aspuru-list November 2013

aspuru-list@lists.fas.harvard.edu

34 participants
83 discussions

[Aspuru-Guzik group list] Flaskbox Update - GREAT NEWS

by Trepte, Kai

Hi Everyone: Thank you for sticking with us through the alpha testing. We have some exciting news. 1. We have turned off system output globally. Many people experienced issues where our file output was swamping their Dropbox and causing synchronization issues. With output turned off you should no longer have this issue. 2. We have added multi-threading for file capture. Many people commented on the slowness of Flaskbox, with this change, we expect that the system will be better able to keep up with file activity. For those of you who un-shared your folders with us, please re-share them so we can check system performance. Also, if there are other folders you can share, please do so. We need activity to continue our tests. For the future - we are adding a very exciting feature: AUTOMATIC DATA PARSING. This process will take MOPAC and QCHEM (and other file types in the future) and parse them into our molecular database so that you can access them directly without having to scan through files; e.g. you will be able to request all of the "free energy" or "homo/lumo" values directly in python or any other language - we could add an export to Excel if that would be helpful. Again, thank you for all of the support. Please let us know if there is anything that we can be doing better. With Respect, Kai

10 years, 5 months

[Aspuru-Guzik group list] Group Slot with Robert Harrison

by Thomas Markovich

Hello All, Just a reminder that we have a group slot to meet with Robert Harrison, our Theochem Speaker, today from 430-530 in the group lounge area. Please drop by and at least meet him, he's a pretty cool guy. His talk title and and abstract are below. Best, Thomas Seeking a sustainable model for scientific simulation Robert J. Harrison Institute for Advanced Computational Science Stony Brook University Many are now questioning whether our current approaches to developing software for science and engineering are sustainable. In particular, can we deliver to society and the nation the full benefits expected from high-performance simulation at the peta and exascales? Or is innovative science being stifled by the increasing complexities of all aspects of our problem space (rapidly changing hardware, software, multidisciplinary physics, etc.)? Focusing on applications in chemistry and materials science, and motivated co-design of exascale hardware and software, I will discuss many of these issues including how chemistry has already been forced to adopt solutions that differ quite sharply to those in the mainstream, and how these solutions position us well for the technology transitions now under way. Radical changes in how we compute, going all the way back to the underlying numerical representation and algorithms used for the simulation, also promise great enhancements to both developer productivity and the accuracy of simulations.

10 years, 5 months

[Aspuru-Guzik group list] [Aspuru-meetings-list] two group meetings this week: Peter Love and Jacob Biamonte

by Ryan Babbush

Hi Everyone, This week we will have two group meetings. First, at our usual time and place of 2:30pm on Thursday in the Division Room, Professor Peter Love will present: =========================================================== Mixed state entanglement: bounds, computation and optimal ensembles =========================================================== Quantifying entanglement has been a longstanding goal of quantum information theory, and many measures for pure states exist. These measures may be extended to mixed states by the convex roof construction. This requires the determination of the convex decomposition of the density matrix into pure states that minimizes the average pure state entanglement. One may regard this as the mean pure-state entanglement cost of synthesizing the density matrix. This minimization is challenging, and exact solutions are only known in a few cases, the most famous of which is the concurrence for two qubits. The next hardest case would seem to be the three-tangle for mixed states of three qubits, for which an analytic form is currently unknown. In this talk I will describe numerical techniques to both compute and bound the three-tangle, and give some properties of the minimal ensembles for this and other polynomial entanglement monotones. On Friday we will be visited by Dr. Jacob Biamonte who will give a presentation that should have special appeal to those doing work on reaction networks. Jacob's talk will be Friday at 1:30pm in the Division Room, ============================================ Quantum Techniques for Chemical Reaction Networks ============================================ Jacob Biamonte, ISI Foundation (jacob.biamonte(a)qubit.org) There is a widely used and successful theory of "chemical reaction networks", which provides a framework describing any system governed by mass action kinetics. Computer science and population biology use the same ideas under a different name: "stochastic Petri nets". But if we look at these theories from the perspective of quantum theory, they turn out to involve creation and annihilation operators, coherent states and other well-known ideas---yet in a context where probabilities replace amplitudes. I will explain this connection as part of a detailed analogy between quantum mechanics and stochastic mechanics which we've produced several results on recently [1, 2, 3], including the recent analytical results uniting quantum physics and complex networks [2]. Our general idea is about merging concepts from quantum physics and complex network theory [1, 2, 3] to provide a bidirectional bridge of relevant analysis tools to address networks in both disciplines. Time permitting, I will close with some work in progress I have towards applying results related to partition functions to rank complexes and transitions in reaction networks. Parts of this talk represent joint work appearing in the following papers: [1] Baez and Biamonte, Quantum Techniques for Stochastic Mechanics, 235 pages to appear in Oxford University Press 2014, ArXiv preprint arXiv:1209.3632 [quant-ph] (2012). http://arxiv.org/abs/1209.3632 [2] Faccin et al., Degree Distribution in Quantum Walks on Complex Networks, Phys. Rev. X 3, 041007 (2013). http://prx.aps.org/abstract/PRX/v3/i4/e041007 [3] Zimboras et al., Quantum Transport Enhancement by Time-Reversal Symmetry Breaking, Sci. Rep. 3, 2361 (2013). http://www.nature.com/srep/2013/130806/srep02361/full/srep02361.html _______________________________________________ Aspuru-meetings-list mailing list Aspuru-meetings-list(a)lists.fas.harvard.edu https://lists.fas.harvard.edu/mailman/listinfo/aspuru-meetings-list

10 years, 5 months

[Aspuru-Guzik group list] -- Special AAG group meeting: Wednesday Nov 6th, 1:30 pm, Division Room.

by Er, Suleyman

Dear all, Dr. Jorge Aguilera-Iparraguirre's talk is on Wednesday-Nov 6th at 1:30 in the Division room. Attached is his updated schedule. "EXPLICITLY-CORRELATED METHODOLOGIES IN THE SEARCH FOR ALTERNATIVE FUELS: THE KORCEK REACTION AND MORE." Abstract: This talk will attempt to explain a three point process: First, the importance of kinetic modeling in the study of alternative fuels. Second, how the implementation of automatic computer generation has had a great impact in the reliability and usability of such models, and third, how the set of explicitly-correlated methods available nowadays (in particular CCSD(T)-F12) has made possible to fill the gaps in accuracy that the kinetic methods have lacked in the pass. As the main topic of the talk, the re-discovery of the Korcek reaction. The subject of our latest research. Using very different techniques, from multireference to explicit- correlated calculations, from Transitions State Theory to liquid phase, all in search for an answer to a thirty years old question. Best, Suleyman

10 years, 5 months

[Aspuru-Guzik group list] Theochem Speaker Tomorrow

by Thomas Markovich

Hi All, We'll have Professor Robert Harrison visiting us tomorrow and giving the theochem lecture on Wednesday at MIT. The group has a group slot from 430-530 but there are available time slots open from 130-230 if you'd like to meet with him individually. Additionally, there's two spots for lunch with him if you're interested. Sorry for this being so last minute! We had another group pull out... Also, I've included his abstract and title below. Best, Thomas Seeking a sustainable model for scientific simulation Robert J. Harrison Institute for Advanced Computational Science Stony Brook University Many are now questioning whether our current approaches to developing software for science and engineering are sustainable. In particular, can we deliver to society and the nation the full benefits expected from high-performance simulation at the peta and exascales? Or is innovative science being stifled by the increasing complexities of all aspects of our problem space (rapidly changing hardware, software, multidisciplinary physics, etc.)? Focusing on applications in chemistry and materials science, and motivated co-design of exascale hardware and software, I will discuss many of these issues including how chemistry has already been forced to adopt solutions that differ quite sharply to those in the mainstream, and how these solutions position us well for the technology transitions now under way. Radical changes in how we compute, going all the way back to the underlying numerical representation and algorithms used for the simulation, also promise great enhancements to both developer productivity and the accuracy of simulations.

10 years, 5 months

[Aspuru-Guzik group list] [qip] Wednesday talk by Troyer

by Edward Farhi

ITAMP/HQOC Joint Quantum Sciences Seminar Matthias Troyer Institute of Theoretical Physics, ETH, Zurich Wednesday, November 6, 4:00 PM, Jefferson 250 "Quantum Annealing" Abstract: Quantum annealing - a finite temperature version of the quantum adiabatic algorithm - combines the classical technology of slow thermal cooling with quantum mechanical tunneling, to try bring a physical system faster towards its ground state. The Canadian company D-Wave systems has recently built and sold programmable devices that are designed to use this effect to find solutions to hard optimization problems. I will present results of experiments designed to shed light on crucial questions about these controversial devices: are they quantum or classical? And are they faster than classical devices? _______________________________________________ qip mailing list qip(a)mit.edu http://mailman.mit.edu/mailman/listinfo/qip

10 years, 5 months

[Aspuru-Guzik group list] Fwd: please post: postdoc position in theoretical QIS at C.N. Yang Institute for Theoretical Physics, Stony Brook University

by Alan Aspuru-Guzik

For those of you looking for first or second postdoctoral opportunities, 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 ---------- Forwarded message ---------- From: Tzu-Chieh Wei <tzu-chieh.wei(a)stonybrook.edu> Date: Mon, Nov 4, 2013 at 11:16 AM Subject: please post: postdoc position in theoretical QIS at C.N. Yang Institute for Theoretical Physics, Stony Brook University To: Dear Colleague, Could you please forward the information on a postdoctoral position in theoretical quantum information science to those who may be interested? Thank you for your assistance, Tzu-Chieh Wei Assistant Professor, C.N. Yang Institute for Theoretical Physics, Stony Brook University "Postdoctoral Position in Theoretical Quantum Information Science at the C.N. Yang Institute for Theoretical Physics, Stony Brook University" The C. N. Yang Institute for Theoretical Physics at Stony Brook University invites applications for a postdoctoral position in the field of theoretical quantum information science with anticipated appointment dates of September 1, 2014. The current interest in quantum information science includes, but is not limited to, quantum computational models (such as measurement-based, topological and adiabatic), computational complexity in many-body systems, and applications of tensor product states. The Institute has a tradition of interaction with the Departments of Physics and Astronomy and Mathematics, and strong connections to the Simons Center for Geometry and Physics. Interested applicants must apply through AcademicJobsOnline. Candidates should upload their curriculum vitae, publication list and research plan, and arrange to have three letters of reference submitted online at https://academicjobsonline.org/ajo/jobs/3513. This job opportunity is also listed at: http://www.stonybrook.edu/cjo (Ref# WC-R-8246/13/10-S). Review of applications will begin December 1, 2013, and continue until the position is filled. Stony Brook University is an Equal Opportunity/Affirmative Action Employer.

10 years, 5 months

[Aspuru-Guzik group list] Add yourselves.

by Alan Aspuru-Guzik

Dear all, Feel free to add yourselves to this cool academic tree... http://academictree.org/chemistry/tree.php?pid=64702 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

10 years, 5 months

[Aspuru-Guzik group list] Special group meeting 2-3pm November 5, 2013 with a postdoctoral candidate

by Dmitry Zubarev

Dear Colleagues, Dr. Brett Savoie (Northwestern U, Ratner Group) will be visiting our group on November 5, 2013. His research interests include organic photovoltaics, amorphous materials, and charge/energy transport in molecular networks. There are five time-slots for personal meetings with Brett in the morning: 9:30 - 10:00am, 10:00 - 10:30am, 10:30-11:00am, 11:00 - 11:30am, and 11:30 - 12:00pm. Please make sure to pick one of these times, let me know, and have your name in the schedule. We also need two (2) volunteers to join our guest for lunch from 12:00pm till 1:30pm. Everyone is strongly encouraged to attend Brett's talk at 2:00pm in the Division Room. The title and abstract follow. *Title:* "Electrons Climbing Trees: The Molecular Networks Responsible for Charge Transport and Generation in Amorphous Organic Materials" *Abstract:* In this talk, I'll walk through the principle challenges to predictively designing amorphous organic materials, using organic photovoltaic materials as an example. A springboard for this discussion is the empirical observation that some structurally disordered organic films manage to macroscopically transport energy and charge, even in the absence of periodic order. I'll show how network theory is the natural language for describing the inherent complexity and richness of these systems, and discuss some recent results. Namely, a new methodology is developed that utilizes network analysis to identify the hierarchical importance of the many possible intermolecular interactions in the amorphous phase. On the basis of results obtained from this methodology, it will be argued that the functional robustness of certain families of organic materials to structural disorder arises from their ability to create spatially extended electrical networks. Best, Dmitry

10 years, 5 months

[Aspuru-Guzik group list] Fwd: [SPS] Physics 95 Wednesday Night Seminar - November 6, 2013 - 7:30pm; Jefferson 453

by Ian Dunn

In case anyone is interested in hearing Professor Hau discuss cold atoms and photosynthesis. This talk will be aimed at grad students and advanced undergraduate students. Professor Hau's group is the one that's famous for trapping light in a BE condensate. Best, Ian Begin forwarded message: > From: "Allen, Angela" <arallen(a)fas.harvard.edu> > Date: November 4, 2013 12:05:32 PM EST > To: "Society of Physics Students (sps-list(a)hcs.harvard.edu)" <sps-list(a)hcs.harvard.edu> > Cc: Lene Hau <hau(a)physics.harvard.edu>, "grads1(a)physics.harvard.edu" <grads1(a)physics.harvard.edu>, "grads2(a)physics.harvard.edu" <grads2(a)physics.harvard.edu>, Jacob Barandes <barandes(a)physics.harvard.edu> > Subject: [SPS] Physics 95 Wednesday Night Seminar - November 6, 2013 - 7:30pm; Jefferson 453 > > > > Wednesday Night Seminar > > November 6, 2013 > Jefferson 453; 7:30 pm > > ________________________________________ > > “Cold Atoms/Nanoscience; > Photosynthesis” > > Professor Lene Hau > > All are welcome! > ICE CREAM WILL BE SERVED. > > _______________________________________________ > sps-list mailing list > sps-list(a)lists.hcs.harvard.edu > https://lists.hcs.harvard.edu/mailman/listinfo/sps-list

10 years, 5 months

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aspuru-list November 2013