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Dr. Andreas Götz: News

Welcome Yu-Ching Hu! Yu-Ching is a graduate student in Materials Science at UCSD. He will spend 2 months with us to learn everything about quantum chemistry, molecular dynamics, and supercomputing.
Andreas gives an invited presentation at ICPP-9 in Nanjing, China, in the session on "Theory and Spectroscopy". The presentation highlights our latest insights into the mechanism that couples oxygen reduction to proton pumping in cytochrome c oxidase, based on quantum chemistry calculations and molecular dynamics simulations.
Welcome back Johannes Brust (UC Merced)! Johannes returns for a 6 week internship. Johannes continues work on large-scale nonlinear optimization methods, related eigenvalue problems, and how these can be employed in electronic structure calculations.
Welcome Adam Kosviner, Erwin Ni, Ryan Nemiroff, Jamie Smith! Adam, Erwin, Ryan and Jamie start a 2 month internship within the REHS (Research Experience for Highschool Students) program. They will work on molecular dynamics simulations of enzymatic reactions with QM/MM methods, automated basis set convergence tests for density functional theory, enhancing Amber's QM/MM codes and optimizing Amber's build system.
SDSC press release on our book "Electronic Structure Theory on Graphics Processing Units", see also corresponding UCSD press release and report on HPCWire.
Our book Electronic Structure Calculations on Graphics Processing Units has been published. Exciting to see this work out and hold an actual copy in my hand! I co-authored 2 chapters and wrote another myself. And we were lucky to have so many excellent contributions from outstanding scientists and software engineers in the book.
ACS spring meeting in San Diego - I am organizing and presiding a symposium on "Computational Chemistry Across Catalysis" (together with Dion Vlachos from University of Delaware and Carine Michel and Philippe Sautet from ENS Lyon).
Rodrigo Ferreira de Morais from ENS Lyon is visiting for 3 weeks to learn about the AMBER molecular dynamics software package and to work on force field development for simulations of biomolecules at aqueous interfaces with polarizable platinum surfaces.
Andreas is visiting the group of Prof. Juan Rodriguez at the Instituto Politecnico Nacional in Mexico City and gives two presentations at the School of Physics and Mathematics. One talk is research focused while the other talk is for a broad audience and also contains an overview of Supercomputing at SDSC.
Press release on our work on mechanisms of Cisplatin to block cancer pathways by inhibition of the mitogen-activated protein kinase MEK1/2. Our contributions are quantum chemistry calculations on binding modes.
Europe visit - Andreas participates in a DFTB workshop in Bremen, Germany, and visits the Chemistry laboratory of the École Normale Supérieure de Lyon in France for the collaboration on multiscale computational methods for catalysis.
Andreas is instructor for the "GPU Computing and Programming" session of the 2015 SDSC Summer Institute.
We received funding from the UC MEXUS program for our joint project "Multiscale simulations of molecular donor-acceptor structures for the design of high-performance organic solar cells" with Prof. Juan Rodriguez from IPN in Mexico City. The funding comes from UC MEXUS and CONACYT and will support undergraduate and graduate student assistants and exchange between our groups.
Welcome Johannes Brust (UC Merced)! Johannes starts a 2 month internship within the UC graduate fellowship program. Johannes is a graduate student in applied math with Dr. RF Marcia and develops large-scale nonlinear optimization methods.
Welcome Grace Li and Ryan Nemiroff! Grace and Ryan start a 2 month internship within the REHS (Research Experience for Highschool Students) program. They will work on molecular dynamics simulations of enzymatic reactions for biofuels production with QM/MM based transition path sampling and related code developments.
Andreas is an invited speaker at the CanBIC-5 conference. He presents results from quantum chemistry and molecular dynamics simulations of cytochrome c oxidase (CcO). CcO is a vital enzyme that reduces oxygen to water and uses the generated energy to pump protons across cell membranes.
Andreas teaches the CUDA module in Mike Norman's parallel computing course.
New NSF award for Andreas Goetz: International Collaboration in Chemistry: Multiscale Simulations of Bifunctional Catalysis. This is a collaboration with Dion Vlachos at UDel and Philippe Sautet, Carine Michel and Paul Fleurat-Lessard at the ENS Lyon (France). We develop models and software to better understand at a molecular level how catalysts function to ultimately improve processes for the production of fuels and raw materials for the chemical industry from renewable biomass. See also the SDSC press release.
We are part of a new Intel Parallel Computing Center at SDSC (PIs Ross Walker, Amit Majumdar, Andreas Goetz). Work focuses on many- and multi-core optimizations for codes in the life science arena, in particular for classical molecular dynamics (AMBER), multi-scale QM/MM simulations (AmberTools) and neuronal simulation (NEURON). The center also offers training in parallel and accelerator programming.
In the news again: Our software development efforts for multiscale QM/MM simulations are highlighted in "Future Medicinal Chemistry" (Future Med. Chem. (2014) 6, 603, article on last page).
Pedro Bello-Maldonado, MSc graduate in electrical engineering from Florida International University, starts a 10 week internship in the framework of the XSEDE student summer engagement program. Pedro will work on optimizing the parallel performance of QM/MM implementations in AMBER. After the internship, Pedro will continue with graduate studies at the University of Illinois, Urbana-Champaign.
We are in the news: Our software development efforts for multiscale QM/MM simulations are highlighted in a UCSD press release. I am particularly proud that Matthew Clark contributed to this project. Matthew was a high school intern who went on to CalTech. He later was an undergraduate intern at SDSC.
Our research on multiscale QM/MM simulation software is featured on the cover of the Journal of Computational Chemistry (Jan 15 issue).
GPU computing event at SDSC (2 day symposium and workshop on technology, tools and research from pharma to geophysics), organized by Andreas Goetz and Ross Walker (both heading the CUDA Teaching Center at SDSC) together with Jon Saposhnik (NVIDIA).
2013 Nobel prize in chemistry "for the development of multiscale models for complex chemical systems". Congratulations to the pioneers who have shaped the field of computational chemistry I am working in!
Good news: NSF awards $12 Million to SDSC to deploy "Comet" Supercomputer.
Supercomputer time on SDSC Gordon and TACC Stampede granted - 755k SUs for QM and QM/MM simulations of biomolecular systems.
Rahul Nori and Keshav Tadimeti presented posters at the XSEDE 13 conference. Topics are numerical precision models for GPU accelerated MD and power consumption of CPU and GPU based MD simulations (a simulation that consumes an equivalent of 1 gallon oil using CPUs, requires only half a gallon on a GPU!).
Supercomputer time on SDSC Gordon granted - 40k SUs for educational purposes (REHS internship: New QM/MM Approaches for High Performance Molecular Dynamics Simulations of Condensed Phase Biological Systems).
Stephen Clark starts a 7 week internship in the framework of the REHS 13 program at SDSC. Stephen will work on benchmarking and improving QM/MM capabilities in AMBER.
Supercomputer time on TACC Stampede granted - 100k SUs for educational purposes (XSEDE student engagement: Effect of numerical noise on molecular dynamics simulations of enzymes).
Rahul Nori, graduate student of scientific computing at the University of North Dakota, starts a 10 week internship in the framework of the XSEDE student summer engagement program. Rahul will study the effect of numerical noise on molecular dynamics simulations.
Newspaper paper article out - life and work of Andreas Goetz highlighted in the Nürnberger Zeitung, the newspaper of the city of Nuremberg.
Original article, English translation
older stuff
A lot of exciting things happened in the past, but these are not recorded here...

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last modification: 2016/08/23