From owner-biophysics@net.bio.net Sun Feb 01 22:00:00 1998 Newsgroups: bionet.biophysics Path: biosci!agate!logbridge.uoregon.edu!ais.net!vixen.cso.uiuc.edu!uchinews!midway.uchicago.edu!aekentsi From: aekentsi@midway.uchicago.edu (alex emil kentsis) Subject: Re: stray light X-Nntp-Posting-Host: howard-nfs.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Organization: The University of Chicago X-Newsreader: TIN [version 1.2 PL2] References: <34D2370B.31A7@york.ac.uk> Date: Mon, 2 Feb 1998 14:18:59 GMT Lines: 17 i am not sure if you are asking about background light levels, as from an ambient light leak, or about this strange phenomenon we've encountered. if the solution level in teh observation cuvette is below a certain level, the fluorimeter produces curved baselines. we think it's due to teh elevation of the meniscus in the cuvette which somehow produces stray light. if the meniscus is covered with a piece of tape or the solution volume increased so that it's far away from teh incident beam, the anomaly disappears. very strange. David Scott (djs17@york.ac.uk) wrote: : Hia : Does anyone out there know anything about stray light in a fluorimeter : and how to calculate/correct/get rid of it? : We have an application where this may be a problem : Thanks in advance : Dave Scott From owner-biophysics@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news From: "Marc W. Slutzky" Newsgroups: bionet.biophysics Subject: APS March Meeting Date: Mon, 02 Feb 1998 11:16:32 -0600 Organization: Northwestern University, Evanston, IL. USA Lines: 13 Message-ID: <34D5FF6F.E7AEFDF0@nwu.edu> Reply-To: mslutzky@nwu.edu NNTP-Posting-Host: jimbob.bme.nwu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) I am looking for a roommate for the American Physics Society March Meeting in L.A. I am a graduate student in Biomedical Engineering at Northwestern University. I'm looking for a non-smoking roommate from March 14th-20th. If interested, please email me at mslutzky@nwu.edu . Thank you -- Marc W. Slutzky Northwestern University, Evanston, IL. USA mslutzky@nwu.edu From owner-biophysics@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!newsfeed.eerie.fr!jussieu.fr!univ-angers.fr!ciril.fr!not-for-mail From: Christophe GOEURY Newsgroups: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Subject: phantom simulated dielectric properties of human tissues Date: Tue, 03 Feb 1998 17:09:46 +0100 Organization: L.I.E.N. Lines: 11 Message-ID: <34D7414A.716@lien.u-nancy.fr> Reply-To: goeury@lien.u-nancy.fr NNTP-Posting-Host: lien1.lien.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold [fr] (WinNT; I) Hello, I'm a french seeker and I'm working in bioelectromagnetism. I would like to use a phantom for simulating the dielectric properties of human tissues in the ELF freqency range(0-100kHz). Would you send me informations and documentations about existing products and phantom if you have. In the negative, would you give me links of whatever else. Thanks very much and I'm waiting for you. Christophe GOEURY -- From owner-biophysics@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!chicago-news-feed2.bbnplanet.com!news.bbnplanet.com!news.itis.com!news.doit.wisc.edu!not-for-mail From: Medical Electronics Lab Newsgroups: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Subject: Re: phantom simulated dielectric properties of human tissues Date: Tue, 03 Feb 1998 12:57:17 -0600 Organization: Dept. Physiology, U. Wisconsin Lines: 10 Message-ID: <34D7688D.38CA@physiology.wisc.edu> References: <34D7414A.716@lien.u-nancy.fr> <34D75184.1CD2@ix.netcom.com> NNTP-Posting-Host: pcaf.neurophys.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (WinNT; I) Uncle Al wrote: > We always use undergraduates. They are abundant, self-housing, > acceptable models for human beings (except the pre-meds and jocks), and > can be charged course credits. If it works in undergrads we go to > rats. There are strict rules for using rats, and they are expensive. :-) Grads and med students make useful phantoms too. Patience, persistence, truth, Dr. mike From owner-biophysics@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!panix!howland.erols.net!ix.netcom.com!news From: Uncle Al Newsgroups: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Subject: Re: phantom simulated dielectric properties of human tissues Date: Tue, 03 Feb 1998 09:19:00 -0800 Organization: The Noble Krell Lines: 27 Distribution: inet Message-ID: <34D75184.1CD2@ix.netcom.com> References: <34D7414A.716@lien.u-nancy.fr> Reply-To: UncleAl0@ix.netcom.com NNTP-Posting-Host: irv-ca5-18.ix.netcom.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NETCOM-Date: Tue Feb 03 11:12:00 AM CST 1998 X-Mailer: Mozilla 3.0 (Win16; U) Christophe GOEURY wrote: > > Hello, > I'm a french seeker and I'm working in bioelectromagnetism. > I would like to use a phantom for simulating the dielectric > properties of human tissues in the ELF freqency range(0-100kHz). > Would you send me informations and documentations about existing > products and phantom if you have. In the negative, would you > give me links of whatever else. > Thanks very much and I'm waiting for you. > > Christophe GOEURY > -- We always use undergraduates. They are abundant, self-housing, acceptable models for human beings (except the pre-meds and jocks), and can be charged course credits. If it works in undergrads we go to rats. There are strict rules for using rats, and they are expensive. -- Uncle Al Schwartz UncleAl0@ix.netcom.com ("zero" before @) http://pw2.netcom.com/~uncleal0/uncleal.htm http://www.ultra.net.au/~wisby/uncleal.htm http://www.guyy.demon.co.uk/uncleal/uncleal.htm (Toxic URLs! Unsafe for children, Democrats, and most mammals) "Quis custodiet ipsos custodes?" The Net! From owner-biophysics@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!enews.sgi.com!news.idt.net!news.maxwell.syr.edu!news-ge.switch.ch!news.unige.ch!news From: david kony Newsgroups: bionet.biophysics Subject: polysaccharides database Date: Tue, 03 Feb 1998 20:03:17 +0100 Organization: Universite de Geneve (CABE) Lines: 9 Message-ID: <34D769F5.41C6@cabe.unige.ch> NNTP-Posting-Host: scsg27.unige.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) hi! I'm looking for NMR or/and X-RAY data concercing polysaccharides. thank you for any information you can give me. bye, david From owner-biophysics@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!199.117.161.1!csn!nntp-xfer-1.csn.net!news.acsu.buffalo.edu!acsu.buffalo.edu!not-for-mail From: Brian M Burkhart Newsgroups: bionet.biophysics Subject: dielectric constant of a membrane bilayer Date: Tue, 03 Feb 1998 14:30:17 -0500 Organization: Hauptman-Woodward Medical Research Institute Lines: 11 Message-ID: <34D77049.794B@hwi.buffalo.edu> NNTP-Posting-Host: galen.hwi.buffalo.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04C-SGI (X11; I; IRIX64 6.2 IP28) I would be interested to see some discussion of the dielectric constant properties of the interior of a membrane bilayer. Gradient towards the center? Or is the 80/2 model sufficient? How similar are various organic solvent systems to the membrane bilayer (n-alcohols, glacial acetic acid, alkanes, fatty acids, etc) -- Brian M Burkhart, Ph.D. Hauptman-Woodward Medical Research Institute 73 High Street Buffalo, NY 14203 Phone: (716)856-9600 x313 FAX: (716)852-6086 From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!nntprelay.mathworks.com!ptdnetP!newsgate.ptd.net!newsfeed00.btx.dtag.de!news.btx.dtag.de!not-for-mail From: Schmidt.GEMETEC@t-online.de (Peter Schmidt) Newsgroups: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Subject: Re: phantom simulated dielectric properties of human tissues Date: 3 Feb 1998 19:53:10 GMT Organization: GEMETEC Aachen mbH Lines: 42 Message-ID: <6b7sj6$ia3$5@news01.btx.dtag.de> References: <34D7414A.716@lien.u-nancy.fr> Reply-To: Schmidt.GEMETEC@t-online.NOSPAM.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Sender: 02418793031-0003@t-online.de X-Mailer: Mozilla 4.04 [en] (WinNT; I) To: goeury@lien.u-nancy.fr, goeury@lien.u-nancy.fr Hello, Christophe GOEURY I made my thesis paper in biotechnological engineering on a field theory topic. Modelling was one of the tasks to do. I cannot instantly give you the proper source, but there is an excellent book on bioelectrical capabilities of tissue written by J. P. Reilly (sp. as far as I can remember). This does not give you the phantom, but for basic research this might be a good point to start. The IEEE Journal on ?Biotechnology or Biomedical Engineering? also regularly delivers articles about modelling. Please mail me (and do not forget to remove the "antispm" thing in the reply-to address;-) if you need more information, i can look it up for you in my paper. You wrote: > ... > I would like to use a phantom for simulating the dielectric > properties of human tissues in the ELF freqency range(0-100kHz). well, there is not only dielecticity, but also ionic conduction. Especially the low range bears some interestin unlinearities (stimulation!). > Would you send me informations and documentations about existing > products and phantom if you have. In the negative, would you > give me links of whatever else. ... CU on the net, Peter Schmidt -- Schmidt.GEMETEC@t-online.de (Dipl.-Ing. Peter B. Schmidt) GEMETEC Aachen mbH, Germany http://home.t-online.de/home/GEMETEC-AC Snail: Pauwelsstrasse 19, D-52074 Aachen, Germany Voice: +49 241 44 68 224, Fax: +49 241 44 68 229 From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!CUB.UCA.EDU!RDJ0288 From: RDJ0288@CUB.UCA.EDU Newsgroups: bionet.biophysics Subject: (none) Date: 4 Feb 1998 13:40:53 -0800 Organization: University of Central Arkansas Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <649A310F61@cub.uca.edu> NNTP-Posting-Host: net.bio.net sUBCRIBE BIOPHYS@NET.BIO.NET RICHARD JOHNSON From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Alex Spirov Newsgroups: bionet.biophysics Subject: Preprint on line: PARASITIC MOBILE GENETIC ELEMENTS IN SIMULATIONS OF EVOLUTION Date: 4 Feb 1998 19:34:17 -0000 Lines: 90 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6bafrp$hjf@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: "'bionet.info-theory'" , "'bionet.general'" , "'bionet.biophysics'" , "'bionet.biology.computational'" , "'bionet.molbio.evolution'" This announcement is being cross-posted to several newsgroups. Please, excuse the duplication. Dear All, The following paper is now available=20 as HTM Pages: http://www.iephb.ru/~spirov/te-tech/te-tech.htm and as ZIP-compressed PostScript file via anonymous ftp from: ftp://ftp.iephb.ru/pub/spirov/te_tech.zip (528 KB) These materials are submitted to "Evol.Comp.Journal".=20 Title: "VARIABLE-LENGTH GENOMES, OPERATORS OF TRANSPOSITION AND = PARASITIC MOBILE GENETIC ELEMENTS IN SIMULATIONS OF EVOLUTION" Authors: Alexander V. Spirov and Alexander B. Kazansky ABSTRACT The progress in the field of evolutionary self-learning algorithms is = primarily associated with the development of the set of operators, = realising the process of evolutionary search and adaptation. It is a = matter of fact, that the low "evolvability" of neo-darwinian population = with the classical set of evolutionary operators put a fundamental = limitation on the effectivity and universality of evolutionary = computations, based on this type of evolving system. The realisation of = this fact stimulates the constant interest of specialists in the field = of evolutionary computations to the achievements in evolutionary and = molecular biology. Godsends of nature can be adapted and applied to = evolutionary algorithms for perfection of the instrument for solving of = the hard optimisation problems. The creative role of viruses and = virus-like elements in evolution attracts nowadays a great interest of = evolutionary biologists as well as specialists in evolutionary = computations. In this work we put forward a new approach to evolutionary algorithms - = Transposable Elements (TE) technique. This technique was evaluated and = tested by the example of solving of biological, as well as classical = test behavioural problems (the John Muir's trail in ant's navigation = problem). The approach is based on the application of new algorithms, modelling = co-evolution of host population and a set of selfish/parasite mobile = genetic elements (transposons). These elements have ability to insertion = in the host's genome and to move from one genome site to another. = Besides, transposons are heritable and can be transmitted to the next = generations as well as to the other host during 'contacts'. Our TE technique presupposes the application of special new TE operators = of evolutionary computations along with classical ones. The TE operators = act on genes-strings of variable length just as known variable-length = operators of duplication, elimination and random addition. The TE technique is effective in cases, when traditional neo-darwinian = populations in framework of classical approaches loses the evolvability. = This technique gives selection advantage to functionally redundant, more = complex programs in the bottlenecks of evolutionary process. The developed method was successfully applied to the simulation of = biological evolution and to solving of ant's navigation test for = non-standard variant of trail. The possibilities for application of = proposed technique for solving GA-hard problems has being discussed as = well. KEYWORDS: self-organisation, evolution, transposons, genetic algorithms, = genetic networks, artificial life, evolutionary biology. (13 pages, 9 color illus.) PS: The PS-file was generated by WinWord 7 and tested by GhostScript viewer for Windows.=20 ________________________ Alexander V.Spirov (PhD) The Sechenov Institute of Evolutionary Physiology & Biochemistry, Thorez = Pr. 44, S.-Petersburg, 194223, Russia phone/fax +7 (812)552 3219; fax + 7 (812)552-3012 = http://www.iephb.ru/~spirov/; Email spirov@iephb.ru and Institute for High-Performance Computing & Data Bases, P.O. Box 71, = St.Petersburg 194291, RUSSIA From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!news.he.net!news.pagesat.net!news1.good.net!news.goodnet.com!news From: Linda Chamberlain Newsgroups: bionet.biophysics Subject: Conference Announcement Date: Wed, 04 Feb 1998 10:16:45 -0700 Organization: Alcor Life Extension Foundation Lines: 121 Message-ID: <34D8A27D.69D2@netzone.com> Reply-To: linda@alcor.org NNTP-Posting-Host: phx-nz-ts6-13.goodnet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) You are invited to attend a conference on advances in life extension and cryopreservation. For more information on the Alcor Life Extension Foundation and this year's Conference: http://www.alcor.org (click on the blue Phoenix icon, then on "Conference") Presentations, Talks and Panels by: Fred Chamberlain Linda Chamberlain Michael Cloud Mike Darwin Robert Ettinger Greg Fahy, Ph.D. Ralph Merkle, Ph.D. Marvin Minsky, Ph.D. (tbc) Dave Pizer Paul Segall, Ph.D. Hal Sternberg, Ph.D. Brian Wowk, Ph.D. Lodging: $99/night, single or double room, $119 for four people. Be sure to tell the reservation clerk that you are attending the Alcor Conference and give them the following code: ALC. Fifty rooms held through March 4, 1998. For additional information, contact the Chamber of Commerce in Scottsdale at (800)877-1117 or in Phoenix at (602)254-5521 (No toll free Ch.Comm in Phoenix!) For frugal conference attendees, there are two Super 8 Motels near the airport and conference hotel with shuttles. The toll-free reservation number is 1-800-800-8000. Conference Cost: Full package includes all presentations and materials, Saturday luncheon and Saturday evening banquet. Regular Rate... if received by March 3, 1998...$149 Late Rate... if received by April 2, 1998...$179 Door Rate......$195 Register by phone: (800) 367-2228 - Ask for Joe Hovey. Visa or MasterCard accepted; you may mail registration - see below: You may mail your registration and payment to: 1998 Alcor Conference, 7895 E. Acoma Dr., Ste. 110, Scottsdale, AZ 85260. Please make check payable to Alcor Foundation, and give us your full name, address, and phone number. Your check will be your receipt; please pick up tickets at the Conference. Friday, April 3, 1998 7:00-10:00 pm Welcome: Registration, Reception Saturday, April 4, 1998 9:00-9:15 am Introduction - Fred Chamberlain, Alcor President/CEO 9:15-10:30 am Greg Fahy, Ph.D. - "CryoPreservation of the Human Brain" 10:30-11:30 am Mike Darwin - "Newly Developed and Emerging Technologies for Human CryoPreservation" 11:30-1:30 pm Luncheon (provided with registration, or available separately, see fee below) 1:30-2:30 pm Brian Wowk, Ph.D. - "Toward Human Vitrification" 2:30-3:30 pm Fred & Linda Chamberlain, , Alcor CEO and Alcor CryoTranport Manager - "Cryonics Rescue Systems" 3:30-4:30 pm Ralph Merkle, Ph.D. - "Nanotechnology Update and Molecular Repair of the Brain" 4:30-5:30 pm Paul Segall, Ph.D. and Hal Sternberg, Ph.D. - "Advances in Low Temperature Medicine" 7:00-7:30 pm Reception; no host bar 7:30-11:00 pm Banquet 8:30-11:00 pm Panel: What's in It for Me? - Marvin Minsky, Ph.D. (tbc) Sunday, April 5, 1998 TRACK-I 8:45-9:30 am Bus to Alcor Facility 9:30-11:15 am Alcor Tour and Sign-up Party 11:15-11:45 am Bus returns to Conference Site TRACK-II 9:30-11:45 Panel: Identity and Reanimation - Fred Chamberlain 11:45 am-1:30 pm Lunch (on your own) 1:30-2:30 pm Alan Stoner & Mark Thompson - Smith Barney's "Cryonics Wealth Preservation Programs" 2:30-3:30 pm Michael Cloud - "How to Make the Idea of Cryonics Infectious" 3:30-4:00 Break 4:00-4:30 pm Dave Pizer - "A Retirement Community and Safe Storage Alternatives" 4:30-5:00 pm Robert Ettinger - "Where are we headed?" 5:00-5:30 pm Closing Comments - Linda Chamberlain END OF EMAIL Linda Chamberlain (linda@alcor.org) CryoTransport Manager Alcor Life Extension Foundation Non-profit cryonic suspension services since 1972. 7895 E. Acoma Dr., Suite 110, Scottsdale AZ 85260-6916 Phone (602) 922-9013 (800) 367-2228 FAX (602) 922-9027 info@alcor.org for general requests http://www.alcor.org From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!news.voicenet.com!nntp.upenn.edu!red.seas.upenn.edu!kfoster From: kfoster@red.seas.upenn.edu (Kenneth R Foster) Newsgroups: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Subject: Re: phantom simulated dielectric properties of human tissues Followup-To: sci.bio.technology,sci.med.physics,sci.physics.electromag,bionet.biophysics,can.med.misc,fr.sci.biometrie,sci.engr.biomed,sci.materials,sci.med.telemedicine Date: 4 Feb 1998 17:21:16 GMT Organization: University of Pennsylvania Lines: 42 Distribution: inet Message-ID: <6ba82c$b3q$1@netnews.upenn.edu> References: <34D7414A.716@lien.u-nancy.fr> <34D75184.1CD2@ix.netcom.com> NNTP-Posting-Host: red.seas.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.3] : > I would like to use a phantom for simulating the dielectric : > properties of human tissues in the ELF freqency range(0-100kHz). : > Would you send me informations and documentations about existing : > products and phantom if you have. In the negative, would you : > give me links of whatever else. : All kidding aside, it depends on how accurately you want to model the body, and what the mechanical properties of the phantom need to be. In this frequency range the loss tangent of tissue is very high, i.e. you do not have to worry too much about the permittivity. For most purposes a simple saline solution should work. If you want to model anatomical structures, you will need to use some kind of gelling agent, taking care to keep the conductivity appropriate for tissue. Some conductivity data are in my review in the CRC Reviews on Biomedical Engineering published a few years ago, but other sources are available also. If you need to correctly model the permittivity as well, you are in trouble since there is no convenient (or feasible, I think() way to get the high permittivity values of tissue at low frequencies using simple phantom liquids. In case you are interested, there will be a conference on electrical bioimpedance in Barcelona, April 5-9, 1998, and a lot of people there would undoubtably be interested in your work. See Contact Prof. Pere Riu priu@eel.upc.es Departament d'Enginyeria Electrsnica Universitat Politicnica de Catalunya Campus Nord, Edifici C-4 C/ Gran Capit` s/n 08071 BARCELONA FAX: 34 - 3 - 401 67 56 http://petrus.upc.es/~wwwdib/homepageuk.html From owner-biophysics@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Dielectric constant of biomembranes Date: 4 Feb 1998 09:34:22 -0000 Lines: 44 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6b9cmu$d43@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Brian M Burkhart wrote:>>>>>>>>>>>> I would be interested to see some discussion of the dielectric constant properties of the interior of a membrane bilayer. Gradient towards the center? Or is the 80/2 model sufficient? How similar are various organic solvent systems to the membrane bilayer (n-alcohols, glacial acetic acid, alkanes, fatty acids, etc)<<<<<<<<<<<<<<<<<<<< I would also like to see a discussion on the same topic and tried to initiate it a few times but failed. There are at least two extremely interesting bioenergetic implications related to a possible variation of the dielectric constant both along and across the membrane. Let me briefly describe them. 1. If the dielectric constant varies ALONG the membrane and if Donnan transmembrane potential difference is established, the combination of the following two universally accepted facts: a) that the potential is uniform on each side of the membrane b) that the transmembrane potential difference is equal to the ratio of the surface charge density and the capacitance - leads inevitably to the incredible result that, even at (Donnan) equilibrium, there are local lateral and, accordingly, transmembrane fluxes of some ion, e.g. H+. 2. Let us consider the following equilibrium system: pH 7 M1 pH 2 M2 pH 7 where M1 and M2 are membranes permeable only to H+ and whose dielectric constants are respectively high and low. What should be noted is that the surface charge density (H+ concentration) is higher on the LEFT side of M1 than on the RIGHT side of M2, but both places are at the SAME electrical potential. In other words, there is a H+ concentration difference between the far sides of the membranes, but no potential difference. If, in a thought experiment, the two membranes approach each other until the space between them becomes microscopic, we obtain a model of a membrane whose dielectric constant varies ACROSS it. What is remarkable however is that in the case of Donnan equilibrium there is a transmembrane concentration but no potential difference, i.e. we can expect a transmembrane H+ flux. My description is incomplete and therefore contains contradictions (it is strange to speak of equilibrium and a transmembrane flux at the same time), but everything could be clarified in a discussion. Pentcho Valev From owner-biophysics@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!CCVAX.SINICA.EDU.TW!mbmtchan From: mbmtchan@CCVAX.SINICA.EDU.TW (ming-tsair Chan) Newsgroups: bionet.biophysics Subject: PI Positions Date: 5 Feb 1998 02:32:34 -0800 Organization: IBAS Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <3250F328.1725@ccvax.sinica.edu.tw> Reply-To: mbmtchan@ccvax.sinica.edu.tw NNTP-Posting-Host: net.bio.net Principal Investigator and Research Fellow Positions Available for The Preparatory Office of Inst. of BioAgricultural Sciences Academia Sinica, Taipei, Taiwan We are seeking to appoint several qualified applicants to serve as Principal Investigators, ranking from assistant, associate to full research fellows. There are five areas within our IBAS Preparatory Office: disease-resistant transgenic plants, bioreactors, aquaculture, animal vaccines, and environmental/industrial enzymes. New recruits can start in May 1998. Requirements for the applicants include a Ph.D. or an equivalent degree. Principal investigators are required to engage in programmatic project, serving as project leaders and/or as collaborative research scientists.. The project leader and the senior research scientist must have at least 10 years of research experience with demonstrated abilities in applied and/or basic research in one of the biotechnology areas indicated above, evidence of creativity and organizational skills. They would greatly benefit from their familiarity with Taiwan*s cultural environment and language. The junior research scientists must have at least 2 years of postdoctoral training. Applicants are expected to conduct research in the above selected areas of biotechnology. Application should include a cover letter, a complete curriculum vitae as well as the names, address and telephone numbers and fax numbers of 5 references. Review of applications will begin around March, 1998, and will continue until suitable candidates are recruited. Several Postdoctoral Fellow positions, each working with the above described research areas are also now available for application. Applications should be addressed to: Ms. S. W. Wang The Preparatory Office of Inst. of BioAgricultural Sciences, Academia Sinica, Taipei 11529, Taiwan, R.O.C. From owner-biophysics@net.bio.net Wed Feb 04 22:00:00 1998 From: mjts@usa.net Newsgroups: bionet.biophysics Subject: help Date: Thu, 05 Feb 1998 08:51:59 GMT Organization: Netvigator Lines: 9 Message-ID: <34d97dab.1618582@news.netvigator.com> Reply-To: mjts@usa.net NNTP-Posting-Host: hhtam007065.netvigator.com X-Newsreader: Forte Free Agent 1.11/32.235 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!202.84.255.3!news.hkt.net!news.netvigator.com!usenet In a photoelectic experiment, if light of wavelength is first 0.0000004m. The wavelength is then changed to 0.0000003m, but the intensity is kept constant. Why for the same intensity, the number of photons is smaller by ¾ and the current is then decreased ? And what actually ‘intensity’ means ? From owner-biophysics@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: "Timothy E. Vaughan" Newsgroups: sci.med.physics,bionet.biophysics Subject: Re: phantom simulated dielectric properties of human tissues Date: Wed, 04 Feb 1998 09:14:26 -0500 Organization: Harvard-MIT Division of Health Sciences and Technology Lines: 24 Message-ID: <34D877C2.49E6F287@epore.mit.edu> References: <34D7414A.716@lien.u-nancy.fr> <6b7sj6$ia3$5@news01.btx.dtag.de> NNTP-Posting-Host: kaytee.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.5.1 sun4m) Peter Schmidt wrote [and I snipped]: > I made my thesis paper in biotechnological engineering on a field theory > topic. Modelling was one of the tasks to do. I cannot instantly give you > the proper source, but there is an excellent book on bioelectrical > capabilities of tissue written by J. P. Reilly (sp. as far as I can > remember). The title of Reilly's book, if it is the one I am thinking of, is"Electrical Stimulation and Electropathology", and it is from Cambridge University Press, 1992. Another potentially useful starting point is and article by K. R. Foster and H. P. Schwan: "Dielectric properties of tissues and biological materials: A critical review", which is in Critical Reviews in Biomedical Engineering, vol. 17, Issue 1 (1989). > This does not give you the phantom, but for basic research this might be > a good point to start. This is true of the Foster and Schwan article, too. From owner-biophysics@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!dca1-hub1.news.digex.net!digex!ais.net!uunet!in3.uu.net!nntp.earthlink.net!usenet From: prismx@scienceweek.com (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: Headlines (6 Feb 98) Date: Thu, 05 Feb 1998 19:25:24 GMT Organization: SCIENCE-WEEK Lines: 52 Message-ID: <6bd3nh$lnk@argentina.earthlink.net> Reply-To: prismx@scienceweek.com NNTP-Posting-Host: 153.35.114.193 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:21308 bionet.biophysics:3968 bionet.cellbiol:8779 bionet.general:29307 SCIENCE-WEEK is a free weekly Email digest of the news of science read each week by 50,000+ people in the scientific community in more than 30 countries. News briefs from the major journals are amplified with enough background material to make them intelligible to nonspecialists: the biology is detailed for physicists and chemists, and the physics and chemistry are detailed for biologists. Each issue contains 15 to 20 news reports, plus annotated listings of new books in the sciences. The SW complete weekly news reports are available free via Email. To subscribe, send SUB SW to . Contents of the Latest Issue Feb 6, 1998: 1. Swiss Government to Preempt Gene Technology Referendum 2. More Controversy Concerning Policy on Xenotransplants 3. Apparent Extensive Plagiarism by Polish Scientist 4. Historical Evidence of Deception by Wireless Inventor Marconi 5. Mounting Evidence for a Sub-Surface Ocean on Jupiter's Europa 6. A Simulation Model for Modern and Glacial Climates 7. Evidence for a Quark-Gluon Plasma 8. A Method for the Synthesis of Durable Organic Gels 9. A Functional Non-Protein Model for an Enzyme Catalyst 10. Rho Enzymes and the Actin Cytoskeleton 11. Intermediate Filaments and Intracellular Scaffolding 12. Motor Proteins and Organelle Transport 13. On the Function of Unconventional Myosins 14. A Criticism of the Prion Hypothesis 15. A New Protein That Acts as an Embryological Head Inducer 16. On the Chemistry and Neurophysiological Action of Vanilloids 17. The Role of Visual Experience in Development of Visual Cortex 18. Phantom Sensations Evoked by Human Thalamic Microstimulation 19. An HIV Protein That Protects the Host Cell Against T-Cells 20. Evidence for Axonal Transection in Multiple Sclerosis Lesions 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. 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 Sat Feb 07 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!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: Dielectric constant of biomembranes Date: Sun, 8 Feb 1998 12:23:18 +0200 Organization: Hebrew University Lines: 28 Message-ID: <6bk12q$dvf$1@news.huji.ac.il> References: <6b9cmu$d43@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-6b9cmu+ACQ-d43+AEA-mserv1.dl.ac.uk+AD4-... ... +AD4- +AD4-1. If the dielectric constant varies ALONG the membrane and if = Donnan +AD4-transmembrane potential difference is established, the combination = of the +AD4-following two universally accepted facts: a) that the potential is +AD4-uniform on each side of the membrane b) that the transmembrane = potential +AD4-difference is equal to the ratio of the surface charge density and = the +AD4-capacitance - leads inevitably to the incredible result that, even = at +AD4-(Donnan) equilibrium, there are local lateral and, accordingly, +AD4-transmembrane fluxes of some ion, e.g. H. +AD4- ... Pentcho, this is really not so mysterious. There are lateral movements = of ions until electroCHEMICAL equilibrium is reached. Once this happens, = there will be no more net ion fluxes. I see no problem with membrane = patches attracting concentrations of particular ions - in fact I expect = that this is documented in the literature. From owner-biophysics@net.bio.net Sat Feb 07 22:00:00 1998 Path: biosci!OUT.HIX.COM!publisher From: publisher@OUT.HIX.COM ("HIX") Newsgroups: bionet.biophysics Subject: *** HIXCD/8 *** HIXCD/8 *** HIXCD/8 *** Followup-To: poster Date: 8 Feb 1998 15:12:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802082312.PAA13175@net.bio.net> Reply-To: "HIXCD" NNTP-Posting-Host: net.bio.net -- English description is at the end -- --------------------------------------------------------------------------- -- Elofordulhat, hogy ezt a levelet tobb peldanyban kapod meg. Ez azt -- jelenti, hogy a HIX-re valaha tobb kulonbozo cimrol irtal, amelyeket a -- program nem tudott megfeleltetni egymasnak. Mivel egyszeri ertesitesrol -- van szo, remelem, ezt a kis kellemetlenseget nem veszed zokon. -- Ez a level a To: mezoben lathato cimedre erkezett. --------------------------------------------------------------------------- Szia! Keszuloben van egy jubileumi HIXCD a HIX 8. szuletesnapjara, februar vegere. A HIXCD/8-on minden rajta lesz, az elso szamoktol kezdve mostanaig, 19,000 megjelent ujsagszam (tobb mint 200,000 cikk!), PLUSZ: - HIX Dokumentumtar (2400 dokument) - Zitaneni Osszes - Kisgyorgy Eva New Yorki utikonyve, es kepes utazasi naploi - Umann Kornel "Tippek viziturazoknak" cimu alapmuve RAADAS: - a teljes Internetto Hirlevel archivum A HIXCD/8-at az Internetto (http://www.internetto.hu) adja ki, onkoltsegi aron, ez vsz. 1000 Ft koruli osszeget jelent (vagy $5). Ha elorelathatolag (ez nem elkotelezettseg!) kersz belole, akkor jelezd a hixcd@hix.com ------------- cimen, mivel a non-profit hozzaallas miatt csak annyit nyomnak, amennyire igeny van - es lehet, hogy nem fog jutni. 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Jozsi. /HIX/ E-mail: help@hix.com Web: http://www.hix.com Arena: telnet arena.hix.com =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= =* Hollosi Information eXchange /HIX/ -- http://www.hix.com *= =* ------------------------------------------------------------------------- *= =* TIPP GURU MOKA RANDI BUDAPEST DOSZ HIR HUNGARY JATEK KORNYESZ KULTURA *= =* MOZAIK NARANCS NY OTTHON SPORT TUDOMANY UK WEBMESTER VITA TANC PARA AZSIA *= =* AGYKONTROLL FILOZOFIA CODER *= =* ------------------------------------------------------------------------- *= =* Automata segitseg: *= =* Ha az nem eleg: *= =* Utolso szalmaszal: Hollosi Jozsi. /HIX/ *= =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*= English description: This letter is to announce a non-profit CDROM containing the 8-year long archives of HIX - discussion and informational forums in Hungarian. This letter has been sent to those who participated in those discussion forums. Some of these addresses might be obsolete by now because of the long timeframe, but there was no way of knowing that without validating them through the distribution of this message. From owner-biophysics@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Membrane capacitance Date: 9 Feb 1998 08:08:17 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6bmdhh$gsq@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Jonathan Marder wrote:>>>>>>>>>>>>>>>>>> Pentcho, this is really not so mysterious. There are lateral movements of ions until electroCHEMICAL equilibrium is reached. Once this happens, there will be no more net ion fluxes. I see no problem with membrane patches attracting concentrations of particular ions - in fact I expect that this is documented in the literature.<<<<<<<<<<<<<<<<<<< It seems to me that there will be lateral fluxes even at equilibrium (although half of my mind rejects this as absurd). Let us have a close look at the situation: pH 2 -------high-capacitance---------low-capacitance----------------------- pH 7 The membrane is permeable only to H+. If (at equilibrium) the potential in each compartment is uniform (this is universally accepted), there will be a lateral gradient of H+ concentration close to the membrane - e.g., in the lower compartment, the H+ concentration will be higher at the high-capacitance patch than at the low-capacitance one. As the potential is uniform, we should expect a lateral H+ flux from the high-capacitance patch to the low-capacitance one (in the lower compartment). The other possible assumption is that, at equilibrium, the potential in each compartment is not uniform. We could analyse this situation as well but it is clear even without analysis that, if correct, the assumption would disturb the established theoretical paradigm to such an extent that practically a new theory will have to be built. Best regards, Pentcho From owner-biophysics@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Membrane capacitance Date: 9 Feb 1998 08:27:13 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6bmel1$hnk@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Jonathan Marder wrote:>>>>>>>>>>>>>>>>>> Pentcho, this is really not so mysterious. There are lateral movements of ions until electroCHEMICAL equilibrium is reached. Once this happens, there will be no more net ion fluxes. I see no problem with membrane patches attracting concentrations of particular ions - in fact I expect that this is documented in the literature.<<<<<<<<<<<<<<<<<<< It seems to me that there will be lateral fluxes even at equilibrium (although half of my mind rejects this as absurd). Let us have a close look at the situation: pH 2 -------high-capacitance---------low-capacitance----------------------- pH 7 The membrane is permeable only to H+. If (at equilibrium) the potential in each compartment is uniform (this is universally accepted), there will be a lateral gradient of H+ concentration close to the membrane - e.g., in the lower compartment, the H+ concentration will be higher at the high-capacitance patch than at the low-capacitance one. As the potential is uniform, we should expect a lateral H+ flux from the high-capacitance patch to the low-capacitance one (in the lower compartment). The other possible assumption is that, at equilibrium, the potential in each compartment is not uniform. We could analyse this situation as well but it is clear even without analysis that, if correct, the assumption would disturb the established theoretical paradigm to such an extent that practically a new theory will have to be built. Best regards, Pentcho From owner-biophysics@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.nacamar.de!uni-erlangen.de!lrz-muenchen.de!not-for-mail From: Gerald Mathias Newsgroups: bionet.biophysics Subject: Re: help Date: Wed, 11 Feb 1998 13:27:32 +0100 Organization: [posted via] Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 4 Distribution: world Message-ID: <34E19934.8CC6ADBF@Physik.Uni-Muenchen.DE> References: <34d97dab.1618582@news.netvigator.com> NNTP-Posting-Host: dial200.lrz-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Intensity means the amount of energy per second per m*m. As the waveleght is shortent the amount of energy per photon is increased, so you nead less photons for the some intensity. From owner-biophysics@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Nick Art Newsgroups: bionet.biophysics Subject: Entropy question Date: 12 Feb 1998 17:48:17 -0000 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6bvcl1$p7v@mserv1.dl.ac.uk> X-Sender: Art@pooh.embl-hamburg.de Original-To: biophys@dl.ac.uk Dear All, I hope if someone could tell me the difference between the statistical entropy and thermodynamic entropy. Many thanks, Nick From owner-biophysics@net.bio.net Wed Feb 11 22:00:00 1998 From: 133@109.com Newsgroups: bionet.biophysics Subject: NLREG - Nonlinear & linear statistical regression program - 34 0212180124 CMI Date: Thu, 12 Feb 98 18:01:25 Organization: Nonlinear Regression Software Lines: 55 Message-ID: <6bte3t$ba7$1@news2.triton.net> NNTP-Posting-Host: 204.181.142.21 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!206.250.193.243!newsfeeder.triton.net!news2.triton.net!not-for-mail ** Announcing NLREG -- Nonlinear Statistical Regression Program ** http://www.sandh.com/sherrod/nlreg.html NLREG is a powerful statistical analysis program for Windows 95 and NT that performs linear and nonlinear regression analysis and curve fitting. 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As a result, it can handle functions that are impossible to linearize such as: Y = Amplitude*SIN(Freq*X+Phase) + A*EXP(X); Another advantage of handing the function in true nonlinear form is that the minimization of the sum of squared residual values (i.e., "least squares") is based on the true nonlinear value rather than some linearized transformation. In addition to computing the optimal values of the parameters, NLREG can generate plots of the data points and the fitted equation. In addition, it can plot the distribution of residual values. In addition to performing classic nonlinear regression, NLREG can be used to find the root or minimum value of a general nonlinear function. It can also be used in a special form where the independent variable is omitted; an interesting application of this is "circular regression" where a circle is fitted to a set of data points. NLREG is in use at hundreds of universities, laboratories, and government agencies around the world (including the U.S. Navy, Harvard, and Duke). NLREG has been validated using the NIST statistical reference datasets; the results are available on the NLREG web page. The price of NLREG is only $65 ($70 if outside the USA), which is far below the cost of comparable commercial regression programs. And you can download a shareware demonstration version of NLREG to try out before you decide to purchase it. To learn more about NLREG and download your free shareware version, visit the web site: http://www.sandh.com/sherrod/nlreg.html -- 34: bionet.biophysics 0212180124 -- From owner-biophysics@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!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: Entropy question Date: 12 Feb 1998 21:26:27 GMT Organization: University of Washington Lines: 16 Distribution: bionet Message-ID: <6bvpe3$4i9$1@nntp3.u.washington.edu> References: <6bvcl1$p7v@mserv1.dl.ac.uk> NNTP-Posting-Host: homer34.u.washington.edu X-Trace: nntp3.u.washington.edu 887318787 4681 (None) 140.142.64.1 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Nick Art writes: >Dear All, >I hope if someone could tell me the difference between >the statistical entropy and thermodynamic entropy. If by statistical entropy, you mean the entropy defined in statistical mechanics, it is assumed that it is the same as the thermodynamic entropy. Measurements of the entropy using the methods of statistical mechanics have always yielded the same result as measurements using the results of thermodynamics. Bryant Fujimoto From owner-biophysics@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!news.shef.ac.uk!not-for-mail From: M.Makris@shef.ac.uk (E Demoncheaux) Newsgroups: bionet.biophysics Subject: General question Date: 13 Feb 1998 14:52:10 GMT Organization: Exp. & Clinical Microbiology, University of Sheffield , UK Lines: 3 Message-ID: <6c1mmq$rnu$1@bignews.shef.ac.uk> NNTP-Posting-Host: pc090018.shef.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Could someone explain the difference between kinetic and thermodynamic stability? From owner-biophysics@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Boltzmann's and thermodynamic entropy Date: 13 Feb 1998 14:23:23 -0000 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6c1l0r$5lm@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote:>>>>>>>>> Nick Art writes: >Dear All, >I hope if someone could tell me the difference between >the statistical entropy and thermodynamic entropy. If by statistical entropy, you mean the entropy defined in statistical mechanics, it is assumed that it is the same as the thermodynamic entropy. Measurements of the entropy using the methods of statistical mechanics have always yielded the same result as measurements using the results of thermodynamics.<<<<<<< We have already discussed that, Bryant, on a suitable model devised by R. Alberty (do you remember?). We found that, in order for Boltzmann's (klnW) and thermodynamic entropy to coincide, some systems must SPONTANEOUSLY move from a MORE probable to a LESS probable state. So I hope you would agree with the following answer: If systems can spontaneously move from a more probable to a less probable state, the two entropies coincide. If not, not. In my opinion, spontaneous movement from a more probable to a less probable state is a LOGICAL absurdity, but I may be wrong. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!209.89.75.15!News.Toronto.iSTAR.net!news.istar.net!mars.online.uleth.ca!jeff.oliver@uleth.ca From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: General question Date: Fri, 13 Feb 1998 12:20:09 -0700 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 16 Message-ID: <34E49CE9.2781@henri.chem.uleth.ca> References: <6c1mmq$rnu$1@bignews.shef.ac.uk> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) E Demoncheaux wrote: > Could someone explain the difference between kinetic and thermodynamic > stability? Easily done by example: Diamonds are thermodynamically unstable relative to graphite at standard temperature and pressure which means that their free energy is higher than that of graphite. Thus, every diamond that has ever been dug out of the ground is slowly converting to graphite. (Contrary to the popular saying, diamonds are not forever.) However, diamonds are kinetically stable in the sense that the rate constant for this conversion is immeasurably small. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!news.sprintisp.com!sprintisp!worldnet.att.net!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's and thermodynamic entropy Date: 13 Feb 1998 20:51:52 GMT Organization: University of Washington Lines: 38 Distribution: bionet Message-ID: <6c2bp8$aln$1@nntp3.u.washington.edu> References: <6c1l0r$5lm@mserv1.dl.ac.uk> NNTP-Posting-Host: homer27.u.washington.edu X-Trace: nntp3.u.washington.edu 887403112 10935 (None) 140.142.64.1 X-Complaints-To: help@cac.washington.edu Pentcho Valev writes: >Bryant Fujimoto wrote:>>>>>>>>> >Nick Art writes: >>Dear All, >>I hope if someone could tell me the difference between >>the statistical entropy and thermodynamic entropy. >If by statistical entropy, you mean the entropy defined in >statistical mechanics, it is assumed that it is the same as >the thermodynamic entropy. Measurements of the entropy using >the methods of statistical mechanics have always yielded the >same result as measurements using the results of thermodynamics.<<<<<<< >We have already discussed that, Bryant, on a suitable model devised by >R. Alberty (do you remember?). We found that, We? Speak for yourself, don't try to speak for me. >in order for Boltzmann's >(klnW) and thermodynamic entropy to coincide, some systems must >SPONTANEOUSLY move from a MORE probable to a LESS probable state. No. In order for them to coincide, experimental measurements of the entropy using statistical mechanics must agree with experimental measurements of the entropy using thermodynamics. Since they do, the assumption that they are the same is accepted. >So I >hope you would agree with the following answer: If systems can >spontaneously move from a more probable to a less probable state, the two >entropies coincide. If not, not. I don't remember how you came to conclude this, but its incorrect. Regards, Bryant From owner-biophysics@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!news.belnet.be!nntp.ulg.ac.be!news From: Thierry Leclipteux Newsgroups: bionet.biophysics Subject: gold conjugates Date: Fri, 13 Feb 1998 14:01:29 +0100 Organization: ulg Lines: 8 Message-ID: <34E44427.248A@stat.fmv.ulg.ac.be> Reply-To: thierry@stat.fmv.ulg.ac.be NNTP-Posting-Host: parasito2.fmv.ulg.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) I have a problem in conjugating a monoclonal antibody to 20 nm gold particles. Monoclonal pi is close to 6.5 and several trials have been performed at ph 7, 8 and even 9 without significant increase in the conjugate sensitivity. In our procedure 0.01 mg IgG are incubated with 1 ml of gold particules (at 0.01 %). I am looking for a protocol which enables me to increase this conjugate sensitivity. Thanks for replying either in the news or by e-mail. From owner-biophysics@net.bio.net Fri Feb 13 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!newshub1.home.com!news.home.com!Supernews60!supernews.com!Supernews69!not-for-mail From: Mike Marsh Newsgroups: bionet.biophysics Subject: Re: General question Date: Sat, 14 Feb 1998 01:09:21 -0600 Organization: All USENET -- http://www.Supernews.com Lines: 28 Message-ID: <34E54321.36E730D6@centenary.edu> References: <6c1mmq$rnu$1@bignews.shef.ac.uk> NNTP-Posting-Host: 17947@198.79.137.162 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (WinNT; I) To: E Demoncheaux E Demoncheaux wrote: > Could someone explain the difference between kinetic and thermodynamic > stability? E. Demoncheaux, for a good explanation, consult a college-level organic chemistry textbook. in short: thermodynamic stability means that the species is at a lower energy relative to some reference value (e.g. the energy of the reactant or the energy of the product) kinetic stability usually denotes a metastable (i.e. thermondynamically metastable) species whose energy could be lowered by a reaction, but the kinetics of such reaction are prohibitive. -mike by the way, can anybody tell me where i should go to do doctoral work in structural biology?? i currently have applications in at scripps research inst, baylor college of medicine, and u.c.s.d. From owner-biophysics@net.bio.net Fri Feb 13 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Boltzmann's vs. thermodynamic entropy Date: 14 Feb 1998 12:45:34 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6c43le$hr7@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote: >So I >hope you would agree with the following answer: If systems can >spontaneously move from a more probable to a less probable state, the two >entropies coincide. If not, not. Bryant Fujimoto replied:>>>>>>>>>>>> I don't remember how you came to conclude this, but its incorrect.<<<<<<< Let me remind you. Consider the following system: --------------------------------------------------------------------------- A + B <-> C + D ---------membrane-permeable-only-to-D-------------------------------------- D ------------------------piston-------------------------------------------- This is a semi-grand ensemble: The EXOTHERMIC gas reaction A + B <-> C + D undergoes an isothermal reversible course as D in the lower compartment pushes a piston and expands. As heat is released by the system, the thermodynamic entropy of the system DECREASES. On the other hand, this reversible course has its spontaneous conterpart (D can expand irreversibly, without pushing the piston). If, in the spontaneous process, the system moves to a MORE probable state, Boltzmann's entropy INCREASES and does not coincide with the thermodynamic entropy. If, in the spontaneous process, the system moves to a LESS probable state (some people claimed so), Boltzmann's entropy decreases, like the thermodynamic entropy. As you can see, the problem is real and quite independent of my personality. Best regards, Pentcho From owner-biophysics@net.bio.net Sat Feb 14 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!feed2.news.erols.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!192.232.20.2!malgudi.oar.net!news.ysu.edu!news.ece.cmu.edu!honeysuckle.srv.cs.cmu.edu!das-news2.harvard.edu!oitnews.harvard.edu!hpngsv01.mgh.harvard.edu!misha.mgh.harvard.edu!user From: mmisha@nmr.mgh.harvard.edu (M. Papisov) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's and thermodynamic entropy Date: Fri, 13 Feb 1998 14:14:03 -0500 Organization: MGH & HMS Lines: 72 Distribution: bionet Message-ID: References: <6c1l0r$5lm@mserv1.dl.ac.uk> NNTP-Posting-Host: misha.mgh.harvard.edu In article <6c1l0r$5lm@mserv1.dl.ac.uk>, Pentcho Valev wrote: The "thermodynamic enthropy" has been invented simply to acknowledge that not all energy can be transformed into work. Nobody could explain why at the time. Entropy was *just a member in the thermodynamic equation*. In the simplest case (a system is being heated, there are no chemical reactions), thermodynamic enthropy equaled to heat capacity. Anyway, nobody knew, at the time where, the heat might go. In turn, the statistical explanation of enthropy was offered simply to demonstrate where the energy actually goes, and why it can not be completely transformed into work. So, there is no "coincidence" or "non-coincidence": "statistical enthropy" is simply a mechanistic explanation of thermodynamic enthropy. If you know *exactly* how energy can be distributed between components of your system, you can calculate a "theoretical" value that is very close to the experimentally determined (thermodynamic) enthropy. If you don't know what is going on in your system (like in old good days), or if the system is too complex, you have no chance to come up with any reasinable theoretical estimate. Obviously, ALL thermodynamic systems can move from a more probable to a less probable states and back. This is what they do all the time. Lower probability does not mean that the state is "more difficult" to reach, it is just that you can encounter that state less frequently. If there is a state to which a system _can not_ move, the probability of that state would be zero. Regards MP PS: Entropy has nothing to do with order. Any objections? > Bryant Fujimoto wrote:>>>>>>>>> > Nick Art writes: > >Dear All, > >I hope if someone could tell me the difference between > >the statistical entropy and thermodynamic entropy. > > If by statistical entropy, you mean the entropy defined in > statistical mechanics, it is assumed that it is the same as > the thermodynamic entropy. Measurements of the entropy using > the methods of statistical mechanics have always yielded the > same result as measurements using the results of thermodynamics.<<<<<<< > > We have already discussed that, Bryant, on a suitable model devised by > R. Alberty (do you remember?). We found that, in order for Boltzmann's > (klnW) and thermodynamic entropy to coincide, some systems must > SPONTANEOUSLY move from a MORE probable to a LESS probable state. So I > hope you would agree with the following answer: If systems can > spontaneously move from a more probable to a less probable state, the two > entropies coincide. If not, not. > > In my opinion, spontaneous movement from a more probable to a less probable > state is a LOGICAL absurdity, but I may be wrong. > > Best regards, > Pentcho ______________He who rides on a tiger never dismounts________________ Please delete the very first letter in my email address to reply. Nobody at all, including my past, current and future employers, is responsible for whatever is written above. From owner-biophysics@net.bio.net Sat Feb 14 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!newsfeed.direct.ca!Supernews60!supernews.com!uunet!in4.uu.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 (13 Feb 98) Date: Sun, 15 Feb 1998 15:38:47 GMT Organization: SCIENCE-WEEK Lines: 54 Message-ID: <6c7280$b30@suriname.earthlink.net> Reply-To: prismx@scienceweek.com NNTP-Posting-Host: 153.35.114.208 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:21387 bionet.biophysics:3994 bionet.cellbiol:8851 bionet.general:29358 SCIENCE-WEEK is a free weekly Email digest of the news of science read each week by 50,000+ people in the scientific community in more than 30 countries. News briefs from the major journals are amplified with enough background material to make them intelligible to nonspecialists: the biology is detailed for physicists and chemists, and the physics and chemistry are detailed for biologists. Each issue contains 15 to 20 news reports, annotated listings of new books in the sciences, a Positions Available section, and other notices of interest to science professionals. The SW complete weekly news reports are available free via Email. To subscribe, send SUB SW to . Contents of the Latest Issue Feb 13, 1998: 1. US Rejects Moratorium on Xenotransplantation Trials 2. Sheep Cloning Research Results: Questions and Answers 3. Comparative US University Chemistry PhDs. 4. On the New Gamma-Ray Astronomy 5. Laboratory Study of a One-Component Crystallized Ion Plasma 6. Detection of Intergalactic Red-Giant Branch Stars in a Cluster 7. Origin of Chondrules and the Formation of Jupiter 8. Discovery of Oldest Known Ant Fossils 9. A Molecular Analysis of Cellulose Biosynthesis 10. Sequence Analysis of an Arabidopsis Chromosome 11. A Model for Energy Transduction in ATP Synthase 12. An X-Ray Crystallography Study of T-Cell Antigen Receptors 13. Recognition of DNA Base Pairs by Synthetic Ligands 14. Yeast Engineered to Synthesize Steroids 15. Structure of a Phosphatidylinositol-Transfer Protein 16. Induction of Apoptosis by Injected Cytochrome C 17. Apoptosis: Release of Cytochrome C is Not Sufficient 18. Integrin-Mediated Short-Term Memory in Drosophila 19. A Gene Mutation Associated with Hereditary Human Hair Loss 20. Prevalence of Suicide After Natural Disasters 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. 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 Sat Feb 14 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!194.168.4.5!newsfeed.cableol.net!not-for-mail From: Alan Loberto Newsgroups: bionet.biophysics Subject: Magnetic affect on growth Date: Sun, 15 Feb 1998 17:13:44 +0000 Organization: Virgin Net Usenet Service Lines: 6 Message-ID: <34E72248.38C@virgin.net> Reply-To: alan.loberto@virgin.net NNTP-Posting-Host: 194.168.64.101 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01C-VN711-003 (Win95; I) I have a dying question and that is; "Will a magnetic field have an affect on Bacterial growth?" I would be very grateful if one would reply via e-mail to alan.loberto@virgin.net Thanks a lot Alan Loberto From owner-biophysics@net.bio.net Sat Feb 14 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!peernews.ftech.net!news.ibm.net.il!ibm.net!news.biu.ac.il!not-for-mail From: shahar stein Newsgroups: bionet.biophysics Subject: what is phantom Date: Sun, 15 Feb 1998 11:21:43 +0200 Organization: Bar-Ilan University, Ramat-Gan, Israel Lines: 1 Message-ID: <34E6B3A7.24B1@inter.net.il> NNTP-Posting-Host: ehrenbrg.ph.biu.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) sorry for the ignorance but what is "phantom"? From owner-biophysics@net.bio.net Sun Feb 15 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!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: Boltzmann's vs. thermodynamic entropy Date: 16 Feb 1998 09:23:48 GMT Organization: University of Washington Lines: 60 Distribution: bionet Message-ID: <6c90j4$mkj$1@nntp3.u.washington.edu> References: <6c43le$hr7@mserv1.dl.ac.uk> NNTP-Posting-Host: homer11.u.washington.edu X-Trace: nntp3.u.washington.edu 887621028 23187 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >I wrote: >>So I >>hope you would agree with the following answer: If systems can >>spontaneously move from a more probable to a less probable state, the two >>entropies coincide. If not, not. >Bryant Fujimoto replied:>>>>>>>>>>>> >I don't remember how you came to conclude this, but its incorrect.<<<<<<< >Let me remind you. Consider the following system: >--------------------------------------------------------------------------- > A + B <-> C + D >---------membrane-permeable-only-to-D-------------------------------------- > D >------------------------piston-------------------------------------------- >This is a semi-grand ensemble: The EXOTHERMIC gas reaction A + B <-> C + D >undergoes an isothermal reversible course as D in the lower compartment >pushes a piston and expands. As heat is released by the system, the >thermodynamic entropy of the system DECREASES. On the other hand, this >reversible course has its spontaneous conterpart (D can expand irreversibly, >without pushing the piston). If, in the spontaneous process, the system >moves to a MORE probable state, Boltzmann's entropy INCREASES and does not >coincide with the thermodynamic entropy. If, in the spontaneous process, >the system moves to a LESS probable state (some people claimed so), >Boltzmann's entropy decreases, like the thermodynamic entropy. >As you can see, the problem is real and quite independent of my >personality. What does your personality have to do with this? I certainly haven't referred to it. Do you want me to? If so, why? It is possible to use thermodynamics to determine the entropy of both the initial and final states, without having to worry about whether the process you wish to use is reversible. Since comparisons of these sorts of calculations with calculations of statistical mechanics yield good agreement, what is the problem? The fact is that, experimental results contradict your assertion. Until you can point to an actual reaction, which behaves the way you think it will, you have nothing comparable. Keep in mind, your system is undergoing an isothermal expansion. If you simply expand a non-reacting gas isothermally, heat will flow _into_ the system. So, how do you know that your exothermal reaction will give off more heat than is necessary to keep the temperature constant due to the expansion? You haven't named the reaction, and until you can, you don't have a demonstration of anything. Regards, Bryant P.S. What does thermodynamics mean by reversible? From owner-biophysics@net.bio.net Sun Feb 15 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!fu-berlin.de!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's vs. thermodynamic entropy Date: 16 Feb 1998 18:43:02 GMT Organization: IIF Lines: 41 Message-ID: References: <6c43le$hr7@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 14 Feb 1998 12:45:34 -0000, Pentcho Valev wrote: >--------------------------------------------------------------------------- > > A + B <-> C + D > >---------membrane-permeable-only-to-D-------------------------------------- > > D > >------------------------piston-------------------------------------------- > > >This is a semi-grand ensemble: The EXOTHERMIC gas reaction A + B <-> C + D >undergoes an isothermal reversible course as D in the lower compartment >pushes a piston and expands. As heat is released by the system, the >thermodynamic entropy of the system DECREASES. On the other hand, this >reversible course has its spontaneous conterpart (D can expand irreversibly, >without pushing the piston). If, in the spontaneous process, the system >moves to a MORE probable state, Boltzmann's entropy INCREASES and does not >coincide with the thermodynamic entropy. If, in the spontaneous process, >the system moves to a LESS probable state (some people claimed so), >Boltzmann's entropy decreases, like the thermodynamic entropy. Pentcho, we discussed this earlier. I'm surprised that you still don't understand this example. Any non-isolated subsystem of a system will spontaneously move from a MORE probable state to a LESS probable state if the WHOLE system can move from a LESS probable state to a MORE probable state by this. That is how life evolved, for example. In other words: if the system is not isolated--and yours is not--then its entropy can spontaneously decrease. In your example, the internal energy of the system decreases during the process. The environment takes up heat and this additional energy is distributed among the degrees of freedom of the environment. This distribution can be done in a very high number of ways, thus the thermodynamic probability (for the WHOLE system) will increase. The entropy of the WHOLE system will increase. Andras From owner-biophysics@net.bio.net Sun Feb 15 22:00:00 1998 Path: biosci!musc.edu!vakseri From: vakseri@musc.edu (Ilya Vakser) Newsgroups: bionet.biophysics Subject: Postdocs/Graduate Students in Protein Docking and Structure Prediction Date: 16 Feb 1998 11:24:59 -0800 Organization: Medical University of South Carolina Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <34E89237.2335225D@musc.edu> NNTP-Posting-Host: net.bio.net Applications are invited for postdoctoral and graduate student positions in my laboratory at the Medical University of South Carolina. The positions were advertised in November, however, due to the delayed release of funds, I post them again. The main subjects of the research in the laboratory are computational studies of molecular recognition, docking methodology, structure prediction, and applications to signal transduction pathways and other molecular systems. For more information, see the lab's web site at http://reco3.musc.edu. The following positions are immediately available: Postdoctoral fellow Development of flexible docking techniques for small ligands. Docking methodology for computer-aided drug design. Postdoctoral fellow Modeling of integral membrane receptors. Structure prediction based on the principles of molecular recognition. Graduate student General development of protein docking methodology. Strong programming skills in C are required for all positions. To apply send or email a letter and CV with names of 3 referees. Ilya A. Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 171 Ashley Avenue Charleston, SC 29425 Email: vakseri@musc.edu, Phone:(803)792-2471, Fax:(803)792-2475 From owner-biophysics@net.bio.net Sun Feb 15 22:00:00 1998 From: mmisha@nmr.mgh.harvard.edu (M. Papisov) Newsgroups: bionet.biophysics Subject: Re: Magnetic affect on growth Date: Mon, 16 Feb 1998 12:29:11 -0500 Organization: MGH & HMS Lines: 76 Message-ID: References: <34E72248.38C@virgin.net> NNTP-Posting-Host: misha.mgh.harvard.edu Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!newsfeed.wizvax.net!news.mv.net!newspump.wustl.edu!news.fas.harvard.edu!oitnews.harvard.edu!hpngsv01.mgh.harvard.edu!misha.mgh.harvard.edu!user In article <34E72248.38C@virgin.net>, alan.loberto@virgin.net wrote: > I have a dying question and that is; > "Will a magnetic field have an affect on Bacterial growth?" > I would be very grateful if one would reply via e-mail to > alan.loberto@virgin.net I personally have no idea, but because it's a "dying question", here is a couple of references: 1 AN 81247674 AU Aarholt E. Flinn EA. Smith CW. TI Effects of low-frequency *magnetic* fields on *bacterial* *growth* rate. SO Physics in Medicine & Biology. 26(4):613-21, 1981 Jul. JC p6j CP England AB A large number of cultures of the bacterium E. coli have been grown in weak alternating *magnetic* fields of square waveform, at frequencies of 50 Hz and 16.66 Hz. Control cultures were simultaneously grown under ambient conditions identical except for the almost complete absence of any *magnetic* *field*. The mean generation time (MGT) for a culture subjected to alternating *magnetic* fields is significantly reduced by comparison with that for the control cultures. Application of the F-ratio test indicates a probability of less than one in two million that the effects observed are due to chance. A marked threshold effect is observed, along with strong indications of periodicity in the graph of MGT against *magnetic* *field* strength. Within the limits of experimental error, these effects correspond to integral changes in the number of *magnetic* flux quanta linking an individual *bacterial* cell during the process of division. DE *Escherichia coli/gd [*Growth* & Development]. *Magnetics. IS 0031-9155 PT Journal Article. LG English EM 8111. 2 AN 87113862 AU Pantev TP. Minkova MI. TI [Direct and mediated action of a permanent *magnetic* *field* on biological objects]. [Russian] TT Priamoe i oposredovannoe deistvie postoiannogo magnitnogo polia na biologicheskie ob''ekty. SO Kosmicheskaia Biologiia i Aviakosmicheskaia Meditsina. 20(6):73-6, 1986 Nov-Dec. JC kxc CP USSR AB The effect of a constant *magnetic* *field* (CMF) of H = 2.3 X 10(5) A/m (2900 Oe) on the viability and radiosensitivity of E. coli B and the effect of magnetically activated water (MAW) on the radioresistance of rats were examined. The exposure did not influence the *growth* kinetics of E. coli B. Cell cultivation in the magnetically pretreated nutrient medium enhanced the *bacterial* *growth*. Preliminary exposure of *bacterial* cells to a CMF for 24 and 48 hrs increased and that for 72 hrs decreased their radioresistance. Twice a day the experimental weanlings were given MAW and the controls--tap water. The postradiation longevity of the MAW rats proved extended as compared to that of the controls. The MAW rats showed a greater osmotic stability of erythrocytes, a higher concentration of nucleic acids, and a larger count of leucocytes. DE Animal. Comparative Study. English Abstract. Escherichia coli/ph [Physiology]. Gamma Rays. *Magnetics. Radiation Dosage. Radiation Tolerance. Rats. Space Flight. Time Factors. Water/pd [Pharmacology]. X-Rays. RN 7732-18-5 (Water). IS 0321-5040 PT Journal Article. LG Russian EM 8705. ______________He who rides on a tiger never dismounts________________ Please delete the very first letter in my email address to reply. Nobody at all, including my past, current and future employers, is responsible for whatever is written above. From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Boltzmann's versus thermodynamic entropy Date: 17 Feb 1998 08:39:09 -0000 Lines: 53 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6cbibd$5m0@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Andras Szilagyi wrote:>>>>>>>>>>>>>>>>>>>>>>>> On 14 Feb 1998 12:45:34 -0000, Pentcho Valev wrote: >--------------------------------------------------------------------------- > > A + B <-> C + D > >---------membrane-permeable-only-to-D-------------------------------------- > > D > >------------------------piston-------------------------------------------- > > >This is a semi-grand ensemble: The EXOTHERMIC gas reaction A + B <-> C + D >undergoes an isothermal reversible course as D in the lower compartment >pushes a piston and expands. As heat is released by the system, the >thermodynamic entropy of the system DECREASES. On the other hand, this >reversible course has its spontaneous conterpart (D can expand irreversibly, >without pushing the piston). If, in the spontaneous process, the system >moves to a MORE probable state, Boltzmann's entropy INCREASES and does not >coincide with the thermodynamic entropy. If, in the spontaneous process, >the system moves to a LESS probable state (some people claimed so), >Boltzmann's entropy decreases, like the thermodynamic entropy. Pentcho, we discussed this earlier. I'm surprised that you still don't understand this example. Any non-isolated subsystem of a system will spontaneously move from a MORE probable state to a LESS probable state if the WHOLE system can move from a LESS probable state to a MORE probable state by this. That is how life evolved, for example. In other words: if the system is not isolated--and yours is not--then its entropy can spontaneously decrease. In your example, the internal energy of the system decreases during the process. The environment takes up heat and this additional energy is distributed among the degrees of freedom of the environment. This distribution can be done in a very high number of ways, thus the thermodynamic probability (for the WHOLE system) will increase. The entropy of the WHOLE system will increase.<<<<<<<<<<<<<<<<<<<<<< Andras, I do not see any contradiction between my statement and your explanation, so there is certainly nothing which I don't understand at that level. Still I find it awkward to accept that, as the system (rather, only D) expands spontaneously and never returns to the initial point, it moves from a MORE probable to a LESS probable state. Your explanation is formally correct but it contradicts my intuition. Unfortunately I am incompetent in statistical mechanics and cannot offer a more reasonable objection. Still my conclusion remains valid: The two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE FROM A MORE PROBABLE TO A LESS PROBABLE STATE. Best regards, Pentcho From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.biophysics Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Feb 1998 02:00:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802171000.CAA11764@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. 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Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. 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You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newspeer.monmouth.com!news.monmouth.com!tr-ppp8.monmouth.com!user From: NOSPAM-Glen@AvivInst.com (Glen Ramsay) Newsgroups: bionet.biophysics Subject: Re: Magnetic affect on growth Date: Tue, 17 Feb 1998 11:31:32 -0500 Organization: Aviv Instruments Lines: 19 Message-ID: References: <34E72248.38C@virgin.net> NNTP-Posting-Host: tr-ppp8.monmouth.com X-Newsreader: Yet Another NewsWatcher 2.1.8 In article , mmisha@nmr.mgh.harvard.edu (M. Papisov) wrote: > > I have a dying question and that is; > > "Will a magnetic field have an affect on Bacterial growth?" > > I would be very grateful if one would reply via e-mail to > > alan.loberto@virgin.net > Check the bionet.journals.contents newsgroup. Periodically they list the table of contents for a journal on the effects of magnetic / eletronic fields on life. Sorry, but I can't remember the name of the journal. Glen -- Glen Ramsay, Ph.D. Aviv Instruments Glen@(NoSpam)AvivInst.com From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's versus thermodynamic entropy Date: 17 Feb 1998 13:50:46 GMT Organization: IIF Lines: 29 Message-ID: References: <6cbibd$5m0@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 17 Feb 1998 08:39:09 -0000, Pentcho Valev wrote: >Andras, I do not see any contradiction between my statement and your >explanation, so there is certainly nothing which I don't understand at >that level. Still I find it awkward to accept that, as the system >(rather, only D) expands spontaneously and never returns to the initial >point, it moves from a MORE probable to a LESS probable state. Your >explanation is formally correct but it contradicts my intuition. >Unfortunately I am incompetent in statistical mechanics and cannot offer >a more reasonable objection. Still my conclusion remains valid: The >two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE >FROM A MORE PROBABLE TO A LESS PROBABLE STATE. So it contradicts your intuition that the entropy of an open system can spontaneously decrease? If yes, then there is something very wrong with your intuition. Personal incredulity is not an argument, it only demonstrates that you have not tried hard enough to understand things. I think that actually it does not make much sense to speak about spontaneous and non-spontaneous processes in an open system. If the system is open (i.e. anything can be made with it from outside) then any processes are spontaneous that are forced by the environment, regardless of any probabilities. Your example would be good if the system were an isolated system. But it is not. Andras From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: General question Date: 17 Feb 1998 22:38:47 GMT Organization: Vollum Institute Lines: 26 Distribution: world Message-ID: <6cd3hn$gg2$1@fremont.ohsu.edu> References: <6c1mmq$rnu$1@bignews.shef.ac.uk> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Tue, 17 Feb 1998 22:46:16 GMT In article <34E49CE9.2781@henri.chem.uleth.ca> Marc Roussel, roussel@henri.chem.uleth.ca writes: > Diamonds are thermodynamically unstable >relative to graphite at standard temperature and pressure which means >that their free energy is higher than that of graphite. Thus, every >diamond that has ever been dug out of the ground is slowly converting to >graphite. Maybe another way to say this is in terms of an energy diagram for the reaction: imagine a bell-shaped curve with the left "foot" higher than the right "foot", so that there is a hill in between. The height of the curve at each point represents the energy of the reaction (e.g., diamond turning to graphite), so that diamond (on the left) has a higher energy than graphite. Given an infinite time, all dimaonds will sooner or later slide across the reaction towards graphite, so diamond is less thermodynamically stable than graphite. However, before diamond can turn to graphite, it has to surmount an energy barrier (the hill). The lower the hill between the two states, the faster things can go over it, and the faster the reaction will proceed. If the hill is very high, then diamond will be kinetically stable, because only very rarely does an individual diamond crystal attain enough energy (from heat in the ground, or whatever) to climb over this energy barrier. Helpful, or more confusing? -Matt From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!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: Boltzmann's versus thermodynamic entropy Date: 17 Feb 1998 21:32:43 GMT Organization: University of Washington Lines: 24 Distribution: bionet Message-ID: <6ccvlr$3pk$1@nntp3.u.washington.edu> References: <6cbibd$5m0@mserv1.dl.ac.uk> NNTP-Posting-Host: homer18.u.washington.edu X-Trace: nntp3.u.washington.edu 887751163 3892 (None) 140.142.64.1 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >Andras, I do not see any contradiction between my statement and your >explanation, so there is certainly nothing which I don't understand at >that level. Still I find it awkward to accept that, as the system >(rather, only D) expands spontaneously and never returns to the initial >point, it moves from a MORE probable to a LESS probable state. Your >explanation is formally correct but it contradicts my intuition. Your intuition is wrong. You haven't even proved which way the heat will flow. How do you know heat will flow out of the chamber? You haven't accounted for the heat necessary to maintain the temperature as you expand your system. >Unfortunately I am incompetent in statistical mechanics and cannot offer >a more reasonable objection. Still my conclusion remains valid: The >two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE >FROM A MORE PROBABLE TO A LESS PROBABLE STATE. If your conclusion is valid, then why is it contradicted by every test ever made to compare statisical mechanical and thermodynamic entropies? Bryant From owner-biophysics@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!UCONNVM.UCONN.EDU!RHODES From: RHODES@UCONNVM.UCONN.EDU Newsgroups: bionet.biophysics Subject: Trying to cut housing cost @ KC Date: 17 Feb 1998 04:03:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <980217.070239.EST.RHODES@UConnVM.UConn.Edu> NNTP-Posting-Host: net.bio.net I know it's pretty close to the last minute, BUT... my plans for the biophys meetings got a little fouled up. I'm looking for someone to share a room at KC. I have made reservations in a place 3 blocks north of the center, but will gladly cancel those if someone has space available. So - - * If you have space in your room and/or * are interested in sharing to reduce your housing costs * (or if you simply need a place) * are male, nonsmoker give me a call or drop me an email. Thanks! - see you there!! |-----------------------------O==O----------------------------| | David G. Rhodes O==O Phone 860-486-5413 | | School of Pharmacy; U-92 O==O Fax 860-486-4998 | | University of Connecticut O==O | | Storrs, CT 06269-2092 O==O rhodes@uconnvm.uconn.edu | |_____________________________O==O____________________________| I love deadlines - especially the "whoosh" sound as they go flying by. From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!CHEM.UFL.EDU!tan From: tan@CHEM.UFL.EDU (Weihong Tan) Newsgroups: bionet.biophysics Subject: Postdoctoral positions at University of Florid Date: 17 Feb 1998 19:44:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4f5k31$6h5@labrat.sedona.net> NNTP-Posting-Host: net.bio.net Applications are invited for two postdoctoral positions at the Department of Chemistry and the UF Brain Institute, University of Florida. The successful applicant should have a strong background in ANY ONE of the following areas: biophysics, optical microscopy and spectroscopy, scanning probe microscopy, bioanalytical chemistry, or neuroscience. We are carrying out exciting research work in the following areas: novel optical microscopy for biomedical imaging and sensing; single biomolecule detection and manipulation; biochemical sensors and in-vivo monitoring; a novel new form of patch clamp technique and its application. We are also studying important biomedical problems such as the molecular and subcellular mechanisms of ischemic stroke, ion channel imaging and manipulation, DNA hybridization in single living cells. These research activities are funded by the National Science Foundation, the Office of Naval Research, Department of Defense and The Arnold Beckman Foundation. These two positions are expected to be as long as three years. The successful applicant will be expected to show both individual initiative and ability to work as a team member. At University of Florida we have excellent working and living environment. Interested applicants should make an initial contact with Prof. Tan through e-mail, or send a CV with two reference letters to the following address: Prof. Weihong Tan Department of Chemistry and The UF Brain Institute University of Florida Gainesville, FL 32611-7200 352-846-2410 E-mail: tan@chem.ufl.edu From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Boltzmann vs. thermodynamic entropy Date: 18 Feb 1998 14:17:58 -0000 Lines: 63 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6ceqim$guo@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote: >Andras, I do not see any contradiction between my statement and your >explanation, so there is certainly nothing which I don't understand at >that level. Still I find it awkward to accept that, as the system >(rather, only D) expands spontaneously and never returns to the initial >point, it moves from a MORE probable to a LESS probable state. Your >explanation is formally correct but it contradicts my intuition. Bryant Fujimoto replied:>>>>>>>>>>>>>>> Your intuition is wrong. You haven't even proved which way the heat will flow. How do you know heat will flow out of the chamber? You haven't accounted for the heat necessary to maintain the temperature as you expand your system.<<<<<<<<<<<<<< I explained this some time ago and still believe that it is obvious. The system is analogous to a liquid-vapor system, the only difference being that in this case the reaction is exothermic. As D (or the vapor in the liquid-vapor system) expands isothermally and reversibly, the chemical reaction releases exothermic heat dQexo and, in addition, the system does work of expansion PdV. So dQabsorbed = PdV - dQexo /1/ where P is the partial pressure of D (or the vapor) and dQexo is positive in this case and negative for the liquid-vapor system. If dQexo > PdV, we obtain dS = dQabs/T < 0 /2/ i.e. the entropy of the system decreases. I don't think there is problem with this. Then I wrote: >Unfortunately I am incompetent in statistical mechanics and cannot offer >a more reasonable objection. Still my conclusion remains valid: The >two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE >FROM A MORE PROBABLE TO A LESS PROBABLE STATE. Bryant replied:>>>>>>>>>>>>>>>>>> If your conclusion is valid, then why is it contradicted by every test ever made to compare statisical mechanical and thermodynamic entropies?<<<<<<<<<<<<<<<<< Bryant, my conclusion is an "if.." statement and is not contradicted by any test. However I have not proved, although my wrong intuition tells me so, that the expanded state is MORE probable than the initial state. So at the moment I am forced to accept Andras' interpretation of probability in terms of entropy: the expanded state is LESS probable than the initial state, but this is compensated for by events in the environment, so the probability of the system + the environment increases in the spontaneous process. If I find a reasonable argument, I will present it for discussion. By the way, why don't you describe an intersting test comparing Boltzmann's and thermodynamic entropy? I know your answer - read the books| - and will certainly do so, but meanwhile you, as you have already read them, can say something interesting - can't you? Otherwise I will have to do this after reading the books, but this will take time. Best regards, Pentcho From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: Boltzmann vs. thermodynamic entropy Date: 18 Feb 1998 15:04:20 GMT Organization: IIF Lines: 17 Message-ID: References: <6ceqim$guo@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 18 Feb 1998 14:17:58 -0000, Pentcho Valev wrote: >By the way, why don't you describe an intersting test comparing Boltzmann's >and thermodynamic entropy? I know your answer - read the books| - and will >certainly do so, but meanwhile you, as you have already read them, can >say something interesting - can't you? Otherwise I will have to do this >after reading the books, but this will take time. Just a suggestion. It was Boltzmann who first proved, using very deep considerations, that the thermodynamic entropy and the thermodynamic probability are always proportional with each other (and the proportionality constant is the Boltzmann constant). Perhaps you should read the original work of Boltzmann if you really want to get to the core of these things. I haven't read them myself, but I would like too. Andras From owner-biophysics@net.bio.net Tue Feb 17 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!helix.nih.gov!malini From: Malini Viswanathan Newsgroups: bionet.biophysics Subject: BIAcore Date: Wed, 18 Feb 1998 17:40:12 -0500 Organization: National Institutes of Health Lines: 17 Message-ID: NNTP-Posting-Host: helix.nih.gov Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have a question regarding BIAcor - are there references about two state kinetic models that have been analyzed or predicted using the BIA. I've tried to look through some references, but have not come across any for a two state kinetic model. Sorry if this newsgroup is not the right one to post to, any suggestions regarding that would also be welcome. Thanks in advance Malini -------------------- Malini Viswanathan Bldg 37, 2B10,NIH Bethesda,MD 20892-4255 From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.direct.ca!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Boltzmann vs. thermodynamic entropy Date: 18 Feb 1998 21:40:00 GMT Organization: University of Washington Lines: 123 Distribution: bionet Message-ID: <6cfkfg$ci0$1@nntp3.u.washington.edu> References: <6ceqim$guo@mserv1.dl.ac.uk> NNTP-Posting-Host: homer03.u.washington.edu X-Trace: nntp3.u.washington.edu 887838004 12864 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Pentcho Valev writes: >I wrote: >>Andras, I do not see any contradiction between my statement and your >>explanation, so there is certainly nothing which I don't understand at >>that level. Still I find it awkward to accept that, as the system >>(rather, only D) expands spontaneously and never returns to the initial >>point, it moves from a MORE probable to a LESS probable state. Your >>explanation is formally correct but it contradicts my intuition. >Bryant Fujimoto replied:>>>>>>>>>>>>>>> >Your intuition is wrong. You haven't even proved which way the >heat will flow. How do you know heat will flow out of the chamber? >You haven't accounted for the heat necessary to maintain the >temperature as you expand your system.<<<<<<<<<<<<<< >I explained this some time ago and still believe that it is obvious. The >system is analogous to a liquid-vapor system, the only difference being >that in this case the reaction is exothermic. As D (or the vapor in the >liquid-vapor system) expands isothermally and reversibly, the chemical >reaction releases exothermic heat dQexo and, in addition, the system does >work of expansion PdV. So > dQabsorbed = PdV - dQexo /1/ You seem to be assuming that the internal energy of the system is constant for an isothermal expansion. This is true for a ideal gas which is not undergoing any reaction. Not necessarily true otherwise. >where P is the partial pressure of D (or the vapor) and dQexo is positive >in this case and negative for the liquid-vapor system. >If dQexo > PdV, we obtain > dS = dQabs/T < 0 /2/ >i.e. the entropy of the system decreases. I don't think there is problem >with this. >Then I wrote: >>Unfortunately I am incompetent in statistical mechanics and cannot offer >>a more reasonable objection. Still my conclusion remains valid: The >>two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE >>FROM A MORE PROBABLE TO A LESS PROBABLE STATE. >Bryant replied:>>>>>>>>>>>>>>>>>> >If your conclusion is valid, then why is it contradicted by every >test ever made to compare statisical mechanical and thermodynamic >entropies?<<<<<<<<<<<<<<<<< >Bryant, my conclusion is an "if.." statement and is not contradicted by >any test. However I have not proved, although my wrong intuition tells >me so, that the expanded state is MORE probable than the initial state. This was supposed to a reversible process. Why should the expanded state always be expected to have a higher entropy than the initial state? Do you know what thermodynamics means by reversible? Perhaps one of the sources of your misunderstandings is that you think that reversible and spontaneous mean the same thing in thermodynamics. >So at the moment I am forced to accept Andras' interpretation of >probability in terms of entropy: the expanded state is LESS probable than >the initial state, but this is compensated for by events in the environment, >so the probability of the system + the environment increases in the >spontaneous process. If I find a reasonable argument, I will present it >for discussion. >By the way, why don't you describe an intersting test comparing Boltzmann's >and thermodynamic entropy? I know your answer - read the books| - and will >certainly do so, but meanwhile you, as you have already read them, can >say something interesting - can't you? Otherwise I will have to do this >after reading the books, but this will take time. Pentcho I have already described it, several times. I pointed out that it is possible to calculate the entropy of a system using the results of thermodynamics and it is possible to calculate the entropy using the results of statistical mechanics. So far, whenever it has been done the results agree to within experimental error. What more is necessary? For example, McQuarrie and Simon calculate the entropy of N2 at 298.15K and 1 atm in two different ways. From thermodynamics, S(T) = Int[0..Ttr] (Cp/T)dT + (Delta H_tr)/T + Int[Ttr..Tm] (Cp/T)dT + (Delta H_fus)/T + Int[Tm..Tb] (Cp/T)dT + (Delta H_vap)/T + Int[Tb..T] (Cp/T)dT where Cp is the heat capacity at constant pressure (1 atm) Int[Ta..Tb] refers to an integral from Ta to Tb, Ttr and (Delta H_tr) are the temperature of a solid phase transition in N2 at 35.61K and the enthalpy change for that transition, Tm and (Delta H_fus) are the melting temperature and heat of fusion, Tb and (Delta H_vap) are the boiling temperature and heat of vaporization. All of these quantities are experimentally measurable, and performing the integrals yields S(298.15K, 1atm) = 191.6 J/(mole K) [Result of Thermodynamics] From statistical mechanics, S = k_B ln(Q) + k_BT (partial ln(Q)/partial T)N,V where k_B is Boltzmann's constant, Q is the cannoical partition function (not to be confused with the reaction quotient which is also called Q), and the last term is the partial derivative of ln(Q) with respect to T at constant composition and volume. Q can be calculated, it depends on the mass of a nitrogen atom, the bond length of N2, and vibrational force constant of N2, the energy and degeneracy of the ground electronic state. These are all measureable by different experiments than that used above. The result is S(298.15K, 1atm) = 191.5 J/(mole K). [Result of Stat. Mech.] Regards, Bryant From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!univ-lyon1.fr!citi2.fr!bomsel.cochin.inserm.fr!user From: bomsel@lovelace.infobiogen.fr (Morgane BOMSEL) Newsgroups: bionet.biophysics Subject: new web site on cell membranes Date: 18 Feb 1998 16:36:40 GMT Organization: CITI2 - Universite Rene Descartes, Paris Lines: 6 Message-ID: NNTP-Posting-Host: bomsel.cochin.inserm.fr a new site on cell membranes has been opened, for information and discussion, on the web at the following address: http://www.univ-paris5.fr/ELM you can also send comments at alfsen@bisance.citi2.fr we are waiting for your prosa ELM , sort of ULM From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 From: mmisha@nmr.mgh.harvard.edu (M. Papisov) Newsgroups: bionet.biophysics Subject: Re: Magnetic affect on growth Date: Wed, 18 Feb 1998 18:24:14 -0500 Organization: MGH & HMS Lines: 30 Message-ID: References: <34E72248.38C@virgin.net> NNTP-Posting-Host: misha.mgh.harvard.edu Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!cam-news-feed2.bbnplanet.com!news.bbnplanet.com!ulowell.uml.edu!newsfeed.wizvax.net!news.mv.net!newspump.wustl.edu!news.fas.harvard.edu!oitnews.harvard.edu!hpngsv01.mgh.harvard.edu!misha.mgh.harvard.edu!user In article , NOSPAM-Glen@AvivInst.com (Glen Ramsay) wrote: > In article , > mmisha@nmr.mgh.harvard.edu (M. Papisov) wrote: > > > > I have a dying question and that is; > > > "Will a magnetic field have an affect on Bacterial growth?" > > > I would be very grateful if one would reply via e-mail to > > > alan.loberto@virgin.net > > > > Check the bionet.journals.contents newsgroup. Periodically they list the > table of contents for a journal on the effects of magnetic / eletronic > fields on life. Sorry, but I can't remember the name of the journal. > > Glen Glen, it was not me who had a dying question. Please make quotations correctly. MP ______________He who rides on a tiger never dismounts________________ Please delete the very first letter in my email address to reply. Nobody at all, including my past, current and future employers, is responsible for whatever is written above. From owner-biophysics@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Pentcho Valev Newsgroups: bionet.biophysics Subject: Boltzmann vs. thermodynamic entropy Date: 18 Feb 1998 15:35:10 -0000 Lines: 63 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6cev3e$lfr@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I wrote: >Andras, I do not see any contradiction between my statement and your >explanation, so there is certainly nothing which I don't understand at >that level. Still I find it awkward to accept that, as the system >(rather, only D) expands spontaneously and never returns to the initial >point, it moves from a MORE probable to a LESS probable state. Your >explanation is formally correct but it contradicts my intuition. Bryant Fujimoto replied:>>>>>>>>>>>>>>> Your intuition is wrong. You haven't even proved which way the heat will flow. How do you know heat will flow out of the chamber? You haven't accounted for the heat necessary to maintain the temperature as you expand your system.<<<<<<<<<<<<<< I explained this some time ago and still believe that it is obvious. The system is analogous to a liquid-vapor system, the only difference being that in this case the reaction is exothermic. As D (or the vapor in the liquid-vapor system) expands isothermally and reversibly, the chemical reaction releases exothermic heat dQexo and, in addition, the system does work of expansion PdV. So dQabsorbed = PdV - dQexo /1/ where P is the partial pressure of D (or the vapor) and dQexo is positive in this case and negative for the liquid-vapor system. If dQexo > PdV, we obtain dS = dQabs/T < 0 /2/ i.e. the entropy of the system decreases. I don't think there is problem with this. Then I wrote: >Unfortunately I am incompetent in statistical mechanics and cannot offer >a more reasonable objection. Still my conclusion remains valid: The >two entropies may coincide but ONLY IF SYSTEMS CAN SPONTANEOUSLY MOVE >FROM A MORE PROBABLE TO A LESS PROBABLE STATE. Bryant replied:>>>>>>>>>>>>>>>>>> If your conclusion is valid, then why is it contradicted by every test ever made to compare statisical mechanical and thermodynamic entropies?<<<<<<<<<<<<<<<<< Bryant, my conclusion is an "if.." statement and is not contradicted by any test. However I have not proved, although my wrong intuition tells me so, that the expanded state is MORE probable than the initial state. So at the moment I am forced to accept Andras' interpretation of probability in terms of entropy: the expanded state is LESS probable than the initial state, but this is compensated for by events in the environment, so the probability of the system + the environment increases in the spontaneous process. If I find a reasonable argument, I will present it for discussion. By the way, why don't you describe an intersting test comparing Boltzmann's and thermodynamic entropy? I know your answer - read the books| - and will certainly do so, but meanwhile you, as you have already read them, can say something interesting - can't you? Otherwise I will have to do this after reading the books, but this will take time. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Feb 18 22:00:00 1998 Path: biosci!UCONNVM.UCONN.EDU!RHODES From: RHODES@UCONNVM.UCONN.EDU Newsgroups: bionet.biophysics Subject: Biophysics meeting housing Date: 19 Feb 1998 04:04:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <980219.070331.EST.RHODES@UConnVM.UConn.Edu> NNTP-Posting-Host: net.bio.net I posted a note here a couple of days ago but am still looking .... If you have space in your room or would like to share mine, please get in touch with me soon so we can save some $$$$. I have a room about 3 blocks from the center, but would like to avoid paying for the whole thing. Once again, male - nonsmoking preferred. Thanks 10^6 - see you in KC! |-----------------------------O==O----------------------------| | David G. Rhodes O==O Phone 860-486-5413 | | School of Pharmacy; U-92 O==O Fax 860-486-4998 | | University of Connecticut O==O | | Storrs, CT 06269-2092 O==O rhodes@uconnvm.uconn.edu | |_____________________________O==O____________________________| I love deadlines - especially the "whoosh" sound as they go flying by. From owner-biophysics@net.bio.net Thu Feb 19 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!206.250.118.17!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 (20 Feb 98) Date: Thu, 19 Feb 1998 21:28:56 GMT Organization: SCIENCE-WEEK Lines: 54 Message-ID: <6ci877$4c@chile.earthlink.net> Reply-To: prismx@scienceweek.com NNTP-Posting-Host: 153.35.114.150 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:21417 bionet.biophysics:4016 bionet.cellbiol:8893 bionet.general:29389 SCIENCE-WEEK is a free weekly Email digest of the news of science read each week by 50,000+ people in the scientific community in more than 30 countries. News briefs from the major journals are amplified with enough background material to make them intelligible to nonspecialists: the biology is detailed for physicists and chemists, and the physics and chemistry are detailed for biologists. Each issue contains 15 to 20 news reports, annotated listings of new books in the sciences, a Positions Available section, and other notices of interest to science professionals. The SW complete weekly news reports are available free via Email. To subscribe, send SUB SW to . Contents of the Latest Issue Feb 20, 1998: 1. An Essay on the Great Asymmetry 2. Determination of HDO/H(sub2)O Ratio in Hale-Bopp Comet 3. Determination of Water in the Stars Betelguese and Antares 4. Stellar Origin of Early Solar System Nuclides 5. On the Bose-Einstein Condensate 6. An Exchange of Letters Concerning Fractality in Nature 7. Electric Field-Induced Demixing in Lipid Bilayer Membranes 8. Discovery of 3-Dimensional Algae and Animal Embryo Fossils 9. Precambrian Sponges with Cellular Structures 10. A Model for the Evolution of the Genetic Code 11. Mitochondrial DNA Recombination in a Natural Population 12. Opening of Liposomal Membranes by Talin 13. Evidence that DNA is a Poor Electron Conductor 14. A Transmembrane Form of the Prion Protein 15. On the Resistance of Bacteria to Antibiotics 16. On the History and Applications of Functional Brain Imaging 17. Identification of HIV-1 Sequence in 1959 Human Viral Sample 18. On the Role of Chemokines in Cell Biology and Disease 19. On Protein Folding in Prion and Amyloid Diseases 20. On Grandmothering, Menopause, and Human Evolution 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. 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 Fri Feb 20 22:00:00 1998 Path: biosci!webtv.net!uunet!in3.uu.net!news.eli.net!news.wolsi.com!news.aros.net!not-for-mail From: smd Newsgroups: bionet.biophysics Subject: ***IT REALLY WORKS***YOU MUST READ THIS!! Date: Sat, 07 Feb 1998 15:24:51 -0700 Organization: ArosNet Inc. Lines: 230 Message-ID: <34DCDF33.D0FD6DE0@aros.net> NNTP-Posting-Host: dm6-29.slc.aros.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; U) A must for you to read:: A little while back, I was browsing these newsgroups, just like you are now, and came across an article similar to this that that said "YOU COULD MAKE THOUSANDS OF DOLLARS WITHIN WEEKS WITH ONLY AN INITIAL INVESTMENT OF $6.00!!!" 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