CUDA Spotlight: Todd Martínez
GPU-Accelerated Quantum Chemistry
This week's Spotlight is on Professor Todd Martínez of Stanford.
Professor Martínez' research lies in the area of theoretical chemistry, emphasizing the development and application of new methods which accurately and efficiently capture quantum mechanical effects.
Professor Martínez pioneered the use of GPU technology for computational chemistry, culminating in the TeraChem software package that uses GPUs for first principles molecular dynamics. He is a founder of the company PetaChem that distributes this software.
This interview is part of the CUDA Spotlight Series.
[Editor's Note: Learn more about GPU-based quantum chemistry at the GPU Technology Conference in March. Stanford graduate student Nathan Luehr will speak on Virtual Molecular Modeling Kits: Playing Games with Quantum Chemistry, on Thurs., March 27.]
Q & A with Todd Martínez
NVIDIA: Todd, tell us about TeraChem.
The primary advantage over empirical force fields (for example, often used for protein structure) is that chemical bond rearrangements and electron transfer can be described seamlessly.
NVIDIA: Who are the users of TeraChem?
Even though TeraChem was designed for ab initio molecular dynamics, it can also carry out simpler tasks such as optimization of the geometry of a molecular structure and calculation of reaction mechanisms.
Many people use TeraChem for these purposes, often referred to as quantum chemistry. Some of the most enthusiastic users have realized that TeraChem makes many simulations possible that were otherwise intractable. They have used TeraChem to optimize molecular structures for proteins, nanotubes, and minerals and to explore chemical reactions happening in these structures.
NVIDIA: What is an example of an industrial research application?
The protein BPTI (Bovine Pancreatic Trypsin Inhibitor) in TeraChem
NVIDIA: How does TeraChem leverage GPU computing?
NVIDIA: When did you first see the promise of GPU computing?
Writing in assembler was very tedious and the idea of rewriting all the code in assembler was unattractive. Thus, we were keeping close tabs on developments in GPGPU computing, which might be a more sustainable approach. Indeed, we were evaluating Brook as a possible avenue to expand that work.
Fortunately, we found out about NVIDIA's plans to release CUDA from Professor Wen-mei Hwu at UIUC and were able to redirect these efforts into CUDA. Our first CUDA electronic structure code was written in late 2007, using a beta release of CUDA.
NVIDIA: What is unique about the TeraChem code?
NVIDIA: In what ways is your team using CUDA?
NVIDIA: Can you talk about how TeraChem is developing into a teaching tool?
We combined TeraChem with 3D visualization and force-feedback input devices so that students can "grab" atoms in a molecule and pull on them – the molecule will "pull back" via the haptic input device.
Students can learn chemistry by playing with molecules directly and they can feel the difference between strong and weak bonds. They also "feel" the difference between favorable and unfavorable reaction pathways. The key here was being able to match human and molecular time scales – this all works fluidly because TeraChem is able to do calculations fast enough so that one second of real time corresponds to several femtoseconds of molecular time.
NVIDIA: What are you looking forward to in the next 5-10 years?
In terms of industrial applications, we expect to be able to design polymers with tailored responses to external stimuli – for example, strengthening by chemical crosslinking as they are stressed to prevent damage. An example would be developing new molecular systems for efficiently converting sunlight into electricity or fuels.
Bio for Todd Martínez
Professor Todd J. Martínez received his B. S. in Chemistry from Calvin College in 1989 and his Ph.D. in Chemistry from the University of California at Los Angeles in 1994. From 1994 to 1996, he was a Fulbright Junior Postdoctoral Researcher at Hebrew University in Jerusalem and a University of California President's Postdoctoral Fellow at UCLA. In 1996, he joined the faculty in the Department of Chemistry at the University of Illinois. In 2009, he was recruited to join the faculty at Stanford University and the SLAC National Accelerator Laboratory, where he is currently David Mulvane Ehrsam and Edward Curtis Franklin Professor.
Professor Martínez has received numerous awards in recognition of his contributions to theoretical chemistry and our understanding of the chemical reactivity of electronic excited states. These include fellowships and awards from the Camille and Henry Dreyfus Foundation, the Alfred P. Sloan Foundation, the Arnold and Mabel Beckman Foundation, the David and Lucille Packard Foundation, and the John D. and Catherine T. MacArthur Foundation.
# # #