aspuru-list March 2016

aspuru-list@lists.fas.harvard.edu

23 participants
63 discussions

[Aspuru-Guzik Group List] [qip] Friday the 18th

by Edward Farhi

Hi Quanta We will meet tomorrow at 11:00 in our usual spot. Shelby is visiting and will say a few words. Also Shalev is supposed to speak. See you then. 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

8 years, 1 month

[Aspuru-Guzik Group List] tomorrow group meeting

by Semion Saikin

Dear Group, I am giving a group meeting tomorrow and have two options for the talk. Could you please let me know what do want to hear? Just reply to me with the number 1 or 2 before 3pm today. Here are the options: 1. The presentation on cavity-assisted spectroscopy of LHCs that I use for my job applications. Some of you heard it already. 2. My current research on plasticity in networks of neurons. I will appreciate your input. Semion --

8 years, 1 month

[Aspuru-Guzik Group List] Group Lunch 3/16 (Wednesday) at 12pm

by Jennifer Wei

Hi Everyone, Just a reminder that we will be having group lunch on Wednesday this week. Please RSVP at this link <https://docs.google.com/forms/d/1klMX0l9K9l48FwJAVlvVjBaFcnRNxsCqttq6MWqFYI…> so I can call ahead and make a reservation. In the future, we'll try to make group lunch a fixed time every few weeks; let me know if you have any suggestions about that. Thanks! See you soon. Jennifer

8 years, 1 month

[Aspuru-Guzik Group List] Themchem, Prof. Eugene Shackhnovich

by Teresa Tamayo

Hello everyone, The next speaker of Theochem lectures will be Prof. Eugene Shackhnovich. We have some spots for both students and postdocs to meet with him on Thursday, March 24th and some spots for lunch. If you want to meet with him or/and to attend lunch, please let me know. Tere PS. These are the details of his lecture: Wednesday, March 13th, MIT Building 4, Room 163. Understanding evolution on multiple scales: from protein physics to population geneticsBiological phenomena unfold in a broad range of scales ranging from molecules to cells to populations and ecosystems. Variation of molecular properties of biomolecules profoundly impact the ability of cells to survive and propagate (fitness). Finally, the fate of a mutation is decided by Darwinian selection on the level of the population, where three outcomes are possible: fixation in the population, elimination by purifying selection or separation in the population in a subdominant clone (polymorphism). In this lecture I will outline my lab’s and others efforts in an emerging new field which merges molecular mechanism with evolution. I will review basic concepts and models that contributed to our multiscale understanding of physical-chemical basis of biological phenomena. First, I will discuss physical chemistry of protein folding. I will present the fundamental heteropolymer model of protein folding and briefly outline the statistical mechanical analysis, which uncovered the energy gap criterion - the necessary and sufficient conditions for a heteropolymer sequence to encode a foldable protein. I will highlight the analogy and fundamental differences between heteropolymer and spin glass models. I will also discuss how understanding of basic principles of protein folding helps in our efforts to design new proteins and decipher the ‘’messages’’ hidden in multiple sequence alignment. I will then discuss the analogy between sequence selection for energy gaps and statistical mechanics of a class of generalized spin models. The statistical mechanical view of sequence selection enjoyed renaissance with the development of statistical methods to derive structural information about proteins from the analysis of variation in multiple sequence alignment. Finally I will discuss the relation between selection for foldable sequences and thermodynamic and kinetic mechanisms of protein folding such as first-order-like cooperativity. Next, I will present recent efforts at modeling evolutionary dynamics that merges molecular mechanisms with population genetics. Traditional population genetics models are agnostic to the physical-chemical nature of mutational effects. Rather they operate with an a’priori assumed distributions of fitness effects (DFE) of mutations from which evolutionary dynamics are derived. Alternatively some population genetics models aim to derive DFE from evolutionary observations. In departure with this tradition the novel multiscale models integrate the molecular effects of mutations on physical properties of proteins into physically intuitive yet detailed genotype-phenotype relationship (GPR) assumptions. I will present a range of models from simple analytical diffusion-based model on biophysical fitness landscapes to more sophisticated computational models of populations of model cells where genetic changes are mapped into molecular effects using biophysical modeling of proteins and ensuing fitness changes determine the fate of mutations in realistic population dynamics. Examples of insights derived from biophysics-based multiscale models include the scale-free character of Protein Universe, the fundamental limit on mutation rates in living organisms, physics of thermal adaptation, co-evolution of protein interactions and abundances in cytoplasm and related results, some of which I will present and discuss. Finally I will briefly present “bottom-up: experimental efforts based on genome editing approaches to test basic assumptions of multiscale biophysics-based models of evolution.

8 years, 1 month

[Aspuru-Guzik Group List] Fwd: Summer Data Science Fellowship Opportunity - 9t

by Alan Aspuru-Guzik

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: Michael Li <michael.li(a)mailg.thedataincubator.com> Date: Tue, Mar 15, 2016 at 9:14 AM Subject: Summer Data Science Fellowship Opportunity - 9t To: alan(a)aspuru.com Hi Aln, Thank you for your interest and support of The Data Incubator. We are grateful for your helping to spread the word about our fellowship program. You can also read about some of our latest fellows on our blog <http://blog.thedataincubator.com/>. Due to its success and increasing demand, we're launching another round. The application is currently live. I would be extremely grateful if you could forward this opportunity on to *masters*, *PhDs*, and *postdocs* in your department. ------------------------------ *Program:* The Data Incubator is an intensive 8 week fellowship that prepares masters students, PhDs, and postdocs in STEM and social science fields seeking industry careers as data scientists. The program is free for Fellows and supported by sponsorships from hundreds of employers across multiple industries. In response to the overwhelming interest in our earlier sessions, we will be holding another fellowship. *Who Should Apply:* Anyone who has already obtained a masters or PhD degree or who is within one year of graduating with a masters or PhD is welcome to apply. Applications from international students are welcome. Everyone else is encouraged to sign-up for a future session <https://www.thedataincubator.com/fellowship.html#apply?ref=wYWxhbkBhc3B1cnU…> . *Locations:* There will be both an in-person (in NYC, DC, SF) and online section of the fellowship. There is a common application for both the online and in-person sections. *Dates:* All sections will be from 2016-06-06 to 2016-07-29 *Application Link*: https://www.thedataincubator.com/fellowship.html#apply?ref=wYWxhbkBhc3B1cnU… *Learn More:* You can learn about our fellows at The New York Times <http://blog.thedataincubator.com/2015/02/alumni-spotlight-dorian-goldman-us…> or Palantir <http://blog.thedataincubator.com/2015/02/moving-to-palantir-from-mathematic…>. To read about our latest fellow alumni, check out blog <http://blog.thedataincubator.com>. To learn more about The Data Incubator, check us out on Venture Beat <http://venturebeat.com/2014/04/15/ny-gets-new-bootcamp-for-data-scientists-…>, The Next Web <http://thenextweb.com/insider/2015/07/02/data-incubator-opens-a-west-coast-…>, or Harvard Business Review <http://blogs.hbr.org/2014/08/the-question-to-ask-before-hiring-a-data-scien…> . Sincerely, Michael Postdoc, Cornell If you would like to stop receiving quarterly notices, please notify us here <http://www.thedataincubator.com/unsubscribe2.html?email_list=marketing>.

8 years, 1 month

[Aspuru-Guzik Group List] Fwd: 5Km run!

by Marlon Cummings

5K runners, please respond to Holly. --------------- *Marlon G. CummingsLab Manager, Aspuru-Guzik GroupMallinckrodt M136Department of Chemistry and Chemical BiologyHarvard University12 Oxford StreetCambridge, MA 02138617-496-9964617-496-9411 (fax)http://aspuru.chem.harvard.edu/ <http://aspuru.chem.harvard.edu/>* ---------- Forwarded message ---------- From: Holly Rees <hollyannerees(a)g.harvard.edu> Date: Mon, Mar 14, 2016 at 3:28 PM Subject: 5Km run! To: aspuru-admin(a)chemistry.harvard.edu Dear Marlon, I’m just writing to see if you could let me know who from your lab ran in the recent Ras na hEireann 5K. I’m trying to compile CCB results and no-one from the Aspuru-Guzik lab has answered my emails! Thanks so much! Holly Rees

8 years, 1 month

[Aspuru-Guzik Group List] paper

by Marlon Cummings

2 boxes for Quantum, 2 for Materials. Come get them please. Thanks, MC ---------- *Marlon G. CummingsLab Manager, Aspuru-Guzik GroupMallinckrodt M136Department of Chemistry and Chemical BiologyHarvard University12 Oxford StreetCambridge, MA 02138617-496-9964617-496-9411 (fax)http://aspuru.chem.harvard.edu/ <http://aspuru.chem.harvard.edu/>*

8 years, 1 month

[Aspuru-Guzik Group List] Grad students: get to John jarvards

by Joey Goodknight

Alans orders

8 years, 1 month

[Aspuru-Guzik Group List] Marlon Away

by Aspuru Lab Email

Team, Alan gave me the day off. Just kidding. Please touch base with Siria if it's absolutely necessary. :) See you on Monday. Marlon G. Cummings

8 years, 1 month

[Aspuru-Guzik Group List] Postdoc candidate visits tomorrow: Special group seminar at 2:30pm

by Steven A. Lopez

Dear Group, I attach the schedule for the visit of our newest postdoctoral candidate Michael Macros from MIT (Van Voorhis group). He will give a special seminar from 2:30-4pm in the Division room entitled "Condensed Phase Charge Transfer: Theory and Applications". His schedule is attached to this e-mail. Double check the time that you're supposed to meet with him! Thanks, Steven -- Steven A. Lopez, PhD Postdoctoral researcher, Aspuru-Guzik group Department of Chemistry & Chemical Biology Harvard University

8 years, 1 month

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aspuru-list March 2016