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Dr. Andreas Götz: News

Andreas and Vinicius attend the annual Amber Developer Meeting.
Welcome Rupin Mittal! We are excited for Rupin to join our group as high school intern. Rupin will work on simulations and data analysis to test an improved constant pH molecular dynamics approach.
Congratulations to Vinicius for winning the Nvidia GPU Award for outstanding research in the use of GPUs for Computational Chemistry. Vinicius presented his PhD thesis work on GPU accelerated constant redox potential MD with Amber, performed in the group of Adrian Roitberg at UFL.
Congratulations to Ethan and Kaushik for winning the "Jeffery Madura Outstanding Research Award" for an excellent undergraduate poster presentation from the Computers in Chemistry Division, presenting work on software for many-body potentials.
The ACS Fall National Meeting is coming to San Diego - we are attending! Teffanie, Ethan, Kaushik and Vinicius are presenting posters.
Welcome Attila Fekete! We are excited for Attila to join our group as postdoctoral research scholar. Attila received his Phd from the University of Debrecen in Hungary where he performed molecular dynamics simulations of biomolecular systems. He also worked at the Hungarian National Supercomputing Center. Vinicius is working on molecular dynamics simulations of cytochrome c oxidase, develops force field parameters, and new QM/MM software in Amber with GPU acceleration.
Our proposal for computer time on NSF XSEDE supercomputer resources was positively reviewed and awarded. Now on to great computational science!
Andreas receives the "SDSC Pi Person of the Year" award. The award recognizes SDSC researchers who have one leg, so to speak, in a science domain and the other in cyberinfrastructure technology.
IJQC cover, Volume 119, Issue 14 IJQC cover, Volume 119, Issue 14: Organic Photovoltaics Check out our cover image on Volume 119, Issue 14 of the International Journal of Quantum Chemistry. Importance of dispersion interactions on structure and electronic properties of organic photovoltaics.
Andreas is giving a talk on quantum chemistry of proton pumping in cytochrome c oxidase at the 7th Canadian International Conference on Bioinorganic Chemistry (CanBIC-7). He is also chair of the theory symposium on 5/24.
Ethan and Kaushik are giving a presentation at the UC San Diego Undergraduate Research Conference. Way to go!
Welcome Vinicius Cruzeiro! We are excited for Vinicius to join our group as postdoctoral research scholar. Vinicius hails from Florida with a PhD in the field of molecular dynamics from Adrian Roitberg's group. Vinicius is working on many-body potentials for molecular simulations as part of CAICE.
Andreas is traveling to Florida for the Amber developer meeting in Safety Harbor and the ACS National Meeting in Orlando. Excited to give presentations on QM/MM capabilities in Amber.
We have a delegation from Osaka University at SDSC for a joint workshop on "Inofmation Science for Future Society". Topics range from information security through database and HPC to computational biology and chemistry. Andreas is giving a talk about multi-scale simulations, many-body models and machine learning.
Andreas and Yaoguang are traveling to Dallas for SC18 - Andreas will give a talk at the Lenovo booth, Yaogung will present a poster.
Welcome Teffanie Goh! Teffanie is a UCSD undergraduate student with interest in quantum chemistry. She will use electronic structure calculations to address open questions in enzymatic reaction mechanisms and atmospheric chemistry.
Welcome Ganesh Ranganath! As a graduate student in UCSD's CSME program with interest and expertise in software engineering, Ganesh will contribute to our efforts in developing molecular simulations software for massively parallel graphics processors.
Andreas visits his alma mater in Erlangen, Germany, and gives a presentation on machine learning of many-body potentials for molecular simulations.
Andreas is named one of 10 global winners of Lenovo's University AI Innovation Challenge! Andreas will present an overview of his research at the Lenovo booth at the Supercomputing conference in Dallas in November.
Congratulations to Yaoguang Zhai! His poster submission to Supercomputing 18 was accepted.
NSF grant ACI-1835144 awarded! I look forward to exciting research (Elements: Software: NSCI: Efficient GPU Enabled QM/MM Calculations: AMBER Coupled with QUICK) with Kennie Merz from Michigan State University. Stand by for some very cool software.
Andreas gives a presentation on automated machine learning of many-body potentials in the symposium "Revolutionizing Chemistry with Artificial Intelligence" at the ACS fall meeting in Boston. Great meeting in a nice city.
Good news - Ronak was accepted into the UCSD MAPS program and will extend his internship in our group.
This week is SDSC Summer Institute 2018! One week of classes on all aspects of Supercomputing and Data Science. Andreas teaches GPU computing and programming.
It is official: NSF-CAICE was renewed for another 5 years! (see NSF award CHE-1801971) 26 senior investigators across 10 institutions. Very excited and proud to be part of this interdisciplinary research center with the goal to understand fundamental chemical processes in aerosol particles and their impact on the environment and climate. We will contribute with accurate molecular simulations of atmospheric gases and sea spray aerosols using many-body potentials and machine learning techniques.
Andreas gives an invited talk on our cytochrome c oxidase work at the 28th Canadian Symposium on Theoretical and Computational Chemistry (CSTCC 2018). It is an honor to speak alongside eminent scientists like Axel Becke, Weitao Yang and many others. Thanks to the organizers James Gauld and Viktor Staroverov!
Andreas participates in the Telluride workshop "Many-body interactions: From quantum mechanics to force fields", presenting our efforts on machine learning of many-body potentials. Very good workshop, a big thanks to the organizers Kenneth Jordan and Jean-Philip Piquemal.
Welcome Aemilia Russ, April Cheng, Conor Sefkow and Ronak Roy! This year we have four outstanding high school students join our group for 2 months of summer internship within SDSC's REHS program. They will work on machine-learning based many-body potentials for simulations of atmospherically relevant molecules, extending our python based workflow tools and generate potentials for hypohalous acids based on quantum chemical reference data.
SDSC press release about our research on machine learning models for many-body potentials that are able to simulate water (and in the future arbitrary molecular systems) with unprecedented accuracy. See also corresponding UCSD press release.
Welcome Spencer Hamilton! Spencer is an undergraduate student at Palomar College and will work on a part-time internship in our group to learn all there is about computational sciences and contribute to our software engineering efforts.
Welcome Tim Tan! Tim is a visiting undergraduate student from Tongji University in Shanghai. Tim joins the group for 8 weeks to profile, optimize and benchmark our Behler-Parinello type neural network C++/OpenMP and CUDA implementation on multi-core CPUs and GPUs.
Congratulations to Thuong Nguyen! Proud that Thuong got accepted into the highly competitive Insight Data Science Fellows Program. Unfortunately this means that she is leaving the group. Best wishes for an exciting career in Data Science!
CAICE is having the 5th annual meeting. Andreas is presenting "Insights into the Aqueous Solvation of dinitrogen pentoxide from computer simulations".
Andreas gives lectures on GPU computing and programming in UCSD's graduate course on Parallel Computing in Science and Engineering (PHYS 244). Fun with all things CUDA and OpenACC.
Congratulations to Sandeep Reddy for his new position as Assistant Professor! Sandeep will join the Centre for Computational and Data Sciences at the prestigious Indian Institute of Technology (IIT) Kharagpur. Good luck Sandeep!
Welcome Ethan Bull-Vulpe! Ethan is a UCSD undergraduate student, software engineering wizard, who joins the group to develop our Python based workflow tools for automated machine learning of many-body potentials for molecular simulations.
Up to Amsterdam to participate in the 2018 ADF developer workshop. Andreas talks about method and software development at SDSC. From QM/MM to machine-learning of many-body potentials. Thanks a lot to SCM for inviting me to this workshop. It's always great to see old friends and discuss great science and software engineering. Love the city.
Andreas visits Adrian Roitberg at UFL to work with Balint Aradi from Bremen, Germany, on coupling DFTB+ to Amber.
AMBER developer meeting. This time in Safety Harbor, Florida. Andreas talks about QM/MM work, the new CMake build system that Jamie Smith developed, and of course the new GAL17 force field from our work with French collaborators Carine Michel, Stephan Steinmann, Philippe Sautet and Paul Fleurat-Lessard.
Andreas is a member of the SDSC Industry Partners Program at the San Diego Supercomputer Center.
Welcome Sandeep Kumar Reddy! Great news for the new year: Sandeep is joining the group as postdoctoral scholar to work on the development of an accurate many-body potential for dinitrogen pentoxide that is compatible with the MB-pol water model with the aim to determine the aqueous solubility from molecular dynamics simulations. This is an exciting CAICE research project!
Welcome Teri Lambros! Teri will spend 4 weeks in our group as a graduate rotation student.
Welcome Derek Tse and Nathaniel Danandeh! Derek and Nathan are UCSD undergraduate students who join the lab to work on software engineering of Python workflow tools for automated machine learning of many-body potentials and C++/OpenMP/CUDA implementations of neural network based molecular simulation models.
The group is now an official member of (NSF-CAICE), the NSF Center for Aerosol Impacts on Chemistry of the Environment. We got funded for our project "Simulations of Solubility and Reactivity of N2O5 at Aqueous Interfaces". We are collaborating with several experimental and theory groups, including Benny Gerber (UCI), Mark Johnson (Yale), Tim Bertram and Gil Nathanson (Wisconsin).
Andreas gives an invited presentation at the 50th anniversary symposium of the solid state physics department of the Instituto Politecnico Nacional in Mexico City. Presenting our new force field for water over Pt(111).
This week is SDSC Summer Institute 2017! One week of classes on all aspects of Supercomputing and Data Science. Andreas teaches GPU computing and programming.
Andreas was promoted to Assistant Research Scientist. Yay!
Congratulations to Aage Skjevik! Aage obtained a prestigious fellowship from the University of Bergen in Norway to pursue 4 years of additional postoctoral research. Unfortunately this means that Aage is leaving the group. Fortunately the fellowship includes one year of research visits abroad, which means we will be able to welcome Aage back, soon.
Congratulations to Yu-Ching Hu! Yu-Ching was accepted into the computer scince and engineering graduate program at North Carolina State University. Good luck with your graduate studies!
Welcome Yaoguang Zhai! Yaoguang is an MSc student in UCSD's Computational Science, Mathematics and Engineering graduate program. He joins our group to work on machine learning methods for the development of many-body potentials and software implementations for molecular simulations on parallel hardware including GPUs.
Welcome Brian Hoh and Ian Wildenhain! Brian and Ian are starting an 8-week internship in our group within SDSC's REHS program. Brian will study the solubility of dinitrogen pentoxide in aerosol particles using molecular dynamics simulations. Ian will investigate the performance and parallel scaling of the ADF density functional code on multi- and many-core Intel architectures.
Andreas participates in the MolSSI workshop on software interoperability.
Andreas chairs the Theory Symposium at the CanBIC-6 International Conference on Bioninorganic Chemistry in Parry Sound (Ontario, Canada) and gives a presentation on Cytochrome c Oxidase.
Andreas gives lectures on GPU computing and programming in UCSD's course on Parallel Computing in Science and Engineering (PHYS 244).
Andreas gives a presentation on force field development for water interacting with Pt surfaces at the ACS spring meeting in San Francisco.
NSF grant ACI-1642336 awarded! This is a collaboration with Co-PI Andrea Zonca from SDSC and PI Francesco Paesani from UCSD's Department of Chemistry. (Title: SI2-SSE: Enabling Chemical Accuracy in Computer Simulations: An Integrated Software Platform for Many-Body Molecular Dynamics)
Welcome Oliver Hamto! Oliver is a graduate student in Francesco Paesani's group and will spend part of his time with us, collaborating on our software for machine learning of many-body potentials.
Welcome Thuong Nguyen! Thuong is joining the group as a postdoctoral scholar. She will work on data science aspects of our research. One of our goals is to develop many-body potentials based on machine learning approaches.
The renewal of our NIH RO1 grant "Quantum Chemistry of Proton Pumping" in collaboration with Professor Noodleman from Scripps Research was awarded! Looking forward to four more years of exciting research.
Andreas is visiting collaborators at the Chemistry laboratory of the École Normale Supérieure de Lyon ENS Lyon in France and gives a department seminar on cytochrome c oxidase simulations.
Welcome Aage Skjevik! Aage is joining the group as postdoc to explore proton pumping mechanisms in Cytochrome c Oxidase using advanced molecular dynamics techniques including constant pH MD and QM/MM MD based on ab initio quantum chemistry methods.
This week is SDSC Summer Institute! Andreas teaches GPU computing and programming.
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: 2020/02/10