Biomolecular Dynamics and Energetics

Below is a list of experimental labs and theoretical groups that study the biomolecular properties.

Champion Lab – Femtosecond spectroscopic techniques to probe protein dynamics

Biomolecules form a class of complex systems that are fundamental to the existence of life. The function of biomolecules can be controlled by very small length scale fluctuations, vibrations, and the “spin” associated with metal ions, all of which involve quantum effects and are associated with the developing field of “Quantum Biology”. Our lab studies the structure and dynamics of biomolecules using a variety of ultrafast laser-based techniques such as vibrational coherence spectroscopy, and broadband pump-probe kinetics that span the femtosecond to millisecond timescales. The vibrational coherence measurements are designed to probe very low frequency motions, within the protein active sites, which have energies that can be thermally excited.  Such motions are used by biomolecules to extract energy from the environment to implement chemical reactions and to do useful biochemical work.   We have also utilized more traditional techniques such as infrared spectroscopy and resonance Raman scattering.  These approaches have excellent time and frequency resolution and can be used as spectroscopic probes of individual biomolecules as well as for imaging biological tissue and cells. Many of our studies have involved heme containing proteins and enzymes, which have roles in oxygen storage, electron and proton transport, signaling and catalysis. Photoactive molecules, such as the green fluorescent protein, have also been intensively investigated to better understand the fundamental aspects of proton transport and tunneling in both the electronically excited and ground states of biological systems. These studies have uncovered important ground state proton tunneling processes that are taking place on sub-nanosecond timescales in biomolecules at room temperature.

Di Pierro Group – The physics of genes: the dynamics of meter-long molecules

The set of instructions that dictates the growth, development, functioning, and reproduction of all known living organisms is stored in the genome. In humans, the genome is composed of 46 DNA molecules known as chromosomes, the combined length of which spans nearly two meters. An array of proteins associates with the genetic material. Together, these interacting macromolecules function as a machine that processes information regulating the transcription of the very genes encoded by the DNA.

Our research is focused on the physical processes involved in the translation of genetic information, a branch of biophysics which we refer to as Physical Genetics. We develop novel theoretical approaches to characterize the structure and function of the genome using the tools of statistical physics, information theory, and computational modeling

Dong Group – Quantum mechanical descriptions of biomacromolecules through physics-based simulations, data-driven methods, and quantum computing

Research in the Dong Lab focuses on developing and applying physics-based and data-driven computational methods on both classical and quantum computers to accelerate molecular and materials discovery for renewable energy, biomedicine, and quantum information science. Currently, we are particularly interested in understanding the tuning of photophysics and chemistry through a macromolecular environment or external field, such as those in photoenzymes. We develop computational tools to allow high-throughput quantum mechanical and multiscale (from electronic structure theory to coarse-grained) simulations of biomolecules, polymers, and heterogeneous systems, and to use insights from first principles simulations to design molecules and materials.

Chakraborty Group – Computational studies of biopolymers and the influence of sugars

Complex biomolecules such as proteins are not just static objects that we are used to seeing in the pages of textbooks and journals. Instead, these are dynamic entities that drive life and health. The functioning of these critical molecular machines depends on their structures, dynamics, and conformational transitions. Experimental techniques for capturing such structures and dynamics, however, can be extremely challenging and resource intensive. This is where computers come to the rescue. The SimBioSys Lab focuses on structure-dynamics modeling of complex biosystems by looking at these through the virtual microscope. The goal of the lab is to solve biomedical problems at the molecular level both from first principles, as well as harnessing data-driven approaches. Our research is at the interface of biochemistry, physics, chemical engineering and computer science where we strive to bridge theoretical modeling, in silico results, and experimental data. The lab currently focuses on the study of glycoproteins and other densely glycosylated systems. Glycans (branching polymers of pyranose sugars) play critical roles in a large number of biological processes, therapeutics, and biomedical devices. However, they are very refractory to experimental studies due to their heterogeneous structures and complex dynamics, The main thrust of this lab is on (i) developing new methods, as well as (ii) applying existing techniques to elucidate the roles of glycoproteins in devastating diseases, harness these systems for better treatment strategies, and get inspired by such systems to design biomaterials.

Whitford Group – Simulating large-scale complex molecular assemblies

We are a theoretical biological physics research group, focusing on the dynamics of large-scale molecular assemblies, such as the ribosome, viral capsids and the SARS-CoV-2 Spike protein. Through the development and use of a variety of models, we are working to identify the physical principles that guide biomolecular dynamics. We are also interested in using molecular simulation approaches to interpret experimental data from a wide range of techniques, including biochemical, small-angle X-ray scattering and cryogenic electron microscopy. With the interdisciplinary nature of this research, we work closely with chemists, biologists, engineers, computational scientists and medical researchers, in order to obtain a comprehensive understanding that spans from the basic sciences to medical applications.

Williams Lab – Measuring the mechanical properties of individual molecules

The Williams lab specializes in the development of single molecule methods for quantitatively probing nucleic acid interactions in order to understand the role of these interactions in processes such as replication and transcription. At the heart of these studies is the search for the mechanism by which proteins interact with nucleic acids to alter their biophysical properties, thereby achieving their specific biological activity. These studies are done in collaboration with experts in each biological system, and the activities of the proteins are monitored in a variety of in vitro and in vivo studies to determine how the observed biophysical mechanism is manifested on the level of a complete biological system.