aspuru-list February 2016

aspuru-list@lists.fas.harvard.edu

34 participants
57 discussions

[Aspuru-Guzik Group List] Excitonics Seminar, Tuesday, Feb 9 at 3PM in 36-428

by Catherine M Bourgeois

Please post and forward to your groups CENTER FOR EXCITONICS SEMINAR SERIES<http://www.rle.mit.edu/excitonics/event-type/seminar-series/> Molecular evolution meets biophysics: the history of the RubisCO enzyme and the Fenna-Matthews-Olson (FMO) complex February 9, 2016 at 3:00pm/36-428* *please note time change to 3:00 pm instead of 4:30 pm Romain Studer The European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI) [studer_romain_web] Ancestral sequence reconstruction allows the inference of a protein's past characteristics at a particular point during its evolution. The inferred ancestral sequence can be modelled in 3D, assuming a structural template exists. Having ancestral structures allows a better understanding of protein evolution and protein function. Ultimately, the ancestral sequence can be resurrected in vitro by synthesis and purification and its properties can be studied using the standard protocols, used its for modern counterparts. Recent successful studies using ancestral sequence reconstruction have focused on old proteins (Groussin et al., Biol Lett. 2013), nuclear receptors (Harms et al., PNAS 2013) or cetacean myoglobins (Dasmeh P. et al., PLOS Comp Biol 2013). In this talk, I will give an introduction to methodologies used to infer ancestral sequences and to identify amino acids under selective pressures. I will present some studies that successfully used these methods. Finally, I will present my recent work on RubisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), the main enzyme responsible for the fixation of CO2 in bacteria and plants (Studer RA et al., PNAS 2014) and our current collaborative project on the Fenna-Matthews-Olson (FMO) complex, which participate in energy transfer in Bacteria. Romain Studer is a postdoctoral fellow within the lab of Dr. Pedro Beltrao at the European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK. He is now studying the evolution of posttranslational modification (PTM) of amino acids. He did his PhD at University of Lausanne (2005-2009), under the supervision of Prof. Marc Robinson-Rechavi. He studied the impact of whole-genome duplications in vertebrates' evolution and initiated the development of Selectome, a database of positive selection. In 2010, he collaborated with Prof. Bernard Rossier (University of Lausanne) to work on the evolution of sodium regulation. He then received a fellowship grant from the Swiss National Science Foundation to continue his research at University College London within the lab of Prof. Christine Orengo (2010-2013). He conducted several evolutionary projects, on the RubisCO enzyme and on the coagulation system. His research interest is to study the evolution of biological systems by integrating knowledge from phylogenetic inference, structural information and biochemical function. Light refreshments will be served. The Center For Excitonics Is An Energy Frontier Research Center Funded By The U.S. Department Of Energy, Office Of Science And Office Of Basic Energy Sciences

8 years, 3 months

[Aspuru-Guzik Group List] [qip] Maris Ozols + Friday group meeting and talk

by Aram Harrow

Dear quanta, 1. Maris Ozols from Cambridge is visiting us from now until mid-April. You can see more about his work here: http://home.lu.lv/~sd20008/ 2. We'll resume our 11am Friday group meetings this week. 3. This Friday at 1:30pm we'll have a talk in the usual place (6C-442). *Marissa Giustina *(University of Vienna) Significant-loophole-free test of local realism with entangled photons Local realism is the worldview in which physical properties of objects exist independently of measurement and where physical influences cannot travel faster than the speed of light. Bell’s theorem states that this worldview is incompatible with the predictions of quantum mechanics, as is expressed in Bell’s inequalities. Previous experiments convincingly supported the quantum predictions. Yet, every experiment requires assumptions that provide loopholes for a local realist explanation. Here, we report a Bell test that closes the most significant of these loopholes simultaneously. Using a well-optimized source of entangled photons, rapid setting generation, and highly efficient superconducting detectors, we observe a violation of a Bell inequality with high statistical significance. http://arxiv.org/abs/1511.03190 -aram _______________________________________________ qip mailing list qip(a)mit.edu http://mailman.mit.edu/mailman/listinfo/qip

8 years, 3 months

[Aspuru-Guzik Group List] [qip] talk + class - both classical

by Aram Harrow

Dear quanta, Today at 4pm there is a talk by Babai about his quasipolynomial time algorithm for graph isomorphism. It is in 32-141. Sadly the algorithm is not quantum, but there is still room for a poly-time quantum algorithm! There are also two classes you may be interested in. Ike is teaching 8.371 / 6.443 / 18.436, which meets at MWF10 in 26-168. And there is also a more classical course on complexity theory, which nevertheless involves many concepts that come up often in quantum complexity. *Course Announcement* *Advanced Complexity Theory *6.841J/18.405J *When: *Tue/Thu 1-2:30pm *Where: *2-190 We will cover many of the highlights of modern complexity theory, including the topics listed below: - Polynomial hierarchy and time-space lower bounds - Approximate counting and Toda's Theorem - Circuit complexity - Relativization, natural proofs - Communication complexity - Pseudorandomness: why randomness only buys polynomial speedups - PCP theorem, Unique Games, and hardness of approximation - And more! *We will have a guest lecture by Avi Wigderson (IAS) on proof complexity on Thursday, Feb 11.* The instructors are Dana Moshkovitz and Mohammad Bavarian. The TA is Govind Ramnarayan. _______________________________________________ qip mailing list qip(a)mit.edu http://mailman.mit.edu/mailman/listinfo/qip

8 years, 3 months

[Aspuru-Guzik Group List] Fwd: Dinner with Romain Studer next Tuesday 9th (typo sorry!)

by Stéphanie Valleau

Hi guys, The dinner will actually be on next Tuesday not on Monday. Sorry for the confusion. Let me know if you can make it!!! Best, Stephanie ---------- Forwarded message ---------- From: Stéphanie Valleau <stephanievalleau(a)gmail.com> Date: Mon, Feb 1, 2016 at 4:25 PM Subject: Dinner with Romain Studer next Monday 8th??? To: A-G Group <aspuru-list(a)lists.fas.harvard.edu> Dear group, Romain Studer (http://www.ebi.ac.uk/about/people/romain-studer) will be visiting next week as part of EFRC, and will be visiting Harvard on Monday the 8th. I collaborate with him on FMO evolution, he seems like a nice guy. We'll take him to dinner in the square, I can take about 2 people - sign up for the free food :) / let me know !!! Cheers, Stephanie

8 years, 3 months

[Aspuru-Guzik Group List] Dinner with Romain Studer next Monday 8th???

by Stéphanie Valleau

Dear group, Romain Studer (http://www.ebi.ac.uk/about/people/romain-studer) will be visiting next week as part of EFRC, and will be visiting Harvard on Monday the 8th. I collaborate with him on FMO evolution, he seems like a nice guy. We'll take him to dinner in the square, I can take about 2 people - sign up for the free food :) / let me know !!! Cheers, Stephanie

8 years, 3 months

[Aspuru-Guzik Group List] Fwd: Romain Studer - Excitonics Speaker Schedule

by Stéphanie Valleau

---------- Forwarded message ---------- From: Catherine M Bourgeois <cmbourg(a)mit.edu> Date: Thu, Jan 28, 2016 at 4:20 PM Subject: Romain Studer - Excitonics Speaker Schedule To: efrc-faculty <efrc-faculty(a)mit.edu>, excitonics-sp < excitonics-sp(a)mit.edu> Dear members: Romain Studer from the European Bioinformatics Institute will be giving a talk at the center on Feb 9 at 3pm in the RLE Haus/Allen room. Alan is hosting his visit. Please CLICK HERE <https://urldefense.proofpoint.com/v2/url?u=http-3A__doodle.com_poll_27rmfh7…> to let me know all the available times you can meet with him. Please note two items: 1. Due to other commitments Alan will be taking him to lunch instead of dinner. Let me know if you can take him to dinner. 2. The talk is schedule for 3 PM instead of the usual 4 pm talk. Please respond by Thursday, Feb 4. Thank you, Cathy Molecular evolution meets biophysics: the history of the RubisCO enzyme and the Fenna-Matthews-Olson (FMO) complex February 9, 2016 at 3:00pm/36-428* *Romain Studer, * *The European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)* [image: studer_romain_web] Ancestral sequence reconstruction allows the inference of a protein’s past characteristics at a particular point during its evolution. The inferred ancestral sequence can be modelled in 3D, assuming a structural template exists. Having ancestral structures allows a better understanding of protein evolution and protein function. Ultimately, the ancestral sequence can be resurrected in vitro by synthesis and purification and its properties can be studied using the standard protocols, used its for modern counterparts. Recent successful studies using ancestral sequence reconstruction have focused on old proteins (Groussin et al., Biol Lett. 2013), nuclear receptors (Harms et al., PNAS 2013) or cetacean myoglobins (Dasmeh P. et al., PLOS Comp Biol 2013). In this talk, I will give an introduction to methodologies used to infer ancestral sequences and to identify amino acids under selective pressures. I will present some studies that successfully used these methods. Finally, I will present my recent work on RubisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), the main enzyme responsible for the fixation of CO2 in bacteria and plants (Studer RA et al., PNAS 2014) and our current collaborative project on the Fenna-Matthews-Olson (FMO) complex, which participate in energy transfer in Bacteria. *Romain Studer* is a postdoctoral fellow within the lab of Dr. Pedro Beltrao at the European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK. He is now studying the evolution of posttranslational modification (PTM) of amino acids. He did his PhD at University of Lausanne (2005-2009), under the supervision of Prof. Marc Robinson-Rechavi. He studied the impact of whole-genome duplications in vertebrates’ evolution and initiated the development of Selectome, a database of positive selection. In 2010, he collaborated with Prof. Bernard Rossier (University of Lausanne) to work on the evolution of sodium regulation. He then received a fellowship grant from the Swiss National Science Foundation to continue his research at University College London within the lab of Prof. Christine Orengo (2010-2013). He conducted several evolutionary projects, on the RubisCO enzyme and on the coagulation system. His research interest is to study the evolution of biological systems by integrating knowledge from phylogenetic inference, structural information and biochemical function. *please note time change to 3:00 pm instead of 4:30 pm -- Stéphanie Valleau PhD student in Chemical Physics Harvard University CCB, 12 Oxford St. Mailbox 312, Cambridge, MA, USA

8 years, 3 months

[Aspuru-Guzik Group List] February 3, 2016 - ITAMP/HQOC Joint Quantum Sciences Seminar: Alexandra Boltasseva

by Ploucha, Clare Dolores

HQOC/ITAMP Joint Quantum Sciences Seminar Wednesday, February 3, 2016 4:00 PM, Jefferson 250 Prof. Alexandra Boltasseva, Purdue University "Practical Nanophotonics with Plasmonic Ceramics" In recent years, two avenues of nanophotonics, namely plasmonics and metamaterials, have seen an explosion of novel ideas and designs that could provide breakthrough devices and exotic functionalities. However, transforming these concepts into practical devices requires a significant amount of effort. The constituent materials in these structures play a crucial role in realizing efficient devices. Similar to the way silicon shaped the nanoelectronics field, efforts toward finding the best set of materials for plasmonic and metamaterial devices could revolutionize the field of nanophotonics. As a potential solution, alternative plasmonic materials have recently gained significant attention. Metals, despite being essential components of plasmonic and metamaterial structures, pose many technological challenges toward the realization of practical devices—primarily due to their high optical loss, integration and fabrication limitations. Hence, searching for an alternative to metals is vital to the success of future nanophotonic devices. In this course, recent developments in the pursuit of better plasmonic materials will be outlined, and several classes of materials including transparent conducting oxides and plasmonic ceramics as potential alternatives to metals will be discussed as material platforms that provide low intrinsic loss, tunability and compatibility with standard semiconductor fabrication processes. Refreshments Served from 4:00-4:30 PM Guest Presentation from 4:30-6:00 PM -- Clare Ploucha Faculty Assistant to Professors Lukin & Greiner and their labs Department of Physics 17 Oxford St., Lyman 324A Cambridge, MA 02138 P. (617) 496-2544

8 years, 3 months

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aspuru-list February 2016