From owner-chemistry@ccl.net Wed Feb 25 00:29:00 2009 From: "Jeff Woodford jwoodfor(-)eou.edu" To: CCL Subject: CCL: Vibrational averaging software Message-Id: <-38716-090225001751-12259-LlVmcsOIAH5Q0wDNKujL+Q#,#server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 24 Feb 2009 22:29:17 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor()eou.edu] All: I'm looking for some software that is capable of performing vibrational averaging of various molecular properties (e.g., rotational constant, chemical shielding, multipole moments), most importantly zero-point vibrational averaging, including of course harmonic averaging but also something that can take into account anharmonicitiy. I'm aware that DALTON has some functionality with this but I'm looking for something that is perhaps a bit more general in anharmonic models that may be considered. Would anyone be able to offer some suggestions? Thanks in advance, -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 From owner-chemistry@ccl.net Wed Feb 25 09:21:01 2009 From: "Michael Fernandez Llamosa michael_llamosa()yahoo.com" To: CCL Subject: CCL: The 3rd Virtual Training Workshop on Bioinformatics Message-Id: <-38717-090225091747-3126-78Oaq1Brrno49z4xyhxwuA ~ server.ccl.net> X-Original-From: Michael Fernandez Llamosa Content-Type: multipart/alternative; boundary="0-627238385-1235567850=:8193" Date: Wed, 25 Feb 2009 05:17:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Michael Fernandez Llamosa [michael_llamosa[#]yahoo.com] --0-627238385-1235567850=:8193 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0AThe 3rd Virtual Training Workshop on=0ABioinformatics=0A=0AAsian Bio= informatics=0AResearch and Education Network (ABREN) is opening its 3rd Vir= tual=0ATraining Workshop on Bioinformatics for March-April, 2009. A variety= =0Aof topics in Bioinformatics are covered by experts in the fields from=0A= various universities and institutions in Asian countries (see the 2nd=0AWor= kshop (2007) site for the list of topics covered). The registered=0Apartici= pants can view the multimedia lectures with video and=0Asynchronized slides= in a video-on-demand (VOD) style from streaming=0Aservers located in diffe= rent parts of Asia. All the lectures are=0Aclassified into Basic, Intermedi= ate and Advanced levels. Participants=0Acan ask teachers questions and get = answers any time during the=0Aworkshop period. The registration is free but= the number of=0Aparticipants may be limited.=0A=0ARegistration site:=0Ahtt= p://www.abren.net/workshop/=0AWorkshop flyer:=0Ahttp://gibk21.bse.kyutech.a= c.jp/abren2009/abren/download/=0AThe 2nd Workshop (2007) site:=0Ahttp://gib= k21.bse.kyutech.ac.jp/abren2007/abren/=0A=0A=0A =A1S=E9 el Bello 51 de= People en Espa=F1ol! =A1Es tu oportunidad de Brillar! Sube tus fotos ya. h= ttp://www.51bello.com/ --0-627238385-1235567850=:8193 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A=0A=09=0A=09=0A=09=0A=09=0A=0A

The 3rd Virtual Training Workshop on=0ABioinformatic= s

=0A


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Asian Bioinformatics=0AResearch and Educ= ation Network (ABREN) is opening its 3rd Virtual=0ATraining Workshop on Bio= informatics for March-April, 2009. A variety=0Aof topics in Bioinformatics = are covered by experts in the fields from=0Avarious universities and instit= utions in Asian countries (see the 2nd=0AWorkshop (2007) site for the list = of topics covered). The registered=0Aparticipants can view the multimedia l= ectures with video and=0Asynchronized slides in a video-on-demand (VOD) sty= le from streaming=0Aservers located in different parts of Asia. All the lec= tures are=0Aclassified into Basic, Intermediate and Advanced levels. Partic= ipants=0Acan ask teachers questions and get answers any time during the=0Aw= orkshop period. The registration is free but the number of=0Aparticipants m= ay be limited.

=0A


=0A

=0A

Registration site:=0Ahttp://www.abren.net/worksho= p/

=0A

Workshop flyer:=0Ahttp://gibk21.b= se.kyutech.ac.jp/abren2009/abren/download/

=0A

The 2nd Workshop (2007) site:=0Ahttp://gibk21.bse.kyutech.ac.jp/abre= n2007/abren/

=0A
 

=0A=0A=0A=0A=0A=0A= =0A

>=A1Sé = el Bello 51 de People en Español!
=A1Es tu oportunidad de Brillar= ! br>Sube tus fotos ya http://www.51bello.com/ --0-627238385-1235567850=:8193-- From owner-chemistry@ccl.net Wed Feb 25 09:55:01 2009 From: "javier sacr jsacristan_+_ictp.csic.es" To: CCL Subject: CCL: TST codes Message-Id: <-38718-090225095245-20869-Xz6VXRcPom54T6vxWSY95g(-)server.ccl.net> X-Original-From: "javier sacr" Date: Wed, 25 Feb 2009 09:52:41 -0500 Sent to CCL by: "javier sacr" [jsacristan]-[ictp.csic.es] Hi all, In an old version of Discover/insigth software there were a couple of macros (gsdiff and gsnet) available to calculate diffusion coefficients and solubilities of small gases through polymers using the TST approach. I would be grateful if anyone can suggest me a name of a software package which can do the same or at least can provide me these two macros and I would try to make them work in Materials Studio.. Thanks in advance. JSB From owner-chemistry@ccl.net Wed Feb 25 10:36:00 2009 From: "Alex A. Granovsky gran a classic.chem.msu.su" To: CCL Subject: CCL: PC GAMESS/Firefly for Mac OS X Message-Id: <-38719-090225093917-12398-++WUUbFq+TBCYyXTIq1BFg~!~server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="koi8-r" Date: Wed, 25 Feb 2009 16:35:41 +0300 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran!=!classic.chem.msu.su] Dear Mac users, The PC GAMESS/Firefly team is proud to announce the availability of the first official release of the PC GAMESS/Firefly package for Mac OS X/Intel platform. List of some key features: Free and fast! Proven reliability and performance of Windows/Linux PC GAMESS/Firefly. Feature rich - supports all the functionality of Windows/Linux-based PC GAMESS/Firefly. Runs on Mac OS X 10.4.x (Tiger) and 10.5.x (Leopard). Parallel jobs run on SMP/multi-core hardware without additional software. Installation is straightforward with a native DMG installer. New drag and drop job submission applications make running jobs significantly easier and more intuitive than most other ab-initio computational chemistry programs on the Mac platform. Just drag and drop your input file on to the appropriate run application for the number of CPU cores desired (or double-click and select) and your job will simply launch and open the output in a suitable text editor. All the necessary output files that may be needed for future follow-up jobs are automatically delivered to the input file directory. Everything is intended to be Mac friendly including a set of Mac-specific step by step Quick Start and Complete install and usage guides that should cover 90%+ of all potential questions for new users. A batch job submission application and a STOP-FIREFLY-JOBS application which allows multiple job management. A good set of third-party Mac native graphical applications is available to prepare input jobs as well as to visualize the output of those runs (e.g., WebMO). Most visualization tools that are not available natively for Mac work fine through Darwine or Crossover Wine. There is an active community of Mac beta testers and Firefly community users to answer questions for new users. For more information, visit the PC GAMESS/Firefly homepage at http://classic.chem.msu.su Enjoy the program! On behalf of the PC GAMESS/Firefly team Alex A. Granovsky From owner-chemistry@ccl.net Wed Feb 25 12:25:01 2009 From: "b wafaa wafaab2~!~yahoo.fr" To: CCL Subject: CCL: IRC+RMS Message-Id: <-38720-090224180402-27841-i8jMrYjTsk0+0klqhf6rpA : server.ccl.net> X-Original-From: b wafaa Content-Type: multipart/alternative; boundary="0-292334253-1235513030=:25581" Date: Tue, 24 Feb 2009 22:03:50 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: b wafaa [wafaab2 . yahoo.fr] --0-292334253-1235513030=:25581 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello Everyone, =A0 Use the GV program in order to print the total energy and the RMS gradient = as a function of the IRC reaction coordinate. What can you say about the to= tal energy and the gradient of the transition state? All the best =0A=0A=0A --0-292334253-1235513030=:25581 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


Hello Everyone,

 

Use the GV program in order to print the total energy and the RMS gradient as a func= tion of the IRC reaction coordinate. What can you say about the total = energy and the gradient of the transition state?

All th= e best


=0A=0A=0A=0A --0-292334253-1235513030=:25581-- From owner-chemistry@ccl.net Wed Feb 25 18:59:00 2009 From: "Elaine Meng meng-.-cgl.ucsf.edu" To: CCL Subject: CCL: NIH Research Resources booth at Biophysical Society 2009, Boston Message-Id: <-38721-090225180258-27375-Y43T7QKpP4tzckOQKIuedQ*o*server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 25 Feb 2009 18:02:54 -0500 Sent to CCL by: "Elaine Meng" [meng**cgl.ucsf.edu] Several NIH Research Resource Centers will be sharing exhibition booth #631 at the Biophysical Society 53rd Annual Meeting in Boston, Feb 28-Mar 4, 2009. The booth schedule is outlined below and a more detailed schedule with abstracts is available at: http://www.cgl.ucsf.edu/events/BPS2009/ Biophysical Society 2009: http://www.biophysics.org/2009meeting/ -------------------------------------------------------------------------- Sunday, March 1, 2009 10am Introduction to UCSF Chimera 11 Systems Biology Linker (SyBiL) - a tool for analysis of BioPAX pathway data and converting it to SBML format noon Interactive Visualization of Spikes, Pores, and Cages with UCSF Chimera 1pm Open Model of Actin Dendritic Nucleation 2 The Computational Microscope 3 Virtual Microscopy 4 Effects of Myocyte Heterogeneity on Ventricular Function: A Multi-Scale Modeling Study using Continuity 6 Monday, March 2 10am Making Animations from Electron Microscope Maps and Molecular Models using UCSF Chimera 11 Viral Entry Strategies - 3D Visualization with Maya & Chimera noon Multi-scale Meshing and Numerical Approaches for Modeling Ca2+ Signaling in Cardiac Muscle Cells 1pm Technologies and Applications in High Resolution Single Particle Cryo-EM 2 Visualizing backbone, side chains and conformational changes in chaperonin by cryo-EM and modeling 3 Visualizing Molecular Mechanisms Using 3D Animation 4 Animation Roundtable Tuesday, March 3 10am Rule-based modelling of signal transduction systems using BioNetGen software 11 Virtual NEURON: Toward a biochemical-electrophysiological model of a cerebellar Purkinje neuron noon Vision based workflow management for computer aided drug discovery application services 1 The Computational Microscope 2 Opal 2.0 for Scientific Applications in the Software as a Service (SaaS) environment 3 The Virtual Cell: from Pathway Models to Spatial Simulations 4 structureViz:Linking Cytoscape to UCSF Chimera -------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Feb 25 21:38:00 2009 From: "K Mannan malie_03 a yahoo.co.in" To: CCL Subject: CCL: MD simulations on the substrate which contains FAD and NADH Message-Id: <-38722-090225100407-29726-eT+1fDwno9rlEa2+Q71RwA^_^server.ccl.net> X-Original-From: "K Mannan" Date: Wed, 25 Feb 2009 10:04:02 -0500 Sent to CCL by: "K Mannan" [malie_03-$-yahoo.co.in] Hi, Is there any reference in which MD simulations done on a substrate with FAD and NADH. Any simple insight will be very helpful. Thanks in advance. Mannan From owner-chemistry@ccl.net Wed Feb 25 22:13:00 2009 From: "Stephen Bush bushsf[]research.ge.com" To: CCL Subject: CCL: CFP: Workshop on Nano, Molecular, and Quantum Communications Message-Id: <-38723-090225180528-27897-KEQd/SIj26adDR6Wr9MtQg^^server.ccl.net> X-Original-From: "Stephen Bush" Date: Wed, 25 Feb 2009 18:05:25 -0500 Sent to CCL by: "Stephen Bush" [bushsf===research.ge.com] ***************************************************************************** Workshop on Nano, Molecular, and Quantum Communications (NanoCom 2009) (in conjunction with ICCCN 2009, August 2 - 6, 2009, San Francisco, CA, USA) http://cms.comsoc.org/eprise/main/SiteGen/Nano/Content/Home/NanoCom_09.html ***************************************************************************** Nanotechnology is fundamentally changing the field of networking in medicine, computing, and sensing. Interesting applications of nano-networking include devices that enable delivery of targeted drugs directly into cancerous tumors or the use of nano robots to conduct inspection in harsh environments. The small size of micro and nanoscale devices imposes constraints on communication, information processing, and propulsion. As the fields of nanotechnology, molecular biology, and quantum computing come together, it has created a rich avenue of interdisciplinary research that will shape the future of nano and molecular information networks. This workshop aims to bring together researchers from the disciplines of information theory, biology, nano-engineering, and computer science to address the communication and information processing issues in nano and molecular networks. This workshop welcomes anyone including researchers, practitioners, and students. The areas of interests include, but are not limited to, the following areas: ** Molecular Communication ** Biological implementation of communications, Molecular Motors, Microtubules, Calcium Signaling, etc... ** Quantum Communication Networks ** Hybrid classical quantum communication networks, repeaters, teleportation, entanglement swapping, nanoscale photon detectors, quantum dot networks, networks and quantum robotics, etc... ** Novel Information and Graph Theory Aspects of Nano-Networks ** Network architectures and topologies, Statistical mechanics approach to nano-communications, Routing/addressing issues in nano-networks, Nano-coding, Applications of complex network theory, Self-organization in nano-scale systems, Modeling of Nano/Bio Communication Channels. ** Applications for Nano-Networks ** Wireless nanoscale transmitters and receivers, nano-sensors and actuators, nanorobotics, medical and in-vivo imaging and sensing, lab on a chip, swarm micro and nano-inspection, embedding sensing, etc... ** Modeling, Simulation, Standards and Architectural Aspects of Nano-Networks ** Physical characterization/modeling of nano-scale interconnects and devices, Fault-tolerant and reliability of nano-devices, Self-healing properties of nano-networks, CAD flows for NoCs and MP-SoC platforms, NoC performance and trade-off analysis, Energy efficiency, Bio-inspired aspects. ** Device Physics and Interconnects ** Nano-technologies and devices for on-chip interconnects (CNTs, graphene nano-ribbons, semic., metallic and DNA-templated nanowires), Molecular, optical and wireless interconnects, Interconnects for non-charge-based devices, emerging 3D-interconnect technologies. ** Nano-Robotics ** Communication systems and networking protocols for sub-inch robotic systems, including low-bandwidth coordination schemes for nano-robot teams and range and bearing devices for inter-robot relative positioning. ** Bio-nano Applications ** Bio-Micro/Nanoelectronics, Molecular scale chemical and biosensors, Bio-MEMS technology, Data and power management, Nano-scale and molecular communications and information processing, Information theory analysis of biological communications, Molecular Computation using molecular cells, Chemical computing. Note that: * The proceedings of the workshop will be included in the IEEExplore digital library and indexed by the EI. * One registration of ICCCN'08 covers up to three papers (including both main conference and workshops). Please refer to ICCCN'08 registration policy for detail. Submission Guidelines Authors are invited to submit original and unpublished papers limited to 6 pages. Please see the Author Information page for submission guidelines in the ICCCN 2009 website. Important Dates Paper submission due................10 Mar 2009 Author notification.......................1 May 2009 Camera-ready due.....................15 May 2009 Author registration.....................15 May 2009 Organizing Committee General Chair * Stephen F Bush, GE Global Research, USA Program Committee Chair * Sanjay Goel, University of Albany, USA Technical Program Committee * Sasitharan Balasubramaniam, TSSG, Ireland * Jian-Qin Liu, NiCT, KARC, Japan * Maggie Cheng, Missouri S&T, USA * Nikolaus Correll, MIT * Andrew Eckford, York University, UK * Darren Brock, Lockheed Martin Nanosystems, USA * James Lyke, USAF * Paul Sotiriadis, Johns Hopkins, USA * Murat Yuksel,University of Nevada, USA * Aristides A. G. Requicha, USC, USA * Guillermo Rueda, Intel Corporation, USA * Alhussein Abouzeid, RPI, USA * Kota Murali, IBM, India * Satoshi Hiyama, NTT DOCOMO, Japan * Feng Cheng, University of Potsdam, Germany * John Barker, University of Glasgow, Scotland * Harish Sethu, Drexel, USA * Michael Shur, RPI, USA * Kevin Mills, NIST, USA * Jir Wiedermann, Academy of Sciences of the Czech Republic * Ian Akyildiz, Georgia Institute of Technology, USA * Jianfeng Wang, Philips Research, North America Contact Us You are welcome to contact Stephen F Bush (bushsf^research.ge.com) for with any questions regarding the workshop or the IEEE Emerging Technologies Committee on Nano-Scale, Molecular, and Quantum Networking.