aspuru-list December 2008

aspuru-list@lists.fas.harvard.edu

12 participants
22 discussions

by Anna B. Shin

Dear Group, Mark Watson will be visiting on Mon/Tue 15-16 Dec. He will present a talk at 4pm on Mon 15 Dec in Room 311 at 60 Oxford Street. I'd like to put together a visit schedule (he will be meeting w/ IIC folks too), so please let me know if you can meet w/ him and your available times Mon and Tue. Thanks, Anna -- Anna B. Shin Aspuru-Guzik Group Administrator Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge, MA 02138 617.496.9964 phone 617.496.9411 fax anna(a)chemistry.harvard.edu Aspuru-Guzik Group URL: http://aspuru.chem.harvard.edu/

15 years, 4 months

[Aspuru-Guzik group list] Group Meeting + Pizza 1 PM

by Roberto Olivares-Amaya

Xavier Andrade will give a lunch group meeting from 1-2.30 at the Division Room today. Author: Xavier Andrade Title: Modified Ehrenfest formalism: A new approach for large scale ab-initio molecular dynamics Abstract: A major drawback of traditional AIMD methods is the necessity to enforce the orthogonalization of the wave-functions, which can become the bottleneck for very large systems. Alternatively, one can handle the electron-ion dynamics within the Ehrenfest scheme where no explicit orthogonalization is necessary, however the time step is too small for practical applications. Here we preserve the desirable properties of Ehrenfest in a new scheme that allows for a considerable increase of the time step while keeping the system close to the Born-Oppenheimer surface. We show that the automatically enforced orthogonalization is of fundamental importance for large systems because not only improves the scaling of the approach with the system size but also allows for a very efficient parallelization. In this work we provide the formal details of the new method, describe its implementation and present some applications to some test systems. Comparisons with the widely used Car-Parrinello molecular dynamics method are made.

15 years, 4 months

[Aspuru-Guzik group list] Fwd: Solar Cloud

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: Kurt Keville <kkeville(a)mit.edu> Date: Tue, Dec 9, 2008 at 10:49 AM Subject: Re: Solar Cloud To: Alan Aspuru-Guzik <alan(a)aspuru.com> Alan, This is great stuff... I think we can put together a couple of Gigacycles to donate to the cause! Hey, we are training up a ton of fresh students in CUDA next month... if you have any students who want to get trained up, I think there is room. <http://sites.google.com/site/cudaiap2009> http://sites.google.com/site/cudaiap2009 The link from the Harvard Energy Forum site is down but we found your article... http://www.reuters.com/article/environmentNews/idUSTRE4B70QS20081208 Kurt Keville

15 years, 4 months

[Aspuru-Guzik group list] [theochem-announce] Wednesday lecture

by Seth Difley

Please take note of the Theochem lecture this Wednesday. Title-- Modeling crowding and confinement of cellular environments Speaker-- Huan-Xiang Zhou (Florida State University) https://people.scs.fsu.edu/~hxzhou/ Time-- Wed, December 10, 2008 4PM Place-- MIT (24-121) http://whereis.mit.edu/map-jpg?mapterms=24-121 More Information-- http://people.bu.edu/theochem _______________________________________________ theochem-announce mailing list theochem-announce(a)mit.edu http://mailman.mit.edu/mailman/listinfo/theochem-announce

15 years, 4 months

[Aspuru-Guzik group list] [iic-colloquium] IIC Colloquium Wednesday, Dec. 10, Hudong Chen: A theory-based approach to computational fluid dynamics

by Rosalind Reid

The IIC's final Colloquium of 2008 will be presented tomorrow afternoon by Hudong Chen, Chief Scientist with Exa Corporation. Please join us! For more information, see the announcement below and online. Rosalind Reid Executive Director, IIC ******************************************* IIC Colloquium Title: Discretization Kinetic Theory-based Approach for Computational Fluid Dynamics December 10, 2008 at 4:00 p.m. Location: 60 Oxford Street, Room 330 Abstract: It has been nearly two decades since formation of the first lattice Boltzmann (LB) algorithm. By now its physics and mathematic underpinnings provide a solid theoretical base. Furthermore, the approach has evolved from a mere academic toy to a major new branch in computational fluid dynamics (CFD), facilitating real-world application. This talk will give an overview of some fundamentals and clarify essential starting points, emphasizing comparison with traditional Navier-Stokes based CFD. The speaker will also present a rigorous general condition for LB to capture necessarily required non- equilibrium physics properties. This is essential for going beyond the Navier-Stokes based CFD. Finally, the speaker is going to outline some basic advantages in LB, especially for handling complex geometry and performing time-dependent flow simulations, and to present some specific numerical examples. Hudong Chen is currently the Chief Scientist at Exa Corporation based in Burlington, Massachusetts, a scientific software company for computational fluid dynamics applications. Hudong has been leading core technology development at Exa for over ten years. The core technology is based on lattice Boltzmann methods in combination with state of the art turbulence modeling. The software is now been widely used in various industries. Hudong received his Ph.D. in physics from Dartmouth College in 1986. He has done post-doctoral work at Los Alamos National Laboratory and elsewhere, and has collaborated with renowned scientists such as Dr. Robert Kraichnan on turbulence theory. Hudong Chen has been a pioneer and leader in the field of lattice Boltzmann methods. In 2000, he was nominated as a Fellow of the American Physical Society. Currently he is also an Affiliated Professor with the aerospace engineering department at Iowa State University. For more information: http://iic.harvard.edu/seminars/iic-colloquium-series-fall-2008-through-spr… _______________________________________________ iic-colloquium mailing list iic-colloquium(a)calists.harvard.edu http://calists.harvard.edu/mailman/listinfo/iic-colloquium

15 years, 4 months

[Aspuru-Guzik group list] Reminder: 2nd Joint Theory Seminar

by Anna B. Shin

Dear Group, Pardon the frequent emails. This is a reminder about tomorrow's Theory Seminar at 4:15pm in Naito 030 (Tue 9 Dec). Dr. Jingzhi Pu of the Karplus Group will be presenting. His title and abstract are as follows: *Coupling Mechanisms in F1-ATPase F1-ATPase is the smallest rotary motor in biology. With ATP binding, hydrolysis, and product release, the motor induces a torque on the central shaft gamma-subunit, which rotates about 1000/sec in one direction. When an applied torque rotates the gamma-subunit in the reverse direction, the motor synthesizes ATP, its normal function in living cells. In this presentation, we will discuss the progress of using a multiscale approach that combines coarse-grained model, targeted molecular dynamics and free energy simulations to elucidate how the rotary motion is achieved via intimate coupling between the ligand binding/catalytic subunit conformations and the gamma-subunit. * Our next seminar will be in January. I'll send out an annoucement after the holiday break. Thanks, Anna

15 years, 4 months

[Aspuru-Guzik group list] Current status of the subversion repository in cleanenergy.harvard.edu

by Sangwoo Shim

Hello group, I just set up the basic setup for subversion repositories at cleanenergy.harvard.edu. As I said, it only has basic feature. Let me explain this to you; The svn access is provided throught WebDAV protocol through ssl-secured http protocol (https). Well, in short, in the viewpoint of a svn client, it is the same as assembla. However, we have two problems; currently we have only system-wide authentication, which mean there is no distinction between users of different project. Only one user/password database for the entire repository. This is because the authentication is entirely relying on the apache's basic authentication mechanism using a htpasswd file. Also, creation of svn repository, and setting email commit notification must be done manually. Please note I don't have any plan to implement more sophiscated authentication mechanism and/or repository management tools unless there already exist installable solutions. So for now, svn users must come to my cubicle and type your password directly through the terminal. Let me know if you have other questions. PS. Cesar, I already set up the HqQIT repository, so the only thing left is come to me and type your password. :-) Best, Sangwoo

15 years, 4 months

[Aspuru-Guzik group list] 2nd Joint Theory Seminar

by Anna B. Shin

Dear Group, Dr. Jingzhi Pu of the Karplus Group will present the second Joint Theory Seminar on Tue 9 Dec at 4:15pm in the Kishi Conference Room (Naito 307 near the Bauer side of Naito). Dr. Pu's title and abstract are as follows: *Coupling Mechanisms in F1-ATPase* *F1-ATPase is the smallest rotary motor in biology. With ATP binding, hydrolysis, and product release, the motor induces a torque on the central shaft gamma-subunit, which rotates about 1000/sec in one direction. When an applied torque rotates the gamma-subunit in the reverse direction, the motor synthesizes ATP, its normal function in living cells. In this presentation, we will discuss the progress of using a multiscale approach that combines coarse-grained model, targeted molecular dynamics and free energy simulations to elucidate how the rotary motion is achieved via intimate coupling between the ligand binding/catalytic subunit conformations and the gamma-subunit.* Our next seminar will be presented by Roberto in January. An announcement will be sent early next month. Best, Anna -- Anna B. Shin Aspuru-Guzik Group Administrator Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge, MA 02138 617.496.9964 phone 617.496.9411 fax anna(a)chemistry.harvard.edu Aspuru-Guzik Group URL: http://aspuru.chem.harvard.edu/

15 years, 4 months

[Aspuru-Guzik group list] Monday December 8

by Edward Farhi

Dear Quanta We will meet on Monday December 8 at 3:00 and Nicolas Cerf will give a presentation. See you then. Eddie ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Edward Farhi Cecil and Ida Green Professor of Physics Director Center for Theoretical Physics Massachusetts Institute of Technology Building 6 Room 300 Cambridge MA 02139 617 253 4871 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

15 years, 4 months

[Aspuru-Guzik group list] HUCE Weekly Calendar Update December 4 - 18

by Center for the Environment

Dear Friends of HUCE, Be sure to check the HUCE calendar on our website, www.environment.harvard.edu, for the most up-to-date listings and complete event descriptions. 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. Feel free to distribute this email to your students, faculty, colleagues, and anyone else who may be interested in environmental events around the community. Highlights: Tuesday, December 9: Catherine Badgley from the University of Michigan department of Ecology and Evolutionary Biology discusses the "Effects of Climate on Mammalian Diversity" in the Earth History and Paleobiology Seminar. Thursday, December 11: Director of the Harvard Center for the Environment Daniel Schrag presents "Confronting the Energy-Climate Challenge" with comments by Kelly Sims Gallagher (HKS) at the Harvard Museum of Natural History's "Earth Matters" lecture series. Saturday, December 13: The School of Engineering and Applied Scienes presents two sessions of, "From Bean to Bar: The Sweet Science of Chocolate," a special holiday lecture for children ages 7 and up. Calendar Listings: Thursday 12/4/2008 4:00p OEB Seminar Series (Bio Labs Lecture Hall, 16 Divinity Ave, Harvard Campus, Cambridge, MA) "Chemical communication among plants and insects." Consuelo de Moraes, Pennsylvania State University. Contact: Katie Parodi, kparodi(a)oeb.harvard.edu, www.oeb.harvard.edu/news_events/semin... 4:00p Climate Seminar (Haller Hall, Geological Museum, 24 Oxford St., Cambridge, MA) "Restoring Balance to the Archean/Paleoproterozoic Carbon Cycle: From Louis Pasteur to the Lomagundi-Jatuli Carbon Isotope Event." Joseph Kirschvink, Div. of Geological and Planetary Science, Caltech. Contact: Shuting Jin , jin(a)fas.harvard.edu, www.seas.harvard.edu/climate/seminars... 6:00p Microbial Sciences Initiative Thursday Evening Seminar Series (HUCE Seminar Room, 24 Oxford St., 3rd Floor, Cambridge, MA) "D-amino acids regulate the composition, structure, amount, and strength of peptidoglycan." Matt Waldor, Professor of Medicine and Microbiology, Harvard Medical School Contact: Christy Herren, herren(a)fas.harvard.edu, www.msi.harvard.edu/thursdays.html 6:30p The Future of Transportation: Ending our Dependence on Oil (JFK Forum, Littauer Building, 79 JFK St., Cambridge, MA) Speaker: Shai Agassi, an Israeli-born entrepreneur who is taking the auto industry by storm with a revolutionary new electric car infrastructure. Contact: Allison Shapira , allison_shapira(a)ksg.harvard.edu , www.surveymonkey.com/s.aspx?sm=25vhyh... Friday 12/5/2008 8:00a - 5:00p The Science of the Human Past: An Invitation to a Symposium on the Scientific Study of the Human Past (Broad Institute, NE30-1154, the Auditorium, 7 Cambridge Ctr., Cambridge, MA) Speakers include Michael Hammer, Pardis Sabeti, Noreen Tuross, and many others. Open to the public; registration required. Contact: www.broad.mit.edu/registration/ 8:30a Restructuring Roundtable (Foley Hoag, 155 Seaport Blvd, Boston, MA) Two panel discussions: "National Priorities for Climate and Energy Policy" and "Regional Climate Initiatives: RGGI and WCI." Contact: www.raabassociates.org/main/roundtabl... 9:00a - 5:00p Stockholm Environmental Institute: US Symposium (Coolidge Room, Ballou Hall Tufts University, Medford, MA) "Taking Climate Change Seriously: Research and Policy Directions for the Next US Administration" Contact: www.sei-us.org/symposium2008.html 11:30a Harvard Forest Seminar Series (Seminar Room at Shaler Hall, Harvard Forest, 324 North Main Street, Petersham, MA) "Plant responses to different environmental stresses in the high tropical Andes ." Fermin Rada - Universidad de Los Andes and Harvard Bullard Fellow. Contact: Audry Barker Plotkin, aabarker(a)fas.harvard.edu, 978-724-3302 x 268, harvardforest.fas.harvard.edu/researc... 2:30p - 4:30p MIT Seminar on Environmetnal and Agricultural History (Building E51, Room 095, MIT, Cambridge, MA) "Neolithic Emergence: the Origin of Agriculture in the Near East." Steven Mithen, Professor of Archaeology, Reading University. Contact: Margo Collett, mcollett(a)mit.edu 6:00p - 8:00p Movie and Guest Speaker from Silent Spring Institute (Emerson Hall 210, Harvard Campus, Cambridge, MA) Sarah Dunagan will talk briefly about the Silent Spring Institute followed by the movie "Toxic Bust." Contact: whxchan(a)yahoo.com 6:45p New England Botanical Club Meeting (Fairchild Lecture Hall, Room 102, 7 Divinity Ave., Cambridge, MA ) "The Ends of Earth: Plant Conservation in Some of the Last Shangri- Las of the World." Dr. Kamaljit Bawa, Distinguished Professor, Department of Biology, University of Massachusetts-Boston Contact: www.rhodora.org/Meetings.html 7:30p Crafting A Sensible National Security Policy (St. Paul Parish, 29 Mt. Auburn St., Cambridge, MA) Andrew J. Bacevich, Boston University. Free and open to the public. Reception to follow. Monday 12/8/2008 8:30a - 5:30p The Pardee Center for the Study of the Longer-Range Future Conference (The Rafik Hariri Building (Boston University School of Management), 4th Floor, 595 Commonwealth Ave, Boston, MA) "Three Decades of Reform and Opening: Where is China Headed?" RSVP required. Contact: pardee(a)bu.edu, www.bu.edu/phpbin/news-cms/news/?dept... 12:00p - 1:00p Harvard Energy Journal Club (HUCE Seminar Room, 24 Oxford St., 3rd Floor, Cambridge, MA) Visit the Energy Journal website for current topics of discussion. Contact: Mark Winkler, mwinkler(a)fas.harvard.edu, www.hcs.harvard.edu/hejc/index.html 4:00p - 5:30p Energy Policy Research Seminar (Perkins Room, 4th Floor, Rubenstein Building, KSG, 79 JFK St., Cambridge, MA) "The Carbonomics of Kissinger's Cartel, Double Dividends, and Global Fairness." Steven Stoft, author, Power System Economics (2002) and Carbonomics (forthcoming) Contact: Louisa Lund, louisa_lund(a)harvard.edu, 617-495-8693 Tuesday 12/9/2008 12:00p Herbaria Seminar Series (Herbaria Seminar Room, 22 Divinity Ave., Cambridge, MA) "Phylogenetic informativeness." Jeffrey Townsend, Yale University. Contact: www.huh.harvard.edu/seminar_series/ 3:00p - 4:00p ClimaTea Lecture/Journal Club (Geological Museum, Room 418, 24 Oxford Street, Cambridge, MA) Visit the Atmosphere, Ocean, and Climate Dynamics website for current speakers and topics of discussion. Contact: Kate Dennis, kdennis(a)fas.harvard.edu, www.seas.harvard.edu/climate/seminars... 4:00p Earth History and Paleobiology Seminar (Haller Hall, Room 102, Geological Museum, 24 Oxford St., Cambridge, MA) "Effects of Climate on Mammalian Diversity." Catherine Badgley, University of Michigan, Ecology and Evolutionary Biology Contact: ehap.seminar(a)gmail.com 5:15p Boston Environmental History Seminar (Massachusetts Historical Society, 1154 Boylston St., Boston, MA ) "'Gold! Gold!! Gold!!!': Mining and Environmental Change in the 19th-Century West." George H. Vrtis, Carleton College. Contact: Jane Becker, jbecker(a)masshist.org, 617-646-0518 Wednesday 12/10/2008 4:00p - 5:00p Origins of Life Initiative Forum (Bio Labs Lecture Hall, 16 Divinity Ave, Harvard Campus, Cambridge, MA) "Marine Microbial Mats and the Search for Life in Deep Time and Space." David J. Des Marais, NASA - Ames. Contact: Sharmon G. Davis, sdavis(a)cfa.harvard.edu, 617.496.1451, origins.harvard.edu/OriginsForum.html Thursday 12/11/2008 4:00p - 5:30p The Potential for Advanced Leadership: Can the Boomer Generation Help Save the World? (Aldrich 112, Harvard Business Scool, Boston, MA) Faculty Seminar sponsored by the Harvard Business School Social Enterprise Initiative in collaboration with the Harvard University Advanced Leadership Initiative and the Harvard Kennedy School. Contact: nbaker(a)hbs.edu, www.hbs.edu/socialenterprise/ 4:00p OEB Seminar Series (Bio Labs Lecture Hall, 16 Divinity Ave, Harvard Campus, Cambridge, MA) "The white-throated sparrow: A natural model uniting genetics, neuroendocrinology, and social behavior." Donna Maney, Emory University. Contact: Katie Parodi, kparodi(a)oeb.harvard.edu, www.oeb.harvard.edu/news_events/semin... 6:00p Harvard Museum of Natural History: Earth Matters (Geological Lecture Hall, 24 Oxford St., Cambridge, MA) "Confronting the Energy-Climate Challenge." A presentation by Dan Schrag (HUCE, EPS/SEAS), with remarks by Kelly Gallagher (HKS). Contact: hmnh(a)oeb.harvard.edu, 617.495.3045, www.hmnh.harvard.edu/lectures_and_spe... Friday 12/12/2008 8:30a - 9:30a Microbial Sciences Friday Chalktalk (HUCE Seminar Room, 24 Oxford St., 3rd Floor, Cambridge, MA) "Genomics on 700 Microbes: An early look at a global analysis of how microbes make and break down small molecules." Michael Fischbach, Department of Molecular Biology, Massachusetts General Hospital Contact: Christy Herren, herren(a)fas.harvard.edu, (617) 495-8643 , www.msi.harvard.edu/fridays.html 11:00a Harvard Forest Seminar Series (Seminar Room at Shaler Hall, Harvard Forest, 324 North Main Street, Petersham, MA) "Do ecologists have GUTS?" Samuel Scheiner, Program Director, National Science Foundation Population & Evolutionary Processes. Contact: Audry Barker Plotkin, aabarker(a)fas.harvard.edu, 978-724-3302 x 268, harvardforest.fas.harvard.edu/researc... Saturday 12/13/2008 10:00a From Bean to Bar: The Sweet Science of Chocolate (Science Center B, 1 Oxford St., Cambridge, MA) Family-friendly holiday lecture with Howard Stone, SEAS, and Amy Rowat, Harvard University. Live experiments and demonstrations; appropriate for ages 7 and up. Repeat session at 1 pm. Contact: ciencetix(a)seas.harvard.edu, www.seas.harvard.edu/cooking Monday 12/15/2008 12:00p - 1:00p Harvard Energy Journal Club (HUCE Seminar Room, 24 Oxford St., 3rd Floor, Cambridge, MA) Visit the Energy Journal website for current topics of discussion. Contact: Mark Winkler, mwinkler(a)fas.harvard.edu, www.hcs.harvard.edu/hejc/index.html Tuesday 12/16/2008 12:00p Herbaria Seminar Series (Herbaria Seminar Room, 22 Divinity Ave., Cambridge, MA) "Sexual dimorphism and floral polymorphism across an island archipelago: hummingbirds and heliconias of the Lesser Antilles." Ethan Temeles, Amherst College. Contact: www.huh.harvard.edu/seminar_series/ ============================================== You are receiving this email because you indicated interest in Harvard University Center for the Environment events. Unsubscribe aspuru-list(a)lists.fas.harvard.edu from this list: http://harvard.list-manage.com/unsubscribe?u=7532d1fbf18f39219ac742ebe&id=5… Our mailing address is: Harvard University Center for the Environment 24 Oxford St. 3rd floor Cambridge, MA 02138 Our telephone: (617) 495-0368 Forward this email to a friend: http://forward-to-friend.com/forward?u=7532d1fbf18f39219ac742ebe&id=a648c13… Update your profile: http://harvard.list-manage.com/profile?u=7532d1fbf18f39219ac742ebe&id=5bea9…

15 years, 4 months

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aspuru-list December 2008