aspuru-list October 2013

aspuru-list@lists.fas.harvard.edu

34 participants
87 discussions

[Aspuru-Guzik group list] Fwd: faculty positions at Notre Dame

by Sarah Mostame

FYI Sent from my iPhone ----- Sarah Mostame, Ph.D. Harvard University 12 Oxford Street, Room M104 Cambridge, MA 02138 email: mostame(a)fas.harvard.edu Begin forwarded message: > From: Ly Do <ly(a)pks.mpg.de> > Date: October 29, 2013 at 4:36:42 AM EDT > To: pksall(a)pks.mpg.de > Subject: Fwd: faculty positions at Notre Dame > > > FYI > > -------- Original Message -------- > Subject: faculty positions at Notre Dame > Date: Mon, 28 Oct 2013 16:51:36 -0400 > From: Zoltan Toroczkai <toro(a)nd.edu> > To: <ly(a)pks.mpg.de> > > > Dear Ly, > > Just a quick announcement for people at Mpipks who would be interested in getting > a faculty position in network science. One is in physics (our place) and the other > is in epidemics (applied math). Is it ok to ask you to please have this posted/advertised > at mpipks? > > in physics > https://academicjobsonline.org/ajo/jobs/3393 > > in applied math: > http://jobs.siam.org/jobseeker/job/15231477/Assistant/Associate%20Professor… > or here > http://acms.nd.edu/job-opportunities/#Faculty%20Positions%20in%20Disease%20… > > many thanks, > > best, > zoltan > > > ------------------------------ > Zoltán Toroczkai, PhD, > Professor of Physics, > Concurrent Professor of Computer Science and Engineering, > Physics Department, 225 Nieuwland Hall of Science, > University of Notre Dame, Notre Dame, IN, 46556, USA > -- > Email: toro(a)nd.edu , Ph: + 574 631-2618 > Admin: Ms. Alejandra (Jasmine) Botello (abotello(a)nd.edu) > Admin Ph: +574 631-7095, Fax: + 574 631-5952 > web: http://www.nd.edu/~toro > > >

10 years, 6 months

[Aspuru-Guzik group list] Mark Tuckerman's Seminar Today at 2pm

by Cynthia M. Chew

Hi Everyone, Just a reminder that Prof. Mark Tuckerman (NYU) is here at Harvard for the joint ITAMP/CCB Seminar series. His talk is at 2pm in Pfizer today. Please join us! Also, our group has the opportunity to meet with Mark from 4-4:45. Please meet in our common area. *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 Cynthia M. Chew Faculty Assistant | Aspuru-Guzik Research Group Department of Chemistry and Chemical Biology | Harvard University 12 Oxford Street | Mallinckrodt 112 | Cambridge, MA 02138 617.496.1716 office | 617.496.9411 fax http://aspuru.chem.harvard.edu/

10 years, 6 months

[Aspuru-Guzik group list] GREAT lecture on MOOCs

by Joey Goodknight

I want to wholeheartedly recommend for viewing the Harvard CS colloquium from October 7 by David Patterson: http://www.seas.harvard.edu/computer-science/computer-science-colloquia# He describes the great success he had with both a mooc and a connected software engineering electronic-textbook at Berkeley. It's really well done, really cool and really inspiring; please check it out! Have a great weekend! -Joey

10 years, 6 months

[Aspuru-Guzik group list] [qip] Friday October 25

by Edward Farhi

Hi Quanta We will meet on Friday at 11:00 in 6-310 as usual. We will have a presentation by Vlad Voroninski and also Daniel Nagaj will be there. At 1:30 Daniel will be speaking in our seminar series. See you there, 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

10 years, 6 months

[Aspuru-Guzik group list] Flaskbox Update

by Trepte, Kai

Hello Everyone: As some of you may have noticed, Flaskbox is back! We have corrected the naming issue for the Flaskbox output directory. We would have had this issue fixed sooner, but we ran into a variable naming issue along the way; we had a variable named "file_" which was a reserved word in one of our libraries - we had to change and test the change in all of our code which took some time. Now that this issue is resolved, Flaskbox should be stay up and running. With respect to the performance issues, we have begun implementing multiprocessing. We are starting with File ingestion (saving files) first because it is one of the most time consuming steps in the process. When this is split out, you should all expect to see a performance improvement in Flaskbox. When this is done we will move to activity tracking. With these changes, the base capability of Flaskbox should be complete. After completing the process we will shift our attention to setting up user login's and preferences. At present we are thinking of the following preferences based on your feedback: 1. Provide the ability to turn off Flaskbox file output. Your "Flaskbox_Output" directory will not be updated if you turn this capability off. 2. Provide the ability to set "ignore files." This will give you the ability to tell Flaskbox about files or file types that do not need to be ingested; e.g. git repository hash files. 3. Provide file search capability by file type, user, date, .... You will be able to search for files by all of the attributes that we capture. 4. Weekly usage charts. You will be able to see how much space and activity you are using in aggregate by file type. 5. Command line file upload tool. You will now be able to upload files without using Dropbox. If there are other capabilities that you would be interested in, please let us know. We have provided four choices that based on what we have heard, but there may be items that are more useful to the group than those listed above. Again, thank you for helping us through the alpha testing process. With Respect, Kai

10 years, 6 months

[Aspuru-Guzik group list] [IACS-events] REMINDER: IACS Seminar featuring Mercè Crosas--- TOMORROW, Friday, October 25

by Baker, Natasha

Date: Friday, October 25, 2013 Location: Maxwell-Dworkin G115, 33 Oxford Street, Cambridge, MA 02138 Speaker: Mercè Crosas, Director of Data Science at the Institute for Quantitative Social Science, Harvard University Time: Informal lunch with speaker, 12:30pm; Talk, 1:00pm. Title: 10 Simple Rules for the Care and Feeding of Scientific Data Abstract: Increasingly, scientific publications and claims are based on ever-increasing volumes of data. Once the publication is complete, it is often difficult for others to locate the data and accompanying analyses, and once located, often challenging to make sense of them. For scientific results to continue being subject to verification and extension, we in the scientific community must ensure that good data management, with sufficient transparency and accessibility of data and analyses, become essential and ordinary elements of the research cycle. In this paper, we present 10 simple rules to help scientists towards this goal. Speaker bio: Mercè Crosas is the Director of Data Science at the Institute for Quantitative Social Science (IQSS) at Harvard University. Her team includes the Dataverse Network project, data acquisition and curation, the Murray Research Archive, statistical programming (Zelig and other R statistical packages), and the Consilience project on text analysis. She is currently collaborating with: 1) the Data Privacy Lab to address concerns about sharing sensitive data for research, 2) PKP's Open Journal System to establish a permanent link between open access publications and their accompanying data, 3) the DataBridge project to develop sociometric tools for research data, 4) the Seamless Astronomy group to link astronomy data to literature, and is co-leading a global initiative to define the Declaration of Data Citation Principles. Mercè Crosas joined IQSS in 2004 as software development lead of a data sharing project, which later became the Dataverse Network. Before joining IQSS, she worked in the educational software and biotech industries, leading software development teams. Prior to that, she was a researcher at the Harvard-Smithsonian Center for Astrophysics, She earned a Ph.D. in Astrophysics from Rice University and a B.S. in Physics from the Universitat de Barcelona, Spain. ************************* Upcoming IACS Seminars Friday, 11/8. "Probabilistic Programming and Probability Processing" presented by Ben Vigoda, Director of Analog Devices Lyric Labs Friday, 11/22: "Deep Learning for Distribution Estimation" presented by Hugo Larochelle, Assistant Professor at the Université de Sherbrooke (UdeS) Please 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

10 years, 6 months

[Aspuru-Guzik group list] new quasi-particles discovered by Levitov :)

by Semion Saikin

http://www.nature.com/news/single-electrons-make-waves-1.14015 -- ******************************************** 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 ********************************************

10 years, 6 months

[Aspuru-Guzik group list] Reminder: visit Prof. Baroni

by Xavier Andrade

Hi all, This is to remind you that today at 11:15 AM (in one hour) in the Division room we have a slot for group members to discuss with Prof. Stefano Baroni. In case you haven't read it, I include the abstract of his talk (today at 4:00 PM in Pfizer), that I think overlaps considerably with the interests of the group. Remember that this is part of the Theochem seminar series that is organized by students and postdocs of Harvard, BU and MIT. As such, it requires the participation of students and postdocs. Xavier ================================================== Ab initio colors Abstract: I will present some recent work addressing the effects of the solvent (water) on the optical properties of natural dyes. I will break the ice with a short presentation of the physics and physiology of color vision, in the style of popular science. I will then introduce some of the theoretical and computational techniques that are currently being used to model the optical properties of complex molecular systems and nano- structured materials, based on time-dependent density-functional perturbation theory. These techniques will be demonstrated with the “prediction” that grass is green, and applied to the optical properties of flavylium, the die that gives aubergines and blueberries their typical deep-purple coloration, as well as of other anthocyanins. I will show that the main effect of the solvent is to provide a medium allowing thermal fluctuations to fill the gaps that would otherwise characterize the spectrum of the dye at low temperature, thus considerably enhancing optical absorption in the visible range, and making blueberries (deep) blue. The uncertainties due to the inadequacies of current energy functionals will be discussed, along with the prospects of predicting and engineering the color optical properties of anthocyanins in solution.

10 years, 6 months

[Aspuru-Guzik group list] [theochem-announce] Theochem Seminar 4:00 PM TODAY @ HARVARD - Prof. Stefano Baroni

by Thomas Robert Avila

Hello all, Prof. Stefano Baroni from the International School for Advanced Studies (Trieste, Italy) will give a talk in the Theochem seminar series today at Harvard at 4:00 PM. Prof. Baroni is known for pioneering different quantum simulation methods, among which the most widely known are density-functional-perturbation theory and reptation quantum Monte Carlo. Title: "Ab-initio colors" Speaker: Prof. Stefano Baroni Date: Thursday, Oct 24th, 4.00-6.00pm Venue: Pfizer Lecture Hall (Mallinckrodt Building, 12 Oxford St., Cambridge) - Harvard University -Thomas Abstract: I will present some recent work addressing the effects of the solvent (water) on the optical properties of natural dyes. I will break the ice with a short presentation of the physics and physiology of color vision, in the style of popular science. I will then introduce some of the theoretical and computational techniques that are currently being used to model the optical properties of complex molecular systems and nano- structured materials, based on time-dependent density-functional perturbation theory. These techniques will be demonstrated with the “prediction” that grass is green, and applied to the optical properties of flavylium, the die that gives aubergines and blueberries their typical deep-purple coloration, as well as of other anthocyanins. I will show that the main effect of the solvent is to provide a medium allowing thermal fluctuations to fill the gaps that would otherwise characterize the spectrum of the dye at low temperature, thus considerably enhancing optical absorption in the visible range, and making blueberries (deep) blue. The uncertainties due to the inadequacies of current energy functionals will be discussed, along with the prospects of predicting and engineering the color optical properties of anthocyanins in solution. _______________________________________________ theochem-announce mailing list theochem-announce(a)mit.edu http://mailman.mit.edu/mailman/listinfo/theochem-announce

10 years, 6 months

[Aspuru-Guzik group list] Administrative Office -- Today

by Marlon Cummings

Dear Friends: I will be away from the office starting at 11:30 am. Cynthia will be here but working on different projects for the group. If you can, please hold off with requests until tomorrow. Thanks, Marlon. ---------------- 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/

10 years, 6 months

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aspuru-list October 2013