aspuru-list March 2015

aspuru-list@lists.fas.harvard.edu

32 participants
64 discussions

[Aspuru-Guzik group list] Postdocs from our group strongly encouraged to apply

by Alan Aspuru-Guzik

9 years, 2 months

[Aspuru-Guzik group list] [IACS-events] IACS Seminar: "Chile-Harvard Innovative Learning Exchange"------ Friday 3/6 @1pm

by Baker, Natasha

Date: Friday, March 6, 2015 Location: Maxwell Dworkin G115, 33 Oxford Street, Cambridge MA 02138 Speakers: Diana Zhang, Sabrina Zhou, Xufei Wang, Lyla Fadden, Kim Minjae Time: Lunch 12:30pm; Talk 1-1:30pm Title: Chile-Harvard Innovative Learning Exchange Abstract: Five Harvard graduate students will discuss their recent research trip to Chile to analyze data from the Dark Energy Camera (DECam). The DECam is one of the instruments used in the Dark Energy Survey<http://www.darkenergysurvey.org/> (DES), an international effort “designed to probe the origin of the accelerating universe" and help uncover the nature of dark energy." Collaborating with students at the University of Chile, Harvard students were separated into small teams and ask to identify and classify objects as galaxies, stars or asteroids. Designed by IACS Scientific Program Director and Lecturer Pavlos Protopapas<http://iacs.seas.harvard.edu/people/pavlos-protopapas>, the two-week Chile-Harvard Innovative Learning Exchange Program is in its second year and aims to provide students the experience of working on international teams with noisy and imperfect data sets. Free and open to the public. No registration required. *********************** UPCOMING SEMINARS 3/27 Jeff Bilmes<http://www.ee.washington.edu/faculty/bilmes/> (University of Washington) 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, 2 months

[Aspuru-Guzik group list] March 10: Meet with Anastasia Alexandrova

by Joey Goodknight

Hello Everyone, Anastasia Alexandrova of UCLA is coming to visit as part of theochem and we've got the chance to meet with her next week on Tuesday 10 March. http://www.chem.ucla.edu/~ana/research.html she works broadly in theory/computation for materials. Let me know if you want to meet with her or grab lunch or dinner with her! -Joey

9 years, 2 months

[Aspuru-Guzik group list] Theochem reminder

by Martin Blood-Forsythe

Just a friendly reminder about the Theochem seminar this Wednesday with Professor Benoit Roux. Please note the changed time and room for this week! The Aspuru-Guzik group also has a discussion slot with Professor Roux at *5pm on Tuesday.* When: Wednesday (March 4, 2015) at 3:00 - 5:00 Where: Building 66 Room 144 at MIT The title and abstract of his talk is given below. Best wishes, -Martin Title: Membrane potential and small charge movement in membrane protein systems Abstract: A theoretical framework is elaborated to account for the effect of a transmembrane potential in explicit solvent computer simulations of membrane proteins [1]. The framework relies on a modified Poisson-Boltzmann equation previously developed from statistical mechanical considerations [2]. It is shown that a simulation with a constant external electric field applied in the direction normal to the membrane is equivalent to the influence of surrounding infinite baths maintained to a voltage difference via ion-exchanging electrodes connected to an electromotive force. It is also shown that the linearly-weighted displacement charge within the simulation system tracks the net flow of charge through the external circuit comprising the electromotive force and the electrodes. Using a statistical mechanical reduction of the degrees of freedom of the external system, three distinct theoretical routes are formulated and examined for the purpose of characterizing the free energy of a protein embedded in a membrane that is submitted to a voltage difference: the W-route constructed from the variations in the voltage-dependent potential of mean force along a reaction path connecting two conformations of the protein, the Q-route based on the average displacement charge as a function of the conformation of the protein, and the G-route based on the relative charging free energy of specific residues, with and without applied membrane potentials. The theory is applied to examine atomic models of the Kv1.2 potassium channel in the active and resting state [2]. Methodologies to treat asymmetric membrane conditions have also been developed [3]. Calculations of the fractional transmembrane potential, acting upon key charged residues of the voltage sensing domain of the Kv1.2 potassium channel, reveals that the applied field varies rapidly over a narrow region of 10 to 15 Angstroms, corresponding to the outer leaflet of the bilayer [4]. The focused field allows the transfer of a large gating charge without translocation of S4 across the membrane. The theory is also applied to examine the binding of sodium and potassium ions to the Na,K ATPase membrane pump. 1. B. Roux. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical Journal. 1997;73(6):2980-9. 2. B. Roux. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J. 2008;95(9):4205-16. 3. F. Khalili-Araghi, B. Ziervogel, J.C. Gumbart, B. Roux. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. J Gen Physiol. 2013;142(4):465-75. 4. F. Khalili-Araghi, V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, K. Schulten. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J. 2010;98(10):2189-98

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aspuru-list March 2015