From chemistry-request@ccl.net Thu Jan 27 21:02:34 2005 Received: from out.esrf.fr (firewall.esrf.fr [193.49.43.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0S22UUI025571 for ; Thu, 27 Jan 2005 21:02:30 -0500 Received: (from uucp@localhost) by out.esrf.fr (1.0.0) id j0PAO1U27640; Tue, 25 Jan 2005 11:24:01 +0100 (MET) Received: from esrf.esrf.fr(160.103.2.9) by firewall via smap (V1.3) id tmp027614; Tue Jan 25 11:23:59 2005 Subject: Re: CCL:[Re]: orbitals and reality Received: from leeloo.esrf.fr (scanscan.esrf.fr [160.103.2.45]) by esrf.esrf.fr (8.9.0/8.9.0) with ESMTP id LAA13295; Tue, 25 Jan 2005 11:23:58 +0100 (MET) Message-Id: <5.1.0.14.0.20050125110312.01ebb080 [a] imap.esrf.fr> X-Sender: vetere [a] imap.esrf.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 25 Jan 2005 11:24:07 +0100 To: Lou Noodleman From: Valentina VETERE Cc: chemistry [a] ccl.net In-Reply-To: <200501242233.j0OMXHR21312 [a] degas.scripps.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL list, since several days I'm reading with interest the e-mail about orbitals and reality. Nevertheless, there is still something not clear in my mind. My point is that since my first lessons on quantum mechanics I belief that all the equations (not excluding Schrodinger or Dirac) were models of a more complex reality that none can describe for instance with numbers. Is this true? If yes, I would like to understand why orbitals give rice to all this discussion. Probably you can say that the orbitals are a rude model with bigger assumptions respect to the all electron wavefunction solution of a Schr. equation. Nevrtheless, also this solution is a model for me...a higher level model? But, my reaction when I first saw the Nature picture was "not too bad the model is not so far from reality.." I thought we were lucky! Can you help me in understanding why I'm wrong? Dr. Valentina Vetere Scientist Theory Group European Syncrothon Radiation Facility (ESRF) Grenoble France From chemistry-request@ccl.net Fri Jan 28 07:37:05 2005 Message-Id: <200412100917.iBA9H0w8022295|at|apex.ibpc.fr> To: CHEMISTRY|at|ccl.net Subject: Data and Knowledge Management Tools for Compuational Chemists Date: Fri, 28 Jan 2005 11:37:24 +0100 From: Marc Baaden Dear All, I am looking for software, tools or general approaches to get hold of the wealth of information that accumulates (mostly) electronically. In particular emails, text/PDF/XML or similar documents, bookmarks to websites and bibliographic references. The main request would be to be able to "store" information as is without having to enter it individually into a curated database. Filtering, indexing or cataloging through a script would be ok, though. A powerful search should be possible. Some specific points: - concerning bibliographic references, there is a wide variety of formats like Pubmed, email-alerts, quotes on websites, ... sometimes with a comment by the person who sent the reference, sometimes with an URL link, ... I would like to be able to gather all information in a first pass without having to parse the format by hand (eg where are authors, title, etc). - concerning bookmarks, it would be nice to also have elimination of duplicates and of dead links - taking it one step further, indexing the sites listed in the bookmarks might also be an additional useful step After some extensive search of the web, I could not come up with a fully satisfactory solution. My current best bet would be to index text and other files and email with a search engine like eg namazu. For bookmarks I'd ideally like to store them in XBEL format, but there seem to be only a limited number of tools, and none or very few that eliminate duplicates and dead links. A useful bookmark tool might be bookmarker. FramerD (a database) seems also an interesting possibility, but probably requires quite some substantial coding. In an ideal world, I'd also love to make use of some artificial intelligence code (eg Self-organizing maps, textual data mining,..) or some machine-learning tools, but my feeling is that those are not (yet) usable by non-experts. My question is what do other people in the field use ? Are there any miracular packages that would do all that I want ? Are there other/better approaches ? Thanks very much in advance. Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden|at|smplinux.de - http://www.marc-baaden.de FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From chemistry-request@ccl.net Fri Jan 28 11:18:44 2005 Received: from mailhub128.itcs.purdue.edu (mailhub128.itcs.purdue.edu [128.210.5.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0SGIhRT023723 for ; Fri, 28 Jan 2005 11:18:43 -0500 Received: from [128.46.108.125] (frny117bpc05.ecn.purdue.edu [128.46.108.125]) by mailhub128.itcs.purdue.edu (8.13.1/8.13.1/scan-smtp) with ESMTP id j0SEmcSX009993 for ; Fri, 28 Jan 2005 09:48:38 -0500 Message-ID: <41FA50C6.8090907)at(purdue.edu> Date: Fri, 28 Jan 2005 09:48:38 -0500 From: Aaron Deskins User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: GULP Questions Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everyone, I'm hoping that there's a GULP expert here on the list. I'm trying to run a simulated annealling run using the shell model, but I'm running into problems. If anyone thinks they can help, please let me know. Thank you, Aaron Deskins Chemical Engineering Purdue University From chemistry-request@ccl.net Fri Jan 28 07:37:05 2005 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0SCb2RT014548 for >ccl.net>; Fri, 28 Jan 2005 07:37:02 -0500 Received: by leitl.org (Postfix, from userid 500) id 283613A84DC; Fri, 28 Jan 2005 11:37:25 +0100 (CET) Date: Fri, 28 Jan 2005 11:37:24 +0100 From: Eugen Leitl >leitl.org> To: chemistry<>ccl.net Subject: [alife] CFP - ECAL WORKSHOP - Artificial Chemistry and Its Applications (fwd from hsuzuki<>atr.jp) Message-ID: <20050128103724.GU1404<>leitl.org> Content-Disposition: inline ----- Forwarded message from Hideaki Suzuki >atr.jp> ----- From: Hideaki Suzuki >atr.jp> Date: Fri, 28 Jan 2005 16:04:10 +0900 To: alife-announce<>lists.idyll.org, genetic_programming<>yahoogroups.com Subject: [alife] CFP - ECAL WORKSHOP - Artificial Chemistry and Its Applications Organization: ATR X-Mailer: Sylpheed version 0.8.5 (GTK+ 1.2.10; i386-vine-linux) -------------------------------------------------------------- *** Apologies for cross-postings. Please circulate. *** -------------------------------------------------------------- Call for Papers: WORKSHOP on Artificial Chemistry and Its Applications (ACA) Submission deadline: May 27th 2005 Organized by Hideaki SUZUKI (ATR Network Informatics Laboratories, JAPAN) Tim HUTTON (University College London, UK) Jian-Qin LIU (ATR Network Informatics Laboratories, JAPAN) Part of ECAL 2005 - 8th European Conference on Artificial Life Monday 5th to Friday 9th September 2005 University of Kent, Canterbury, Kent (UK) * AIMS AND SCOPE As a promising branch of artificial life, artificial chemistry has been extended into a broad domain that includes the studies on theories, models, algorithms and applications. Using a strong comparison to biochemical reactions in living cells, artificial chemistry provides a powerful method to study why and how complex living creatures have evolved on the earth, and at the same time provides a nice workbench on which we can deepen an understanding of: (a) emergence -- in the sense of artificial life, (b) complexity -- in the sense of non-linear complex systems, (c) evolvability -- in the sense of generalized evolution for biologically inspired information processing systems, and (d) network -- in the sense of complex systems for artificial life. Following the success of the previous workshops held in conjunction with ECAL2003 at Dortmund and with ALIFE9 at Boston, this workshop will be arranged as a place for concise tutorials of established works that present particular uses of artificial chemistry, and for active discussion on new progress in the field of artificial chemistry. This workshop is seeking the submission on the following aspects but not limited to: - Modeling molecular interactions and chemical processes - Simulating the chemical evolution of life - Catalysis and auto-catalysis - Self-replication and von Neumann machines - Origin of information and translation - Requirements for the evolutionary growth of complexity - Self-organization - Self-assembly in nanotechnology and abstract systems - Membranes and cellular structure - Membrane computing (P-systems) - Co-evolution and evolvability - Enzymes and chemical engineering - Experimental technology for artificial life - Biophysics and simulation - Networks - Hybrid systems - Applications of AC approaches to parallel computation, etc. * IMPORTANT DATES Paper submission in PDF : May 27th 2005 Acceptance notices : June 10th 2005 Camera-ready submission in PDF : June 24nd 2005 * SUBMISSION Original papers in English are welcome for submission. Papers should follow the ECAL style, be formatted in PDF, and be directly emailed to >atr.jp> no later than the deadline shown above. Papers should be limited to twelve pages, but ten pages are preferable. * REVIEW AND PUBLICATION All submitted papers are reviewed by at least 2 independent reviewers using the ECAL review form, and accepted papers will be included in the workshop proceedings that will be published in the form of a CD-ROM. Also, all accepted papers are encouraged to be extended, revised, and submitted to a special issue on artificial chemistry, which is scheduled to be published in Artificial Life Journal, MIT Press. More detailed announcement will be made after the workshop. * PROGRAM COMMITTEE (Tentative; in alphabetical order) Dominique Chu (University of Birmingham, UK) Peter Dittrich (University of Jena, Germany) Rudolf Freund (Vienna University of Technology, Austria) Tim Hutton (University College London, UK) Christian Jacob (University of Calgary, Canada) Jian-Qin Liu (ATR, Japan) Duraid Madina (University of New South Wales, Australia) Naoaki Ono (ATR, Japan) Hiroki Sayama (University of Electro-Communications, Japan) Moshe Sipper (Ben-Gurion University, Israel) Pietro Speroni di Fenizio (University of Jena, Germany) Peter F. Stadler (University of Leipzig, Germany) Hideaki Suzuki (ATR, JAPAN) Yasuhiro Suzuki (Tokyo Medical and Dental University, Japan) From chemistry-request@ccl.net Fri Jan 28 18:39:33 2005 Received: from out.esrf.fr (firewall.sfn.asso.fr [193.49.43.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0SNdVRT004873 for ; Fri, 28 Jan 2005 18:39:31 -0500 Received: (from uucp@localhost) by out.esrf.fr (1.0.0) id j0RAuRb27483 for ; Thu, 27 Jan 2005 11:56:27 +0100 (MET) Received: from esrf.esrf.fr(160.103.2.9) by firewall via smap (V1.3) id tmp027151; Thu Jan 27 11:56:00 2005 Subject: orbital and reality Received: from leeloo.esrf.fr (scanscan.esrf.fr [160.103.2.45]) by esrf.esrf.fr (8.9.0/8.9.0) with ESMTP id LAA24833 for ; Thu, 27 Jan 2005 11:56:00 +0100 (MET) Message-Id: <5.1.0.14.0.20050127112924.01f23c48 {} imap.esrf.fr> X-Sender: vetere {} imap.esrf.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 27 Jan 2005 11:56:16 +0100 To: chemistry {} ccl.net From: Valentina VETERE Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I post my letter again..I received a warning message of no-distribution: >Dear CCL list, >since several days I'm reading with interest the e-mail about orbitals and >reality. > >Nevertheless, there is still something not clear in my mind. My point is >that since my first lessons on quantum mechanics I belief that all the >equations (not excluding Schrodinger ) were models of a more complex >reality that none for instance is able to describe exactly with numbers. >Is this true? For me Schrodinger model of atom is a smart model, that >scientist are using since 80 years ..but is a model. Moreover we are not >computing Schrodinger solution most of the time...no? HF, DFT, CI >..etc..separation of nuclei and electron motions..etc..still models >to end up with something we can work with ..no? I'm I rigth? >If yes, I would like to understand why orbitals give rice to all this >discussion. >Probably you can say that the orbitals are a rude model with bigger >assumptions respect to the all electron wavefunction solution of a Schr. >equation. Nevrtheless, also this solution is a model for me...a higher >level model? But, my reaction when I first saw the Nature picture was "not >too bad the model is not so far from reality.." >I thought we were lucky! > >Can you help me in understanding why I'm wrong? > >Dr. Valentina Vetere >Scientist Theory Group >European Syncrothon Radiation Facility (ESRF) >Grenoble France > > From chemistry-request@ccl.net Fri Jan 28 17:23:50 2005 Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0SMNmRT002820 for ; Fri, 28 Jan 2005 17:23:49 -0500 X-Envelope-To: Received: from [192.168.5.1] (CPE0050bfacfe11-CM00122573bb18.cpe.net.cable.rogers.com [70.25.0.168]) (authenticated bits=0) by sycorax.delfa.net (8.13.1/8.13.1/Sycorax.Delfa) with ESMTP id j0SKqIR0031133 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Fri, 28 Jan 2005 23:52:20 +0300 Message-ID: <41FAA602.80203 {} xenon.spb.ru> Date: Fri, 28 Jan 2005 15:52:18 -0500 From: Dmitri Rozmanov User-Agent: Mozilla Thunderbird 0.9 (X11/20041124) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: Re: CCL:[Re]: orbitals and reality References: <5.1.0.14.0.20050125110312.01ebb080 {} imap.esrf.fr> In-Reply-To: <5.1.0.14.0.20050125110312.01ebb080 {} imap.esrf.fr> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear, CCL Yes, I would agree. For me this discussion look like: "Muffin is a torus, look.", "No way! Nobody can show me the torus, as it is just a math abstraction." Honestly I have not read the paper. But ;) read all the messages in the thread. In fact that was very interesting. I am glad that so many people answered. I think that all this just a matter of what we want to express. If an electron standing wave at some specific state in the atom has some specific density of charge, probability, etc. Then if we can visualize it in some way and the same thing is described by an orbital at some level of theory and many people understand this. I guess it is fair and acceptable to say that the orbital is visualized, in some sense. Regards, --- Dmitry. Valentina VETERE wrote: > Dear CCL list, > since several days I'm reading with interest the e-mail about orbitals > and reality. > > Nevertheless, there is still something not clear in my mind. My point is > that since my first lessons on quantum mechanics I belief that all the > equations (not excluding Schrodinger or Dirac) were models of a more > complex reality that none can describe for instance with numbers. Is > this true? > If yes, I would like to understand why orbitals give rice to all this > discussion. > Probably you can say that the orbitals are a rude model with bigger > assumptions respect to the all electron wavefunction solution of a Schr. > equation. Nevrtheless, also this solution is a model for me...a higher > level model? But, my reaction when I first saw the Nature picture was > "not too bad the model is not so far from reality.." > I thought we were lucky! > > Can you help me in understanding why I'm wrong? > > Dr. Valentina Vetere > Scientist Theory Group > European Syncrothon Radiation Facility (ESRF) > Grenoble France > >