aspuru-list May 2016

aspuru-list@lists.fas.harvard.edu

26 participants
50 discussions

[Aspuru-Guzik Group List] talk at 11.00 in Pfizer Auditorium Hall by Nimrod Moiseyev

by Uri Peskin

Dear Friends, Please allow me to recommend tomorrow's talk at 11.00 in Pfizer Auditorium Hall by Nimrod Moiseyev from the Technion - A chance to learn about non-Hermitian Quantum mechanics and enjoy a fun speaker! Uri

8 years

[Aspuru-Guzik Group List] Jennifer Ogilvie talks today at MIT

by Doran Bennett

Hi Everyone, This is just a reminder that Jennifer Ogilvie is speaking today at MIT about "Understanding coherence in photosynthetic reaction centers by multidimensional electronic spectroscopy." The event announcement is below. I will be leaving around 4pm to attend. Best, Doran [image: Inline image 1]

8 years

[Aspuru-Guzik Group List] ITAMP lunch seminar - Mike Crescimanno & Lee Liu (05/05)

by Stefan Pabst

8 years

[Aspuru-Guzik Group List] You have been unsubscribed from the Iacs-events mailing list

by iacs-events-bounces＠seas.harvard.edu

8 years

[Aspuru-Guzik Group List] Last Reminder :) Blankenship's talk in less than 10 min, Naito 205

by Semion Saikin

Learn about photosynthesis! If you do not know where it is, stop by my office

8 years

[Aspuru-Guzik Group List] Oriole: Jupyter noteooks with synced video online

by Benjamin Sanchez Lengeling

HI group, Just wanted to shared an awesome use of jupyter notebooks, will probably be one of the future ways of teaching online code stuff: https://www.oreilly.com/learning/regex-golf-with-peter-norvig Ben

8 years

[Aspuru-Guzik Group List] Fwd: FW: Gevorg Grigoryan Seminar, Tue, May 3rd at 4:15 in the Division Room

by Siria Serrano

Seminar Tomorrow! ---------- Forwarded message ---------- From: Torres, Roel Rosalio <rtorres(a)chemistry.harvard.edu> Date: Mon, May 2, 2016 at 12:44 PM Subject: FW: Gevorg Grigoryan Seminar, Tue, May 3rd at 4:15 in the Division Room To: "Siria Serrano (aspuru.facultyassistant(a)gmail.com)" < aspuru.facultyassistant(a)gmail.com> Hi Siria, Could you please advertise tomorrow’s seminar to the members of your group? Thanks! Cheers, Roel *From:* Torres, Roel Rosalio *Sent:* Sunday, May 01, 2016 10:16 PM *To:* hellergroup(a)googlegroups.com; Alex Park; Anna Whitney; araguram(a)college.harvard.edu; Bauer, Nicholas C; Bershtein, Shimon; Bharat Adkar; Bhattacharyya, Sanchari; Cetinbas, Murat; Cheron, Nicolas; Choi, Jeong-Mo; Eric Zinn; Gilson, Amy Ilana; Jacobs, William Monroe; Jason Park; Woodard, Jaie Christina; Magaly Gutierrez (maguti2095(a)gmail.com); Manhart, Michael; Michael Musharbash; Michael Zimet; Muyoung Heo; Naveen Jasty; Niamh Durfee; Raynor Kuang; Robert Lin; Rodrigues, Joao Vierira; rrazban(a)g.harvard.edu; Serohijos, Adrian; Shakhnovich, Eugene; Tijda Argun; Torres, Roel Rosalio; Victor Zhao; xiaole Xia; Yan, Jin; Zhang, Yanmin *Subject:* Gevorg Grigoryan Seminar, Tue, May 3rd at 4:15 in the Division Room Dear Shakhnovich and Heller Groups, Prof Gevorg Grigoryan from Dartmouth will be giving a seminar on *Universal Tertiary Structural Alphabet Describes Protein Sequence-Structure Relationships *on Tuesday, May 3rd at 4:15 in the Division Room. Please see the abstract below for the content of the seminar. This seminar will replace the regular Shakhnovich GM. Thanks! Cheers, Roel *Universal Tertiary Structural Alphabet Describes Protein Sequence-Structure Relationships* We systematically decompose the known protein structural universe into its basic tertiary motifs, which we call TERMs. A TERM is a compact structural fragment that captures the secondary, tertiary, and quaternary environments around a given residue. We seek the set of universal TERMs that capture all structural environments observed in the PDB, finding remarkable degeneracy. Strikingly, only ~600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. Further, the PDB appears to be close to converged with respect to TERM usage. On the other hand, more rare geometries also exist and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective means of describing structure-sequence relationships. First, we demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones, with little difference between the two classes (28% and 24% sequence identity, respectively). Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Second, we show that TERM statistics can discriminate between accurate and erroneous structural models (R = 0.69 between true model accuracy and a TERM-based metric), providing information on poorly predicted regions. Finally, we demonstrate that amino-acid frequencies within TERM instances can be used to predict changes in the free energy of folding upon single mutations on par with or better than existing methods. Structural biology has benefited greatly from previously observed degeneracies in structure space, particularly on secondary and super-secondary structural levels. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities towards better understanding, design, and prediction of protein structure. -- *Siria Serrano* *Faculty Assistant* *Aspuru-Guzik Group* *Harvard University **Department of Chemistry and Chemical Biology* *12 Oxford St. M 136* *Cambridge, MA 02138* *P:** (617) 496-1716 <%28617%29%20496-1716>** F: **617-496-9411 <617-496-9411>*

8 years

[Aspuru-Guzik Group List] Prof. Chris Wolverton visiting from Northwestern

by Sawaya, Nicolas Per Dane

Hey Group, Prof. Chris Wolverton of Northwestern will be visiting Harvard on Tuesday, May 3. His theochem talk at MIT will be the day after. Website: http://www.mccormick.northwestern.edu/research-faculty/directory/profiles/w… Wolverton is a well-known name, especially in materials discovery for energy applications. He researches topics that a lot of our group studies as well, including substantial work in: * hydrogen storage, batteries, light-weight metals, fuel cells, thermoelectrics * first-principles simulation methods (e.g. DFT) * predicting phase diagrams * big data/ML for materials discovery Please let me know if you're interested in meeting with him (lunch and dinner too). Cheerio, Nicolas

8 years

[Aspuru-Guzik Group List] Group lunch tomorrow

by Jennifer Wei

Hi everyone, A reminder that tomorrow we will be having group lunch at Fire and Ice. Please let me know by 10am tomorrow if you can make it so I can make a reservation. Enjoy the rest of the weekend, Jennifer

8 years

[Aspuru-Guzik Group List] Reminder: Bob Blankenship's talk today at 2:30pm in Naito 205 (NOTICE Unusual location)

by Semion Saikin

Guys, Bob Blankenship, http://pages.wustl.edu/blankenshiplab, one of the experts in bacterial photosynthesis is visiting our group today. He will give a talk on Molecular Mechanisms of Photosynthetic Antenna Regulation at 2:30pm in Naito 205. Please join us! Semion -- ******************************************** 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 ********************************************

8 years

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aspuru-list May 2016