From chemistry-request@ccl.net Wed Mar 11 13:27:25 1992 Date: Wed, 11 Mar 92 11:31:41 EST From: "Michael A. Lee" Subject: Cutt offs To: chemistry@ccl.net Status: R I am afraid I must disagree with the mail about the need for cutoffs even in the case when dealing with real coulomb interactions. Previous mail states: Even if you use "infinite" range potentials, you must remember that force interacts at the speed of light (3 x 10^18 angstroms/sec) and given a timestep of 10^-16 seconds would mean that you should still limit "infinite" potentials to a cutoff of a few hundred angstroms. I say: Does that mean that if I make my timestep 10^-20 that the cutoff becomes a few angstroms? SO, my conclusion is that 1) if you want to worry about the finite speed of light, it is a much more complex question and the subject of interactions between bodies in that case reqires an analysis involving special relativity. and 2) It is irrelevant and the correct thing to do when dealing with coulomb forces is to use coulomb forces and not cutoffs. If you use a cutoff that does not arise for some physical reason (screening for instance), then you are making an approximation. That is OK sometimes, but you still have to worry about the impact of the approximation on the calculation. From chemistry-request@ccl.net Wed Mar 11 14:18:26 1992 Date: Wed, 11 Mar 1992 11:24:32 EST From: carmen@tethys.ph.albany.EDU Subject: Albany Conference Announcement To: chemistry@ccl.net Status: R * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * UPDATE: SECOND ALBANY CONFERENCE ON COMPUTATIONAL BIOLOGY "PATTERNS OF BIOLOGICAL ORGANIZATION" * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * GENERAL DESCRIPTION The Second Albany Conference on Computational Biology will be held October 8-11, 1992 in Rensselaerville near Albany, New York. The aim of this conference (like that of the 1990 Albany Conference) is to explore the computational tools and approaches being developed in diverse fields within biology, with emphasis this year on topics related to organization and self-assembly. The conference will be designed to provide an environment for a frank and informal exchange among scientists and mathematicians that is not normally possible within the constraints of topical, single-discipline meetings. The theme of the Conference, "Patterns of Biological Organization", will be developed in five sessions on topics ranging from the level of sequence to the level of embryo development. Leading specialists in the various disciplines are being invited, with the degree of involvement in novel computational approaches as one of the most important criteria for selection. We are seeking an interdisciplinary audience, mathematicians, and computer scientists as well as biologists. All participants will be invited to submit abstracts for posters, although submission is not mandatory. Also, if funding permits, we will sponsor "young investigator" travel awards as we did in 1990 for the first Albany Conference on Computational Biology. CONFERENCE FORMAT The conference will consist of three morning and two evening sessions over a period of three nights and days (Thursday afternoon through Sunday morning). Each session will be comprised of four 30-minute talks interspersed by question-and-answer periods of 15-20 minutes. Afternoons are free for discussion and workshops (some planned, others impromptu). Tentative workshop topics include visualization tools and structure data bases. In addition, a workshop is planned for Thursday afternoon that will introduce non-biologists to the main issues of macromolecular and cellular structure to be addressed at the meeting. The following is an outline of the conference sessions, including a partial listing of confirmed speakers: Session 1 Sequence analysis and secondary structure ---------------------------------------------------- Discussion leader: Charles Lawrence Wadsworth Center, and State Univ. of New York, Albany 518-473-3382 CEL@BIOMETRICS.PH.ALBANY.EDU Speakers: David L. Waltz Thinking Machines, Inc., and Brandeis University Waltham, MA Jean Michel Claverie National Center for Biotechnology Information, NIH, Bethesda, MD Michael Zucker Stanford University Stanford, CA Session 2 Tertiary structure prediction ---------------------------------------- Discussion leader: George Berg State Univ. of New York, Albany 518-442-4267 BERG@CS.ALBANY.EDU Speakers: Rick Fine Biosym Technologies, Inc. San Diego, CA Stephen Bryant National Center for Biotechnology Information, NIH Bethesda, MD James Bowie University of California Los Angeles, CA Francois Michel Centre de Genetique Moleculaire, CNRS Gif-sur-Yvette, France Session 3 Macromolecular function ---------------------------------- Discussion leader: Jacquelyn Fetrow State Univ. of New York, Albany 518-442-4389 JACQUE@ISADORA.ALBANY.EDU Speakers: Judith Hempel Biosym Technologies, Inc. San Diego, CA Fred Cohen University of California San Francisco, CA Chris Lee Stanford University Stanford, CA Session 4 Recognition and assembly ----------------------------------- Discussion leader: Joachim Frank Wadsworth Center and State Univ. of New York, Albany 518-474-7002 JOACHIM@TETHYS.PH.ALBANY.EDU Speakers: David DeRosier Brandeis University Waltham, MA Phoebe Stewart University of Pennsylvania Philadelphia, PA John Sedat University of California San Francisco, CA Session 5 Development ---------------------- Discussion leader: John Reinitz Yale Univ., New Haven, CT 203-785-7049 REINITZ-JOHN@CS.YALE.EDU Speakers: Michael Levine University of California San Diego, CA John Reinitz Yale University New Haven, CT George Oster University of California Berkeley, CA Brian Goodwin Open University Milton Keynes, UK Questions about individual sessions may be sent to the respective Discussion Leaders (phone numbers and email addresses provided above). For general conference information, you may contact any of the discussion leaders or any other member of the Organizing Committee (chair: Carmen Mannella) or Program Committee (chair: Joachim Frank). Phone numbers and email addresses of the other members of these committees are listed below: Jeff Bell, Rennselaer Polytechnic Institute, Troy, NY 518-276-4075 BELL@VAX1.CHEM.RPI.EDU Stephen Bryant, National Center for Biotechnology Information, NIH, Bethesda, MD 301-496-2475 (ext. 65) BRYANT@NCBI.NLM.NIH.GOV Carmen Mannella, Wadsworth Center and State Univ. of New York, Albany 518-474-2462 CARMEN@TETHYS.PH.ALBANY.EDU Patrick Van Roey, Wadsworth Center, Albany, NY 518-473-1336 VANROEY@TETHYS.PH.ALBANY.EDU CONFERENCE SITE The conference, one of the Albany Conference series held annually since 1984, will take place at the Rensselaerville Conference Center, located 30 miles southwest of Albany, NY in the Helderberg Mountains. The Institute offers on-campus facilities including a large auditorium with all necessary audio-visual equipment, and smaller conference halls for informal workshops and poster sessions. The Weathervane Restaurant, located on-campus and formerly the carriage house of the Huyck estate, provides meals and refreshments, while overnight lodging is available in the modern and classic estate houses. Rooms are assigned in advance to registrants, and transportation to and from Rensselaerville is provided from the airport, as well as train and bus stations. The rural, secluded setting of the conference, the limited number of participants and the scheduling of sessions in the morning and the evening -- leaving the afternoons free -- are intended to facilitate informal discussions among conference participants. REGISTRATION INFORMATION CONFERENCE FEE: $475 includes registration, accomodations (double occupancy), meals and transportation between the conference center and Albany airport. A limited number of single occupancy accomodations are available for an extra $100. Payment of the full fee will be required by AUGUST 31, 1992. Please note that neither the Albany Conferences nor the Rensselaerville Conference Center accepts credit cards. APPLICATION DEADLINE: July 31, 1992. For further registration information and a copy of the application form for the 1992 Albany Conference on Computational Biology, please call the conference coordinator, Carole Keith, 518-442-4327, FAX 518-442-4767, Bitnet: CAROLE@ALBNYVM1, or write to The 1992 Albany Conference, P.O. Box 8836, Albany, NY 12208-0836. - - - - - - - - - - - - - - - - - - - - - - - - Individuals may also use the following "E-Mail application form" to register for this meeting: Name: Organization: Business Address: City: State: Zip: Business Phone: Fax: Because attendance is limited, please describe briefly your research interests or activities which explain your interest in participating in this conference. If you plan to submit a poster, please include its title and (if ready) a short abstract. (You will be asked to provide a one-page, camera-ready version of the poster abstract, using 1.5 inch borders, for the meeting workbook.) Send this E-mail application to CAROLE@ALBNYVM1 before the registration deadline (July 31). TRAVEL AWARDS Graduate students and postdocs who would like to be considered for a Young Investigators travel award should submit with their registration form a brief letter explaining his/her research interests. Graduate students should also include a letter of recommendation from a faculty advisor. Applications from members of groups that are underrepresented in this field (women and racial minorities) are encouraged. From jkl@ccl.net Wed Mar 11 16:45:30 1992 To: chemistry@ccl.net Subject: QTP Course on Applied MO Theory Date: Wed, 11 Mar 92 16:45:21 EST From: jkl@ccl.net Status: R QTP COURSE ON APPLIED MOLECULAR ORBITAL THEORY Dear Colleague: In your research, do many questions about molecular structure, spectra and reactivity arise? The Florida Quantum Theory Project offers the seventh edition of their popular one-week short course which will help you to answer the following questions: What is the structure of a proposed novel compound? What is the activation barrier for a potential reaction mechanism? How can I predict where to look for the vibrational or electronic spectra of a molecule to identify it? What are the structures, spectra and energetics of transient reaction intermediates? How can I assess the effect of adding a substituent on the color of a dye molecule without synthesis? Can I inexpensively screen functional molecules like drug derivatives to identify the best prospects for success? How can computer graphics provide a new perspective on chemistry? How can I better understand and evaluate the quantum chemical analysis which accompanies more and more articles in the best chemical journals? If such questions are important to you, we invite you to attend our course on molecular orbital theory. The course is designed for scientists who are active researchers and recognize the potential for applying molecular orbital theory to molecules in order to provide information that is otherwise unavailable; and for managers, supervisors and research directors who may be interested in an overview of recent advances in computational quantum chemistry and how they may be employed to enhance the productivity of their research unit. We invite you to learn the current developments in empirical potentials from Nigel Richards; semiempirical molecular orbital methods MINDO and AM1 and their organic chemistry applications from M.J.S. Dewar; spectroscopic CNDO and INDO from Michael Zerner; basis sets and ab initio SCF theory from Yngve Ohrn; and correlated methods, many-body perturbation theory (MBPT; also known as MP) and coupled-cluster (CC) theory from Rod Bartlett; augmented with computer graphics by George Purvis of the Tektronix CAChe group. John Stanton coordinates the laboratory exercises. The staff's expertise spans the range from biomolecular applications, through organic chemistry, to the highest levels of ab initio methods. The course includes discussion of methods for the determination of energy "derivatives" and their application to locating minima and transition states on potential energy surfaces and to predictions of vibrational spectra. Applications are brought to life by employing a wide variety of graphics techniques to visualize the formation of chemical bonds, or the potentials that molecules exert upon each other. Computer applications in chemistry are becoming essential. This is an opportunity for your research group to add a computational capability that can provide results to complement the other instrumental techniques at your disposal. Besides providing lecture material to assist you to select the right methods and to appreciate their limitations, the intent of this course is to provide "hands-on" experience with state-of-the-art computer programs executing on the project's computers through a special arrangement with Tektronix, Inc., CAChe workstations. Versions of most of the Florida computer program system used in this course are provided to each participant in order to apply these electronic structure methods on computers at their home institutions. To take advantage of inexpensive plane fares that include a Saturday night stay, the course is scheduled for semester break on the campus of the University of Florida, with arrival on Sunday, May 3, and recommended departure on Sunday, May 10, 1992. Lectures are presented in the morning and early afternoon, with computer lab sesafternoon. Optionally, the computers are also available to participants in the evenings and all day Saturday, May 9, for additional work on applications. We also devote time to hear about your research problems, and try to assist you in using theoretical methods to help solve them. Social events include a welcoming reception Sunday evening, and dinners Monday, Wednesday, and Friday, held at the best restaurants in the area. Tuition, including room, dinners, coffee, a computer tape of the programs used in the course, and detailed lecture notes are at an inclusive $1250 per person. Enrollment will be limited to 25 participants, housed in single rooms at the Reitz Union on campus. Spouses are invited to accompany a participant by payment of an additional $100 to cover the social affairs and room increment. Registration plus a check or purchase order payable to the University of Florida -- Research Foundation will be required before April 15, 1992, and should be sent directly to me at the Quantum Theory Project, University of Florida, Gainesville, FL 32611--2085. We hope that you or some of your colleagues will find our course to be of interest. If we can provide any further information, please call us. Sincerely, Rodney J. Bartlett Graduate Research Professor of Chemistry and Physics Phone: 904-392-1597 FAX: 904-392-8722 email: bartlett@qtp.ufl.edu From chemistry-request@ccl.net Wed Mar 11 19:14:17 1992 Date: Wed, 11 Mar 92 18:11:10 -0500 From: jle@world.std.COM (Joe M Leonard) Subject: Re: comments regarding speed of light To: chemistry@ccl.net Status: R I'm not sure the math is correct, but if the speed of light's a problem vis-a-vis event horizons, what about the uncertainty principle? If the MD simulation's done on a femtosecond time-scale, what is the minimum uncertainty in the energies and/or momenta? Anybody in or teaching or TA'ing a P-chem course should be able to check this one :-)... Joe Leonard jle@world.std.com