From owner-biophysics@net.bio.net Mon Sep 01 23:00:00 1997 Path: biosci!classic.msn.com!rcb5 From: rcb5@classic.msn.com ("Ronald Blue") Newsgroups: bionet.biophysics Subject: Neutrotranmitters frequencies? Date: 1 Sep 1997 19:17:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Do the neurotransmitters have unique radio frequencies which will cause them to viberate or move quickly. Could use these to seperate the chemicals? What are the frequencies? Ron Blue From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!logbridge.uoregon.edu!newsfeed1-hme1!newsfeed.internetmci.com!204.238.120.130!jump.net!jumpnet.com!news From: Br. Michael Newsgroups: bionet.biophysics Subject: St. Anthony of Padua Date: 3 Sep 1997 04:40:53 GMT Organization: St. Anthony Center Lines: 7 Message-ID: <5uipol$4er@news.jumpnet.com> NNTP-Posting-Host: jump-dialup-0026.jumpnet.com September 1, 1997 We need your help NOW! The Order of St. Anthony/St. Anthony Center is an ecumenical tax exempt Religious Order dedicated to helping the oppressed. One group of oppressed is the alcoholics and addicts. A few months ago we entered into an escrow contract with owner financing, to purchase 152 acres just southeast of Austin. This property would provide a larger home for the monastery and those who want to work with us, as well as property on which to develop the first St. Anthony Detox and Recovery Center. This contract requires a $250,000 down payment. We planned an 84 hour music festival for this weekend called The Cow Pasture Special.We were featuring Blood Sweat & Tears, the Ricky Van Shelton Band, Willie Nelson and many local groups. This would have covered the down payment and more. At the last minute our financial backers for the festival reneged on their commitments. We could not find alternative backing fast enough and had to cancel the festival. Now we are asking for donations or loans of approximately $300,000 to cover the down payment and liabilities we acquired in having to cancel the festival.Closing on the property is this Thursday, 9/4/97. If you or people you know have a special interest in the desperate need for detox and recovery facilities, please contact us immediately at (512) 467-0613; FAX (512) 467-9027; 7511 Carriage Drive; Austin, Texas 78752 or e-mail at stanthony@jumpnet.com. For The St. Anthony Center: With Love and Peace; I am, Br. Michael, OSA From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!sloan.org!trance From: trance@sloan.org Newsgroups: bionet.biophysics Subject: POSTDOCS: Comp. Molec. Biol. Date: 3 Sep 1997 08:17:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 213 Sender: daemon@net.bio.net Distribution: world Message-ID: <40DA4980.1801@sloan.org> NNTP-Posting-Host: net.bio.net Alfred P. Sloan Foundation and U.S. Department of Energy Postdoctoral Fellowships in Computational Molecular Biology (Round III) APPLICATION DEADLINE: JANUARY 19, 1998 The Alfred P. Sloan Foundation and the U.S. Department of Energy believe that a nexus with exceptional scientific potential is emerging between the powerful theoretical and practical tools of molecular biology and the revolutionary power of modern computational techniques. However, too few scientists possess the cross-disciplinary skills in both molecular biology and computation that are needed to further such advances. The purpose of these fellowships is to catalyze career transitions into computational molecular biology from physics, mathematics, computer science, chemistry, and related fields. Ideal candidates will have strong educational backgrounds in such fields and wish to bring these backgrounds to bear upon computational molecular research questions. In exceptional cases, we will also consider applications from more traditional biological orientations in transition to computational molecular biology. Applicants already firmly rooted in computational molecular biology, or who are proposing to continue pursuit of research undertaken for their Ph.D.s, may be more appropriate candidates for other postdoctoral opportunities. This postdoctoral program is designed to give computationally sophisticated young scientists an intensive postdoctoral opportunity in an appropriate molecular biology laboratory. We particularly wish to encourage applications from those holding doctorates in mathematics, physics, computer science, chemistry, or other relevant fields who would like to develop the capacity to apply their computational sophistication to the complex problems that increasingly face molecular biology. The focus of this program is upon computational molecular biology related to data and information from studies of human and other genomes. Computational molecular biology is taken broadly to include the application of mathematics (continuous and discrete), statistics, probability, and computer science to fundamental problems of molecular biology. The goal is to foster interactions between the mathematical and biological sciences and to provide rigorous training for scientists in this new interdisciplinary area. Of special interest are important problems in structural biology and genome analysis, including analysis of protein and nucleic acid sequence, protein and nucleic acid structure, genome structure and maps, cross-species genome analysis, multi-genic traits, and structure-function relationships where the structures are from genomes, genes, or gene products. Applications will be reviewed by: Philip P. Green, University of Washington Barry Honig, Columbia University Leroy E. Hood, University of Washington Michael Levitt, Stanford University Michael S. Waterman, University of Southern California Awards will support up to two years of research work in an appropriate molecular biology department or laboratory in the U.S. or Canada selected by the applicant. The principal selection criteria will be the potential of the applicant and the proposed postdoctoral research and training plan for furthering rigorous computational approaches to analysis of important molecular biological problems, both theoretical and empirical. The capabilities of the proposed laboratory and senior scientist in computational molecular research, and support for the postdoctoral research by the senior scientist (department chair or laboratory director) will be an important element considered in selection. In addition, where possible, applicants are encouraged to seek a secondary faculty sponsor from the mathematical/computer sciences sector of the same campus. Only one proposal per applicant will be considered, and a senior scientist should endorse only one applicant for this competition. There are no formal application forms needed for this program. Further details and application procedures are as follows: Number, Starting Date and Grant Period: Up to 10 fellowships will be granted during 1998, each with a total budget of $100,000 (including indirect and overhead costs, which together will be limited to 15% of direct costs). These funds are to be spread over a grant period of two years ($50,000 per year). Selections for this third round will be announced in May, 1998. Funding may begin any time after September 1, 1998. Stipend: -$42,000 per year to Fellow, inclusive of benefits. -$ 1,500 per year in research expenses to be allocated at the discretion of the Fellow. -Institutional overhead of up to 15% of direct costs. Eligibility: Fellow - Applicants must be citizens or legal permanent residents of the United States. Ph.D. earned within the past 5 years or expected by June, 1998, in mathematics, physics, computer science, chemistry or other relevant fields. (Initiation of postdoc requires completion of Ph.D.) Applications to extend an existing postdoc cannot be considered. Institution - Non-profit private or public institution of higher education or research, located in the United States or Canada. Applicant must make formal arrangements with a senior scientist (e.g. laboratory director) at the institution where the postdoctoral fellowship would be held before applying for the award. Materials Needed for Application: From Applicant (8 copies, fully collated): Cover Page, including: - Applicant's name, address, telephone, fax and e-mail - Applicant's current department and institution - Title of proposed postdoctoral research project and institution at which it would be conducted (including mail and email addresses and telephone and fax numbers) - Planned starting date of postdoctoral fellowship - Applicant's Ph.D. granting institution and year of receipt (or date realistically expected) - Brief educational history indicating the year and institution of graduate study and of any postdoctoral research - Laboratory, department and institution in which postdoctoral fellowship would be held - Name, address and telephone of senior scientist - Names, addresses, telephone numbers, etc., of references Abstract of proposed research (not to exceed 300 words) Proposed research/training plan describing scientific importance of subject, with considerable specificity as to analytic methods and data to be employed, and reason for choice of proposed sponsoring scientist and institution (with a firm maximum of 1,500 words, including selected citations). If desired, copies of up to two reprints may be attached to each collated copy of proposal. Statement of applicant's reasons for interest in computational molecular biology, current career goals, and potential role of postdoctoral fellowship in attaining such goals (ca. 250 words). A summary of the major findings of the applicant's dissertation research (250 words). Curriculum vitae including educational background, topic of doctoral dissertation, positions held to date, scientific awards and grants received citing source, duration and amount (direct costs),full titles, and references of all publications. Formal institutional endorsement of proposal may be included, but is not required unless and until a formal award offer has been made. A stamped, self-addressed postcard (if applicant desires) to confirm that application materials have been received (allow at least 3 weeks for processing; no telephone calls, please). All applications should be final and complete; no substitutions or additions. From Sponsoring Senior Scientist (8 copies, fully collated): Letter of agreement to host and supervise the research of postdoctoral applicant, including any necessary institutional clearances, e.g. animal experimentation, human subjects, recombinant DNA, etc. Letter must include qualitative comments concerning scientific merit of proposed research and training plan. Brief description (500 words) of current research, sources of funding, relevance of applicant's proposed research, and personnel with whom applicant would work. Curriculum vitae including educational background, current and former positions, scientific awards and grants received citing source, duration and amount (direct costs), full titles and references of publications related to computational molecular biology. From References (8 copies): The applicant must request reference letters from three scientists (excluding sponsoring scientist) in relevant disciplines who are knowledgeable about applicant's capabilities and previous research, and to whom he/she has sent a copy of the research/training plan proposed for the postdoctoral fellowship. If possible, one of these three should have personal knowledge of the applicant's doctoral research, and all must comment on the applicant's summary of the major findings of his/her recent research. Reference letters should include comments on overall ranking of applicant, e.g. top 1% of Ph.D.s, top 10%, etc. It is the applicant's responsibility to assure that reference letters (8 copies) are sent. Deadline and Announcements: The deadline for receipt of all application materials from applicant, sponsoring scientist, and related reference letters is January 19, 1998 (firm). Announcements will be made by May, 1998. Send Application To: Dr. Michael S. Teitelbaum Sloan/DOE Joint Postdoctoral Fellowships in Computational Molecular Biology Alfred P. Sloan Foundation 630 Fifth Avenue, Suite 2550 New York, NY 10111-0242 From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Question about Eyring Rate Theory Date: 3 Sep 1997 19:08:01 GMT Organization: Vollum Institute Lines: 35 Distribution: world Message-ID: <5ukcih$h76$2@fremont.ohsu.edu> 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: Wed, 3 Sep 1997 20:18:52 GMT Hi all, In describing chemical reactions, people often use the Theory of Absolute Reaction Rates, also known as Eyring Rate Theory. As you know, the idea is that reactants and products are separated by a "transition state" which is less favorable (thermodynamically, has a higher energy) than either products or reactants. Thus, after forming, it quickly disintegrates leaving either the initial reactants again or the products. The energy difference between the reactants and the transition state indicates the rate of the forward reaction, whereas the difference between the transition state and the reactants indicates the rate of the backward reaction. Usually, the reaction is drawn schematically on X and Y axes, in which the Y axis represents the energy at each point in the reaction pathway, and the X axis is usually labelled "Reaction Coordinate". My questions are these: 1) What is the physical meaning of "Reaction Coordinate"? Is it related to the physical distance between reactant molecules? Does it have units, and if so what are they? 2) Is there actually an equation that uses the Reaction Coordinate as the independent variable, with energy as the dependent variable, that one can use to generate these Eyring diagrams? What is this equation, and where can I find a published derivation (The Eyring 1935 paper that I read does not really give such an equation, or if it does, I didn't recognize it). Thanks much, Matt Jones The Vollum Institute Portland, OR USA From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!loop.mdy.univie.ac.at!hs From: hs@mdy.univie.ac.at (Hellfried Schreiber) Newsgroups: bionet.biophysics Subject: ICMSB97 - Final Programme Date: 3 Sep 1997 18:56:21 GMT Organization: Vienna University, Austria Lines: 262 Sender: hs@loop.mdy.univie.ac.at (Hellfried Schreiber) Message-ID: <5ukbsl$1c0q@www.univie.ac.at> NNTP-Posting-Host: loop.mdy.univie.ac.at ------------------- Final Programme ------------------- S E C O N D I N T E R N A T I O N A L C O N F E R E N C E O N M O L E C U L A R S T R U C T U R A L B I O L O Y >> I C M S B 97 << SEPTEMBER 10 - 14, 1997 VIENNA, AUSTRIA Organized by the Austrian Chemical Society Working Group Biophysical Chemistry ---------------------------------------------------------------------- Scientific Schedule and Social Programme ======================================== * Wednesday 10.9.97 From 14:00 Registration 19:00 Dr. Max Perutz (Honorary) Glutamine Repeats and Inherited Neurodegenerative Diseases 20:00 Welcome Get-Together * Thursday 11.9.97 STRUCTURE AND PREDICTION +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 H. Michel (Plenary) Structure and Possible Mechanism of Action of the Cytochrome c Oxidase from Paracoccus denitrificans 9:55 R. Crowther (Plenary) The Fold of the Core Protein of Hepatitis B Virus Determined by Electron Cryo-Microscopy 10:40 Coffee Break 11:10 T. Richmond (Plenary) X-Ray Structure of the Nucleosome Core Particle at 2.8A Resolution 11:55 R. Dutzler (Short Commun.) Sugar Transport through Maltoporin: From Structure to Mechanism of a Facilitated Diffusion Channel 12:15 J.-P. Renaud (Short Commun.) Ligand Binding to Retinoid Receptors 12:35 Lunch 14:00 G. Rose (Plenary) Simulation of Protein Folding Using LINUS 14:45 B. Rost (Plenary) Learning from Evolution to Predict Protein Structure 15:30 L. LoConte (Short Commun.) Visible Volume: A New Way of Exploring Protein Structures 15:50 Coffee Break 16:20 S. Benner (Plenary) Natural History and the Physical Sciences: Predicting the Structure of Proteins 17:05 M. Sippl (Plenary) Molecular Forces in Protein Folding and Prediction 17:50 M. Rodionov (Short Commun.) Amino Acid Interaction Patterns and Sequence Conservation in Protein Superfamilies 18:10 Close 20:00 Cocktail Reception for all participants and accompanying people at the City Hall of Vienna "Wiener Rathauskeller" * Friday 12.9.97 MACROMOLECULAR INTERACTIONS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 W. van Gunsteren (Plenary) Calculation of Free Energy and Binding Constants for Biomolecular Complexes 9:55 A. Frankel (Plenary) Design and Evolution of RNA-Binding Proteins 10:40 Coffee Break 11:10 T. Steitz (Plenary) DNA and RNA Polymerases: Structural Diversity and Common Mechanisms 11:55 P. Walsh (Short Commun.) RNA Binding by the N-Terminus of the Wilms, Tumor 1 Tumor Suppressor Protein 12:15 J. Forbes (Short Commun.) Probing the Hydrophobic Interactions of Surfaces, Peptides, and Macromolecules with the Atomic Force Microscope 12:35 Lunch 14:00 Poster Session I 15:30 Coffee Break 16:00 R. Rigler (Plenary) Fluorescence Correlation Spectroscopy, Detection and Selection of Single Molecules 16:45 A. Watts (Plenary) Atomic Resolution of Bound Ligands in Functionally Active, Membrane Receptors using Non-Crystallographic Methods 17:30 G. Miller (Short Commun.) Molecular Dynamics Simulations on G Protein-Coupled Receptors: Implementation and Validation of a Membrane Mimetic 17:50 Close This evening has been left free for participants to enjoy Vienna * Saturday 13.9.97 CATALYSIS AND DESIGN +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 O. Jardetzky (Plenary) Protein Dynamics and Conformational Transitions in Allosteric Proteins 9:55 A. Wlodawer (Plenary) Retroviral Integrases - the Last Frontier in Designing Drugs against AIDS 10:40 Coffee Break 11:10 R. Goody (Plenary) Problems and Perspectives in Designing Drugs against AIDS 11:55 H. Bjrkbacka (Short Commun.) Conformational Changes Induced Upon Oxidation of Chloroplastic Carbonic Anhydrase Studied by Intrinsic Tryptophan Fluorescence 12:15 K. Sakakibara (Short Commun.) Molecular Design of the Amide Transition-state Analog by Molecular Mechanics 12:35 Lunch 14:00 Poster Session II 15:30 Coffee Break 16:00 M. Weir (Plenary) Role of Structural Biology in Drug Discovery 16:45 K. Mueller (Plenary) Combined Rational and Random Design Concepts in Drug Discovery 17:30 J. Priestle (Plenary) A Target Based Strategy for Drug Discovery 18:15 Close On this evening, participants are encouraged to attend the dinner at a wine cellar in the city centre. The "Heurigen" atmosphere, with wine and Viennese food is very characteristic of Vienna * Sunday 14.9.97 FOLDING +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 R. Baldwin (Plenary) Nature of the Apomyoglobin Folding Pathway 9:55 K. Dill (Plenary) Sightseeing along the Landscapes of Protein Folding 10:40 Coffee Break 11:10 C. Dobson (Plenary) Exploring the Structural Basis of Protein Folding 11:55 A. N=94ppert (Short Commun.) Initial Hydrophobic Collapse is not Necessary for Protein Folding: A Study by Stopped-Flow Dynamic Light Scattering and Stopped-Flow Circular Dichroism 12:15 I. Bahar (Short Commun.) Simulation of Protein Folds Using a Low Resolution Model 12:35 Lunch 14:00 P. Schuster (Plenary) RNA Structures Beyond the One Sequence-One Structure Paradigm 14:45 F. Hartl (Plenary) Chaperone-Assisted Protein Folding 15:30 End of Conference -------------------------------------------------------------------------- For further information contact: Dr. Andreas Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: ++ 43 1 5874249 or ++ 43 1 5873980 FAX.: ++ 43 1 5878966 e-mail: biophys@goech.co.at ============================================================================ Distribution: Followup-To: Organization: Univ. of Vienna, Inst. for Theoretical Chemistry Keywords: -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 4028525 | | | | +-----------------------------------------------------------------------------+ From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!www.nntp.primenet.com!globalcenter1!news.primenet.com!nntp.primenet.com!feta.direct.ca!newsfeed.direct.ca!news.he.net!news.pagesat.net!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Re: Question about Eyring Rate Theory Date: Wed, 03 Sep 1997 18:20:08 -0500 Organization: BioKin Consulting Lines: 56 Message-ID: <340DF0A8.83B27D08@biokin.com> References: <5ukcih$h76$2@fremont.ohsu.edu> NNTP-Posting-Host: wa3.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Matt Jones wrote: > 1) What is the physical meaning of "Reaction Coordinate"? Is it related > to the physical distance between reactant molecules? Does it have > units, and if so what are they? There are probably better qualified people reading this group (I think Bob Alberty does) who could answer your question, but here is my $0.02 worth. For a two-atom reaction such as H. + H. ----> H2, the reaction coordinate simply is the distance of the two atoms, or geometrically a straight line. When more than two atoms are involved, things get a little hairy, because now we are in multi-dimensional space: no one single interatomic distance will suffice. Still, you can think of the reaction coordinate in geometric terms if you accept the notion of multidimensional spaces. It is a winding "curve" running on the "surface" of potential energy. BTW, did you try to type "reaction coordinate" into the Infoseek search engine? Here is what came out on http://www.chem.ucalgary.ca/groups/ziegler/IRC.html I cut and pasted from the above Web site (Tom Ziegler's group at Calgary): The starting point of studying chemical reactions in computational chemistry is to locate and characterize the reactants, products, and transition states on the potential energy surface (PES). For some reactions the PES can be rather complicated so that it is not obvious to determine if the transition state (TS) connects to desired reactant(s) and product(s). In such cases tracing reaction path from the TS to reactant(s) and product(s) becomes essential for understanding the reactions. Besides, the information of the PES along the reaction path is also desired for detailed kinetic and dynamic studies. A nature definition of reaction path is the steepest descent path from the TS down to both reactant and product sides on the PES. When mass-weighted Cartesian coordinates are used, this path is so-called intrinsic reaction coordinate (IRC). Physically, IRC is the solution of equation of motion of the nuclei which move on the PES with infinitesimal velocity. Mathematically, IRC proves to be a quasi-geodesic curve in the Riemannian space corresponding to the PES and hence the shortest path connecting the reactant to product via the TS. The IRC is thus a simple yet rigorous approach for probing complicated reaction processes. So there you have it, it is a curve in Riemanian space. Doesn't it tell us chemists that math is worth looking at? ------------------------+------------------------ Petr Kuzmic, Ph.D. | (608) 256-4790 BioKin Consulting | fax (708) 256-1269 P.O. Box 8336 | pkuzmic@biokin.com Madison WI 53708 | http://www.biokin.com ------------------------+------------------------ From owner-biophysics@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!news.bc.net!rover.ucs.ualberta.ca!news.ucalgary.ca!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: Question about Eyring Rate Theory Date: Wed, 03 Sep 1997 16:24:33 -0600 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 68 Message-ID: <340DE3A1.167E@henri.chem.uleth.ca> References: <5ukcih$h76$2@fremont.ohsu.edu> 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) To: Matt Jones Matt Jones wrote: > In describing chemical reactions, people often use the Theory of > Absolute Reaction Rates, also known as Eyring Rate Theory. It's generally called Transition State Theory (TST) now. > My questions are these: > > 1) What is the physical meaning of "Reaction Coordinate"? Is it > related to the physical distance between reactant molecules? Does it > have units, and if so what are they? The reaction coordinate can be any coordinate which varies monotonically during the reaction. For instance, during an AB + C -> A + BC reaction, you might take the reaction coordinate to be either the distance from atom A to atom B or the distance from B to C. The former increases during the reaction while the latter decreases. For the purposes of calculating rate constants using TST however, some choices are better than others. Some of the most beautiful work on this problem has been done by Marcus: @article{Marcus64a, Author="R.A. Marcus", Journal="J. Chem. Phys.", volume=41, number=9, pages="2614-2623", year=1964, Title="Generalization of the activated complex theory of reaction rates. I. Quantum mechanical treatment", Annote="A version of transition state theory not requiring a Cartesian metric is derived." } @article{Marcus64b, Author="R.A. Marcus", Journal="J. Chem. Phys.", volume=41, number=9, pages="2624-2633", year=1964, Title="Generalization of the activated complex theory of reaction rates. II. Classical mechanical treatment", Annote="It is shown that, in the right metric (constructed from geodesics of the potential energy surface), there is always a separable coordinate in the classical transition state theory that may be used as a reaction coordinate." } These papers are classics and well worth reading by anyone with an interest in TST. It takes a little background in non-Euclidean geometry to understand them fully though. > 2) Is there actually an equation that uses the Reaction Coordinate as > the independent variable, with energy as the dependent variable, that > one can use to generate these Eyring diagrams? The whole point of TST is that you don't need to know much about the reaction coordinate or about how the energy varies along it. You need only identify the transition state and know a few things about the geometry of the energy surface there (esp. the curvature along the reaction coordinate which gives you the "frequency" which enters into TST calculations; at the TS, the reaction coordinate is the direction of steepest descent from the saddle point so there is no problem identifying it there). This information is (at least in principle) available from high-precision ab initio calculations. The "Eyring diagrams" you refer to are just pedagogical aids. When needed to make a point in a paper, I think most people just sketch them. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Wed Sep 03 23:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: Question about Eyring Rate Theory Date: 4 Sep 1997 19:55:38 GMT Organization: Vollum Institute Lines: 94 Distribution: world Message-ID: <5un3nq$r93$1@fremont.ohsu.edu> References: <5ukcih$h76$2@fremont.ohsu.edu> 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: Thu, 4 Sep 1997 21:06:27 GMT In article <340DF0A8.83B27D08@biokin.com> Petr Kuzmic, pkuzmic@biokin.com writes: >So there you have it, it is a curve in Riemanian space. > >Doesn't it tell us chemists that math is worth looking at? > Thanks for both of the very helpful responses I've gotten so far. After looking up some these references, I have this to say: Ouch! I definitely should have paid more attention in BOTH chemistry and math class! I also have a few more questions: This is from the Ziegler web page: "A nature definition of reaction path is the steepest descent path from the TS down to both reactant and product sides on the PES." So, tell me if I have this right. One way to think of the reaction coordinate is to first figure out the "energy surface" for a reaction. Let's say we're dealing with the reaction A+BC-->ABC, where A, B and C are single atoms. We could calculate the energy change with distance for A and B, and for A and C seperately (B and C remain at a fixed distance from each other, so their relative energy in isolation doesn't change). Then we could plot this as energy versus the coordinate plane defined by the A-B distance as one axis and the A-C distance as the other axis. We'll probably get a sheet with a lump sticking up out of it, right? The tip of this lump is the transition state. I guess this would really be a saddle point if there were a lot of lumps, which there must be because there are very high energies associated with some distances that could possibly exist. Now, the reaction coordinate is the curve we would trace if we followed the steepest descent down from the saddle to the products on one side and the reactants on the other. That's the shortest distance between reactants and products that goes through the transition state. I guess we could calculate the length of this curve, keeping our units straight. So the energy coordinate is _related_ to the spatial distance, but it's not really a spatial distance because it's going to have units of energy per angstrom per angstrom or something like that (for this example). If we had a system with several atoms on different molecules, then instead of a sheet, we'd have a solid or a hypersurface of some sort, but still the reaction coordinate would represent the shortest distance _along_ this energy vs space surface that contained the transition state. Is this a reasonable layman's summary of the main idea, or am I still getting something grossly wrong? At the moment, for me, understanding Hamiltonian operators and tensor products and Riemann spaces is right out of the question. Maybe next week ;-). One more thing. In the Marcus paper (J. Chem. Phys. 41:2624-2633), he says: "For the reaction to occur some n-1 dimensional hypersurface in the n-dimensional configurational space must be crossed. (The hypothetical system constrained to exist on this surface is the 'activated complex.' The surface is called the 'reaction hypersurface'.)" In light of what I wrote above, I'm confused about which surface is which here. I would first imagine that the 'reaction hypersurface' he's referring to is what I had in mind when I talked about the "reaction coordinate" above. "Surface" would apply in the case where there's lots of atoms in the system. Instead of a line or curve (n-1 dimensional when dealing with 2D space, A-B and A-C axes), you have a sheet for 3D, a solid for 4D etc. The activated complex lies on this surface (because of the way you define the surface, i.e. the shortest distance that contains the transition state). OK. But at the beginning he talks about the system _"crossing"_ the hypersurface. In my example above, this would be analogous to crossing (intersecting?) the reaction coordinate, which I don't think makes any sense. The reaction moves along it, but doesn't cross it. Or does he mean to cross in the sense of "to traverse" or "to travel along"? Can anyone help clear up my confusion on this point (and any others that I may be confused about)? Oh, yeah. One final, final question (for now). Those "Eyring Diagrams" that people draw in 2D: are they analogous to making a cross-sectional slice through the energy surface that contains the entire curve of steepest ascent and descent containing the transition state (in my example above, the energy surface is a lumpy plane, and the cross section along the reaction coordinate would be a lumpy line, which is what people usually draw)? If so, then when they label the X-axis "reaction coordinate" they're not really talking about what I was talking about above (units: energy per angstrom per angstrom) but rather just the straight line where that cross section intersects the A-B x A-C plane (units: angstrom per angstrom). I realize that people don't intend those things to be taken too literally, but still I'd like to understand what's going on. If you made it this far, thanks a lot for your patience! Matt From owner-biophysics@net.bio.net Wed Sep 03 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!EU.net!news0.Belgium.EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!usenet From: Guy Droogmans Newsgroups: bionet.biophysics,bionet.neuroscience,bionet.software Subject: WinASCD: analysis of single channel and whole cell currents Date: Thu, 04 Sep 1997 09:46:50 +0200 Organization: kuleuven.ac.be Lines: 46 Message-ID: <340E676A.3433D85D@med.kuleuven.a.c.be> NNTP-Posting-Host: fysiologie-12.med.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Xref: biosci bionet.biophysics:3494 bionet.neuroscience:20217 bionet.software:19430 WinASCD is a program to analyze single channel and whole-cell pClamp data (Clampex, Fetchex, AxoTape). It is a 32-bit (WIn95/NT) updated version of an original DOS program that I started writing more than 10 years ago. It includes the following main features: 1. a data correction module for baseline restoration (drift correction) background subtraction (correction for leak and capacitative current) 2. a module for calculating average and peak currents ensemble averaged current avg current for continuous data avg and peak current for triggered data 3. a module to construct linear combinations of records belonging to the same or different files 4. a module to fit sum of exponentials or a kinetic model to indivudual current traces, ensemble averaged currents and composed records 5. a module for the Analysis of Single Channel Data, including Amplitude histogram construction and fit with Gauss peaks Kinetic Analysis: idealization, dwell time histograms, first latencies, burst analysis, analysis of the number of events 6. a module for the analysis of current fluctuations, including current variance analysis and FFT. Each window (graphical or text) can be printed (not a screen dump) or saved as a TAB delimited ASCII file for import in e.g. a presentation software package. A demo version of the program in which output is disabled is available from ftp://cc5.kuleuven.ac.be/pub/droogmans/winascd.zip -- Guy Droogmans Laboratorium voor Fysiologie Campus Gasthuisberg, KU Leuven B-3000 Leuven (Belgium) Tel 32 16 345 726 Fax 32 16 345 991 From owner-biophysics@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!agate!howland.erols.net!feta.direct.ca!newsfeed.direct.ca!news.he.net!news.pagesat.net!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Software available: Biochemical kinetics and equilibria Date: Fri, 05 Sep 1997 11:25:51 -0500 Organization: BioKin Consulting Lines: 51 Message-ID: <3410328F.B04B504C@biokin.com> NNTP-Posting-Host: j29.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) _____________________________________________________ PUBLIC DOMAIN PROGRAM DYNAFIT AVAILABLE DynaFit is a program for simulation and least-squares fitting of biochemical kinetic data. The user enters the reaction mechanism symbolically, such as this: ; "Slow, tight" inhibition of HIV proteinase [mechanism] E + S <==> ES : k ks ES ---> E + P : kr E + I <==> EI : k1 k2 EI <==> EJ : k3 k4 The machine then derives the underlying system of differential equations (to compute the time-course of the reaction) or algebraic equations (to compute the composision at equilibrium). _____________________________________________________ TEST PROBLEMS The program should be downloaded along with a set of test examples, all of them based on real experimental mostly from biochemical kinetics, but the same methods can be used for other areas of chemistry and biology. _____________________________________________________ REVIEWS A reviewer had this to say about DynaFit: "If you do any kind of kinetic data analysis as part of your research program, be sure to download DynaFit from the BioKin Web site." (HMS Beagle Newsletter "Software Alert", volume 1997 No. 9). _____________________________________________________ LINKS http://www.biokin.com/ BioKin home http://www.biokin.com/dynafit/index.shtml ... DynaFit _____________________________________________________ REFERENCES P. Kuzmic (1996) Anal. Biochem. 237, 260-273. _____________________________________________________________ Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA pkuzmic@biokin.com * http://www.biokin.com * 608.256.1269 fax From owner-biophysics@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!TTUHSC.EDU!phyan From: phyan@TTUHSC.EDU (Alan Neely) Newsgroups: bionet.biophysics Subject: Neutrotranmitters frequencies? Date: 5 Sep 1997 06:38:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.1.32.19970905084542.006c00b4@ttuhsc.edu> NNTP-Posting-Host: net.bio.net What are you talking about ? I am sure that neurotransmitter like any other molecule has an NMR spectra related to the rotation of nuclei. Vibration in on the infrared range and I am afraid that movement is pretty random. Cromatography and electroforesis are more likely to help you in this. Waht is your background ? What are you really up to ? Alan From owner-biophysics@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!agate!howland.erols.net!feta.direct.ca!newsfeed.direct.ca!news.he.net!news.pagesat.net!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Re: Question about Eyring Rate Theory Date: Fri, 05 Sep 1997 00:13:23 -0500 Organization: BioKin Consulting Lines: 50 Message-ID: <340F94F3.34B8779A@biokin.com> References: <5ukcih$h76$2@fremont.ohsu.edu> <5un3nq$r93$1@fremont.ohsu.edu> NNTP-Posting-Host: q41.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Matt Jones wrote: > Then we could plot this as energy versus the coordinate plane defined > by the A-B distance as one axis and the A-C distance as the other axis. > We'll probably get a sheet with a lump sticking up out of it, right? > The tip of this lump is the transition state. Not really: your second idea is better: > I guess this would really be > a saddle point > Is this a reasonable layman's summary of the main idea, or am I still > getting something grossly wrong? I think you are on the right track. Especially the part about saddle points. A friend of mine did his Ph.D. and then a post-doc with Roald Hoffmann finding methods to get from an energy minimum (say, a minimum according to the molecular orbital theory) UP TO THE SADDLE POINT, where the transition state actually "is". (You see, the energy minimum is relatively easy to find, compared to finding the structure of the saddle point, because there you have to climb up the hill but only in a certain very intelligent way.) > Oh, yeah. One final, final question (for now). Those "Eyring Diagrams" > (snip) > they're not really talking about what I was talking about > above (units: energy per angstrom per angstrom) Be careful: the "Intrinsic Reaction Coordinate" of Ziegler is a more exotic beast then drawings of "r.c." in undergaduate texts. Really what most people mean is just an interatomic distance between two atoms making and breaking a bond, while all the other atoms (if any) in the system follow along their respective least "expensive" pathway. Why don't you mail Dr. Ziegler himself and ask him about the Web page his group posted? Maybe he can unleash someone on you to explain the details, or send you some reprints and other info on R.C. ------------------------+------------------------ Petr Kuzmic, Ph.D. | (608) 256-4790 BioKin Consulting | fax (708) 256-1269 P.O. Box 8336 | pkuzmic@biokin.com Madison WI 53708 | http://www.biokin.com ------------------------+------------------------ From owner-biophysics@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed1-hme1!newsfeed.internetmci.com!205.219.188.10!news.lr.net!usenet From: lin Newsgroups: bionet.biophysics Subject: Laser WANTED Date: Fri, 05 Sep 1997 17:36:16 -0400 Organization: LRNet, Inc. Lines: 6 Message-ID: <34107B50.ECF79FE8@worldpath.net> NNTP-Posting-Host: ndur2-3.worldpath.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) Wanted old PHASE-R Pulse dye lasers. Re mail if you got one !!! From owner-biophysics@net.bio.net Fri Sep 05 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX.wco.com!feta.direct.ca!newsfeed.direct.ca!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.45.32.37!world1.bellatlantic.net!news From: CASH4U@dream.com Newsgroups: bionet.biophysics Subject: GET THE CASH YOU NEED //////////// Date: Sat, 6 Sep 1997 16:43:58 Organization: Bell Atlantic Internet Solutions Lines: 34 Message-ID: <5usfd8$d3n@world1.bawave.com> NNTP-Posting-Host: client-110-27.bellatlantic.net CASH GRANTS CASH GRANTS CASH GRANTS Foundations all over the United States GIVE CASH GRANTS. ANYONE can apply for a Grant from 18 years and up... This money HAS to be given away, WHY not to YOU? Grants from $500.00 to $50,000.00 possible, in some instances. Grants don't have to be paid back. Grants can be ideal for people who are or were bankrupt or just have bad credit. 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From owner-biophysics@net.bio.net Sun Sep 07 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!206.229.87.50!news-pull.sprintlink.net!news-in-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news.bc.net!rover.ucs.ualberta.ca!news.ucalgary.ca!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: Question about Eyring Rate Theory Date: Mon, 08 Sep 1997 15:46:10 -0600 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 31 Message-ID: <34147222.167E@henri.chem.uleth.ca> References: <5ukcih$h76$2@fremont.ohsu.edu> <5un3nq$r93$1@fremont.ohsu.edu> 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) To: Matt Jones Matt Jones wrote: > If we had a system with several atoms on different molecules, > then instead of a sheet, we'd have a solid or a hypersurface of some > sort, but still the reaction coordinate would represent the shortest > distance _along_ this energy vs space surface that contained the > transition state. Not exactly. The reaction path would be the lowest energy path connecting the saddle point to the reactant and product minima. This is almost certainly not the shortest distance. > One more thing. In the Marcus paper (J. Chem. Phys. 41:2624-2633), he > says: > "For the reaction to occur some n-1 dimensional hypersurface in the > n-dimensional configurational space must be crossed. (The hypothetical > system constrained to exist on this surface is the 'activated > complex.' The surface is called the 'reaction hypersurface'.)" Let's take the simplest case. If you think about the traditional diagrams, the energy is shown as a one-dimensional curve. The product and reactant are separated by a maximum (a point, which is a zero-dimensional object). Now think about an energy surface. The surface is two-dimensional and the reactants and products are separated by a line (one-dimensional) running through the saddle point and perpendicular to the direction of steepest descent. The generalization to higher dimensions is obvious :-). Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Mon Sep 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!news1.chicago.cic.net!iagnet.net!newsspool.doit.wisc.edu!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Henri (1902) translation Date: Mon, 08 Sep 1997 22:47:11 -0500 Organization: BioKin Consulting Lines: 24 Message-ID: <3414C6BF.9A360377@biokin.com> NNTP-Posting-Host: wa48.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Greetings, I have posted on the BioKin website (http://www.biokin.com) an English translation of Victor Henri (1902) "General Theory of Action of Certain Hydrolases" Compt. rend. hebd. Acad. Sci. Paris 135, 916-919 (1902). I think it is particularly amusing from today's perspective that Mr. Henri imagined the enzyme exerting its catalytic influence without a direct physical contact with the substrate (see problem 2.2 p. 37 of Athel Cornish-Bowden "Fundamentals..." 1979 edition). If anyone (especially native French speakers) would care to comment on the translation, it would be much appreciated (I depended on my dictionary to do this). Petr _____________________________________________________________ Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA pkuzmic@biokin.com * http://www.biokin.com * 608.256.1269 fax From owner-biophysics@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.erols.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!news1.chicago.cic.net!iagnet.net!nntp.earthlink.net!usenet From: specpress@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol Subject: SCIENCE-WEEK: This Week's Headlines (5 Sep 97) Date: Wed, 10 Sep 1997 01:13:26 GMT Organization: SCIENCE-WEEK Lines: 22 Message-ID: <5v4sb3$17i@argentina.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.35.118.102 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20258 bionet.biophysics:3506 bionet.cellbiol:8037 Headlines in This Week's SCIENCE-WEEK (September 5, 1997) [complete digests free at http://members.aol.com/sciweek] Karolinska Institute Accuses One of Its Researchers of Fraud University of California Loses Important Insulin Patent Law Suit An International Group to Search for Supernova Neutrinos Mesospheric Water Data Supports Small-Comet Theory Report of First Quantum Mechanical Entanglement of Atoms RNA Polymerization a Focus at Origin of Life Meeting New Investigations of RNA Structure and Catalysis First Emission of Low-Energy UV Photons from an Atomic Nucleus Mechanism of Macrophage Invasion by Tuberculosis Pathogen Receptor-Mediated Retrograde Chemical Signaling in Neurons A New Technique for Localizing Intracellular Calcium Ions Evidence for Retrovirus Involvement in Autoimmune Diabetes The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!194.162.162.196!newsfeed.nacamar.de!news-feed.inet.tele.dk!news.misty.com!nntp.upenn.edu!axe1.med.upenn.edu!axelsen From: axelsen@axe1.med.upenn.edu (Paul H Axelsen) Newsgroups: bionet.biophysics Subject: POSTDOCTORAL POSITIONS: Molecular Recognition and Membrane Biophysics Date: 10 Sep 1997 15:38:16 GMT Organization: University of Pennsylvania Lines: 31 Message-ID: <5v6et8$h1g$2@netnews.upenn.edu> NNTP-Posting-Host: axe1.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] POSTDOCTORAL POSITIONS AVAILABLE: Molecular Recognition and Membrane Biophysics Projects involve the use of novel spectroscopic techniques (infrared and UV) and mass spectrometry to study the behavior of antibiotics, fusogenic peptides, and blood coagulation proteins on lipid membranes with a view towards rational drug design. The laboratory is stably funded and the positions are available immediately. Applicants MUST be available for interview prior to appointment. Persons with a talent for mastering sophisticated new technology, and seeking to work on important biomedical problems, should inquire by email to axe@pharm.med.upenn.edu or Prof. Paul H. Axelsen Departments of Pharmacology and Medicine, Infectious Diseases Section University of Pennsylvania Rooms 130/131 John Morgan Bldg 3620 Hamilton Walk Philadelphia, PA 19104-6084 215-898-9238 / 9766 (tel) 215-573-2236 (fax) http://axe2.med.upenn.edu (www) -- ------------------------------------------------------------------------------ Axe@pharm From owner-biophysics@net.bio.net Wed Sep 10 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!bullseye.news.demon.net!demon!newsgate.unisource.nl!surfnet.nl!ruu.nl!gillies From: Malcolm Gillies Newsgroups: bionet.biophysics,bionet.molec-model,sci.bio.technology,sci.chem Subject: [2nd Announce] Molecular Graphics & Modelling Electronic Conference 2 Followup-To: poster Date: 11 Sep 1997 14:46:01 GMT Organization: Virtual Environments International, Oxford UK Message-ID: <5v9079$qr0$1@newshost.cc.ruu.nl> NNTP-Posting-Host: cmcind.far.ruu.nl Originator: gillies@cmcind.far.ruu.nl Lines: 96 Xref: biosci bionet.biophysics:3509 bionet.molec-model:1787 [please note that the deadline for submissions has been extended until September 15 for abstracts and September 22 for papers and posters] Second Electronic Molecular Graphics and Modelling Conference ************************************************************* October 6-17, 1997 World Wide Web: http://www.vei.co.uk/mgmec2/ Email: mgmnorg@vei.co.uk The Second Electronic Molecular Graphics and Modelling Conference (MGM EC-2) will be held on the Internet and World Wide Web from Oct 6-17, 1997 and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates and Protein-Carbohydrate Interactions; Enzyme Mechanisms; Conformational Sampling; Nucleic Acids; Quantum Chemistry; Structure-based Design; Visualization; and Perspectives. Presentations of papers or posters must be prepared in Hypertext Markup Language (HTML) with figures in GIF or other Web-compatible formats so that participants can view the papers via the World Wide Web (The presentations may also include enhancements such as 3D structures, VRML, Java, RealAudio, Quicktime movies etc.) Authors may submit WWW presentations for non-permanent display during the conference, or for refereed print or electronic publication in the Journal of Molecular Graphics or the Internet Journal of Chemistry (IJC), http://www.ijc.com/ During the conference, interaction, presentations and discussions will take place via the Internet using a Java-based virtual conference centre, WWW-based discussion forums and an electronic mailing list. Before the conference, a timetable for lectures and discussion sessions for each section will be posted. The Conference will feature a Virtual Exhibition where exhibitors will be able to describe the activities of their organization, display their products and services and interact with registrants. Potential exhibitors should contact the conference organisers. Further information regarding the conference is available from the conference WWW site at http://www.vei.co.uk/mgmec2/ Inquiries may also be sent by email to the conference organisers at mgmnorg@vei.co.uk REGISTRATION ************ If you intend to participate in MGM EC-2 please use the special registration form accessible via http://www.vei.co.uk/mgmec2/. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 45 pounds sterling (75 US dollars) with a special rate for students of 30 pounds sterling (50 US dollars). DEADLINES AND DATES ******************* 1) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is September 15. 2) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is September 22. 3) Refereeing Period The refereeing period will commence upon completion of the conference. Molecular Graphics & Modelling Network (MGMN) mailing list ********************************************************** Conference-related news and announcements will be posted regularly to the MGMN mailing list (mgmn@vei.co.uk). If you wish to subscribe to the MGMN list send the following one line message to mgmn-request@vei.co.uk subscribe your_email@address To unsubscribe send the following message: unsubscribe your_email@address -- Posted by Malcolm Gillies Molecular Modelling Coordinator Virtual Environments International, Oxford UK http://www.vei.co.uk/ From owner-biophysics@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!panix!howland.erols.net!iagnet.net!nntp.earthlink.net!usenet From: specpress@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol Subject: SCIENCE-WEEK: This Week's Headlines (12 Sep 97) Date: Fri, 12 Sep 1997 03:31:26 GMT Organization: SCIENCE-WEEK Lines: 23 Message-ID: <5vad5l$qsa@chile.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.135.18 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20275 bionet.biophysics:3510 bionet.cellbiol:8048 Headlines in This Week's SCIENCE-WEEK (September 12, 1997) [complete digests free at http://members.aol.com/sciweek] First Annual Decline in Number of U.S. Graduate Science Students Anthropological Evidence for Earliest Known Net Hunters No Evidence of Nearby Galactic or Intergalactic Hydrogen Reserves First Production of Matter From Light First Evidence of an Exotic Meson Evidence for Decline of Sea-Ice Surrounding Antarctica First Commercial Catalytic Antibody for Chemical Synthesis Animal Virus Engineered to Attack HIV Virus A Possible Novel Mechanism of Gene Mutation in Cancer More Evidence for Cofactors in Prion Pathogenesis Prenatal Lead Exposure and Postnatal Lead Toxicity First Mice Engineered for Duchenne Muscular Dystrophy New Multi-Drug Resistance of Plague Pathogen The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!newsfeed.dacom.co.kr!europa.clark.net!205.252.116.205!howland.erols.net!ix.netcom.com!news From: Alex Damien Newsgroups: bionet.biophysics Subject: International Symposium Date: Sat, 13 Sep 1997 09:00:53 -0700 Organization: Netcom Lines: 14 Message-ID: <341AB8B5.1F52@ix.netcom.com> Reply-To: AlexDn@ix.netcom.com NNTP-Posting-Host: wfd-nj1-21.ix.netcom.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NETCOM-Date: Sat Sep 13 9:29:14 AM CDT 1997 X-Mailer: Mozilla 3.0C-NC320 (Win16; I) The following page contains the program schedule for the 1st INTERNATIONAL SYMPOSIUM on Enigmatic and Uncertain Substances and Microorganisms in Bucaramanga, Colombia, South America. AIDS WITHOUT HIV: Myth or Reality? http://www.netcom.com/~alexdn/sympos.html Please spread this message to all Internet sites (www, newsgroups, mailing lists, etc.) that would be of interest. Thank you. George DeCarlo From owner-biophysics@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!raw From: raw@healthcareforums.com (Ruth Ann) Newsgroups: bionet.biophysics Subject: * Biomedical COMMUNICATIONS Freeware * Date: Sat, 13 Sep 1997 02:57:08 -0800 Organization: Worldwide Healthcare Forums Lines: 49 Message-ID: NNTP-Posting-Host: 38.28.33.14 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 *NEW* Please excuse any cross-posting. Instant Online Communication with your Family + BioNET Colleagues & Friends. Free: PeopleLink is a new communications service that lets people stay in touch no matter where they are on the Internet. The PeopleLink application notifies users whenever selected friends, colleagues or family members appear online, and enables them to instantly communicate in real-time. Combining the interactivity of chat with the selectivity and privacy of email. PeopleLink provides the simplest, safest, and most dependable way for online Healthcare Professionals to connect and communicate. PeopleLink is free to users, takes less than 5 minutes to download at 28.8, sets up easily, and is available for Windows 95, Windows 3.x, Macintosh PowerPC and 68K platforms. Download at http://www.healthcareforums.com/plink.html ---------------------------------- Visit 200 Healthcare Forums in English - http://www.healthcareforums.com BIOMEDICAL FORUM found under the main topic - Field of Medical Specialty Worldwide Healthcare Forums SITE TRANSLATIONS: Deutsch Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index4.html Español Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index5.html Français Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index6.html *COMING SOON* Japanese Healthcare FORUMS Chinese Healthcare FORUMS ---------------------------------- NEW SUPER SEARCH ENGINE PAGE with 28 ENGINES http://www.healthcareforums.com/Sengines.html ---------------------------------- POST A MESSAGE & START THREAD AT ||||||||||||||||||||||||||||||||||||||||||||||||||| www.healthcareforums.com ||||||||||||||||||||||||||||||||||||||||||||||||||| From owner-biophysics@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeeds.sol.net!news.pagesat.net!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Software available: (bio)chemical kinetics and equilibria Date: Sat, 13 Sep 1997 14:43:15 -0500 Organization: BioKin Consulting Lines: 51 Message-ID: <341AECD3.CDB146A2@biokin.com> NNTP-Posting-Host: k11.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) _____________________________________________________ PUBLIC DOMAIN PROGRAM DYNAFIT AVAILABLE DynaFit is a program for simulation and least-squares fitting of biochemical kinetic data. The user enters the reaction mechanism symbolically, such as this: ; "Slow, tight" inhibition of HIV proteinase [mechanism] E + S <==> ES : k ks ES ---> E + P : kr E + I <==> EI : k1 k2 EI <==> EJ : k3 k4 The machine then derives the underlying system of differential equations (to compute the time-course of the reaction) or algebraic equations (to compute the composision at equilibrium). _____________________________________________________ TEST PROBLEMS The program should be downloaded along with a set of test examples, all of them based on real experimental mostly from biochemical kinetics, but the same methods can be used for other areas of chemistry and biology. _____________________________________________________ REVIEWS A reviewer had this to say about DynaFit: "If you do any kind of kinetic data analysis as part of your research program, be sure to download DynaFit from the BioKin Web site." (HMS Beagle Newsletter "Software Alert", volume 1997 No. 9). _____________________________________________________ LINKS http://www.biokin.com/ BioKin home http://www.biokin.com/dynafit/index.shtml ... DynaFit _____________________________________________________ REFERENCES P. Kuzmic (1996) Anal. Biochem. 237, 260-273. _____________________________________________________________ Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA pkuzmic@biokin.com * http://www.biokin.com * 608.256.1269 fax From owner-biophysics@net.bio.net Tue Sep 16 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.biophysics Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Sep 1997 02:00:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199709170900.CAA27951@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-biophysics@net.bio.net Wed Sep 17 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!139.130.235.93!news.telstra.net!loomi.telstra.net!not-for-mail From: John Wickham Newsgroups: bionet.biophysics Subject: JRAK equipment Date: Thu, 18 Sep 1997 22:17:24 -0700 Organization: Sonic Seeker Developments Lines: 68 Message-ID: <34220AE4.2178@real.net.au> NNTP-Posting-Host: mercury.real.net.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I; 16bit) Cache-Post-Path: mercury.real.net.au!unknown@syd-pm2-26.real.net.au ********************* JRAK Biosignals Close Out Sale ******************************** JRAK Biosignals has made quality equipment for the medical and physiological research fraternerty for over 10 years. We are quitting this market as the world of physiological reaserch has moved on to other areas such as biotechnology etc. Thus we are offering a final opportunity to our customers to get equipment at a 50% discount. JRAK will continue to service and support our existing customers, but will not make any more equipment of this type. This is a list of our current stock, selling for 50% of the list price. List Price Instrumentation Racks 1x RK8 Instrumentation Rack (240V) $1285 Rack-mounted modules 1x SA.1 Dual channel Scaling Amplifier $620 1x PA.2 Pressure Amplifer $920 1x WD.1 Window Discriminator $790 1x ST.1 Isolated Stimulator $880 1x BA.1 Biological Amplifier $1090 1x BA.2 Isoloated biological amplifier $1425 2x NR.1 Nerve Ratemeter $1090 ea 1x EI.1 EMG Integrator $870 1x IA.1 Intracellular/Microelectrode $1090 Amplifier 1x F.1 Dual channel Signal Filter $795 1x MA.1 Audio Monitor $590 Stand-Alone Units 2x BA.2b Isolated Biological Amplifiers $1425 ea 1x IA.1b Intracellular/Microelectrode Amplifier $1290 1x MA.1b Audio Monitor $790 Analogue-Digital Converter 1x JLINK A/D Converter - with JVIEW software $2250 Note: Prices are in $AUS, FOB melbourne and exclude sales tax. Reply to johnshel&real.net.au or david.walker@med.monash.edu.au for further information. From owner-biophysics@net.bio.net Wed Sep 17 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!prodigy.com!not-for-mail From: york@ibm.net Newsgroups: bionet.biophysics Subject: Manuscripts/Wanted/writers Date: Thu, 18 Sep 1997 02:54:48 Organization: Prodigy Services Corp Lines: 19 Message-ID: <5vqj47$rma$12@newssvr04-int.news.prodigy.com> NNTP-Posting-Host: port66.myer.prodigy.net We/are the International Literary Agency of New York. We also have 2 other branches, one in the Lake George region of New York and the other in Marco Island, Florida, consequently we are able to accept new clients. Please adhere strictly to the following guidelines for submission of all fiction & nonfiction. Fiction: Brief synopsis, first chapter, self-addressed, stamped envelope (S.A.S.E.) Nonfiction: Brief synopsis, first chapter, S.A.S.E. Screenplays: (for TV & Movies) Brief synopsis, first 20 pages, S.A.S.E. Short Stories: Brief synopsis, first 3 pages, S.A.S.E. Poetry: Send in 3 of your best poems only, S.A.S.E. >>>Woodside International Literary Agency 33-29 58 Street Woodside, New York 11377 (718) 651-8145 Please do not send in complete manuscript unless invited. From owner-biophysics@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!usenet From: prismx@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol Subject: SCIENCE-WEEK: This Week's Headlines (19 Sep 97) Date: Fri, 19 Sep 1997 02:00:47 GMT Organization: SCIENCE-WEEK Lines: 25 Message-ID: <5vsmge$s5e@suriname.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.139.39 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20337 bionet.biophysics:3518 bionet.cellbiol:8086 Headlines in This Week's SCIENCE-WEEK (September 19, 1997) [complete digests free at http://members.aol.com/sciweek] A Criticism of Nomenclature in Molecular Biology Heavy Elements Finally Named India Sterile-Mosquito Project to be Revived A Summary of Current Mars Mission Results On Coherent Spin States of Optically Excited Electrons On Analysis of Self-Organizing Polymeric Materials Lungfish Replaces Coelacanth As Closest to Land Animals Complete Sequencing of E. Coli Genome On the Use of Yeast as a Model for Eukaryotic Biology First Determination of Prion Protein Structure Induced Reversal of Kinesin Motion in Cells Fluorescent Protein Analysis of Eukaryotic Cell Secretion Evidence for Differing Roles of the Two Estrogen Receptors An Analysis of Sickle Cell Disease Evidence for Linkage Between AIDS and Malaria The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Fri Sep 19 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: How much is the useful work? (Pentcho Valev) Date: 20 Sep 1997 10:13:30 +0100 Lines: 62 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <60043q$fmg@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk (I am sorry for writing my name in the subject space - the reason is that my messages are archived under somebody else's name). Some time ago I tried to start a discussion about useful work and the validity of the second law in general, but my arguments were either vague or wrong so the group was probably right not to pay much attention to them. Still everybody would agree that research of this kind is too painful - it always seems psychopathic at first, most often it is, so the reaction is always hostile and the author doomed to failure. Yet I do not think that problems of this kind should not be discussed - after all, heresy has always been an important factor in science (although heretics are sometimes burned). This time I am presenting an almost obvious example showing a violation of the second law. What is even more interesting is the theoretical generalization which is in fact a development of the classical thermodynamic concept of useful work. If correct, the new results will have a tremendous effect on quantitative bioenergetics. Please consider the following system: NaCl (high concentration) M NaCl (low concentration) where M is a membrane permeable only to Na+ (not even to water). At equilibrium, a capacitor-like double layer will be formed at the membrane, positive on the right side and negative on the left one. Accordingly, there will be a transmembrane potential difference which will be maximal at equilibrium. But this means that the process can be presented in the following way: Na+(left) = Na+(right) + el. potential (work) /1/ In fact, this is a reaction which produces work at equilibrium, in violation of the second law| We can easily imagine an isothermal cyclical process in which work is gained: The electrical potential does some work (e.g. pushes some different ions through the membrane or just shifts the electrometer) and decreases. This shifts /1/ to the right. As the work production stops, the initial equilibrium is restored. I cannot see how one can refute this perpetuum mobile. One will have to prove either that the el. potential cannot do work (?|) or that the reaction is not reversible (?|). The generalization of this case leads to the following result: The meximum useful work that can be extracted from a chemical reaction is not -(delta G), but rather -(delta G + delta H). In this particular case delta G = 0, so, as can be seen, Wmax = -(delta H). It would be interesting to examine other cases. For galvanic reactions, the delta H component cannot be done, i.e. the heat of reaction is immaterial to the work done. Vice versa, if the same reaction occurs not in a galvanic system, i.e. the electron transfer is direct, the delta G component is not normally produced, i.e. W = -(delta H). Tha last case is representative of many bioenergetic processes. For the ATP-ADP system, again, W = -(delta H). This is an expression of the obvious fact that, in the elementary chemical act, one molecule ATP can only use its internal energy for doing work. At the moment I can only present theoretical cases in which the maximum work Wmax = -(delta G + delta H) is done, but am sure that somewhere in the living system this work is obtained - Nature cannot have missed this opportunity. Pentcho Valev From owner-biophysics@net.bio.net Sat Sep 20 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.icm.edu.pl!newsfeed.nacamar.de!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed.inet.tele.dk!news.misty.com!nntp.upenn.edu!axe1.med.upenn.edu!axelsen From: axelsen@axe1.med.upenn.edu (Paul H Axelsen) Newsgroups: bionet.biophysics Subject: POSTDOCTORAL POSITIONS AVAILABLE: Molecular Recognition and Membrane Biophysics Date: 21 Sep 1997 23:22:19 GMT Organization: University of Pennsylvania Lines: 29 Message-ID: <604a7b$15q$4@netnews.upenn.edu> NNTP-Posting-Host: axe1.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] Projects involve the use of novel spectroscopic techniques (infrared and UV) and mass spectrometry to study the behavior of antibiotics, fusogenic peptides, and blood coagulation proteins on lipid membranes with a view towards rational drug design. The laboratory is stably funded and the positions are available immediately. Applicants MUST be available for interview prior to appointment. Persons with a talent for mastering sophisticated new technology, and seeking to work on important biomedical problems, should inquire by email to axe@pharm.med.upenn.edu or Prof. Paul H. Axelsen Departments of Pharmacology and Medicine, Infectious Diseases Section University of Pennsylvania Rooms 130/131 John Morgan Bldg 3620 Hamilton Walk Philadelphia, PA 19104-6084 215-898-9238 / 9766 (tel) 215-573-2236 (fax) http://axe2.med.upenn.edu (www) -- ------------------------------------------------------------------------------ Axe@pharm From owner-biophysics@net.bio.net Sun Sep 21 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!mic.fibernet.net!newsfeed.direct.ca!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!169.226.1.109!rebecca!euclid.wadsworth.org!tivol From: tivol@news.wadsworth.org (William Tivol) Newsgroups: bionet.biophysics Subject: Re: How much is the useful work? (Pentcho Valev) Date: 22 Sep 1997 20:53:32 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 97 Distribution: bionet Message-ID: <606lsc$r2h@euclid.wadsworth.org> References: <60043q$fmg@mserv1.dl.ac.uk> NNTP-Posting-Host: alcor.wadsworth.org X-Newsreader: TIN [version 1.2 PL2] RUMYM@BGEARN.ACAD.BG wrote: : Some time ago I tried to start a discussion about useful work and the : validity of the second law in general, but my arguments were either vague : or wrong so the group was probably right not to pay much attention to : them. One of the questions you addressed at that time was about the mole- cular dynamics of how to get more work out of ATP hydrolysis than delta H. I read up on this, and here is what I found: First, consider a simpler system--a solution of ADP and Pi. Since the equilibrium constant for the reaction ATP + H2O -> ADP + Pi is not in- finite, the second law predicts that in a solution of ADP and Pi there will be condsensations which produce ATP. On the molecular level this can be explained by considering collisions between ADP and Pi. The molecules in this system have a distribution of kinetic energies, vibrational and rota- tional states, etc., which I will assume are Maxwellian. Therefore, some of the collisions will be between ADP and Pi molecules which have enough total energy to produce ATP. Of these collisions, a fraction will occur with the correct orientation, and ATP will, indeed, be produced. As this process continues, there will come a time when there are just the right concentrations of ADP, ATP, Pi and H2O so that for each collision which produces ATP there will be a collision of ATP with H2O which produces ADP and Pi. At this point, the system is in equilibrium. As for your example, which concerned ATP hydrolysis and electrical potentials across a membrane, similar considerations of the energy content in the individual molecules undergoing the reaction can be sufficient to produce the reaction (and ra- pidly, if the concentrations of reactants and products make delta G nega- tive). As you pointed out, the total energy of the system is unchanged, and, therefore, the energy which went into the chemical bonds must be sub- tracted from the total kinetic (& vib + rot, etc.) energy of the system, so the temperature will decrease. : Still everybody would agree that research of this kind is too painful - : it always seems psychopathic at first, most often it is, so the reaction is : always hostile and the author doomed to failure. Yet I do not think that : problems of this kind should not be discussed - after all, heresy has : always been an important factor in science (although heretics are sometimes : burned). If one can't stand the flames, one shouldn't think about these things (At least one shouldn't post them on the internet. ;-)) : This time I am presenting an almost obvious example showing a violation : of the second law. What is even more interesting is the theoretical : generalization which is in fact a development of the classical thermodynamic : concept of useful work. If correct, the new results will have a tremendous : effect on quantitative bioenergetics. : Please consider the following system: : NaCl (high concentration) M NaCl (low concentration) : where M is a membrane permeable only to Na+ (not even to water). : At equilibrium, a capacitor-like double layer will be formed at the : membrane, positive on the right side and negative on the left one. : Accordingly, there will be a transmembrane potential difference which will : be maximal at equilibrium. But this means that the process can be : presented in the following way: : Na+(left) = Na+(right) + el. potential (work) /1/ : In fact, this is a reaction which produces work at equilibrium, in violation : of the second law| We can easily imagine an isothermal cyclical process in : which work is gained: The electrical potential does some work (e.g. pushes : some different ions through the membrane or just shifts the electrometer) : and decreases. This shifts /1/ to the right. As the : work production stops, the initial equilibrium is restored. : I cannot see how one can refute this perpetuum mobile. One will have to : prove either that the el. potential cannot do work (?|) or that the : reaction is not reversible (?|). If you look at the electrical potential far from the membrane, it goes to zero on each side. There are enough excess Cl- on the left and Na+ on the right to balance everything. The excess Cl- will be distributed on the left such that [Cl-] = const*exp(-eV/kT), where one still has to cal- culate V, and the same applies to the Na+ on the right. Since there are just as many + charges as -, virtually all the electric field lines will be confined to a finite distance from the membrane (yes, some of the lines will loop around through a plane at any finite distance from the membrane, but they will assymtotically approach zero at large distances). If you put electrodes near the membrane in an attempt to extract work from the system, you will move it off equilibrium, and some work can be extracted as equilibrium is re-established, but you will not get perpetual motion. : Tha last case is representative of many bioenergetic processes. For : the ATP-ADP system, again, W = -(delta H). This is an expression of : the obvious fact that, in the elementary chemical act, one molecule ATP : can only use its internal energy for doing work. It can also use its kinetic energy and any vib, rot & electronic energy if it is not in the ground state. Thermodynamics predicts that some molecules will not be in the ground state. : Pentcho Valev Yours, Bill Tivol From owner-biophysics@net.bio.net Sun Sep 21 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.direct.ca!news.he.net!news.pagesat.net!news.itis.com!not-for-mail From: Petr Kuzmic Newsgroups: bionet.biophysics Subject: Re: How much is the useful work? (Pentcho Valev) Date: Mon, 22 Sep 1997 14:41:34 -0500 Organization: BioKin Consulting Lines: 19 Message-ID: <3426C9EE.1E1E808B@biokin.com> References: <605tr4$1lo@mserv1.dl.ac.uk> NNTP-Posting-Host: s22.itis.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) Timothy J. Kordas wrote: > You've just re-invented the battery. Your potential drops steadily (doing > work) until equilibrium is reached. Congratulations. > > ** > > Does anyone else read these things, or am I just a sucker ? I read 'these things' as brain-teasers on coffee-breaks. My strategy is to skip the details that describe exactly how the newest perpetuum mobile works. At this stage of the game, I simply wait for an elegant and insightful refutation... -Petr _____________________________________________________________ Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA pkuzmic@biokin.com * http://www.biokin.com * 608.256.1269 fax From owner-biophysics@net.bio.net Sun Sep 21 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!cs.utexas.edu!news.uh.edu!news.uth.tmc.edu!farmr37.med.uth.tmc.edu!user From: tkordas@gsbs3.gs.uth.tmc.edu (Timothy J. Kordas) Newsgroups: bionet.biophysics Subject: Re: How much is the useful work? (Pentcho Valev) Date: Mon, 22 Sep 1997 12:56:04 -0600 Organization: UT Houston Medical School Lines: 54 Distribution: bionet Message-ID: References: <605tr4$1lo@mserv1.dl.ac.uk> NNTP-Posting-Host: farmr37.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: MT-NewsWatcher 2.3.1 wrote: [given a system as illustrated here] > NaCl (high concentration) M NaCl (low concentration) < > > where M is a membrane permeable only to Na+ (not even to water). < [we get] > At equilibrium, a capacitor-like double layer will be formed at the < > membrane, positive on the right side and negative on the left one. < > Accordingly, there will be a transmembrane potential difference which will > be maximal at equilibrium. But this means that the process can be < > presented in the following way: < > > Na+(left) = Na+(right) + el. potential (work) /1/ < [and a situation is proposed:] > For instance: Some neutral molecule > approaches the membrane where an enzyme splits it into a positive and a > negative part: > > A = B+ + C- > > Obviously B+ will be pushed to the left and C- to the right, i.e. they can > be separated at the membrane and this is electrical work. Again, this is not > exactly perpetuum mobile, but the more important conclusion remains: the > system can do work at equilibrium. So let me present the problem in its most > general form. In your hypothetical situation you've used the membrane potential to split the species B and C into different compartments. However, by adding anions to the cation-compartment (the left-hand one in your illustration) while at the same time added cations to the anion-compartment (the right-hand compartment in your illustration). When calculating the membrane potential, you must account for all ions involved, regardless of their ability to permeate the membrane. Your membrane model does work just fine, but you had to put work into it! You only maintain the Na and Cl distributions across the membrane by putting work into the system: biological membranes, mostly, use the Na/K-ATPase powered by ATP generated from oxidation of fuel. You've just re-invented the battery. Your potential drops steadily (doing work) until equilibrium is reached. Congratulations. ** Does anyone else read these things, or am I just a sucker ? -Tim -- Timothy J. Kordas UT-Houston Medical School Dept. of Pharmacology From owner-biophysics@net.bio.net Sun Sep 21 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: How much is the useful work? (Pentcho Valev) Date: 22 Sep 1997 15:03:16 +0100 Lines: 66 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <605tr4$1lo@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk There is a mistake in my message of 20 September, in the interpretation of the following system: NaCl (high concentration) M NaCl (low concentration) < where M is a membrane permeable only to Na+ (not even to water). < At equilibrium, a capacitor-like double layer will be formed at the < membrane, positive on the right side and negative on the left one. < Accordingly, there will be a transmembrane potential difference which will be maximal at equilibrium. But this means that the process can be < presented in the following way: < Na+(left) = Na+(right) + el. potential (work) /1/ < < In fact, this is a reaction which produces work at equilibrium, in violation of the second law| We can easily imagine an isothermal cyclical process in < which work is gained: The electrical potential does some work (e.g. pushes < some different ions through the membrane or just shifts the electrometer) < and decreases. This shifts /1/ to the right. As the < work production stops, the initial equilibrium is restored. < First of all, perpetuum mobile is impossible if MACROwork is done, i.e. "shifting the electrometer" is a wrong example. Secondly, the reaction on which work is done must be IRREVERSIBLE. For instance: Some neutral molecule approaches the membrane where an enzyme splits it into a positive and a negative part: A = B+ + C- Obviously B+ will be pushed to the left and C- to the right, i.e. they can be separated at the membrane and this is electrical work. Again, this is not exactly perpetuum mobile, but the more important conclusion remains: the system can do work at equilibrium. So let me present the problem in its most general form. Let the reaction A = B drive the reaction C = D: A + C = B + D A = B itself is at equilibrium, but the concentration of D is zero so the coupled reaction still goes to the right. Also, A = B is exothermic and C = D is endothermic. What is this? A = B drives C = D by giving it some of its energy; is this work done by A = B on C = D or just heat exchange? The question is not only theoretical: if C = D is some biopolimer synthesis, the concentration of D is practically zero (there is no reverse reaction), so does ATP do work in this case or not? In fact, all problems arise when classical thermodynamics face irreversibility. My approach differs from irreversible thermodynamics and is based on the following obvious (in my opinion) definition: When a system transfers energy to another system and the process is ISOTHERMAL, the system DOES WORK on the other system. It follows that, when the system is a chemical reaction, the maximum work that can be produced in this way is equal to the enthalpy of reaction. I hope that this purely chemical aspect will attract more attention than the teasing examples demonstrating violation of the second law. It can also be shown that the delta G component of the maximal work is always macroscopic (as could be expected - it comes from classical thermodynamics), whereas the delta H component is in fact chemical work in the narrow sense - it is always microscopic. Pentcho From owner-biophysics@net.bio.net Sun Sep 21 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsxfer3.itd.umich.edu!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.biophysics Subject: US-CT-JOB OPPORTUNITY IN BONE RESEARCH Date: 22 Sep 1997 13:07:51 GMT Lines: 14 Message-ID: <19970922130701.JAA00957@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com SnewsLanguage: English I am looking for a Scientist to lead a lab unit in the Osteoporsis Research department to support the identification of therapeutic targets for osteoporosis. You will participate in the analysis of potential therapeutics through the use of biochemical and cellular biological assays. The candidate will develop new approaches to the determination of drug action on bone cells and tissues both in vitro and ex vivo. You should possess a PhD in Biology, Cell Biology, Biochemistry, or related field with 2 years postdoctoral experience. We are a leading pharmaceutical company with research facilities in Conneticut and can provide excellent benefits (health insurance, dental, and vision plan, bonus program, paid vactation and more). A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 Ext. 218, fax CV and cover letter to 609-584-9575 or E-Mail to sis@dmc10.com From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Yu Wai Chen Newsgroups: bionet.biophysics Subject: question about EPR Date: 23 Sep 1997 09:00:02 -0700 Organization: MRC Centre for Protein Engineering Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <3427B81E.452E1C7F@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net Dear all, I am interested in obtaining structural information about a protein which forms aggregates in physiological conditions. Do you think I can use site-directed spin labelling and then EPR to get side-chain mobility data? Can EPR be run on aggregated samples? What other techniques would you suggest? Thanks. Any advice would be appreciated. -- =================================================================== Yu Wai CHEN, Ph.D. .................. email: ywc@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel: 44-(1223) 402148 MRC Centre, Cambridge CB2 2QH, U.K. fax: 44-(1223) 402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/people/wai.html From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Work done by ATP (Pentcho Valev) Date: 23 Sep 1997 15:07:17 +0100 Lines: 68 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <608iel$gaf@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bill Tivol wrote: One of the questions you addressed at that time was about the mole- < cular dynamics of how to get more work out of ATP hydrolysis than delta H. < I read up on this, and here is what I found: < First, consider a simpler system--a solution of ADP and Pi. Since < the equilibrium constant for the reaction ATP + H2O -> ADP + Pi is not in- < finite, the second law predicts that in a solution of ADP and Pi there will< be condsensations which produce ATP. On the molecular level this can be < explained by considering collisions between ADP and Pi. The molecules in < this system have a distribution of kinetic energies, vibrational and rota- < tional states, etc., which I will assume are Maxwellian. Therefore, some < of the collisions will be between ADP and Pi molecules which have enough < total energy to produce ATP. Of these collisions, a fraction will occur < with the correct orientation, and ATP will, indeed, be produced. As this < process continues, there will come a time when there are just the right < concentrations of ADP, ATP, Pi and H2O so that for each collision which < produces ATP there will be a collision of ATP with H2O which produces ADP < and Pi. At this point, the system is in equilibrium. As for your example,< which concerned ATP hydrolysis and electrical potentials across a membrane,< similar considerations of the energy content in the individual molecules < undergoing the reaction can be sufficient to produce the reaction (and ra- < pidly, if the concentrations of reactants and products make delta G nega- < tive). As you pointed out, the total energy of the system is unchanged, < and, therefore, the energy which went into the chemical bonds must be sub- < tracted from the total kinetic (& vib + rot, etc.) energy of the system, < so the temperature will decrease. < Let me state again the concrete example. An ATPase transports H+ against an electrical but not pH gradient, and the process is close to equilibrium. The concentrations of ATP, ADP and P are such that delta G = delta Go + RTln((ADP)(P)/(ATP)) = -50 KJ/mole As delta H of ATP hydrolysis is -20 KJ/mole, the heat absorbed in the reaction is Qr = 30 KJ/mole, i.e. as one mole ATP does work, it uses not only its internal energy, delta H, but also absorbs 30 KJ heat from the environment and converts it into work too. If we refer these values to one molecule ATP, we will have to divide them by the Avogadro number. What is bothering is that, as we examine the elementary chemical act, we can easily imagine how the internal energy, delta H, is converted into work (e.g. something like discharge of a spring) but can by no means imagine a mechanism allowing absorbtion of heat from the environment. The only possible assumption is that only molecules ATP which have enough kinetic energy can react, but in this case there would be a piston-like mechanism somewhere in the ATPase allowing convertion of this kinetic energy into work. Moreover, the ADP and P molecules must strike the piston from the other side so that, as their concentrations decrease, the work produced in this way get more. Quite an unrealistic picture - the only way to accept it is to refrain from thinking in physical terms and adopt thermodynamic formalism only. In fact, the delta G work can only be macroscopic - e.g. in galvanic reactions. It can even be PV work - in fact, this is implicit in all textbook derivations, but authors do not state it explicitly as they remember the dogma that delta G is useful and not PV work. However V, by definition, is the volume of the system = as long as it does not change, we can take portions of the system, expand them etc.-the work done belongs to delta G. However no one wants to consider this physical picture (some time ago I made an unsuccesful attempt to discuss it in the btk-group). In conclusion: delta G is statistical work, a result of the simultaneous action of many particles. Applied to a limited number of particles (the participants in the elementary molecular act) it gets wrong. However thermodynamics has left to the opponents to find a way to verify the concept, and this is extremely difficult. I believe the example above offers the only possible verification - one should determine, calorimetrically, the heat of reaction as an ATPase transports, almost reversibly, H+ against an electrical gradient. Pentcho From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: How much is the useful work? (Pentcho Valev) Date: 23 Sep 1997 09:53:28 +0100 Lines: 46 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <608028$o1p@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bill Tivol wrote: : NaCl (high concentration) M NaCl (low concentration) < < : where M is a membrane permeable only to Na+ (not even to water). < < If you look at the electrical potential far from the membrane, it < goes to zero on each side. There are enough excess Cl- on the left and Na+< on the right to balance everything. The excess Cl- will be distributed on < the left such that [Cl-] = const*exp(-eV/kT), where one still has to cal- < culate V, and the same applies to the Na+ on the right. Since there are < just as many + charges as -, virtually all the electric field lines will < be confined to a finite distance from the membrane (yes, some of the lines < will loop around through a plane at any finite distance from the membrane, < but they will assymtotically approach zero at large distances). If you < put electrodes near the membrane in an attempt to extract work from the < system, you will move it off equilibrium, and some work can be extracted < as equilibrium is re-established, but you will not get perpetual motion. < Bill, your first sentence is quite correct, but unfortunately it contradicts thermodynamics. If, far from the membrane, the electrical potential goes to zero on each side, the Na+ electrochemical potential is not uniform throughout the system. This can also solve the problem with my unfortunate perpetuum mobile. I would like to ask electrochemists: As we measure the transmembrane potential difference, the membrane is made impermeable (e.g. another impermeable one is placed beside it). What will happen to the value shown by the electrometer? If it decreases, perpetuum mobile is possible. The decrease can only be due to diffusion of ions from the membrane to the depth of the compartments, so the electrical potential there will slightly increase in magnitude. Restoring the permeability of the membrane will restore the value of the electrometer, since new Na+ will cross from left to right. This process can continue until, theoretically, the potentials in the two phases get uniform, different and corresponding to the concentration difference. All shiftings of the electrometer constitute the work gained. Then the membrane remains permeable and the initial equilibrium (in which the electrical potential far from the membrane is zero) is restored. There are two independent and easy ways to verify all this experimentally. The first one is to measure the electrical potential far from the membrane (I suspect your first statement is based on such a measurement). The second one (maybe not so easy) is to "open" and "close" the membrane consecutively and register the value shown by the electrometer. If I had the slightest opportunity, I would do both experiments. Pentcho From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!spool.mu.edu!uwm.edu!gsl-penn-ns.gsl.net!news-peer.gsl.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!169.226.1.109!rebecca!euclid.wadsworth.org!tivol From: tivol@news.wadsworth.org (William Tivol) Newsgroups: bionet.biophysics Subject: Re: How much is the useful work? (Pentcho Valev) Date: 23 Sep 1997 21:38:11 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 56 Distribution: bionet Message-ID: <609cs3$pbt@euclid.wadsworth.org> References: <608028$o1p@mserv1.dl.ac.uk> NNTP-Posting-Host: alcor.wadsworth.org X-Newsreader: TIN [version 1.2 PL2] RUMYM@BGEARN.ACAD.BG wrote: : Bill Tivol wrote: : : NaCl (high concentration) M NaCl (low concentration) < : < : : where M is a membrane permeable only to Na+ (not even to water). < : < : If you look at the electrical potential far from the membrane, it < : goes to zero on each side. : Bill, your first sentence is quite correct, but unfortunately it contradicts : thermodynamics. If, far from the membrane, the electrical potential goes : to zero on each side, the Na+ electrochemical potential is not uniform : throughout the system. I think not. The concentration differences should balance the electrical potential differences to produce the same electrochemical potential throughout each compartment. I haven't calculated either the electrical potential or the Na & Cl distributions, so I can't prove this. : This can also solve the problem with my unfortunate perpetuum mobile. : I would like to ask electrochemists: As we measure the transmembrane : potential difference, the membrane is made impermeable (e.g. another : impermeable one is placed beside it). What will happen to the value shown : by the electrometer? Since the electric field will penetrate a membrane unless it's a conductor, placing an impermeable membrane beside the first one should not change things--if the system is at equilibrium. Placing an infinite metal foil next to the membrane will cause the electric field between the membrane and the foil to change to that which would be produced by a com- bination of the membrane and another located behind the foil and of oppo- site charge, and the field on the other side of the foil will be that due to the excess Na+ or Cl- plus the appropriate mirror charges. Once the appropriate charge distribution is known, the potential can be calculated. : There are two independent and easy ways to verify all this experimentally. : The first one is to measure the electrical potential far from the membrane : (I suspect your first statement is based on such a measurement). Actually, it's based on my recent reading. : The second : one (maybe not so easy) is to "open" and "close" the membrane consecutively : and register the value shown by the electrometer. If I had the slightest : opportunity, I would do both experiments. There are many biomembranes whose permeabilities can be altered by changing experimental parameters, so this experiment is certainly possible. The electronics necessary to make the measurements and the skill to produce the appropriate membrane across a small hole dividing two compartments can be obtained for a reasonable commitment of time (I'd guess ~ 1 year) and $$$ (I'd guess ~$10k). A lab where I worked ~20 years ago did these kinds of things routinely. Yours, Bill Tivol From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ix.netcom.com!news From: Universal Light Tones Newsgroups: bionet.biophysics Subject: FASCINATING BOOKS, VIDEOS, MUSIC Date: Tue, 23 Sep 1997 10:55:09 -0700 Organization: Universal Light Tones Lines: 13 Message-ID: <3428027C.D2E@ix.netcom.com> Reply-To: zybernet@ix.netcom.com NNTP-Posting-Host: lap-ca2-09.ix.netcom.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NETCOM-Date: Tue Sep 23 10:49:00 AM PDT 1997 X-Mailer: Mozilla 3.0C-NC320 (Win95; U) FASCINATING & POWERFUL VIDEOS, BOOKS, MUSIC AND VIBRATIONAL HEALING FEATURING WORLD-CLASS ARTIST & PERFORMERS WITH BEST SELLING AUTHORS IN MIND & BODY MEDICINES AND THE SCIENCE. Sound Healing, Contemporary Jazz/ New Age Music, Guided Relaxation, Super Health, Documentation-Fire Walk, The Healing Sounds of Nature-Cymatics, Mechanics of Consciousness & Creation and more. For more info. Visit Universal light Tones Web Page. http://www2.netcom.com/~zybernet/links.html or http://www.igdesign.com/ult From owner-biophysics@net.bio.net Mon Sep 22 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!169.226.1.109!rebecca!euclid.wadsworth.org!tivol From: tivol@news.wadsworth.org (William Tivol) Newsgroups: bionet.biophysics Subject: Re: Work done by ATP (Pentcho Valev) Date: 23 Sep 1997 22:01:46 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 70 Distribution: bionet Message-ID: <609e8a$ppb@euclid.wadsworth.org> References: <608iel$gaf@mserv1.dl.ac.uk> NNTP-Posting-Host: alcor.wadsworth.org X-Newsreader: TIN [version 1.2 PL2] RUMYM@BGEARN.ACAD.BG wrote: : Bill Tivol wrote: : One of the questions you addressed at that time was about the mole- < : cular dynamics of how to get more work out of ATP hydrolysis than delta H. < : I read up on this, and here is what I found: < : First, consider a simpler system--a solution of ADP and Pi. Since < : the equilibrium constant for the reaction ATP + H2O -> ADP + Pi is not in- < : finite, the second law predicts that in a solution of ADP and Pi there will< : be condsensations which produce ATP. On the molecular level this can be < : explained by considering collisions between ADP and Pi. The molecules in < : this system have a distribution of kinetic energies, vibrational and rota- < : tional states, etc., which I will assume are Maxwellian. [skip] : Let me state again the concrete example. An ATPase transports H+ against an : electrical but not pH gradient, and the process is close to equilibrium. : The concentrations of ATP, ADP and P are such that : delta G = delta Go + RTln((ADP)(P)/(ATP)) = -50 KJ/mole : As delta H of ATP hydrolysis is -20 KJ/mole, the heat absorbed in the reaction : is Qr = 30 KJ/mole, i.e. as one mole ATP does work, it uses not only its : internal energy, delta H, but also absorbs 30 KJ heat from the environment : and converts it into work too. If we refer these values to one molecule ATP, : we will have to divide them by the Avogadro number. : What is bothering is that, as we examine the elementary chemical act, we : can easily imagine how the internal energy, delta H, is converted into work : (e.g. something like discharge of a spring) but can by no means imagine : a mechanism allowing absorbtion of heat from the environment. The only : possible assumption is that only molecules ATP which have enough kinetic : energy can react, but in this case there would be a piston-like mechanism : somewhere in the ATPase allowing convertion of this kinetic energy : into work. Moreover, the ADP and P molecules must strike the piston from : the other side so that, as their concentrations decrease, the work produced : in this way get more. Quite an unrealistic picture - the only way to accept : it is to refrain from thinking in physical terms and adopt thermodynamic : formalism only. Consider that the H+ is initially occupying a particular location in a channel of the protein on the more negative side of the membrane, and the H+ has no access to the far side: | __|__ H+_ / \ | | Suppose that ATP hydrolysis alters the channel so that the H+ no longer has access to the original side of the membrane, but its spatial location (and perhaps the electrical potential there) is unchanged: | __|__ |H+_ ~~ \ | | The ADP and Pi readily leave the ATPase, since their concentrations are low (necessary for the concentration term in your eqn to be large & negative). At this point, it is easy to see how energy transfer to the H+ could leave it with enough energy to travel to other parts of the far side compartment, whereupon the ATPase can revert to its original conformation. No special mechanism is required to transfer energy from the environment. Your pro- posal to measure the heat change of the environment may be difficult, but I think it can be done with modern calorimeters. Yours, Bill Tivol From owner-biophysics@net.bio.net Tue Sep 23 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.erols.com!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!alan From: alan@ebi.ac.uk (Alan Robinson) Newsgroups: bionet.biophysics Subject: ANNOUNCE: Conference on Visualisation for the Life Sciences Date: 24 Sep 1997 08:45:25 GMT Organization: EBI - European Bioinformatics Institute Lines: 146 Message-ID: <60ajv5$4q$3@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: uranus.ebi.ac.uk X-Newsreader: TIN [version 1.2 PL2] =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Frontiers in Visualisation and Human-Computer Interaction '97 "Visualising the Future of the Life Sciences" The Wellcome Trust Genome Campus, Cambridge, UK. 10th and 11th December, 1997 http://www.ebi.ac.uk/fiv97/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Conference Theme This two day conference will provide an outstanding opportunity to hear some of the world's leading speakers in the related areas of human- computer interaction and visualisation. Review talks on the current uses of visualisation in the biosciences. An arena for professionals in the biosciences and pharmacology to meet with the leading graphics and interaction experts and to develop new ideas and synergies. Hence a major Conference Theme could be expressed as "How can Visualisation be used to extract Information and Knowledge from the Data of these Sciences?" Keynote Speakers on Visualisation The two keynote speakers are: Professor Andries van Dam, Thomas J. Watson, Jr., University Professor of Technology and Education and Professor of Computer Science, Brown University, Providence, RI and Prof. Dr. Josi Luis Encarnagco, Professor Technical University of Darmstadt and Director of the Fraunhofer Institute for Computer Graphics in Darmstadt. Both speakers have been visionary pioneers in establishing the discipline of computer graphics, Van Dam being a founder of SIGGRAPH and Encarnagco being the driving force behind the founding of EUROGRAPHICS. Invited Speakers Professor Paolo Zanella, Head of the European Bioinformatics Institute and Chair in the Faculty of Sciences, Department of Informatics of the University of Geneva. Dr. Jonathan K.C. Knowles, formerly Director of Glaxo Wellcome Research Europe and now Director of Global Research of Hoffmann-La Roche. Dr. Detlev Kroemker, Head of the Animation and HD-Image Communication Department of the Fraunhofer Institute for Computer Graphics. Dr. Jean-Francis Balaguer, Technology Manager for 3D Graphics, artemedia online, Lausanne, Switzerland. Professor Philip E. Bourne, Senior Staff Scientist at the San Diego Supercomputer Center , an Associate Adjunct Professor in the Department of Pharmacology at the University of California San Diego, and an Adjunct Senior Scientist at the Burnham Institute. Dr. Michael Berman, General Manager of Silicon Graphics Biomedical Ltd., a subsidiary of SGI based in Jerusalem, Israel. Dr. Alan Robinson, Visualisation Support for the BioStandards Initiative at the European Bioinforatics Institute. John Wise, currently Head of IT at the Imperial Cancer Research Fund, soon to be Head of Non-Clinical Development Information Management at Roche. Dr. Chris Jones is currently on sabbatical leave at the European Bioinformatics Institute from CERN where he has been responsible for most IT services including a virtual reality project prototyping the next major accelarator and experiments for the year 2005. Conference Programme The Conference Agenda will cover: Frontiers in 3D Human Interactions Applications of Virtual Reality Distributed Computer-Supported Collaborative Working, CSCW-VR Visualisation in the Biosciences Panel discussion on the Conference Theme of how visualisation could be used to extract knowledge from the data Live Demonstrations of the state of the art of Visualisation, including 3D stereo projection in the auditorium and high speed link to Darmstadt There will also be an opportunity for poster submissions and a trade show. Conference Location The Conference will take place in the newly completed conference facilities at the Wellcome Trust Genome Campus in the grounds of Hinxton Hall, Cambridge, UK. The campus is the site of The European Bioinformatics Institute, The Sanger Centre and the UK MRC Human Genome Mapping Project Resource Centre. The Conference Banquet will take place in the Dining Hall of King's College, Cambridge. Conference Registration The Closing Date for early registration and submission of abstracts is 10th November, 1997. Late registration will be possible from the 11th November, however the registration fee will increase by 50 GBP. Registration forms are available at the conference web site: http://www.ebi.ac.uk/fiv97/ Frontiers in Visualisation '97 is supported by the Astra Bioinformatics Centre. Requests for further information and questions should be addressed to Chris Jones (Chris.Jones@cern.ch) or Alan J. Robinson (alan@ebi.ac.uk). -- ============================================================ Alan J. Robinson Tel:+44-(0)1223 494625 EMBL Outstation Fax:+44-(0)1223 494468 European Bioinformatics Institute Email: alan@ebi.ac.uk Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1RQ, UK