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Professor Todd Martinez Launches Molecular Theory and Simulation Program at Stanford

Todd Martinez with graduate student

Professor Todd Martinez with Research Associate Robert Parrish at a Molecular Theory and Simulation Bootcamp

Photo Credit: Binhong Lin
Nov 1 2017

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By Stefanie Pietkiewicz


Professor Todd Martinez is leading a Molecular Theory and Simulation Program at Stanford, which aims to foster interdisciplinary collaboration for the design of molecular structures. In this interview, he discusses his experience growing up in Central America, lifelong captivation with chemistry and computing, and vision for the newly established program.

The Big C’s

Although born in New York, Martinez spent most of his childhood in Central America, where he first developed an interest in chemistry. Due to the region’s more relaxed safety standards, he was able to freely experiment with strong acids and bases obtained from his neighborhood supply house. He recalls with amazement that, as a child, he could walk to a shop only a few blocks away from his home in Nicaragua to purchase nitric and sulfuric acid.

“You could go there and buy anything you wanted,” he laughed. “If an eight year old tried to do that in the US, it would probably lead to a Homeland Security investigation, but it meant that I was able to do a lot of cool experiments.”

When he was a teenager, Martinez moved with his family back to the US, landing in Texas. With the move, his interests shifted, and he became obsessed with computer programming. He started spending all of his free time in computer stores, secretly writing video games when the storeowners were distracted.

“I went on to write and sell video games, but in the end I figured out that it wasn’t as much fun to play video games that you wrote because you know how to beat them,” he said with a smile.

The Ah-Ha Moment

While earning his B.S. in chemistry, Martinez discovered he could marry his interests in chemistry and computers when he stumbled upon a computational chemistry course during Calvin College’s interim break period. “That was the epiphany moment where I realized these two things didn’t have to exist in separate worlds,” he said.

This dual passion for chemistry and computer science has served as the foundation of a prolific career. Today, Martinez is a theoretical chemist in the Stanford Department of Chemistry focused on developing new methods to explain quantum mechanical behavior and designing new molecules.

“In many ways my research looks a lot more like what I would have wanted to do as a kid, than it did when I started out 25 years ago as an assistant professor,” he noted.

From a young age, Martinez has been drawn to the possibility of working directly with small molecules — a determination which cultivated his fixation with computers in the first place. “The computer is a tool that allows you to interact directly with atoms, protons and electrons. You can try to make inferences from experiments, but it’s not the same as actually interacting with molecules,” he said. 

A New Era

While theoretical chemists have spent the past two decades proving to the scientific community that they can in fact predict certain phenomena, Martinez believes the field is entering a new era.

In the future, he foresees that scientists will have the ability to interact with molecules in a more tangible way, predict new reactions, and design individual molecules and molecular material.

Molecular Theory and Simulation Program

Martinez is leading a new Molecular Theory and Simulation Program at Stanford, which will focus specifically on molecular design.

Todd Martinez and graduate students

Because chemists now have the ability to generate data about molecules and the motivation to find meaning in the data, Martinez predicts that significant progress in designing molecular systems is on the horizon. Furthermore, he feels collaboration with individuals outside of theoretical chemistry is essential to making any headway.

“Theoretical chemistry has a lot of overlap with the burgeoning fields of machine learning, artificial intelligence and big data. We are all analyzing large amounts of data to try to find patterns,” he said. “We need to look outside of chemistry itself and work with people who are also analyzing data patterns in different fields.”

Center for Quantum Molecular Design

Martinez was recently awarded a $1.8 million grant from the NSF to develop a Center for Quantum Molecular Design, which will enable these types of multidisciplinary collaborations to occur. The center will focus on developing models for quantum mechanical molecular dynamics for the design of molecules and materials.

Martinez’s collaborators include Michael Fayer (Stanford), Steven Boxer (Stanford), Thomas Markland (Stanford), Mark Tuckerman (NYU), Gabriella Schlau-Cohen (MIT) and Kelly Gaffney (SLAC).

“The primary goal of phase one is to establish that this kind of collaboration is fruitful and to make it clear that the ability to design is promising. In phase two, we would like to double the size of the collaboration,” he explained.

A Collaborative Work Space

The Molecular Theory and Simulation Program will reside in the Keck Building, which is currently undergoing a major overhaul. Over half of the first floor has been gutted and redesigned to create a more communal atmosphere and workplace.

Molecular Theory and Simulation Space in Keck

Slated to open in April 2018, the new space will feature several shared areas as well as private offices to maximize lab interactions while preserving individual research group identities.

“The communal spaces are areas where we can try out new, computational technologies,” said Martinez. “One is a sort of a mini electronics workstation, and the other is a visualization space where we can go in and play with three dimensional molecules.”

The new space will eventually house more than 40 graduate students, postdoctoral scholars and faculty members, including chemistry Professor Thomas Markland.

Building a Network

Under his leadership, Martinez hopes the Molecular Theory and Simulation Program will lead to stronger interdisciplinary partnerships between departments like chemistry, statistics, mathematics, computer science as well as the SLAC National Accelerator Laboratory.

“The present is really the time when those connections can catalyze a big change in what we are able to do with molecules. Chemists alone are not going to be able to do this. It is going to happen because of a lot of communication between many different areas,” he said.