aspuru-list March 2015

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32 participants
64 discussions

[Aspuru-Guzik group list] Group discussion time with Prof. Miller today moved to 3PM

by Jarrod McClean

Hi All, Due to last minute schedule adjustments, the group meeting time with Professor Miller is now 3PM in the common area (instead of 10 AM). Thank you for your flexibility! Also, if you weren't at his seminar yesterday, no worries, but he has some very cool new results where he gets better results than PIMD with an almost entirely classical theory (apart from an effective quantization that is achieved only through coarse binning of classical trajectories!), worth asking him about or reading about regardless! Jarrod

9 years, 1 month

[Aspuru-Guzik group list] ITAMP lunch seminar- K. Rajibul Islam, Harvard University (03/27)

by Richard Schmidt

Dear colleagues, this week we are happy to have Rajibul Islam from the Greiner group at our seminar, speaking about their very recent work on entanglement. Kind regards, Richard and Swati ITAMP Topical Lunch Discussion Date: Friday, March 27th Time: 12:00-1:30 pm Pizza will be served. Location: B-106 @ Center for Astrophysics (60 Garden Street) Directions: after entering the lobby of the CfA, turn right to enter the hallway of the B building. In the hallway, turn right again, and B-106 is there. Speaker: K. Rajibul Islam, Harvard University Title: Entanglement detection by interfering quantum many-body twins Abstract: Entanglement is a hallmark of quantum many-body physics, and is increasingly used to explore long range correlations near quantum phase transitions, and topological order. Detecting entanglement, however, is hard as it often requires a full reconstruction of the state of the system or a prior knowledge about the state itself. In our experiments with bosonic ultra cold atoms, we detect entanglement by comparing the quantum states of two identically prepared copies of a few-body system. This is achieved by bosonic interference between the copies, similar to the two photon Hong-Ou-Mandel interference. We directly measure the second order Renyi entanglement entropy in the ground state of an interacting few-body system, and observe entanglement dynamics in a quench experiment. --------------------------- Dr. Richard Schmidt Institute for Theoretical Atomic, Molecular, and Optical Physics (ITAMP) Harvard-Smithsonian Center for Astrophysics MS-14 60 Garden St. Cambridge, MA 02138 U.S.A. richard.schmidt(a)cfa.harvard.edu Tel. +1 (617) 496-7610 Fax +1 (617) 496-7668

9 years, 1 month

Re: [Aspuru-Guzik group list] David Wales talk TODAY at 2pm

by Semion Saikin

For those who (like me) reads the subject line only On Wed, Mar 25, 2015 at 1:14 PM, McClean, Jarrod <jmcclean(a)fas.harvard.edu> wrote: > Hi all, > Don't forget about David Wales talk today at 2pm also! It will be good! > > Jarrod > > > *From:* "Schwickrath, Helen" <schwickrath(a)chemistry.harvard.edu> > *Date:* March 24, 2015 at 2:47:38 PM EDT > *To:* "Schwickrath, Helen" <schwickrath(a)chemistry.harvard.edu> > *Subject:* *[G5] FW: David Wales talk tomorrow* > > Wednesday, 25 March > > 2:00 p.m. > > Pfizer Lecture Hall > > ITAMP Series > > Prof David Wales from the University of Cambridge will be giving a talk at > 2pm tomorrow in Pfizer, as part of the ITAMP series. It will probably be > of interest to members of the department, so if you could post this to the > list, it would be appreciated. > > I include an abstract: > > David Wales: > Energy Landscapes and Prediction of Molecular Properties > > ------------------------------------------------------------------------------ > > The potential energy landscape provides a conceptual and computational > framework for investigating structure, dynamics and thermodynamics in > atomic and molecular science. This talk will summarise new approaches for > global optimisation, quantum dynamics, the thermodynamic properties of > systems exhibiting broken ergodicity, and rare event dynamics. Applications > will be presented that range from prediction and analysis of > high-resolution spectra, to conformational changes of biomolecules and > coarse-grained models of mesoscopic structures. > > Selected Publications: > D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010) > D.J. Wales, J. Chem. Phys., 130, 204111 (2009) > B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008) > D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006) > D.J. Wales, Int. Rev. Phys. Chem., 25, 237-282 (2006) > D.J. Wales, "Energy Landscapes", Cambridge University Press, Cambridge, > 2003 > > _______________________________________________ > Ccb-g5 mailing list > Ccb-g5(a)lists.fas.harvard.edu > https://lists.fas.harvard.edu/mailman/listinfo/ccb-g5 > > > _____________________________________________ > Aspuru-list mailing list > Aspuru-list(a)lists.fas.harvard.edu > https://lists.fas.harvard.edu/mailman/listinfo/aspuru-list > > -- ******************************************** Semion K. Saikin, PhD Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street, Cambridge, MA 02138 email: saykin(a)fas.harvard.edu phone: (619)212-6649 ********************************************

9 years, 1 month

[Aspuru-Guzik group list] Fwd: [G5] FW: David Wales talk tomorrow

by McClean, Jarrod

Hi all, Don't forget about David Wales talk today at 2pm also! It will be good! Jarrod From: "Schwickrath, Helen" <schwickrath(a)chemistry.harvard.edu<mailto:schwickrath@chemistry.harvard.edu>> Date: March 24, 2015 at 2:47:38 PM EDT To: "Schwickrath, Helen" <schwickrath(a)chemistry.harvard.edu<mailto:schwickrath@chemistry.harvard.edu>> Subject: [G5] FW: David Wales talk tomorrow Wednesday, 25 March 2:00 p.m. Pfizer Lecture Hall ITAMP Series Prof David Wales from the University of Cambridge will be giving a talk at 2pm tomorrow in Pfizer, as part of the ITAMP series. It will probably be of interest to members of the department, so if you could post this to the list, it would be appreciated. I include an abstract: David Wales: Energy Landscapes and Prediction of Molecular Properties ------------------------------------------------------------------------------ The potential energy landscape provides a conceptual and computational framework for investigating structure, dynamics and thermodynamics in atomic and molecular science. This talk will summarise new approaches for global optimisation, quantum dynamics, the thermodynamic properties of systems exhibiting broken ergodicity, and rare event dynamics. Applications will be presented that range from prediction and analysis of high-resolution spectra, to conformational changes of biomolecules and coarse-grained models of mesoscopic structures. Selected Publications: D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010) D.J. Wales, J. Chem. Phys., 130, 204111 (2009) B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008) D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006) D.J. Wales, Int. Rev. Phys. Chem., 25, 237-282 (2006) D.J. Wales, "Energy Landscapes", Cambridge University Press, Cambridge, 2003 _______________________________________________ Ccb-g5 mailing list Ccb-g5(a)lists.fas.harvard.edu<mailto:Ccb-g5@lists.fas.harvard.edu> https://lists.fas.harvard.edu/mailman/listinfo/ccb-g5

9 years, 1 month

[Aspuru-Guzik group list] Group time with Prof. Miller tomorrow at 10am

by Jarrod McClean

Hi all, As you know, Prof Miller is giving his theochem presentation today at 4 pm at MIT. He will also be visiting tomorrow, and we will have group time with him at 10 am at the theory couches. See you there! Jarrod

9 years, 1 month

[Aspuru-Guzik group list] David Wales visit

by Edward Pyzer-Knapp

Hi all During the next week, David Wales from Cambridge will be visiting. David is a specialist in energy landscape exploration. If you would like to chat with him, I will be setting up a few sessions. Additionally he will be speaking at ITAMP on Wednesday, so I have a few lunch spots up for grabs. Get in touch :) Ed

9 years, 1 month

[Aspuru-Guzik group list] [Aspuru-meetings-list] Group Meeting, WEDNESDAY, 3/25, 10:30am, Div Room

by Jennifer Wei

Hi Everyone, Please note the change in time of the group meeting to tomorrow at 10:30 am. This week, Martin will be giving us group meeting. Please see below for his abstract. Jennifer --------------------------- Accurate treatment of the long-range electron correlation energy, including dispersion, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate treatments of dispersion is the range-separated many-body dispersion (MBD@rsSCS) method [A. Ambrossetti* et al., J. Chem. Phys.* 2014, *140*, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range energy by a model system of coupled quantum harmonic oscillators. However, computing the gradient of the MBD energy has been limited to finite difference techniques, which require SCF calculations at multiple nuclear configurations. Thomas and I have developed analytic energy gradients of the MBD@rsSCS energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the stockholder partitioning of the density. This gives an accurate and efficient scheme for geometry optimizations (and with future work to accelerate the code will allow for molecular dynamics simulations). The method has been implemented in a development version of the open-source *QuantumEspresso* software package. I will provide an introduction to the DFT+MBD method, discuss details of our derivation and implementation of MBD forces, and provide a few examples of how MBD changes the optimized geometries of gas-phase and condensed phase structures. _______________________________________________ Aspuru-meetings-list mailing list Aspuru-meetings-list(a)lists.fas.harvard.edu https://lists.fas.harvard.edu/mailman/listinfo/aspuru-meetings-list

9 years, 1 month

[Aspuru-Guzik group list] FW: Student/postdoc lunch with Seminar Speaker, Sharon Glotzer

by Sawaya, Nicolas

Hi friends, See below and email Adrian Serohijos if interested. cheers nico ________________________________ From: Serohijos, Adrian Sent: Monday, March 23, 2015 8:55 PM To: Sawaya, Nicolas; Saykin, Semion Subject: Student/postdoc lunch with Seminar Speaker, Sharon Glotzer Hi Nicolas and Simeon, There are free slots for the lunch with Dr. Glotzer (the TheoChem Seminar Speaker) on Thursday. Could you ask your group if anybody is interested? Thanks a bunch. Best, Adrian /-- Adrian W.R. Serohijos, Ph.D. Postdoctoral Fellow Biophysics Program Department of Chemistry and Chemical Biology Harvard University serohij(a)fas.harvard.edu<mailto:serohij@fas.harvard.edu> www.people.fas.harvard.edu/~serohij<http://www.people.fas.harvard.edu/~serohij> On Mar 23, 2015, at 5:48 PM, Schwickrath, Helen <schwickrath(a)chemistry.harvard.edu<mailto:schwickrath@chemistry.harvard.edu>> wrote: Dear Adrian, Many thanks for serving as host! (I thought I had sent this but just found the draft.) The time available is 12:00 – 1:25. Sharon has a meeting scheduled for 1:30 p.m. (I’m moving some faculty around on her schedule.) I would recommend no more than a total of 9 for lunch – any larger, and it becomes difficult to have a conversation. If you would like me to try for a table at the Faculty Club, please let me know. (Faculty Club will directly bill the seminar.) Otherwise, you can go out for lunch and see me for reimbursement. Many thanks! Helen From: Serohijos, Adrian Sent: Thursday, March 19, 2015 2:50 PM To: Morrison, Judy Cc: Schwickrath, Helen Subject: Re: host for student/postdoc lunch with Sharon Glotzer Yes! I’ll be happy to do that! Adrian /-- Adrian W.R. Serohijos, Ph.D. Postdoctoral Fellow Biophysics Program Department of Chemistry and Chemical Biology Harvard University serohij(a)fas.harvard.edu<mailto:serohij@fas.harvard.edu> www.people.fas.harvard.edu/~serohij<http://www.people.fas.harvard.edu/~serohij> On Mar 19, 2015, at 2:48 PM, Morrison, Judy <morrison(a)chemistry.harvard.edu<mailto:morrison@chemistry.harvard.edu>> wrote: Hi Adrian, Eugene is hosting next week’s PChem speaker Sharon Glotzer from University of Michigan. He asked me to ask you if you are available to host her lunch with students and postdocs at noon next Thursday March 26. Please let me know if you are able to do this. I’ve copied Helen Schwickrath on this email as she will help you to make the necessary arrangements (if your answer is yes!). Thanks! Judy From: Shakhnovich, Eugene Sent: Wednesday, March 18, 2015 2:53 PM To: Morrison, Judy Subject: RE: host for student/postdoc lunch with Sharon Glotzer Adrian if he is available Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Morrison, Judy" Date:03/18/2015 1:05 PM (GMT-05:00) To: "Shakhnovich, Eugene" Subject: host for student/postdoc lunch with Sharon Glotzer Hi Eugene, Who would you like to host the student/postdoc lunch with PChem speaker Sharon Glotzer next Thursday? Thanks, Judy From: Schwickrath, Helen Sent: Thursday, March 12, 2015 11:20 AM To: Joanna Aizenberg; James Anderson; aspuru(a)chemistry.harvard.edu<mailto:aspuru@chemistry.harvard.edu> forwards to aspuru.com<http://aspuru.com/>; Balskus, Emily; Betley, Theodore; Cohen, Adam; Friend, Cynthia (cfriend(a)seas.harvard.edu<mailto:cfriend@seas.harvard.edu>); Corey, Elias; Gordon, Roy; Heller, Eric; Dudley Herschbach; Kahne, Daniel; Kishi, Yoshito; Lieber, Charles; Liu, David; William Klemperer; Myers, Andrew; Efthimios Kaxiras; Ni, Kang-Kuen; Nocera, Daniel; O'Shea, Erin; Park, Hongkun; ritter(a)chemistry.harvard.edu<mailto:ritter@chemistry.harvard.edu> forwards to gmail.com<http://gmail.com/>; Stuart Schreiber; Shair, Matthew; Shakhnovich, Eugene; Szostak, Jack; Verdine, Gregory; Whitesides, George; Xie, Xiaoliang; Zhuang, Xiaowei Cc: Marina McLaughlin; Aspuru-Assistant; Schaal, Tracey; Fosdick, Jeffrey; Kenar, Magdalena; Howard, Teri; Morrison, Judy; Quinn, Michael; Quilty, Sarah; Donlon, Renee; Markovic, Aleks; Kinsella, Susan; Lubarr, Lisa; Arvidson, Peter; Creson, Jeffrey; Pearson, Anita; fneville(a)broadinstitute.org<mailto:fneville@broadinstitute.org>; Carmosino, Lydia; LeGrand, Melissa; Kilroy, Matthew Subject: visit by Sharon Glotzer Good morning! Please let me know your scheduling preference(s) and if you are available for dinner. Many thanks! Professor Sharon Glotzer http://sitemaker.umich.edu/glotzergroup/home Center for Assembly Science & Engineering University of Michigan Thursday, 26 March 2015 Host: Eugene Shakhnovich 9:00 – 9:40 9:45 – 10:25 10:30 – 11:10 11:15 – 12:00 12:00 – 1:30 p.m. Lunch with graduate students and postdocs Meet in Mallinckrodt Lobby 1:45 – 2:30 2:30 – 3:10 3:15 – 4:00 4:00 – 4:15 Seminar Preparation, Coffee & Cookies Outside Pfizer Lecture Hall Introductions: Professor Shakhnovich 4:15 p.m. The Entropic Chemistry of Shape 5:45 p.m. Dinner with faculty Helen L. Schwickrath Seminar & Events Coordinator Harvard University Department of Chemistry & Chemical Biology 12 Oxford St. Cambridge, MA 02138 Phone (617) 496-8190 Fax (617) 496-5618 http://www.chemistry.harvard.edu<http://www.chemistry.harvard.edu/>

9 years, 1 month

[Aspuru-Guzik group list] [IACS-events] IACS Seminar: "Summarizing Large Data Sets"--- Friday 3/27 **NEW LOCATION**

by Baker, Natasha

Date: Friday, March 27, 2015 Time: Lunch: 12:30pm; Talk: 1pm Location: Science Ctr. Hall E, 1 Oxford Street, Cambridge MA 02138 Speaker: Jeff Bilmes, Professor of Electrical Engineering at the University of Washington Title: Summarizing Large Data Sets Abstract: The recent growth of available data is both a blessing and a curse for the field of data science. While large data sets can lead to improved predictive accuracy and can motivate research in parallel computing, they can also be plagued with redundancy, leading to wasted computation. In this talk we will discuss a class of approaches to data summarization and subset selection based on submodular functions. We will see how a form of "combinatorial dependence" over data sets can be naturally induced via submodular functions, and how resulting submodular programs (that often have approximation guarantees) can yield practical and high-quality data summarization strategies. The effectiveness of this approach will be demonstrated based on results from a wide range of applications, including document summarization, machine learning training data subset selection (for speech recognition, machine translation, and handwritten digit recognition), image summarization, and assay selection in functional genomics. Speaker Bio: Jeffrey A. Bilmes is a professor in the Department of Electrical Engineering at the University of Washington, Seattle and an adjunct professor in the Department of Computer Science and Engineering and the Department of Linguistics. He received his Ph.D. in Computer Science from the University of California, Berkeley. He is a 2001 NSF Career award winner, a 2002 CRA Digital Government Fellow, a 2008 NAE Gilbreth Lectureship award recipient, and a 2012/2013 ISCA Distinguished Lecturer. Prof. Bilmes has been working on submodularity in machine learning for more than twelve years. He received the best paper award at ICML 2013 and a best paper award at NIPS 2013 for work in this area. Prof. Bilmes is also a recipient of a 25-year paper award from the International Conference on Supercomputing for his 1997 paper on high-performance matrix optimization. Prof. Bilmes has authored the graphical models toolkit (GMTK), a dynamic graphical-model based software system that is widely used in speech and language processing, bioinformatics, and human-activity recognition. Free and open to the public. No registration required. *********************** UPCOMING SEMINARS 4/10 Budhendra Bhaduri<http://web.ornl.gov/sci/gist/staff_bios/staff_bhaduri.shtml> (Oak Ridge National Laboratory<http://www.ornl.gov/>--- Geographic Information Science and Technology) 4/24 Christian Rudder<http://www.okcupid.com/about> (OkCupid) Click here<https://lists.seas.harvard.edu/mailman/listinfo/iacs-events> to subscribe to our events list. _______________________________________________ Iacs-events mailing list Iacs-events(a)seas.harvard.edu https://lists.seas.harvard.edu/mailman/listinfo/iacs-events

9 years, 1 month

[Aspuru-Guzik group list] Bill Miller Visiting Next Thursday 3/26

by Jarrod McClean

Hi All, Next Thursday (3/26) Prof. William Miller of Berkeley ( http://www.cchem.berkeley.edu/millergrp/ ) will be visiting us after his Wednesday Theochem seminar (info below). If you would like to meet with him or attend lunch with him, please let me know as soon as possible! Talk Info: Time: 4:00 PM Date 3/25 Place: MIT 4-163 Title: Symmetrical Quasi-Classical Model for Classical Molecular Dynamics Simulations of Electronically Non-Adiabatic Processes Abstract: A recently described symmetrical windowing methodology [J. Phys. Chem. A 117, 7190 (2013)] for quasi-classical trajectory simulations is applied here to the Meyer-Miller [J. Chem. Phys. 70, 3214 (1979)] model for the electronic degrees of freedom in electronically non-adiabatic dynamics. Results generated using this classical approach are observed to be in very good agreement with accurate quantum mechanical results for a variety of test applications, including cases where coherence effects are significant and also the challenging asymmetric spin-boson system. Jarrod

9 years, 1 month

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