aspuru-list December 2009

aspuru-list@lists.fas.harvard.edu

29 participants
57 discussions

[Aspuru-Guzik group list] Fwd: [mpp-users] Hopper Accounts Enabled

by Alan Aspuru-Guzik

Alán Aspuru-Guzik | Assistant Professor Harvard University | Department of Chemistry and Chemical Biology 12 Oxford Street, Room M113 | Cambridge, MA 02138 (617)-384-8188 | http://aspuru.chem.harvard.edu ---------- Forwarded message ---------- From: Katie Antypas <kantypas(a)lbl.gov> Date: Mon, Dec 14, 2009 at 2:14 PM Subject: [mpp-users] Hopper Accounts Enabled To: mpp-users(a)nersc.gov Dear NERSC Users, All user accounts have been enabled on the first phase of Hopper, NERSC's newest HPC resource, a Cray XT5. The system was installed earlier this fall and is currently in the pre-production phase, a time when NERSC users are given access to the machine, and also when NERSC and Cray staff are still making improvements to the system. You are invited to run on the Hopper system free of charge in exchange for providing feedback to NERSC staff about your experiences using Hopper. The Hopper Phase I system has 664 nodes and 5312 cores and a number of enhancements and new features including: ** Support of python and other shared libraries on the compute nodes ** High I/O bandwidth and capacity 2PB disk and ~25 GB/sec from each scratch file system ** 8 login nodes which are external to the main system with large amounts of memory (128 GB) and swap space The Hopper Phase I system will be targeting mid-sized jobs using roughly a couple hundred cores. Users running applications larger than ~1000 cores will see better throughput on Franklin until the second phase of Hopper arrives late next year when it will be joined with the first phase of Hopper to create NERSC's first peta-flop system with over 150,000 cores. More information about Hopper can be found on our website. http://www.nersc.gov/nusers/systems/hopper/ Please be aware that during the pre-production period the system may be taken down with little or no advance warning and support may be more limited. Additionally, during this period you must: ** Report all bugs, problems, and usability issues you have with the system to consult(a)nersc.gov. ** Report the performance of your code and your experience using Hopper to consult(a)nersc.gov. ** Not publish any machine performance results without the consent of NERSC. It is OK to publish science results, but since the machine has not yet been accepted we can not release information about specific code performance or I/O performance as Cray is still making configuration improvements. ** Understand that your job may be aborted at any time if Cray or NERSC staff need to do testing or maintenance on the system. ** Back up your data often. The file systems will not be backed up and the file system could be reformatted with little or no warning. We look forward to receiving your feedback on Hopper. Best regards, Katie Antypas NERSC User Services Group _______________________________________________ mpp-users mailing list mpp-users(a)nersc.gov

14 years, 4 months

[Aspuru-Guzik group list] Harkless Afternoon Schedule

by J D Whitfield

Hi everyone, Feel free to join us for lunch. We'll be leaving shortly after 12. Give me a buzz if you want to come (301) 520-7847. So far the schedule for Prof J. Harkless is - 1:30-2:00 Dmitrij and Semion(?) - 2:00-2:30 V and JDW - 2:30-3:00 Sigi - 3:00-4:00 Sangwoo and Stephanie - 4:00-4:30 Joel and David - 4:30-5:00 [YOU] Its a very flexible schedule so please let me know if you want to change times. JDW J. D. Whitfield Aspuru-Guzik Group Department of Chemistry and Chemical Biology Harvard University tel: 301-520-7847 web: aspuru.chem.harvard.edu/people/James_Whitfield

14 years, 4 months

[Aspuru-Guzik group list] REMINDER: Dec. 15, 2009 - Dr. Sergei Tretiak - Excitonics Seminar

by rtavilla＠rle.mit.edu

Center for Excitonics Seminar Series Announcement The Center for Excitonics is an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science and Office of Basic Energy Sciences The Center for Excitonics invites you to join us at the next seminar of the 2009 series. Please forward this information on to others who might be interested in attending this and other center seminars. Title: Dynamics of Excitons and Phonons in Disordered Nanoscale Materials Presenter: Dr. Sergei Tretiak Organization: Theoretical Division, Center for Nonlinear Studies and Center for Integrated Nanotechnologies Los Alamos National Laboratory Date: December 15, 2009 Time: 3:00 - 4:00pm Place: Haus Room - 36-428 MIT Campus Center URL: http://www.rle.mit.edu/excitonics Seminar URL: http://www.rle.mit.edu/excitonics/tretiak-121509.html Abstract Prediction of the optical response and photoinduced processes of molecular and nanomaterials is fundamental to a myriad of technological applications, ranging from sensing, imaging, solar energy harvesting, to future optoelectronic devices. In this talk I will overview several applications of emerging quantum-chemical approaches to model photoinduced dynamics in a number of molecular materials over multiple length and time scales. Using concept of strongly bound excitons, we develop exciton scattering (ES) model, allowing multiscale calculation of electronic spectra in large molecules. Consequently, computational design of molecular structures with desirable electronic and optical properties can be performed using graph-like representation of molecules. To simulate non-adiabatic excited state molecular dynamics and concurrent energy transfer processes in dendrimetrs, we use surface hopping techniques combined with the semiempirical approaches. The results show intricate details of photoinduced vibronic relaxation leading to ultrafast energy transfer. In quantum dots we study the role of surface ligands on the electronic structure and observe strong surface-ligand interactions leading to formation of hybridized states and polarization effects. This opens new relaxation channels for high energy photoexcitations simulated using non-adiabatic time-domain DFT molecular dynamics technique. In the amorphous clusters of conjugated polymers, we find that electron trap states are induced primarily by intra-molecular configuration disorder, while the hole trap states are generated primarily from inter-molecular electronic interactions. All these phenomena define important properties of materials suitable for various technologies such as solar energy conversion. Representative publications: 1. C. Wu, S. Malinin, S. Tretiak, and V. Chernyak, "Multiscale Modeling of Electronic Excitations in Branched Conjugated Molecules Using Exciton Scattering Approach," Phys. Rev. Lett. 100, 057405 (2008). 2. S. Kilina, E.R. Batista, P. Yang, S. Tretiak, A. Saxena, R.L. Martin, and D.L. Smith ”Electronic structure of amorphous polyfluorene aggregates”, ACS Nano 2 1381-1388 (2008). 3. D.A. Yarotski, S.V. Kilina, A. Talin, S. Tretiak, O.V. Prezhdo, A.V. Balatsky and A.J. Taylor ”Scanning tunneling microscopy of DNA-wrapped carbon nanotubes”, Nano Lett. 9 12-17 (2009). 4. S. Kilina, S. Ivanov, V.I. Klimov, and S. Tretiak ”Effect of Surface Ligands on Optical and Electronic Spectra of Semiconductor Nanoclusters”, J. Am. Chem. Soc., 131, 7717-7726 (2009). 5. S. F. Alberti, V. Kleiman, S. Tretiak, A. Roitberg, ”Nonadiabatic molecular dynamics simulations of the energy transfer between building blocks in a phenylene ethynylene dendrimer”, J. Phys. Chem. A, 113, 7535-7542 (2009). 6. J. Tao, S. Tretiak, ”Optical absorptions of new blue-light emitting oligoquinolines bearing pyrenyl and triphenyl endgroups investigated with time-dependent density functional theory”, J. Chem. Theory and Comput., 5, 866-872 (2009). Bio Sergei Tretiak received his M.Sc. degree (highest honors, 1994) from Moscow Institute of Physics and Technology (Russia) and his Ph.D. degree in 1998 from the University of Rochester where he worked with Prof. Shaul Mukamel. Afterwards he was Director-funded Postdoctoral Fellow (1999-2001) and subsequently became a Technical Staff Member (2001-present) at LANL. Since 2006 he is a member of the DOE funded Center for Integrated Nanotechnologies (CINT). Dr. Tretiak’s research interests center on the relation between optical and chemical properties of organic and semiconductor materials; development of modern computational methods for molecular optical properties; time-dependent density functional theory and semiempirical methods; nonlinear optical response of organic chromophores; adiabatic and non-adiabatic molecular dynamics of the excited states; collective electronic excitations and optical response of confined excitons in conjugated polymers, carbon nanotubes, semiconductor nanoparticles, and molecular aggregates; charge and energy transfer in biological and artificial antenna complexes. Dr. Tretiak has published over 110 scientific publications and has presented more than 90 invited talks. ergydrade, J.L Alonso, Pablo Echenique, L. Wirtz, A. Marini, M. Gruning, C. Rozzi, D. Varsano and E.K.U. Gross.

14 years, 4 months

[Aspuru-Guzik group list] Group meeting tomorrow: "Quantum Monte Carlo and Procedural Wavefunction Design"

by J D Whitfield

Hi everyone, Prof. Harkless will be visiting with us tomorrow and he will give group meeting at 10am in Naito 030. The title of his talk is "Quantum Monte Carlo and Procedural Wavefunction Design." See you tomorrow, James J. D. Whitfield Aspuru-Guzik Group Department of Chemistry and Chemical Biology Harvard University tel: 301-520-7847 web: aspuru.chem.harvard.edu/people/James_Whitfield

14 years, 4 months

[Aspuru-Guzik group list] John Harkless is visiting us on Monday Dec 14

by J D Whitfield

Hi group, Professor John Harkless is a visiting professor currently at MIT on loan from Howard University. He studies QMC and applications to metallic systems and electronic excitations. He will be visiting our lab on Monday. Please let me know if you would like to get on his schedule. He will also be giving us a talk with the details to be announced. Cheers, James J. D. Whitfield Aspuru-Guzik Group Department of Chemistry and Chemical Biology Harvard University tel: 301-520-7847 web: aspuru.chem.harvard.edu/people/James_Whitfield

14 years, 4 months

[Aspuru-Guzik group list] HUCE Weekly Calendar Email December 10 - 24

by Center for the Environment

Highlight: Monday, December 14: Wendy Jacobs, Associate Professor at the Harvard Law School, discusses "Exploring a Legal Framework for Achieving Commercial-Scale Carbon Capture and Sequestration in the US" in the final Energy Policy Research seminar this fall. Good luck during finals! Calendar Listings: December 10, 2009 3:00pm - 4:00pm Discussion with the Commissioner of the Massachusetts Department of Environmental Protection Dunster Small Dining Room Harvard University Cambridge, MA Interested in environmental conservation? Want to know how to use the law for environmental protection and environmental justice? As Commissioner of MassDEP, Laurie is now at the head of the state's largest environmental regulatory agency. Come with questions! 3:00pm - 5:00pm The Great Climate-gate Debate Massachusetts Institute of Technology 77 Massachusetts Avenue Building 26, Room 100 Come and listen to five experts give their views on what this really means for climate science, the integrity of the Intergovernmental Panel on Climate Change, public perception of climate, and the ongoing policy negotiations in the Congress and at Copenhagen. Agnes Budnik scnc(a)mit.edu 617-253-8900 6:00pm Six Years on Mars Location: Geological Lecture Hall, 24 Oxford St. Cambridge, MA Knoll will reflect on six years of NASA Mars Rover exploration; what the evidence tells us about the history of water and its implication for life on the ancient surface of the Red Planet. hmnh-lectures(a)oeb.harvard.edu 617-495-2773 7:30pm Boston Area Solar Energy Association Forum First Parish in Cambridge Unitarian Universalist 3 Church Street , Harvard Square, Cambridge Chad Laurent, formerly with Massachusetts Energy Consumers' Alliance, and now with the Meister Consultants Group, will cover this technology segment, based on geothermal, solar thermal, and biomass energy. info(a)basea.org December 11, 2009 8:30am - 9:30pm MSI Chalktalk Breakfast HUCE Seminar Room 24 Oxford St. Cambridge, MA “Keeping up with the "-ologys" - An intro to Geomycology” with Cara Santelli, Harvard School of Engineering and Applied Sciences. Host: Colleen Hansel MSI-Info(a)hms.harvard.edu 11:30am - 1:00pm Energy Integration : Helping to Achieve Energy Security and Independence MIT E19-319 Cambridge, MA Jameson Twomey jtwomey(a)mit.edu Speaker: Gary Feldman, Lockheed Martin. December 12, 2009 8:30am - 3:00pm Cambridge Climate Emergency Congress Cambridge City Hall 795 Massachusetts Avenue Cambridge, MA While world leaders delay on taking serious action on climate change, the City of Cambridge, along with other cities world-wide, is weighing in. 100 delegates will be selected to represent the full diversity of Cambridge’s population, institutions, and organizations. 617-349-4321 http://www.cambridgema.gov December 14, 2009 11:45am - 12:45pm Harvard Energy Journal Club HUCE Seminar Room, 24 Oxford St., 3rd Floor, Cambridge, MA Visit the Energy Journal website for current topics of discussion. http://www.hcs.harvard.edu/hejc/ Kate Dennis kdennis(a)fas.harvard.edu 1:00pm - 2:30pm Energy Technology Innovation Policy & Consortium for Energy Policy Research Seminar Series Fainsod Room (Littauer 324, HKS) 79 JFK St. Cambridge, MA "Exploring a Legal Framework for Achieving Commercial-Scale Carbon Capture and Sequestration in the US." Wendy Jacobs, Harvard Law School. Louisa Lund louisa_lund(a)hks.harvard.edu 3:00pm - 4:00pm MIT Energy Initiative Lecture: "All that Gas..." Jameson Twomey jtwomey(a)mit.edu MIT 66-110 Cambridge, MA Speaker: Leonardo Maugeri, Senior Executive Vice President of Eni S.p.A. and MIT Energy Initiative External Advisory Board member. --- Always check the calendar on the website for updated information. If you would like to submit an event to the calendar, contact Lisa Matthews at the Center for the Environment: lisa_matthews(a)harvard.edu. You are receiving this email because you indicated interest in Harvard University Center for the Environment events. [22]Unsubscribe aspuru-list(a)lists.fas.harvard.edu from this list. Links: 22. http://harvard.us1.list-manage.com/unsubscribe?u=7532d1fbf18f39219ac742ebe&… Our mailing address is: 24 Oxford St. Cambridge, MA 02138 (T) 617-495-0368 www.environment.harvard.edu Copyright (C) 2008 Harvard University. All rights reserved.

14 years, 4 months

[Aspuru-Guzik group list] Fwd: Charge Carrier Motion in Disordered Conjugated Polymers: A Multiscale Ab Initio Study - Nano Letters (ACS Publications)

by Alan Aspuru-Guzik

Hi guys, I just got this URL from Joshua Schrier. Good paper. I added this to the Mendeley. It is quite interesting full ab initio study of charge transport. Best, Alan http://pubs.acs.org/doi/full/10.1021/nl9021539 <http://pubs.acs.org/doi/full/10.1021/nl9021539> -- Joshua Schrier Assistant Professor of Chemistry Haverford College 370 Lancaster Ave Haverford, PA 19041-1392 office: 610-896-1388

14 years, 4 months

[Aspuru-Guzik group list] ANNOUNCEMENT: Dec. 15, 2009 - Dr. Sergei Tretiak - Excitonics Seminar

by rtavilla＠rle.mit.edu

14 years, 4 months

[Aspuru-Guzik group list] leftovers in Converse

by Anna B. Shin

Dear Group, I've just done a walk-through of the old lab space in Converse. As you know, the wet lab in Cv 002 needs to be cleared out. There are many books, papers, 2 coffee machines, boxes, posters, etc spread out all over the benches, cabinets and desks. The group printer is still downstairs as well. Ville and David have volunteered to move the printer to the big office. We need volunteers to move the remaining items to the big office, or they will be thrown out by the end of tomorrow. There are gray plastic crates on wheels and a moving shelf to help with the move. All the items can be moved in 1 trip; we just need 3-4 people. Thanks, Anna Anna B. Shin Laboratory Administrator Aspuru-Guzik Research Group Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge, MA 02138 617.496.9964 office 617.694.9879 cell 617.496.9411 fax 617.495.9676 lab http://aspuru.chem.harvard.edu/

14 years, 4 months

[Aspuru-Guzik group list] Female postdocs at Harvard.

by Alan Aspuru-Guzik

Dear Group, This is insightful, and our own group has not a 35% women representation. I will try my best to recruit the top women theoreticians! This is for the women in the group, as well, to note the statistics. Also remember, statistics are just that: Individuals matter and no career track is the same. http://www.insidehighered.com/news/2009/08/17/chemistry Best, Alan Alán Aspuru-Guzik | Assistant Professor Harvard University | Department of Chemistry and Chemical Biology 12 Oxford Street, Room M113 | Cambridge, MA 02138 (617)-384-8188 | http://aspuru.chem.harvard.edu

14 years, 4 months

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aspuru-list December 2009