aspuru-list October 2013

aspuru-list@lists.fas.harvard.edu

34 participants
87 discussions

[Aspuru-Guzik group list] AAG Administrative Office

by Marlon Cummings

Dear friends, The office will be closed tomorrow between 9-5. Please hold off on requests until Tuesday. If you have an appointment with Alan, Marlon, or Cynthia, those are still on. Best, Marlon.

10 years, 6 months

[Aspuru-Guzik group list] Fwd: [Cgrgt] DE Shaw Tech Talk next Tuesday at 6pm

by Adrian Jinich

DE Shaw Tuesday, Maxwell Dworkin. This should be great. ---------- Forwarded message ---------- From: Stern, Bodo <Bstern(a)cgr.harvard.edu> Date: Sun, Oct 6, 2013 at 3:08 PM Subject: [Cgrgt] DE Shaw Tech Talk next Tuesday at 6pm To: SYSBIOPHD_STUDENT(a)listserv.med.harvard.edu * * *D. E. Shaw Research Tech Talk and Information Session* Date: Tuesday, October 8, 2013 Time: 6:00 - 8:00 PM Location: Maxwell Dworkin, room 119 Company Website: http://www.deshawresearch.com/ Refreshments will be served! Please RSVP: https://docs.google.com/forms/d/1LOMjkZYIiRlipiVX6N21QDt9bctxXqE9_AZE-B9n7Y… *About The Talk* D. E. Shaw Research is an independent research laboratory that conducts basic scientific research in the field of computational biochemistry under the direct scientific leadership of Dr. David E. Shaw. Our group is currently focusing on molecular simulations involving proteins and other biological macromolecules of potential interest from both a scientific and a pharmaceutical perspective. Members of the lab include computational chemists and biologists, computer scientists and applied mathematicians, and computer architects and engineers, all working collaboratively within a tightly coupled interdisciplinary research environment. Our lab has designed and constructed a massively parallel supercomputer called Anton specifically for the execution of molecular dynamics (MD) simulations. Each Anton computer can simulate a single MD trajectory as much as a millisecond or so in duration -- a timescale at which biologically significant phenomena occur. Anton has already generated the world’s longest MD trajectory. Join us for an overview of our work on parallel algorithms and machine architectures for high-speed MD simulations and a description of the simulations that have helped elucidate the dynamics and functional mechanisms of biologically important proteins. *About The Speakers* *Andrew Taube *Andrew is involved in the development of improved force fields for biomolecular simulation. Prior to joining DESRES, Andrew was a John von Neumann Post Doctoral Research Fellow at Sandia National Laboratories. His work focused on using quantum mechanical methods to improve the accuracy of chemical simulations. Andrew received a Ph.D. in physical chemistry from the University of Florida, and a B.S. in chemistry and mathematics from Duke University. *Thomas Mildorf* Thomas focuses on analysis of molecular dynamics simulations and associated numerical and statistical issues. Thomas graduated from MIT with dual S.B. degrees in mathematics and biology. In 2006, he was a William Lowell Putnam prize winner. _______________________________________________ Cgrgt mailing list Cgrgt(a)lists.fas.harvard.edu https://lists.fas.harvard.edu/mailman/listinfo/cgrgt

10 years, 6 months

[Aspuru-Guzik group list] Fwd: Physical Chemistry Faculty Search at the University of Utah

by Felipe Herrera

Open position at the University of Utah, see below. Felipe -------- Original Message -------- Subject: Physical Chemistry Faculty Search at the University of Utah Date: Fri, 4 Oct 2013 14:09:37 -0700 From: <head(a)chem.ubc.ca> To: <grad(a)chem.ubc.ca>, <postdoc(a)chem.ubc.ca>, <reassoc(a)chem.ubc.ca> Hi Everyone, Position available -- please see attached and below. Cheers, Laura Partland Assistant to the Head, Michael Fryzuk Faculty of Science | Department of Chemistry The University of British Columbia | 2036 Main Mall, D225 Phone 604 822-2471 headsec(a)chem.ubc.ca <mailto:first.last@ubc.ca> The Department of Chemistry at the University of Utah invites applications for one or two tenure track positions in the area of physical chemistry, with primary focus on experimentalists, but with the possibility of a hire in theory. I would appreciate your help identifying outstanding candidates who show exceptional promise in your group, your department or whom you know from their work at other institutions. We are eager to invite them to send an application. Therefore, please forward the attached advertisement to these folks. Applications should be uploaded in PDF format directly to: /http://utah.peopleadmin.com/postings/24957/. Application review will begin Oct. 15 and continue until suitable candidates are identified. The University of Utah values candidates who have experience working in settings with students from diverse backgrounds, and possess a strong commitment to improving access to higher education for historically underrepresented students. The University of Utah is an Equal Opportunity/Affirmative Action employer and educator. Minorities, women, and persons with disabilities are strongly encouraged to apply. Veterans preference. Reasonable accommodations provided. For additional information: http://www.regulations.utah.edu/humanResources/5-106.html. I would like to thank you for any help in advance. Respectfully, Scott L. Anderson, Distinguished Professor of Chemistry /Attachment/ ********************* Debbie Olson Assistant to the Chair University of Utah Department of Chemistry 315 S 1400 E RM 2020 Salt Lake City, Utah 84112-0850 T: 801-581-3164 F: 801-581-8433 dolson(a)chem.utah.edu <mailto:dolson@chem.utah.edu> -- This message has been scanned for viruses and dangerous content by MailScanner believed to be clean.

10 years, 7 months

[Aspuru-Guzik group list] Flaskbox Update

by Trepte, Kai

Hi Everyone: A quick update. We have learned a lot this week. The most important thing is that we have hit an internal limit within Dropbox, not with the number of files, but with the amount of data that can be pulled in a single request. This has the effect of forcing us to rewrite our user initialization process so that it can take in data in smaller chunks. What this means is that if you share a folder with us, you will not see the initialization event that earlier users did due to the Dropbox limit. We have some more research to decide how to address the user initialization issue, but will keep you in the loop as we work through this issue. Other than that, Flaskbox appears to be operating as designed. If you notice any odd behavior, please let us know. As always, please let us know if you have an suggestions or improvements that we can make. With Respect, Team Flaskbox

10 years, 7 months

[Aspuru-Guzik group list] [qip] today

by Edward Farhi

Hi Quanta We are meeting this morning at 11:00 in 6-310. We will have a presentation by Michael Kastoryano. 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, 7 months

[Aspuru-Guzik group list] AQC 2014

by Ryan Babbush

Hey Everyone, This is still 8 months away but the 3rd annual conference in Adiabatic Quantum Computing was announced recently. Its in June, in Southern California. I went to this last March and it was an incredibly valuable experience for me - I suggest that everyone interested in adiabatic start thinking about a way to get funding to go! Here is the link: http://www.isi.edu/events/aqc2014/home Ryan

10 years, 7 months

[Aspuru-Guzik group list] Apartment Assiatance

by Marlon Cummings

Dear Group: Edward Pyzer-Knapp will be starting in January and has begun the apartment hunting process. As you know, Cambridge and Boston is a jungle and I am writing to ask if you can forward any leads or the names of honest agents he can work with. Please feel free to contact Edward directly (e.o.pyzerknapp(a)gmail.com) 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, 7 months

[Aspuru-Guzik group list] Moshe Shapiro, 10/9/2013 - HQOC/ITAMP Joint Quantum Sciences Seminar

by Hamilton, Joan

HQOC/ITAMP Joint Quantum Sciences Seminar Wednesday, October 9, 2013, Jefferson 250 4:00 - Student Presentation 4:10-4:30 - Refreshments 4:30 - Moshe Shapiro, Departments of Chemistry and Physics, The University of British Columbia, Vancouver, Canada, and Department of Chemical Physics, The Weizmann Institute, Rehovot, Israel Title: Dark states and the incoherent encoding of molecular motions Abstract: Contrary to conventional wisdom that all dynamics is a result of interference (or “dephasing”) between many (at least 2) energy eigenstates, we show that when a continuum of states is present, even a single molecular eigenstate undergoes “steady-state” quantum dynamics. Moreover, this type of dynamics can be initiated by incoherent (e.g.,solar) light sources. Continua are invariably involved in molecular systems due to a variety of sources such as the ever present bath modes; spontaneously emitted photons; the detachment of electrons; or the dissociation of chemical bonds. Contrary to a single bound energy-eigenfunction which is a real(“standing-waves”) function that carries no flux, hence has no dynamics, a single(complex) continuum energy-eigenfunction carries “steady-state” flux given by the group velocity of the energetically narrow wave packet it represents. We then proceed to discuss the possibility of encoding programmed molecular motions using the above incoherent dynamics. The encoding is attained by ordering the molecular eigenstates to have a specific sequence of "overlapping resonances". Using the prediction we already made in 1972 concerning the formation of "dark states" as a result of interference between overlapping resonances (giving rise to the development of the celebrated "Electromagnetically Induced Transparency" 17 years later), we show how "dark states" give rise to a very efficient transfer between eigenstates, thereby executing a desired sequence of molecular events (such as that involved in protein folding). We also show that "dark states" may enable us to attain the "holy grail" of chemical dynamics: the production of a molecular beams containing just one pre-selected internal (vib-rotational) state. 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

10 years, 7 months

[Aspuru-Guzik group list] Moshe Shapiro, 10/9/2013 - HQOC/ITAMP Joint Quantum Sciences Seminar

by Hamilton, Joan

HQOC/ITAMP Joint Quantum Sciences Seminar Wednesday, October 9, 2013 4:00 - Student Presentation 4:10-4:30 - Refreshments 4:30 - Moshe Shapiro, Departments of Chemistry and Physics, The University of British Columbia, Vancouver, Canada, and Department of Chemical Physics, The Weizmann Institute, Rehovot, Israel Title: Dark states and the incoherent encoding of molecular motions Abstract: Contrary to conventional wisdom that all dynamics is a result of interference (or “dephasing”) between many (at least 2) energy eigenstates, we show that when a continuum of states is present, even a single molecular eigenstate undergoes “steady-state” quantum dynamics. Moreover, this type of dynamics can be initiated by incoherent (e.g.,solar) light sources. Continua are invariably involved in molecular systems due to a variety of sources such as the ever present bath modes; spontaneously emitted photons; the detachment of electrons; or the dissociation of chemical bonds. Contrary to a single bound energy-eigenfunction which is a real(“standing-waves”) function that carries no flux, hence has no dynamics, a single(complex) continuum energy-eigenfunction carries “steady-state” flux given by the group velocity of the energetically narrow wave packet it represents. We then proceed to discuss the possibility of encoding programmed molecular motions using the above incoherent dynamics. The encoding is attained by ordering the molecular eigenstates to have a specific sequence of "overlapping resonances". Using the prediction we already made in 1972 concerning the formation of "dark states" as a result of interference between overlapping resonances (giving rise to the development of the celebrated "Electromagnetically Induced Transparency" 17 years later), we show how "dark states" give rise to a very efficient transfer between eigenstates, thereby executing a desired sequence of molecular events (such as that involved in protein folding). We also show that "dark states" may enable us to attain the "holy grail" of chemical dynamics: the production of a molecular beams containing just one pre-selected internal (vib-rotational) state. 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

10 years, 7 months

[Aspuru-Guzik group list] Group meeting tomorrow

by Ryan Babbush

Hi Everyone, Tomorrow I will be presenting group meeting at 2:30pm in the Division Room. I'll be speaking on a subject I know you are all very excited about: compiling problems for adiabatic quantum computing using perturbative gadgets. Perturbative gadgets provide a "scalable" methodology for encoding the eigenspectra of an n-qubit Hamiltonian in the lowest 2^n eigenstates of a more constrained (>n)-qubit Hamiltonian. For instance, gadgets might be used to lower the locality of a Hamiltonian or get rid of unwanted, difficult to implement couplings. While gadgets have been essential to many important proofs in quantum complexity theory, there has been little work done to characterize and improve upon the resources required to physically implement a gadget. I aim to provide a gentle introduction to the theory of perturbative gadgets while also discussing prospects and challenges for using gadgets to compile electronic structure problems to a form suitable for experimental implementation on an adiabatic quantum computer. -- 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

10 years, 7 months

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aspuru-list October 2013