer.kren.nm.kr!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Let's reach an agreement about chemical work Date: 8 Jan 1998 10:10:30 -0000 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6928mm$av0@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I still believe that the concept of chemical work is important so no question should remain unanswered. If, for the reaction ATP -> ADP + P /1/ the chemical work that can be extracted isothermally and isobarically is given by delta G = delta Go + RTln((ADP)(P)/(ATP)) /2/ then the following questions should sooner or later be answered: 1. Can this work be really done? Under what conditions? 2. Can this work be regarded as a limit for the real work done? Under what conditions is this limit approached? One can find in textbooks a positive answer to the first part of the second question. But then any teacher should be able to answer the second part of the second question. Otherwise science would not be fair. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!ananke.salford.ac.uk!not-for-mail From: CHS292@news.salford.ac.uk (John) Newsgroups: bionet.biophysics Subject: Lasers and Optics (WWW page) Date: Thu, 08 Jan 98 18:55:20 GMT Organization: University of Salford Lines: 11 Message-ID: <692lsd$ehv$1@ananke.salford.ac.uk> NNTP-Posting-Host: cockcroft-061.salford.ac.uk X-Newsreader: News Xpress Version 1.0 Beta #3 Lasers-Optics-UK is at: http://members.aol.com/WSRNet/optics.htm and Lasers-Optics-USA is at: http://members.aol.com/WSRNet/laser.htm John From owner-biophysics@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Towards an agreement about chemical work Date: 8 Jan 1998 16:52:02 -0000 Lines: 31 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <69307i$47i@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Delta G gives the chemical work only for a REVERSIBLE process, i.e. one for which dQ = TdS: Wu = -delta G = Tdelta S - delta H = Q - delta H /1/ where Q is the heat ABSORBED from the environment as work is done REVERSIBLY. It is said in textbooks that, if delta G for the ATP system is -50 KJ/mole, one can expect maximum 50 KJ/mole work to be done by the ATP system. As delta H for ATP hydrolysis is 20 KJ/mole, it follows from /1/ that Q, the heat absorbed as maximum work is done, is 30 KJ/mole. Everybody would agree that the ATP system NEVER does the maximum work, i.e. work production in this case cannot be REVERSIBLE. What is not clear however is whether the value of 50 KJ/mole can be APPROACHED. In other words, as the ATP system drives the reaction B -> C in ATP + B -> ADP + P + C /3/ when is the work production ALMOST REVERSIBLE so that almost 50 KJ/mole work is done and almost 30 KJ/mole heat are absorbed from the environment? Please note that the answer to this question is essential - the concept of "maximum work" makes sense only if this value can be APPROACHED under certain conditions. If it cannot be approached under any REAL conditions (e.g. delta G = -50 KJ/mole but really Wmax < 20 KJ/mole), we should certainly define a new concept giving us the REAL MAXIMUM WORK. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!news-xfer.netaxs.com!news1.chicago.iagnet.net!iagnet.net!nntp.earthlink.net!usenet From: prismx@scienceweek.com (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: Headlines (9 Jan 98) Date: Fri, 09 Jan 1998 01:13:27 GMT Organization: SCIENCE-WEEK Lines: 54 Message-ID: <693tje$ors@ecuador.earthlink.net> Reply-To: prismx@scienceweek.com NNTP-Posting-Host: 153.35.118.75 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:21085 bionet.biophysics:3886 bionet.cellbiol:8640 bionet.general:29082 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. 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A Method for Patterning of Orientated Mesoscopic Domains 10. Analysis of Monolayer Film Catalysis 11. Synthesis of Multidimensional Large-Cage Zeolite Structures 12. Selection of Broad-Scope Enzymes by Antibody Catalysis 13. Analysis of Intracellular Signaling Mechanisms 14. Abscisic Acid Signaling in Plants 15. Evidence for Cyclic AMP Signaling in Higher Plants 16. Transgenic Sheep Expressing Human Clotting Factor Protein 17. More Evidence that Prion Protein Binds Copper In Vivo 18. Involvement of Immune System B-Cells in a Prion Disease 19. Regeneration of Axons in Central Nervous System White Matter 20. Animal Models of HIV-1 Disease Book Notes Notices - Positions Available Notices - Miscellaneous 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. 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The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@scienceweek.com http://scienceweek.com From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!207.5.0.44!nntp.mainstreet.net!feeder.swcp.com!fugu!SantaFe!not-for-mail From: Erik Van Nimwegen Newsgroups: bionet.biophysics Subject: Re: Counterexample against thermodynamics Date: Thu, 08 Jan 1998 18:47:06 -0700 Organization: The Santa Fe Institute Lines: 59 Message-ID: <34B5819A.7274@santafe.edu> References: <68qdmm$er7@mserv1.dl.ac.uk> NNTP-Posting-Host: aztec.santafe.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5 sun4u) I've been trying to follow this discussion a bit and I'm getting kind of confused about what the problem is. > Still let me give the counterexample > you so much insist upon. The maximum work that can be extracted from the > reaction > > ATP -> ADP + P /1/ > > is, according to thermodynamics, the negative if > > delta G = delta Go + RTln((ADP)(P)/(ATP)) /2/ > > This work is a fiction. Never, under any conditions, can this work be > extracted. However, in this discussion, you have deliberately made the > verification impossible. For quite a long time I have been trying, in > accordance with textbooks and other people's opinions, to specify the > conditions under which the work /2/ is done - the ATP system does the > maximum work on another system, e.g. B -> C, when the coupled reaction > > ATP + B -> ADP + P + C /3/ > > is CLOSE TO EQUILIBRIUM - only then can the work production be regarded as > (almost) REVERSIBLE. Imitating Lucasz Salwinski, you gave in one of your > previous postings a simple and unambiguous answer - "No". Moreover, you > explicitly recognized that you have no idea how a solute reaction can be > carried out REVERSIBLY. In fact, this is tantamout to recognizing that > you see no conditions under which the work /2/ can be done. This is exactly > what I claim - one cannot even imagine, let alone create, conditions under > which the work /2/ is done - this work is just fiction. > Ok, first, as far as I know, a reversible process is a process for which the entropy of the system remains fixed, i.e. dS = 0. Therefore, all energy lost by the system most be lost in the form of work, therefore the work done is maximal along a reversible path (that's how I have come to understand it, if I'm wrong somebody should enlighten me.) Now, the problem you raise is: How do I set up the system such that it actually DOES go along a reversible path, instead of a reversible one. As far as I know, that question does not have a general answer. So, to me it seems that: Yes, thermodynamics is fine. Yes, the maximal work thermodynamics predicts a process can deliver can in general not be obtained by a real system because we don't know how to set up the system such that it remains arbitrarily close to equilibrium. Does that solve the problem? Erik Erik From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!musc.edu!nowakm From: nowakm@musc.edu (Mark W Nowak) Newsgroups: bionet.biophysics Subject: Post-Doctoral Position: Role of Ion Channels in Drug-Dependence Date: 9 Jan 1998 11:36:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Mark W Nowak NNTP-Posting-Host: net.bio.net Neuroscience Post-Doctoral Position A post-doctoral position is immediately available for a candidate (must be a US citizen or permanent resident) with a strong background in electrophysiological recording from mammalian cells, neuronal cultures and slices (both whole cell and single-channel recording techniques). Studies will examine the role of nAChRs and other ligand-gated ion channels in mediating the effects of nicotine and ethanol by employing viral-mediated gene expression methodologies. These in vitro studies will provide a foundation for in vivo expression studies using mouse behavioral models of nicotine- and ethanol-dependence. The overall aim is to understand how changes in ion channel function at the cellular level are related to drug-seeking behavior. My laboratory contains a 1) mammalian cell/neuron electrophysiology rig, 2) whole-cell Xenopus oocyte rig, 3) tissue culture facility and 4) molecular biology facility. The candidate will have the opportunity to apply his/her existing knowledge of ion channel function in collaborative projects with researchers employing animal models of drug-dependence. My laboratory is located in The Center for Drug and Alcohol Programs (CDAP) within the Institute of Psychiatry at the Medical University of South Carolina. CDAP integrates the latest basic and clinical advances in alcohol and drug abuse research with direct patient care and education. Thus, the candidate will have a unique opportunity to interact with pre-clinical and clinical researchers in the area of drug-dependence. In addition, I have a joint appointment in the Department of Cell and Molecular Pharmacology and Experimental Therapeutics where there is an emphasis on signal transduction research. Candidates should send a CV and a brief statement of research interests to: Dr. Mark W. Nowak Room 461N, Institute of Psychiatry 171 Ashley Avenue Medical University of South Carolina Charleston, SC 29425 E-mail address: nowakm@musc.edu MUSC is an equal opportunity employer. From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!newsfeed.direct.ca!newshub1.home.com!news.home.com!zdc!szdc!super.zippo.com!newsp.zippo.com!snews2 From: "M. Muz Zviman" Newsgroups: bionet.biophysics Subject: Low emission computer monitor Date: Fri, 9 Jan 1998 11:28:34 -0500 Organization: Monell Chemical Senses Center Lines: 14 Message-ID: <695j17$7b9@snews2.zippo.com> NNTP-Posting-Host: p-686.newsdawg.com X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hi, We are looking for a low em emission SVGA monitor for electrophysiology rig. I would appreciate any recommendations. Muz ******************************************************************** M. Muz Zviman, Ph.D. Monell Chemical Senses Center Philadelphia, PA 19104 From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!newsrelay.netins.net!nntp.kreonet.re.kr!news.maxwell.syr.edu!ais.net!news1.chicago.iagnet.net!iagnet.net!news.uiowa.edu!not-for-mail From: Toshinori Hoshi Newsgroups: bionet.biophysics Subject: Postdoctoral position Date: Fri, 09 Jan 1998 11:08:59 -0600 Organization: The University of Iowa Lines: 21 Message-ID: <34B659A6.4465@uiowa.edu> Reply-To: toshinori-hoshi@uiowa.edu NNTP-Posting-Host: hoshi-k.physiology.uiowa.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Macintosh; U; PPC) === Postdoctoral Position in Neurophysiology === A postdoctoral position is available to study how oxidation affects ion channel properties and other neuronal properties, such as synaptic transmission. My laboratory focuses on oxidation of methionine and nitration of tyrosine. Electrophysiology experience using single-channel and macroscopic patch-clamp recordings as demonstrated by publication is required. Knowledge of molecular biology, optical methods, and organ-level physiology is desirable. Send curriculum vitae, names of references and description of previous research experience to: T. Hoshi, Ph.D. Department of Physiology and Biophysics The University of Iowa Iowa City, IA 52242 FAX: 319-335-7330 Email: Toshinori-Hoshi@uiowa.edu From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Newsgroups: bionet.biophysics Path: biosci!bloom-beacon.mit.edu!howland.erols.net!recycled.news.erols.com!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!bris.ac.uk!usenet From: "Ulrich T. Riedel" Subject: Desperate Search for Polymer Layer X-Nntp-Posting-Host: dig1.enm.bris.ac.uk Content-Type: text/plain; charset=us-ascii Message-ID: <34B64BAC.281AB82E@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, 9 Jan 1998 16:09:16 GMT X-Mailer: Mozilla 4.04 [en] (Win16; I) Lines: 28 ___Desperate Search for Polymer Layer___ Dear everybody! After three months of never-ending investigation I am (re)searching, more desperately than ever, for a material with which I can cover an inorganic surface. This material seems to have to be a polymer. The ideal polymer should have the following properties: - it should be soluble in a completely evaporating organic liquid - it must not be soluble in - water and - acids - it must not swell/shrink in or react with - water and - acids - it must stick quite well to inorganic surfaces - it must have a strong solid surface - it should not shrink during storage under normal conditions (room temperature, normal pressure etc.) Any ideas which polymer this could be would be APPRECIATED VERY MUCH INDEED! Thanks a lot for your efforts Ulrich Riedel Dipl.-Ing., Univ. of Bristol, UK & Univ. of Techn. Aachen, Germany From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Chemical work (reply to Erik Van Nimwegen) Date: 9 Jan 1998 09:34:04 -0000 Lines: 59 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <694quc$mlj@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Erik wrote:>>>>>>>>>> I've been trying to follow this discussion a bit and I'm getting kind of confused about what the problem is. Ok, first, as far as I know, a reversible process is a process for which the entropy of the system remains fixed, i.e. dS = 0.<<<<<<<<<<<< Only for an isolated system. For a normal closed system dS is not zero. One can easily imagine this in the particular case in which a solute reaction releases a gas, e.g. A + B <-> C + D where D is a gas. Then we can carry out the reaction reversibly in both directions with the help of a piston. The reaction can be either endo- or exothermic, and, in addition, some work is done as the piston is pushed. The sum of the endothermic heat dQend and the work done dW gives dS: dQabsorbed = dQend + dW = TdS /1/ In fact, this is a true REVERSIBLE process - when I started the discussion I intended to prove in the end that delta G work is done only in such processes - it is statistical work which comes from a simultaneous conversion of the thermal energy of a great number of particles. However in chemical systems there is a different and independent kind of work - when in the elementary chemical act a molecule (e.g. ATP) transfers some of its internal energy to another molecule. So the solution is simple - when, in a thought experiment, a TRUE REVERSIBLE process is possible (e.g. for galvanic and osmotic systems) we can expect delta G work to be done or approached. When such a process is impossible (as in all cases in which ATP does work), delta G work is also impossible - then only molecular work is done which obeys a different quantitative description. Of course, there are complications - in the chemiosmotic process for instance the two types of work are interconvertible. My dream was to constructively discuss this as well, but at the moment I am still trying to prove that I am not just ignorant. >>>>>>>>>>>>>>>>>>> So, to me it seems that: Yes, thermodynamics is fine. Yes, the maximal work thermodynamics predicts a process can deliver can in general not be obtained by a real system because we don't know how to set up the system such that it remains arbitrarily close to equilibrium. Does that solve the problem? <<<<<<<<<<<<<<<<<<<<< To some extent. If the reversible process is possible and definable, delta G is the maximum work and a small deviation from reversibility decreases slightly the work. (This is strictly analogous to what is valid for an ideal gas system). If the reversible process is not definable at all (as in the cases in which ATP does work), we should just see "what transfers energy to what". If the process is isothermal, this energy transfer cannot be heat exchange - then it is WORK DONE. I would agree that thermodynamics is fine, but we should not ignore any REAL physical event just because thermodynamics does not adequately describe it. I still believe that a quantitative theory describing energy transfer at the molecular level is much needed. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!199.60.229.5!newsfeed.direct.ca!Supernews60!supernews.com!nntp.flash.net!news.mira.net.au!harbinger.cc.monash.edu.au!newshost.carno.net.au!torda From: Andrew.Torda@anu.edu.au Newsgroups: bionet.molbio.proteins,bionet.biophysics,bionet.xtallography Subject: Post-doc in computational chemistry, Canberra, Australia with Andrew Torda Date: 9 Jan 1998 06:00:32 GMT Organization: Research School of Chemistry, Australian National University Lines: 69 Sender: Andrew.Torda@anu.edu.au Message-ID: <694ee0$df5$1@clarion.carno.net.au> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: 150.203.35.129 Originator: torda@rsc.anu.edu.au Xref: biosci bionet.molbio.proteins:12093 bionet.biophysics:3888 bionet.xtallography:3972 POST DOCTORAL POSITION Computational Chemistry in The Research School of Chemistry, Canberra, Australia with Andrew Torda Available immediately. The research group of Andrew Torda is oriented towards biomolecular calculation and simulation. We are working in areas such as low-resolution (protein fold recognition) force fields, refinement of experimental structures using MD simulation, mixing knowledge-based force fields with experimental data and combinatorial algorithms for protein sequence optimisation. All the projects in the group involve coding and development - not just applications. It would be an advantage to have a reasonable knowledge of data structures and algorithms and programming experience in a civilized language (not fortran). Possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. These might include some entertaining ideas such as quasi-Newtonian dynamics in amusing spaces. Projects are negotiable. Salary: more than $40,963 - $43,834 per annum (the rates just increased a week ago). Grants are provided towards travel and removal. Positions are initially for two years with a possible extension to a third year. There is a housing office to help find accommodation. The Research School of Chemistry is part of the Institute of Advanced Studies which runs special research schools in parallel to the normal teaching schools. There are no undergraduate teaching duties. The university is in the centre of Canberra (the nation's capital). Given the research orientation of the school, there is a lively academic environment. We have close contacts with the school's other theoretical groups in statistical mechanics, polymer theory, quantum chemistry and chemical physics. From the point of view of experimental groups, we maintain close ties to the school's NMR, X-ray crystallography and molecular biology groups. Anyone interested in the Torda group should look at http://www.rsc.anu.edu.au/~torda That also contains a pointer to a page of recent publications. Anyone interested should contact me directly (Andrew.Torda@anu.edu.au). The closing date for applications will be March 3 1998. The administrative procedure is that, if you are interested, you are sent an official application (by slow mail). Applicants then have to fill this out and mail it back (again by slow mail). The official forms will include a request for comments from three referees. There is an old advertisement from a previous school-wide job offer at http://www.rsc.anu.edu.au/RSC/AcademicPositions/RSC_Academic_Positions.html and read under "Postdoctoral Fellowships". Andrew Torda From owner-biophysics@net.bio.net Fri Jan 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!Cabal.CESspool!bofh.vszbr.cz!serra.unipi.it!news.caspur.it!news From: Leopoldo Silvestroni Newsgroups: bionet.biophysics Subject: organic anions flux Date: Sat, 10 Jan 1998 11:34:13 +0100 Organization: Università di Roma 'La Sapienza' Lines: 23 Message-ID: <34B74EA5.DFBF30A2@caspur.it> NNTP-Posting-Host: silves.dfm.med.uniroma1.it Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.04 [en] (Win95; I) dear Colleagues, I'm looking for some good/recent rviews/papers dealing with outward flux mechanisms of organic anions across the cell (plasma) mebrane upon permeability changes. Of course, contacts from experienced people are welcome. thank You all in advance Leopoldo Silvestroni,MD -- Leopoldo Silvestroni Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I, Università di Roma "La Sapienza" Viale del Policlinico, 00161 - ROMA tel. +39-6-49970710; fax +39-6-4461450 e-mail L.SILVESTRONI@CASPUR.IT http://w3.uniroma1.it/MEDICFISIO/labpag1.html From owner-biophysics@net.bio.net Fri Jan 09 22:00:00 1998 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: Illustration of delta G and delta H works (correction) Date: 10 Jan 1998 09:37:02 -0000 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <697ffu$712@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Sorry, there is a mistake in the following text from my previous message: >>>>>>>>>>>>>>>>>>>>>>> The reaction A -> B is at equilibrium in the container above, and not at equilibrium in the container below. Also, the concentration of A is greater below so that there is an upward transmembrane flux of A, whereas the concentration of B is greater in the equilibrium system so that there is a downward flux of B.<<<<<<<<<<<<<<<<<<<<<<<< Please replace it with the correct version: The reaction A -> B is at equilibrium in the container above, and not at equilibrium in the container below. Also, BOTH A AND B HAVE GREATER CONCENTRATIONS IN THE NON-EQUILIBRIUM SYSTEM (SO THAT BOTH SPONTANEOUS FLUXES ARE UPWARD). Best regards, Pentcho From owner-biophysics@net.bio.net Fri Jan 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!europa.clark.net!205.252.116.205!howland.erols.net!recycled.news.erols.com!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Illustration of delta G and delta H works Date: 10 Jan 1998 09:01:47 -0000 Lines: 39 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <697ddr$5p4@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk The following idealised system can give us some rough physical picture of the two types of work that can be extracted from a chemical reaction - statistical suitably described by delta G and molecular suitably described by delta H. ------------------------------------------------------------------------- A <-> B (equilibrium) membrane-permeable-only-to-A////////////membrane-permeable-only-to-B////// A -> B (non-equilibrium) --------------------------------------------------------------------------- The reaction A -> B is at equilibrium in the container above, and not at equilibrium in the container below. Also, the concentration of A is greater below so that there is an upward transmembrane flux of A, whereas the concentration of B is greater in the equilibrium system so that there is a downward flux of B. As A and B cross the membrane, they can do OSMOTIC work. It is not difficult to see that, for one mole A going up and returning to the non-equilibrium system as B, the maximum osmotic work that can be obtained is the negative of delta G = delta Go + RTln((B)/(A)) /1/ On the other hand, as A is converted into B within the non-equilibrium system, the energy released in each elementary chemical act can be transfered to some other molecule in the form of MOLECULAR work. If it is not transfered, it will be dissipated as heat. At constant temperature and pressure, this heat is represented, at the macroscopic level, by the enthalpy of reaction. So the enthalpy gives the maximum work of this type. This work depends on the coupling mechanism (if it is not perfect, much of the energy is dissipated), but is independent of the concentrations and the distance from equilibrium. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Thermodynamic problems Date: 11 Jan 1998 13:17:39 -0000 Lines: 110 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <69agpj$bff@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>>>>>>> Weren't you the one who was insisting earlier that the amount of work done shouldn't depend on the concentrations? How does anything I have said lead you to conclude that I consider specifying conditions unimportant?<<<<<<<<<<<<<<<<<< Misunderstanding. By specifying the conditions I mean a definition of a reversible course of the reaction A -> B. If you know the definition, please give it - I have some problems with it and, besides, my incompetence in this case is not very important. >>>>>>>>>>>>>>>>>> The only sense in which this is abstract is that we don't normally run reactions under conditions where we can extract the maximum work. The energy transfered in a reaction is a function only of the initial and final states, and therefore does not depend on whether the reaction was performed reversibly or not. It is not, however the work.<<<<<<<<< Bryant, here you obviously mean delta U = Q + W, where U is a state function whereas Q and W are not. Formally this gives us the right to think of any, even miraculous, combinations of Q and W for any constant value of delta U (just one equation with two variables). However our knowledge of chemical systems is not so indefinite - when a molecule transfers 5/L KJ energy to another molecule (L is the Avogadro number), this energy transfer is CHEMICAL WORK, although, for the second molecule, thermodynamics allows us to say that it has received 500000/L KJ work but simultaneously has released 499995/L KJ heat. >>>>>>>>>>>>>>> You keep using the word reversible. Do you know what thermodynamics means by reversible? I keep asking, and the impression I get is that you don't know. Since you want to rexamine thermodynamics, why don't you know? How do you expect to be able to say any thing sensible about thermodynamics if you don't know how it is formulated, or what it predicts?<<<<<<<<<<<<<< You are not very serious here. Obviously there are OBJECTIVE problems with the definition of reversiblity of a chemical reaction (e.g. A -> B). Please give your version and let us expect, as one of the hypotheses, that a correct definition is impossible - this sometimes happens in science. >>>>>>>>>>>>>>>>>>>>>>>> You say you are interested in REAL work. You need to define it (a definition which doesn't conflict with the first law of thermodynamics would be nice). And after that, you need to tell us why we should be interested. What would we learn from knowing the REAL work, that we wouldn't know from measurements of things like equilibrium constants, changes in the concentrations, temperature or pressure, or from the usual thermodynamic quantities (Delta H, G or S).<<<<<<<<<<<<<< As I tried to demonstrate in my previous posting, the work (both real and maximal) done in an isothermal chemical CYCLE is not zero. If this is not interesting....... >>>>>>>>>>>>>>>>>>>> You appear to know what it means when Delta G is negative, it represents the maximum amount of non-PV work the system can do on its surroundings. Have you considered what it means when Delta G is positive? I am fairly sure I mentioned this long ago, but it then represents the mimimum amount of work necessary to drive the reaction under those conditions. If the coupling is not perfect, you will need more free energy from the driving reaction, and the excess is wasted. I suppose you could define the chemical work done as the Delta G of the driven reaction.<<<<<<<<<<<<<<<< The issue is interesting - we will discuss this but I need to think a bit more. It seems to me that "imperfect coupling" has different physical meanings when delta G and delta H works are done. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore, one obvious requirement for a reversible reaction is that the Delta G for the reaction being driven has to be equal in magnitude and opposite in sign to the Delta G for the driving reaction. i.e. Delta G for the overall reaction must be zero. Getting a reaction to go forward while remaining at equilibrium would require you to be constantly manipulating the concentrations and/or equilibrium constant. That I didn't know how to do this, doesn't mean it isn't possible. I simply haven't thought about how you would go about doing this. I did post a few ideas latter, and one of them might work. Since you think this is important, it is your responsibility to think about them.<<<<<<<<<<<<<<<<<<<<<<<<< I have already given such an example. You have commented on it in another posting - I will reply. >>>>>>>>>>>>>>>>>>> I asked some questions a while back, and I think nothing will be cleared up until you address them. Here they are again (modified in view of some of your more recent comments). 1) What does thermodynamics mean by a reversible process? (The same definition applies to all processes.) 2) What does the first law of thermodynamics say? And why do you claim that the energy transfered equals the work, since that contradicts the first law? 3) Why is testing the predictions made by the laws of thermodynamics not a valid test of those laws? 4) Where is your counter example? (i.e. an experiment whose results are predicted incorrectly by thermodynamics.)<<<<<<<<<<<< I hope my recent messages address questions 1), 2) and 4) enough. (By the way, is the first question in 2) fair?) As to 3), I answered earlier - some tests may be valid, others not - it is up to theoreticians to analyse the situation and develop the science further. I do not feel competent enough in statistical mechanics, but if you insist that the most reliable verification of the second law is there (or anywhere else) I will have to complete my knowledge and turn the discussion in that direction. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Delta H work Date: 11 Jan 1998 11:56:20 -0000 Lines: 92 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <69ac14$8g9@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote:>>>>>>>>>>>>>> >The following idealised system can give us some rough physical picture >of the two types of work that can be extracted from a chemical reaction - >statistical suitably described by delta G and molecular suitably described >by delta H. >------------------------------------------------------------------------- > A <-> B (equilibrium) >membrane-permeable-only-to-A////////////membrane-permeable-only-to-B////// > A -> B (non-equilibrium) >--------------------------------------------------------------------------- >The reaction A -> B is at equilibrium in the container above, and not at >equilibrium in the container below. Also, the concentration of A is greater >below so that there is an upward transmembrane flux of A, whereas the >concentration of B is greater in the equilibrium system so that there is >a downward flux of B. >As A and B cross the membrane, they can do OSMOTIC work. It is not difficult >to see that, for one mole A going up and returning to the non-equilibrium >system as B, the maximum osmotic work that can be obtained is the negative of > delta G = delta Go + RTln((B)/(A)) /1/ >On the other hand, as A is converted into B within the non-equilibrium >system, the energy released in each elementary chemical act can be transfered >to some other molecule in the form of MOLECULAR work. If it is not transfered, >it will be dissipated as heat. At constant temperature and pressure, this >heat is represented, at the macroscopic level, by the enthalpy of reaction. >So the enthalpy gives the maximum work of this type. This work depends on >the coupling mechanism (if it is not perfect, much of the energy is >dissipated), but is independent of the concentrations and the distance from >equilibrium.<<<<<<<<<<<<<<<<<<< Bryant Fujimoto replied:>>>>>>>>>>>>>> Since at constant pressure, (Delta H) = Q + Wu, what happens when Q is positive? In that case, if (Delta H) is negative, the magnitude of Wu (the work done by the system on the environment) is larger than the magnitude of (Delta H). So (Delta H) does not give the maximum amount of work possible.<<<<<<<<<<<<<<< Bryant, for this type of (molecular) work Q cannot be positive. Let us have a look at the molecular process: a molecule (e.g. ATP) releases some energy. This energy is either transfered to some other molecule in the form of chemical work, or dissipated as heat (in free hydrolysis). In the former case the coupling mechanism is normally not perfect, so part of the energy is still dissipated as heat. There can be no description more adequate than (delta H)/L = Q/L + Wu/L /2/ where (delta H)/L is the (negative of the) MAXIMUM work the molecule can do, Wu/L is the (negative of the) REAL work done, Q/L is the dissipated energy (since the coupling mechanism is not perfect) and L is the Avogadro number. There is no HEAT ABSORPTION in the process, so Q cannot be positive. Of course, heat absorption may occur in other simultaneous processes - the future development of the theory will analyse such complications. Also, if Q is positive, we can expect the molecule to be ACCEPTING and not GIVING work - formally /2/ can describe this too. As you can see, I am strictly using Wu (i.e. the thermodynamic definition of chemical work) in my analysis, whereas delta H gives only the upper limit which would be reached if the coupling mechanism were perfect and the whole energy released by the molecule is converted into chemical work (i.e. stored as chemical energy of some other molecule). Now we can solve all problems by considering a cycle undergone by the nonequilibrium system A -> B (see the drawing above): 1. One mole of A is converted into B in the nonequilibrium system. The reaction is coupled to another reaction and the coupling mechanism is PERFECT, so Q in /2/ is zero and Wu = delta H. 2. One mole of B is REVERSIBLY transfered from the nonequilibrium to the equilibrium system. OSMOTIC work is done. 3. One mole of A is REVERSIBLY transfered from the equilibrium to the nonequilibrium system. OSMOTIC work is done. Calculations show that the MAXIMUM CHEMICAL WORK that can be obtained from a chemical system as it undergoes a CYCLE is Wch,max = -(delta H - delta G) /3/ This result contradicts the second law, but, on the other hand, I expect it to be very useful in analysing bioenergetic cycles. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!wnfeed!204.127.130.5!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Chemical work (reply to Erik Van Nimwegen) Date: 11 Jan 1998 09:47:28 GMT Organization: University of Washington Lines: 76 Distribution: bionet Message-ID: <69a4fg$n3q$1@nntp3.u.washington.edu> References: <694quc$mlj@mserv1.dl.ac.uk> NNTP-Posting-Host: homer11.u.washington.edu X-Trace: nntp3.u.washington.edu 884512048 23674 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Erik wrote:>>>>>>>>>> >I've been trying to follow this discussion a bit and I'm getting kind of >confused about what the problem is. >Ok, first, as far as I know, a reversible process is a process for which >the entropy of the system remains fixed, i.e. dS = 0.<<<<<<<<<<<< >Only for an isolated system. For a normal closed system dS is not zero. One >can easily imagine this in the particular case in which a solute reaction >releases a gas, e.g. A + B <-> C + D where D is a gas. Then we can carry out >the reaction reversibly in both directions with the help of a piston. The >reaction can be either endo- or exothermic, and, in addition, some work is >done as the piston is pushed. The sum of the endothermic heat dQend and the >work done dW gives dS: > dQabsorbed = dQend + dW = TdS /1/ Pentcho, Where did you get this equation? Assuming you define your system correctly, dQabsorbed = TdS for a reversible reaction. However, I see no reason why they should necessarily equal dQend + dW. >In fact, this is a true REVERSIBLE process - when I started the discussion >I intended to prove in the end that delta G work is done only in such >processes - it is statistical work which comes from a simultaneous >conversion of the thermal energy of a great number of particles. However >in chemical systems there is a different and independent kind of work - >when in the elementary chemical act a molecule (e.g. ATP) transfers some >of its internal energy to another molecule. So the solution is simple - when, >in a thought experiment, a TRUE REVERSIBLE process is possible (e.g. for >galvanic and osmotic systems) we can expect delta G work to be done or >approached. When such a process is impossible (as in all cases in which >ATP does work), delta G work is also impossible - then only molecular work >is done which obeys a different quantitative description. >Of course, there are complications - in the chemiosmotic process for instance >the two types of work are interconvertible. My dream was to constructively >discuss this as well, but at the moment I am still trying to prove that I am >not just ignorant. >>>>>>>>>>>>>>>>>>>> >So, to me it seems that: >Yes, thermodynamics is fine. >Yes, the maximal work thermodynamics predicts a process can deliver can >in general not be obtained by a real system because we don't know how to >set up the system such that it remains arbitrarily close to equilibrium. >Does that solve the problem? <<<<<<<<<<<<<<<<<<<<< >To some extent. If the reversible process is possible and definable, delta G >is the maximum work and a small deviation from reversibility decreases >slightly the work. (This is strictly analogous to what is valid for an ideal >gas system). If the reversible process is not definable at all (as in the cases >in which ATP does work), Pentcho, What ever gave you the idea that it wasn't definable? Carrying out such a reaction would be a problem, but that doesn't make it undefinable. >we should just see "what transfers energy to what". >If the process is isothermal, this energy transfer cannot be heat exchange - >then it is WORK DONE. I would agree that thermodynamics is fine, but we should >not ignore any REAL physical event just because thermodynamics does not >adequately describe it. I still believe that a quantitative theory describing >energy transfer at the molecular level is much needed. Pentcho, If the thing you want is energy transfer, thermodynamics already has it. Its called (Delta U). Regards, Bryant From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!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: Counterexample against thermodynamics Date: 11 Jan 1998 09:31:30 GMT Organization: University of Washington Lines: 116 Distribution: bionet Message-ID: <69a3hi$mj7$1@nntp3.u.washington.edu> References: <68qdmm$er7@mserv1.dl.ac.uk> NNTP-Posting-Host: homer11.u.washington.edu X-Trace: nntp3.u.washington.edu 884511090 23143 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >In reply to Bryant Fujimoto >Bryant, I find my activity more and more meaningless - I also suspect that >the group is already bored to tears. Still let me give the counterexample >you so much insist upon. The maximum work that can be extracted from the >reaction > ATP -> ADP + P /1/ >is, according to thermodynamics, the negative if > delta G = delta Go + RTln((ADP)(P)/(ATP)) /2/ >This work is a fiction. Never, under any conditions, can this work be >extracted. However, in this discussion, you have deliberately made the >verification impossible. For quite a long time I have been trying, in >accordance with textbooks and other people's opinions, to specify the >conditions under which the work /2/ is done - the ATP system does the >maximum work on another system, e.g. B -> C, when the coupled reaction > ATP + B -> ADP + P + C /3/ >is CLOSE TO EQUILIBRIUM - only then can the work production be regarded as >(almost) REVERSIBLE. Imitating Lucasz Salwinski, you gave in one of your >previous postings a simple and unambiguous answer - "No". Moreover, you >explicitly recognized that you have no idea how a solute reaction can be >carried out REVERSIBLY. In fact, this is tantamout to recognizing that >you see no conditions under which the work /2/ can be done. This is exactly >what I claim - one cannot even imagine, let alone create, conditions under >which the work /2/ is done - this work is just fiction. >I realize with horror that I am the only one interested in REAL work done >under REAL conditions. If so, you are right - I am just ignorant - I simply >do not know what thermodynamics is interested in. So please tell me - do >you really believe that specifying the conditions makes no sense? Weren't you the one who was insisting earlier that the amount of work done shouldn't depend on the concentrations? How does anything I have said lead you to conclude that I consider specifying conditions unimportant? >That we >should speak about the work done by the ATP system only in abstract terms, >without caring of any energy transfer in any real reaction? The only sense in which this is abstract is that we don't normally run reactions under conditions where we can extract the maximum work. The energy transfered in a reaction is a function only of the initial and final states, and therefore does not depend on whether the reaction was performed reversibly or not. It is not, however the work. >If this is >true science, I should obviously give up everything. Pentcho You keep using the word reversible. Do you know what thermodynamics means by reversible? I keep asking, and the impression I get is that you don't know. Since you want to rexamine thermodynamics, why don't you know? How do you expect to be able to say any thing sensible about thermodynamics if you don't know how it is formulated, or what it predicts? What you posted above isn't a counter example. A counter example would be an experiment for which thermodynamics makes an incorrect prediction of the results. You say you are interested in REAL work. You need to define it (a definition which doesn't conflict with the first law of thermodynamics would be nice). And after that, you need to tell us why we should be interested. What would we learn from knowing the REAL work, that we wouldn't know from measurements of things like equilibrium constants, changes in the concentrations, temperature or pressure, or from the usual thermodynamic quantities (Delta H, G or S). You appear to know what it means when Delta G is negative, it represents the maximum amount of non-PV work the system can do on its surroundings. Have you considered what it means when Delta G is positive? I am fairly sure I mentioned this long ago, but it then represents the mimimum amount of work necessary to drive the reaction under those conditions. If the coupling is not perfect, you will need more free energy from the driving reaction, and the excess is wasted. I suppose you could define the chemical work done as the Delta G of the driven reaction. Furthermore, one obvious requirement for a reversible reaction is that the Delta G for the reaction being driven has to be equal in magnitude and opposite in sign to the Delta G for the driving reaction. i.e. Delta G for the overall reaction must be zero. Getting a reaction to go forward while remaining at equilibrium would require you to be constantly manipulating the concentrations and/or equilibrium constant. That I didn't know how to do this, doesn't mean it isn't possible. I simply haven't thought about how you would go about doing this. I did post a few ideas latter, and one of them might work. Since you think this is important, it is your responsibility to think about them. I asked some questions a while back, and I think nothing will be cleared up until you address them. Here they are again (modified in view of some of your more recent comments). 1) What does thermodynamics mean by a reversible process? (The same definition applies to all processes.) 2) What does the first law of thermodynamics say? And why do you claim that the energy transfered equals the work, since that contradicts the first law? 3) Why is testing the predictions made by the laws of thermodynamics not a valid test of those laws? 4) Where is your counter example? (i.e. an experiment whose results are predicted incorrectly by thermodynamics.) Regards, Bryant From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 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: Illustration of delta G and delta H works Date: 11 Jan 1998 08:05:30 GMT Organization: University of Washington Lines: 49 Distribution: bionet Message-ID: <699uga$ieg$1@nntp3.u.washington.edu> References: <697ddr$5p4@mserv1.dl.ac.uk> NNTP-Posting-Host: homer11.u.washington.edu X-Trace: nntp3.u.washington.edu 884505930 18896 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >The following idealised system can give us some rough physical picture >of the two types of work that can be extracted from a chemical reaction - >statistical suitably described by delta G and molecular suitably described >by delta H. >------------------------------------------------------------------------- > A <-> B (equilibrium) >membrane-permeable-only-to-A////////////membrane-permeable-only-to-B////// > A -> B (non-equilibrium) >--------------------------------------------------------------------------- >The reaction A -> B is at equilibrium in the container above, and not at >equilibrium in the container below. Also, the concentration of A is greater >below so that there is an upward transmembrane flux of A, whereas the >concentration of B is greater in the equilibrium system so that there is >a downward flux of B. >As A and B cross the membrane, they can do OSMOTIC work. It is not difficult >to see that, for one mole A going up and returning to the non-equilibrium >system as B, the maximum osmotic work that can be obtained is the negative of > delta G = delta Go + RTln((B)/(A)) /1/ >On the other hand, as A is converted into B within the non-equilibrium >system, the energy released in each elementary chemical act can be transfered >to some other molecule in the form of MOLECULAR work. If it is not transfered, >it will be dissipated as heat. At constant temperature and pressure, this >heat is represented, at the macroscopic level, by the enthalpy of reaction. >So the enthalpy gives the maximum work of this type. This work depends on >the coupling mechanism (if it is not perfect, much of the energy is >dissipated), but is independent of the concentrations and the distance from >equilibrium. Pentcho Since at constant pressure, (Delta H) = Q + Wu, what happens when Q is positive? In that case, if (Delta H) is negative, the magnitude of Wu (the work done by the system on the environment) is larger than the magnitude of (Delta H). So (Delta H) does not give the maximum amount of work possible. Regards, Bryant From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!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: Towards an agreement about chemical work Date: Sun, 11 Jan 1998 17:59:11 +0200 Organization: Hebrew University Lines: 34 Message-ID: <69aqag$eut$1@news.huji.ac.il> References: <69307i$47i@mserv1.dl.ac.uk> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: quoted-printable X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Pentcho Valev wrote in message = +ADw-69307i+ACQ-47i+AEA-mserv1.dl.ac.uk+AD4-... ... +AD4-It is said in textbooks that, if delta G for the ATP system is -50 = KJ/mole, +AD4-one can expect maximum 50 KJ/mole work to be done by the ATP = system. +AD4-As delta H for ATP hydrolysis is 20 KJ/mole, it follows from /1/ = that +AD4-Q, the heat absorbed as maximum work is done, is 30 KJ/mole. +AD4- +AD4-Everybody would agree that the ATP system NEVER does the maximum = work, i.e. +AD4-work production in this case cannot be REVERSIBLE. What is not = clear however is +AD4-whether the value of 50 KJ/mole can be APPROACHED. ... Pentcho, You need look no further than chemiosmotic coupling. The normal = consensus is coupling of 3 protons per ATP. Typical proton motive forces = are up to 180 meV which translates to roughly 52kJ per 3 protons+ACE- = This would represent perfect coupling. Even with a 2 protons per ATP coupling ratio, deltaH is still = insufficient to account for the work done. Does this meet your criterion = of +ACI-APPROACHing+ACI- reversibility? Jonathan B. Marder +ADw-MARDER+AEA-agri.huji.ac.il+AD4- Department of Agricultural Botany, The Hebrew University of Jerusalem Faculty of Agriculture, P.O.Box 12, Rehovot 76100, ISRAEL Phone: +-972 8 9481918 Fax: +-972 8 9467763 =20 Web page: http://www.agri.huji.ac.il/+AH4-marder From owner-biophysics@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Chemiosmotic mechanism Date: 11 Jan 1998 19:15:12 -0000 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <69b5o0$pdv@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Jonathan Marder wrote:>>>>>>>>>>>> You need look no further than chemiosmotic coupling. The normal consensus is coupling of 3 protons per ATP. Typical proton motive forces are up to 180 meV which translates to roughly 52kJ per 3 protons This would represent perfect coupling. Even with a 2 protons per ATP coupling ratio, deltaH is still insufficient to account for the work done. Does this meet your criterion of APPROACHing reversibility?<<<<<<<<<<<<<<<< Jonathan, I am not very competent in this but my interest is great. Let us first clarify a few things. 1. How do we know the number of protons per molecule ATP? I have read a few times that it is derived thermodynamically, but is there an independent experimental confirmation? 2. How do we know the real proton motive force? For instance, the transmembrane potential difference is inversely proportional to the capacitance of the membrane. The ATPase complex is thick and hydrophilic, i.e. the capacitance of that spot can be enormous and, accordingly, the transmembrane potential difference almost zero. 3. If delta H (20 KJ/mole) is insufficient to account for the work done (e.g. 52 KJ/mole), where does the rest of the energy come from? It could only be heat absorbed, but Bryant would object (I do not know why). 4. I am surprised to hear that this maximal value (52 KJ or 3 protons) corresponds to "perfect coupling". Isn't it assumed that the reaction ATP + (nH+)in -> ADP + P + (nH+)out /1/ is close to equilibrium? (At least papers say so). Then why did you and Bryant reject the same interpretation in other cases? Best regards, Pentcho From owner-biophysics@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Entropy change for a chemical reaction Date: 12 Jan 1998 09:26:02 -0000 Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <69cnja$2ue@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote: >For a normal closed system dS is not zero. One >can easily imagine this in the particular case in which a solute reaction >releases a gas, e.g. A + B <-> C + D where D is a gas. Then we can carry out >the reaction reversibly in both directions with the help of a piston. The >reaction can be either endo- or exothermic, and, in addition, some work is >done as the piston is pushed. The sum of the endothermic heat dQend and the >work done dW gives dS: > dQabsorbed = dQend + dW = TdS /1/ Bryant Fujimoto replied:>>>>>>>>>>>>>>> Where did you get this equation? Assuming you define your system correctly, dQabsorbed = TdS for a reversible reaction. However, I see no reason why they should necessarily equal dQend + dW.<<<<<<<<< Just consider a liquid-vapour system. As it expands isothermally and reversibly, heat is absorbed as the liquid turns into vapour (the process is endothermic) and, in addition, work dW = PdV is done by the vapour. dQabsorbed is to compensate for both heat-consumming processes. Theoretically much more interesting is the case in which dQend is negative (i.e. the chemical reaction is exothermic). Then dQend and dW have opposite signs and we can easily imagine concentrations of the reagents such that dQend = -dW. Then, accoring to /1/, dS = 0 /2/ for a reversible and, therefore, for the respective SPONTANEOUS chemical chemical process. This is even more than an absurdity and can be regarded as a counterexample against thermodynamics. Best regards, Pentcho From owner-biophysics@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!not-for-mail From: jhmiller@helix.nih.gov (Jay Miller) Newsgroups: bionet.biophysics Subject: NASA and biologists Date: 12 Jan 1998 14:27:46 GMT Organization: National Institutes of Health Lines: 5 Distribution: world Message-ID: <69d992$a20$1@light.nih.gov> Reply-To: jhmiller@helix.nih.gov NNTP-Posting-Host: ams06057.niams.nih.gov X-Newsreader: IBM NewsReader/2 2.0 Dan Goldin, dir. of NASA, gave one of the invited talks at the just concluded American Astronomical Soc. meeting in Washington, DC. He said that, while NASA has a general hiring freeze on, it is looking for "biologists". They are interested in the possibilities and criteria for life in the universe. I have no specifics on who actually to contact, but I guess you could just contact HQ for more info. From owner-biophysics@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!ais.net!newsm.ibm.net!ibm.net!uunet!in5.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!bootp-18-241.bootp.virginia.edu!user From: saj3y@mcconnell.chem.virginia.edu (sajith jayasinghe) Newsgroups: bionet.biophysics Subject: Deuterated Zwitterionic Detergent Date: 10 Jan 1998 17:25:18 GMT Organization: department of chemistry Lines: 10 Message-ID: NNTP-Posting-Host: bootp-18-241.bootp.virginia.edu X-newsreader: MT-NewsWatcher 2.2.2 Hello all, Where would I be able to find a deuterated Zwitterionic detergent suitable for NMR spectroscopy (perdeuterated). I am in the process of taking NMR spectra of a 11-mer peptide in detergent and would like the detergent to be Zwitterionic. I can obtain SDS deuterated but this detergent is -vely charged. Any help would be greatly appreciated. Thanks in advance. Regards, Sajith Jayasinghe. From owner-biophysics@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news-ber1.dfn.de!news-fra1.dfn.de!news-kar1.dfn.de!news.embl-heidelberg.de!embl-heidelberg.de!schlichting From: schlichting@embl-heidelberg.de Newsgroups: bionet.biophysics Subject: Postdoctoral position in Protein Crystallography, MPI Date: 7 Jan 98 19:58:52 +0100 Organization: European Molecular Biology Laboratory Lines: 28 Distribution: world Message-ID: <1998Jan7.195852@hera> NNTP-Posting-Host: hera.embl-heidelberg.de The Max Planck Institute for Molecular Physiology, Dortmund invites applications for a Postdoctoral position in Kinetic Crystallography A post-doctoral fellowship is availabe in the Department of Physical Biochemistry. The aim is to study the enzymatic mechanism of tryptophan synthase. The work is interdisciplinary providing opportunities to apply (and learn) techniques of time-resolved crystallography and possibly of transient enzyme kinetics. Applicants must have a strong background in biochemistry and experience in protein crystallography. Previous work using transient enzyme kinetics would be a big asset. The successful applicant will join an international group. The Max Planck Society is an equal opportunity employer. The project is funded by the BMBF for initially 2 years. The salary is up to BAT Ib depending on experience. For details of the post please contact me informally. To apply please submit a full CV with names and addresses of two referees to: Ilme Schlichting, Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Rheinlanddamm 201, 44139 Dortmund, Germany. e-mail:ilme.schlichting@mpi-dortmund.mpg.de FAX +49.231-1206-622, TEL: +49.231-1206-273 From owner-biophysics@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!news.maxwell.syr.edu!news2.chicago.iagnet.net!news1.chicago.iagnet.net!iagnet.net!ihug.co.nz!clear.net.nz!news.hn.netlink.co.nz!southern.co.nz!not-for-mail From: bsandle@southern.co.nz (Brian Sandle) Newsgroups: sci.bio.ecology,bionet.biophysics Subject: Overheating of elephant seals in warm sea? Date: 13 Jan 1998 03:34:55 GMT Organization: Southern InterNet Services Lines: 13 Message-ID: <69encv$eii$1@mnementh.southern.co.nz> NNTP-Posting-Host: kalessin.southern.co.nz X-Newsreader: TIN [UNIX 1.3 950621BETA PL0] I have felt too hot swimming in a 6mm wet suit. Will an elephant seal lose fat if the water temperature is say over 21 degrees? Our Christchurch, New Zealand, sea surf temperature has been 21.5 or more degrees recently. Our local summer visiting elephant seal, Dumbo, has been losing weight in the last few weeks. Is that because he was doused with petrol and lost his insulation (now pretty much back) and so is losing energy, or because he is too hot? White Robbit Dodo Dolphin From owner-biophysics@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!DNA-DIAGNOSTICS.COM!mmunzer From: mmunzer@DNA-DIAGNOSTICS.COM (dna-diagnostics.com) Newsgroups: bionet.biophysics Subject: Re: New DNA Technologies Date: 13 Jan 1998 07:32:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BD200E.3C28CDE0@cygene-2.biotech.ufl.org> NNTP-Posting-Host: net.bio.net Thank you all for your overwhelmingly positive response to our = announcement of new DNA Diagnostic technologies. Due to the volume of = inquiries, we have compiled a series of FAQ's, to respond to the = majority of your questions. We have posted them on our CyGene web site = along with several letters of opinion from professionals who have = reviewed the TPA and RFTA patent documents. RFTA opinion letters will be = posted on our AGENDA site shortly. We will respond to all other inquiries as soon as possible. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Martin Munzer=20 AGENDA, Inc. http://www.dna-diagnostics.com a.k.a. Advanced Genetic Diagnostic Associates=20 Confirming "Heirlines" Through State of the Art DNA Analysis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-biophysics@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!willihigh.schnet.edu.au!rodonovan From: rodonovan@willihigh.schnet.edu.au ("Richard O'Donovan") Newsgroups: bionet.biophysics Subject: (none) Date: 12 Jan 1998 21:01:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801130504.PAA27848@gateway.willihigh.schnet.edu.au> NNTP-Posting-Host: net.bio.net I am embarking upon some research into the effect of a particlar technique on increasing limb strength. The effect is claimed to be immediate, so I am wondering if anyone would have any suggestions regarding appropriate experimental design and/or analysis. My current thinking is to have subjects (who will be reclining) to lift a weight by a pulley system for a set period of time. I was intending to videotape the movement of the weight against a scale so that a paired t-test could be performed on the results, or perhaps a non-parametric Mann-Whitney test. Any suggestions or comments would be gratefully received. Richard O'Donovan rodonovan@willihigh.schnet.edu.au From owner-biophysics@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news.belwue.de!news.uni-freiburg.de!bergert.physiol.uni-freiburg.de!kraushaa From: kraushaa@hotmail.com (Udo Kraushaar) Newsgroups: bionet.biophysics Subject: Ion permeability of amphotericin B pores Date: Tue, 13 Jan 1998 18:30:53 +1000 Organization: Uni Freiburg Lines: 8 Message-ID: NNTP-Posting-Host: bergert.physiol.uni-freiburg.de X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Hi, does anyone know a paper where the permeability of several ions tof ampho B is tested? In detail I'm interested in the permeability of Cl- in comparison to nystatin and gramicidin, respectively. Thanks for any hint Udo From owner-biophysics@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!xfer.kren.nm.kr!fnews.nuri.net!news.nuri.net!not-for-mail From: Tae-Young Ahn Newsgroups: bionet.biophysics Subject: Re: Ion permeability of amphotericin B pores Date: Wed, 14 Jan 1998 14:21:58 +0900 Organization: A-Lab, CNS, Seoul, Korea Lines: 34 Message-ID: <34BC4B75.A3F7C23F@nuri.net> References: NNTP-Posting-Host: ts242-63.nuri.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Udo Kraushaar X-Priority: 3 (Normal) Udo Kraushaar wrote: > Hi, > does anyone know a paper where the permeability of several ions tof > ampho B is > tested? In detail I'm interested in the permeability of Cl- in > comparison to > nystatin and gramicidin, respectively. > > Thanks for any hint > > Udo Sure, Udo.You must only read following papers: Journal of Neuroscience Methods (1991) Vol. 37., 15-26 Biophysical Journal (1995) Vol., 69., 2541-2557 And click here. Refer to following web site. http://www.axonet.com/pub/tech/focus/FOCUS002.txt In case of my experimental experience, you must carefully solubilize (sonicate) Amphotericin B powder in DMSO in appropriate time range. Tae-Young Ahn http://members.iWorld.net/tyahn/ From owner-biophysics@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!ag