aspuru-list April 2013

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54 participants
81 discussions

[Aspuru-Guzik group list] [IACS-events] IACS Seminar Friday, April 26: Franziska Michor (HSPH) on Evolution of the Cancer Genome

by Info, IACS

Dear friends, Please join us for the final IACS seminar of the semester, which will feature Dr. Franziska Michor with a presentation on the "Evolution of the Cancer Genome". Videos of previous seminars can be viewed here: https://www.seas.harvard.edu/news-events/video/iacs-seminar-series. Date: Friday, April 26, 2013 Speaker: Franziska Michor, Associate Professor in the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Department of Biostatistics, Harvard School of Public Health Location: Maxwell-Dworkin G125, 33 Oxford Street, Cambridge, MA 02138 Time: Informal lunch with speaker, 12:30pm; Talk, 1:00pm Title: Evolution of the Cancer Genome Abstract: Cancer emerges through an evolutionary process in somatic tissue. The fundamental laws of evolution can best be formulated as exact mathematical equations; therefore, the process of cancer initiation and progression is amenable to mathematical investigation. Current areas of research of the Michor lab include cancer stem cells, the evolution of drug resistance, and the dynamics of metastasis formation. In this talk, I will introduce two examples of the application of evolutionary theory to cancer genomics and treatment. Speaker bio: Franziska Michor studied molecular biology and mathematics at the University of Vienna, Austria, and medical biotechnology at the Università degli Studi di Trieste, Italy. She received her PhD from Harvard's Department of Organismic and Evolutionary Biology in 2005. Afterwards, she was a Junior Fellow in the Harvard Society of Fellows and worked at the Dana-Farber Cancer Institute. From 2007 to 2010, she was assistant professor at the Memorial Sloan-Kettering Cancer Center. In 2010, she moved to the Dana-Farber Cancer Institute and Harvard School of Public Health. Her lab investigates the evolutionary dynamics of cancer. Visit http://iacs.seas.harvard.edu/events to subscribe to our Google calendar, manage your subscription to this mailing list, or access video and audio recordings of previous seminars. _______________________________________________ Iacs-events mailing list Iacs-events(a)seas.harvard.edu https://lists.seas.harvard.edu/mailman/listinfo/iacs-events

11 years

[Aspuru-Guzik group list] Marlon Away on Friday

by Marlon Cummings

Have a lovely weekend. ---------------------- Marlon G. Cummings Lab Manager, Aspuru-Guzik Group Mallinckrodt M112 Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge, MA 02138 617-496-9964 617-496-9411 (fax) http://aspuru.chem.harvard.edu/

11 years

[Aspuru-Guzik group list] Mark Tuckerman Tomorrow!

by Cynthia M. Chew

Hi Group, Here are the details of Prof. Mark Tuckerman's CCB-ITAMP seminar tomorrow. Following the talk, Mark will be attending our group meeting and then will be available for further discussion (4-4:45pm). Seminar Location & Time: Friday April 19, 2pm @ Pfizer Prof. Mark Tuckerman Department of Chemistry and Courant Institute of Mathematical Sciences New York University https://files.nyu.edu/mt33/public/index.html “Structure and transport of topological defects in hydrogen bond networks: Studies of water and phosphates using first-principle molecular dynamics" Proton transport in aqueous and non-aqueous hydrogen-bonded media has long been an area of intense study due to its fundamental importance in emerging energy technologies such as hydrogen fuel cells and in biological problems such as proton pumping. Our understanding of proton transport phenomena is based on the concept structural diffusion of a topological defect in the hydrogen bond network originally proposed by C. J. T. von Grotthuss in 1806. Within this picture, long-range proton transport is driven by specific structural rearrangements in the local hydrogen bonding environment, however, pinning down the specific microscopic mechanisms in different media remains an immense challenge that has an immediate impact on the problem of designing novel materials for enhancing the proton transport process. In this talk, I will show how first-principles molecular dynamics has contributed to our understanding of proton transport phenomena in a variety of systems including aqueous acidic and basic solutions, pure phosphoric acid, and phosphoric acid doped with water or imidazole. It will be shown that proton transport in aqueous systems relies largely on local fluctuations in the hydrogen bond network while phosphate systems, by contrast, transport protons along extended, polarized chains in a manner much closer to the original picture suggested by von Grotthuss. Best, Cynthia

11 years

[Aspuru-Guzik group list] [qip] Friday

by Edward Farhi

Hi Quanta We will meet on Friday at 11:00 in our usual spot. Juan is going to tell us about what he has been doing. At 2:00 on FridayThomas Vidick will give the QI seminar in 6C 442. His title is "Truly device-independent quantum key distribution". See you there. Best, Eddie ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Edward Farhi Cecil and Ida Green Professor of Physics Director Center for Theoretical Physics Massachusetts Institute of Technology 6-300 Cambridge MA 02139 617 253 4871 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: _______________________________________________ qip mailing list qip(a)mit.edu http://mailman.mit.edu/mailman/listinfo/qip

11 years

[Aspuru-Guzik group list] [Aspuru-meetings-list] group meeting this Friday: Dr. Takatoshi Fujita

by Ryan Babbush

Hi Everyone, Immediately following the ITAMP seminar being presented this Friday by Professor Mark Tuckerman, our own Dr. Takatoshi Fujita will present his current work in excitonics. We will meet in the Division Room as soon as possible after Professor Tuckerman's talk (so probably around 3:05). A title and abstract for group meeting is included below. Title: Dynamics of an exciton coupled to a classical phonon bath Abstract: In this talk, I will discuss dynamics of an exciton system coupled to a classical phonon bath and a relationship between atomistic and stochastic bath models. If the phonon bath is treated classically, dynamics of the exciton and phonon systems are described by the Ehrenfest equations. I will show by introducing Mori's projection operator technique that stochastic bath models can be regarded as an approximation of the Ehrenfest equations. Deficiencies of stochastic models can be explained by the derivation. Then, I will propose an idea to include reorganization effects into the stochastic model and apply it to study Stokes shifts in model J-aggregates. Finally, I will describe possible idea to correct quantum effects of the phonon bath. -- Ryan Babbush | PhD Student in Physics (949) 331-3943 | babbush(a)fas.harvard.edu Harvard University | Aspuru-Guzik Group 12 Oxford Street | Cambridge, MA 02138 _______________________________________________ Aspuru-meetings-list mailing list Aspuru-meetings-list(a)lists.fas.harvard.edu https://lists.fas.harvard.edu/mailman/listinfo/aspuru-meetings-list

11 years

[Aspuru-Guzik group list] HQOC/ITAMP Seminar - Today at 4:00 PM - J250

by Hamilton, Joan

***HQOC/ITAMP Joint Quantum Sciences Seminar*** **April 17, 2013 - 4:00 PM - Jefferson 250** *Prof. Harald Hess, HHMI - Janelia Farm Research Campus* "3D Imaging at the Limits with Photo-Activated Labels and Electrons" Fluorescence microscopy, is limited in its ability to resolve densely labeled features smaller than the optical diffraction limit, however special photoactivated fluorescent proteins or dyes can be harnessed in a technique called Photo-Activated Localization Microscopy, PALM. A series of personal challenges in fiber optics, fly height testing, and high throughput disk drive screening provided a diverse foundation in interferometry that inspired a new 3D imaging concept. This multiphase interferometry one can measure the vertical position of fluorescent molecules to nanometer precision with the highest photon efficiency and can be combined with PALM to give full 3 dimensional molecular coordinates of genetically tagged proteins with ~ 10-20 nm resolution. In a complimentary 3D project, electron microscopes, EM, can be customized for high throughput imaging for neural tissue or cells. Correlating PALM and electron microscopy gives EM images, which can be colorized with specific protein locations. Student Presentation by Yat Shan Au, Graduate Student, Doyle Lab "Cold Collision Studies with ThO" Student Presentation will begin at 4:00 PM Guest Presentation will begin at 4:30 PM Refreshments will be provided Joan Hamilton Faculty Assistant to Profs. Greiner and Lukin HQOC Laboratory Administrator HUCTW Local Union Representative Harvard University Department of Physics 17 Oxford Street Cambridge, MA 02138 P: (617) 496-2544 F: (617) 496-2545

11 years

[Aspuru-Guzik group list] Tuckerman visit Friday lunch

by Sawaya, Nicolas

Hi everyone, Let me know if you're interested in going to lunch with Professor Mark Tuckerman (of NYU), visiting this Friday. I was still waiting to find out how many people we can have and where we're going, but I'll keep track of the order in which people email me. Three spots taken so far. Cheers, Nicolas

11 years

[Aspuru-Guzik group list] ITAMP topical lunch discussion: Thursday April 18 @ 12:00

by Mikhail Lemeshko

Dear Friends, On Thursday, April 18, there will be an ITAMP topical lunch discussion. Tea Room (P-226) @ CfA (60 Garden Street) Time: 12:00-1:30 As always pizza will be served. Speaker: Chris Laumann Title: The hardness of approximating quantum optimization problems Abstract: The quest for quantum computers is motivated by their potential for solving problems that defy existing, classical, computers. The theory of computational complexity provides a rigorous framework for classifying the hardness of problems according to the computational resources, most notably time, needed to solve them. Its extension to quantum computers allows the relative power of quantum computers to be analyzed. This framework identifies families of problems which are likely hard for classical computers (“NP-complete”) and those which are likely hard for quantum computers (“QMA-complete”) by indirect methods. That is, they identify problems of comparable worst-case difficulty without directly determining the individual hardness of any given instance. Statistical mechanical methods can be used to complement this classification by directly extracting information about particular families of instances by studying random ensembles of them. These pose unusual and interesting (quantum) statistical mechanical questions and the results shed light on the difficulty of problems for large classes of algorithms as well as providing a window on the contrast between typical and worst case complexity. In this lunch talk, I will provide a brief background tour of the theory of computational complexity and its extension to quantum computers with reference to the quantum satisfiability problem. I will also introduce some of the related notions of 'hard' free energy landscapes in spin glasses and how they apply to ensembles of typical optimization problems. This will lead us to a study of the phase diagram of quantum satisfiability where we will find transitions between classically easy, classically hard and intrinsically quantum phases as a function of clause and energy density. Looking forward to seeing you there, Misha Lemeshko -- Dr. Mikhail Lemeshko 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. mlemeshko(a)cfa.harvard.edu http://sites.google.com/site/mishalemeshko/ Tel. +1 (617) 496-7610 Fax +1 (617) 496-7668

11 years

[Aspuru-Guzik group list] Prof. Harald Hess - HQOC/ITAMP Joint Quantum Sciences Seminar

by Hamilton, Joan

***HQOC/ITAMP Joint Quantum Sciences Seminar*** **April 17, 2013 - 4:00 PM - Jefferson 250** *Prof. Harald Hess, HHMI - Janelia Farm Research Campus* "3D Imaging at the Limits with Photo-Activated Labels and Electrons" Fluorescence microscopy, is limited in its ability to resolve densely labeled features smaller than the optical diffraction limit, however special photoactivated fluorescent proteins or dyes can be harnessed in a technique called Photo-Activated Localization Microscopy, PALM. A series of personal challenges in fiber optics, fly height testing, and high throughput disk drive screening provided a diverse foundation in interferometry that inspired a new 3D imaging concept. This multiphase interferometry one can measure the vertical position of fluorescent molecules to nanometer precision with the highest photon efficiency and can be combined with PALM to give full 3 dimensional molecular coordinates of genetically tagged proteins with ~ 10-20 nm resolution. In a complimentary 3D project, electron microscopes, EM, can be customized for high throughput imaging for neural tissue or cells. Correlating PALM and electron microscopy gives EM images, which can be colorized with specific protein locations. Student Presentation by Yat Shan Au, Graduate Student, Doyle Lab Student Presentation will begin at 4:00 PM Guest Presentation will begin at 4:30 PM Refreshments will be provided Joan Hamilton Faculty Assistant to Profs. Greiner and Lukin HQOC Laboratory Administrator HUCTW Local Union Representative Harvard University Department of Physics 17 Oxford Street Cambridge, MA 02138 P: (617) 496-2544 F: (617) 496-2545

11 years

Re: [Aspuru-Guzik group list] K20 test

by Alan Aspuru-Guzik

Thank you Jerry for doing this! I copy my group so they can test the GPU rig! Alán Aspuru-Guzik | Professor of Chemistry and Chemical Biology Harvard University | 12 Oxford Street, Room M113 | Cambridge, MA 02138 (617)-384-8188 | http://aspuru.chem.harvard.edu | http://about.me/aspuru On Mon, Apr 15, 2013 at 3:51 PM, Lotto, Gerald <lotto(a)harvard.edu> wrote: > Well, I had to fabricate the mounting hardware but: > [root@c8000eval ~]# lspci | grep NV > 03:00.0 3D controller: NVIDIA Corporation Device 1028 (rev a1) > 81:00.0 3D controller: NVIDIA Corporation Device 1028 (rev a1) > > Happy GPGUing! > > From: Alan Aspuru-Guzik <alan(a)aspuru.com> > Date: Wednesday, April 10, 2013 3:46 PM > To: Jerry Lotto <lotto(a)harvard.edu> > Cc: "christophkreisbeck(a)gmail.com" <christophkreisbeck(a)gmail.com>, > hanspeter pfister <pfister(a)seas.harvard.edu>, "hpfister(a)seas.harvard.edu" > <hpfister(a)seas.harvard.edu>, "lgreenhill(a)cfa.harvard.edu" < > lgreenhill(a)cfa.harvard.edu> > Subject: Re: K20 test > > Dear Jerry, > I would say take it out right away from our point of view. > > Best, > Alan > > Alán Aspuru-Guzik | Professor of Chemistry and Chemical Biology > Harvard University | 12 Oxford Street, Room M113 | Cambridge, MA 02138 > (617)-384-8188 | http://aspuru.chem.harvard.edu | http://about.me/aspuru > > > On Wed, Apr 10, 2013 at 3:45 PM, Lotto, Gerald <lotto(a)harvard.edu> wrote: > >> The K20s have arrived and I wish to arrange a downtime to swap them for >> the teslas. When would a convenient time be to take c8000eval down? >> >> From: "christophkreisbeck(a)gmail.com" <christophkreisbeck(a)gmail.com> >> Date: Sunday, March 10, 2013 7:46 PM >> To: Jerry Lotto <lotto(a)harvard.edu> >> Cc: Alan Aspuru-Guzik <alan(a)aspuru.com>, hanspeter pfister < >> pfister(a)seas.harvard.edu>, "hpfister(a)seas.harvard.edu" < >> hpfister(a)seas.harvard.edu>, "lgreenhill(a)cfa.harvard.edu" < >> lgreenhill(a)cfa.harvard.edu> >> Subject: Re: K20 test >> >> Hi Jerry, >> >> my code was developed on a NVIDIA C2075 and hence is optimized to this >> architecture. >> When we installed new K20 cards in Regensburg we did a comparison >> between the C2075 and K20's. We obtain an increase in performance of the >> K20 >> of about 10%-20%. Therefore, it makes sense that your installed card is a >> M2090 >> and not a K20. >> >> The 10%-20% is indeed not much of performance gain and we are still >> investigating the reason for this low factor. There is not much data >> transfer between CPU and GPU. >> My impression is that our code might run into bandwidth problems when >> accessing >> GPU memory. But as I mentioned we are still in the early process of >> investigations. >> >> Best Christoph >> >> >> >> >> >> >> 2013/3/10 Lotto, Gerald <lotto(a)harvard.edu> >> >>> This is what led me to be concerned about it:**** >>> >>> [root@c8000eval ~]# lspci | grep NVIDIA**** >>> >>> 03:00.0 3D controller: NVIDIA Corporation Tesla M2090 (rev a1)**** >>> >>> 81:00.0 3D controller: NVIDIA Corporation Tesla M2090 (rev a1)**** >>> >>> ** ** >>> >>> looking at the BOM and it lists**** >>> >>> 1 320-3773 NVIDIA M2090 PCIe x16 GPGPU card for C8220X**** >>> >>> 1 320-9364 NVIDIA M2090 PCIe x16 GPGPU, 2nd card for C8220X**** >>> >>> ** ** >>> >>> *From:* Alan Aspuru-Guzik [mailto:alan@aspuru.com] >>> *Sent:* Sunday, March 10, 2013 2:12 PM >>> *To:* Lotto, Gerald >>> *Cc:* pfister(a)seas.harvard.edu; christophkreisbeck(a)gmail.com; >>> hpfister(a)seas.harvard.edu; lgreenhill(a)cfa.harvard.edu >>> *Subject:* Re: K20 test**** >>> >>> ** ** >>> >>> How can it be Tesla if Christoph is comParing with a K20!! Christoph can >>> you query the card to see what model it is? **** >>> >>> ** ** >>> >>> Alan **** >>> >>> ** ** >>> >>> -- >>> Alan Aspuru-Guzik >>> Associate Professor of Chemistry and Chemical Biology >>> Harvard University >>> http://aspuru.chem.harvard.edu**** >>> >>> ** ** >>> >>> On Sunday, March 10, 2013 at 2:10 PM, Lotto, Gerald wrote:**** >>> >>> I sent that request a while back. Will try again. >>> >>> Sent from my Android Galaxy Nexus phone >>> >>> -----Original Message----- >>> *From:* Hanspeter Pfister [pfister(a)seas.harvard.edu] >>> *Received:* Sunday, 10 Mar 2013, 12:27pm >>> *To:* Lotto, Gerald [lotto(a)harvard.edu] >>> *CC:* christophkreisbeck(a)gmail.com [christophkreisbeck(a)gmail.com]; >>> hpfister(a)seas.harvard.edu [hpfister(a)seas.harvard.edu]; >>> lgreenhill(a)cfa.harvard.edu [lgreenhill(a)cfa.harvard.edu]; >>> aspuru(a)chemistry.harvard.edu forwards to aspuru.com [alan(a)aspuru.com] >>> *Subject:* Re: K20 test**** >>> >>> ** ** >>> >>> Hi Jerry,**** >>> >>> ** ** >>> >>> Can you please remedy this mistake and tell Dell to send us K20s >>> instead, and as quickly as possible? We already have two Tesla clusters, so >>> the current Dell configuration is essentially useless. **** >>> >>> ** ** >>> >>> I am actually surprised it's only 10% difference. I assume the >>> benchmark application is not GPU bound and either uses the CPU or moves >>> data a lot. Christoph - can you tell us more about it?**** >>> >>> ** ** >>> >>> Thanks!**** >>> >>> ** ** >>> >>> - HP**** >>> >>> ** ** >>> >>> On Mar 10, 2013, at 12:21 PM, "Lotto, Gerald" <lotto(a)harvard.edu> wrote: >>> **** >>> >>> >>> >>> **** >>> >>> Looks like the test system dell sent you is actually tesla, not kepler >>> (k20). >>> >>> Sent from my Android Galaxy Nexus phone >>> >>> -----Original Message----- >>> *From:* Alan Aspuru-Guzik [alan(a)aspuru.com] >>> *Received:* Sunday, 10 Mar 2013, 11:17am >>> *To:* Christoph Kreisbeck [christophkreisbeck(a)gmail.com]; Lotto, Gerald >>> [lotto(a)harvard.edu]; Hanspeter Pfister [hpfister(a)seas.harvard.edu]; >>> Lincoln Greenhill [lgreenhill(a)cfa.harvard.edu] >>> *Subject:* Re: K20 test**** >>> >>> Dear Christoph **** >>> >>> 10 percent is 10 percent. Can you work with Jerry to see the difference >>> in specs between Regensburg and the demo setup to see if we can 'regain' >>> that performance?**** >>> >>> ** ** >>> >>> Alan **** >>> >>> ** ** >>> >>> -- >>> Alan Aspuru-Guzik >>> Associate Professor of Chemistry and Chemical Biology >>> Harvard University >>> http://aspuru.chem.harvard.edu**** >>> >>> ** ** >>> >>> On Friday, March 8, 2013 at 6:23 PM, Christoph Kreisbeck wrote:**** >>> >>> Dear Alan, >>> >>> today I did some benchmark tests with the k20eval queue. >>> Everything worked pretty nice. I got GPU-HEOM running >>> and did comparisons with Tobias' K20's in Regensburg. >>> For the tested parameter the wokstation solution in Regensburg >>> is a little bit faster (about 10%) >>> >>> Best Christoph >>> >>> **** >>> >>> ** ** >>> >>> ** ** >>> >>> ** ** >>> >> >> >

11 years

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aspuru-list April 2013