Computational & Theoretical Chemistry

The computational and theoretical chemistry group, supported by Boston University’s world class computational resources, is widely considered to form one of the “top 30” theoretical chemistry programs in the United States. There are five associated faculty whose research areas span quantum dynamics, photo-ionization and electron-molecule scattering theory, classical statistical mechanics of dynamical processes in liquids and protein structure and dynamics. Resources and affiliations include the Boston University Center for Computational Science, the Scientific Visualization Group, and the Greater Boston Area, the Atlantic Center for Atomistic Modeling.

Core Faculty

David Coker – Quantum dynamics and statistical mechanics
The Coker Group develops semi-empirical methods to compute electronic excited state potential energy surfaces for many-body systems, as well as mixed quantum-classical and semi-classical molecular dynamics methods which allow for electronic transitions. These methodologies are combined to study photo-dissociation dynamics in liquids, solids and clusters, charge transfer reactions in different environments, and how electronic states and electronic relaxation dynamics are influenced by solvent.

Tom Keyes – Theoretical biophysical chemistry
The Keyes Group investigates the mechanism and dynamics of protein folding, binding of ligands to proteins, all-atom descriptions of viruses, and ‘theory of experiment’ for the associated spectral probes. Their themes are: (1) the broad applicability of classical mechanics when induction or polarization (creation of dipoles by local electric fields) is accurately included. The Group has classical theories of nonlinear IR and Raman spectroscopy and consider that ligand binding occurs via classical ‘electrostatic bonds; (2) formulation of theories in terms of the multidimensional potential energy surface, or landscape; and (3) development of intelligent or accelerated simulation algorithms for computationally intensive problems.

John Straub – Protein structure and dynamics
The Straub Group focuses on the theoretical and computational modeling of biophysical systems. Particular areas of interest include: (1) probing the pathways and time scales of ultrafast quantum dynamics and energy transfer in proteins; (2) the development of computational algorithms and coarse-grained models of proteins for use in protein structure prediction and large-scale simulations; and (3) probing the principles of peptide and protein aggregation associated with amyloid disease.

Feng Wang - High-quality force fields & multi-scale molecular dynames & Monte Carlo simulations
The Wang Group develops high-quality force fields and multi-scale molecular dynamics and Monte Carlo simulations. Systems of particular interest include methane clathrate and metal hydrides. Projects involve development of high quality force fields for methane clathrate and metal hydrides and studies of the thermo-stability and the nucleation rate of methane clathrate. A new method is being developed to study the escape kinetics of methane from a clathrate lattice.

Brandon Xia – Protein bioinformatics
The Xia Group applies computational techniques to study the structure, function, and evolution of complex bio-molecular systems such as proteins and protein networks. Specific projects include reconstruction of protein interaction and regulatory networks by genomic data integration; comparative and evolutionary analysis of proteins and protein networks; protein sequence-structure-function relationships; prediction of protein structure and function.

Associated Faculty

Sandor Vajda, Department of Biomedical Engineering
Gene Stanley, Department of Physics

Resources and Affiliations

Center for Computational Science – provides a forum for the multidisciplinary exchange of ideas among researchers, educators, and students. CCS offers seminars, workshops, and symposia to highlight advances in computational science and facilitates computationally based research projects and education, working with scientists from 20 different departments and centers.

Scientific Computing & Visualization Group – Boston University’s high-performance computing and visualization systems include the IBM Blue Gene, IBM pSeries 690, an IBM pSeries 655, an Intel Pentium III Linux Cluster, a Deep Vision Display Wall, an Access Grid Conference Facility, a Laboratory for Virtual Environments and a Computer Graphics Laboratory.

GBA (Greater Boston Area) Theoretical Chemistry Lecture Series – Designed for and run by graduate students and postdoctoral research associates at Boston University, Boston College, Harvard University, and the Massachusetts Institute of Technology, this series attracts top researchers from the fields of theoretical chemistry and physics. The twice-monthly lectures enable students from the four institutions to exchange ideas and build relationships with scientists from all over the academic world. Topics vary from Density Functional theory to Network Biology, but the majority focus on theoretical chemistry and condensed matter physics.

ACAM bridges research between scientists in North America and Europe and provides valuable training opportunities for Boston University graduate students and postdoctoral fellows.

ACAM (Atlantic Center for Atomistic Modeling) – Boston University has strong international research connections in computational and theoretical chemistry through ACAM. ACAM is the Irish “node” (University College of Dublin) of the “European Center for Calculations on Atoms and Molecules” (CECAM) and is led by Professor David Coker (2009-2012). ACAM aims to take advantage of the global connectivity between researchers to enable them to collaborate and begin building a new generation of algorithms to address important challenges in materials, biological, and energy science with the most advanced theoretical and computational tools.