Dmitrii E. Makarov

makarov@mail.utexas.edu

Associate Professor, Faculty

Research Group

Makarov Group

Education

PhD, Institute of Chemical Physics, Moscow, 1992
BS, Moscow Institute of Physics and Technology, 1990

Affiliations

Center for Computational Biology and Bioinformatics; Institute for Cellular and Molecular Biology; Institute for Computational and Engineering Sciences; Center for Nano- and Molecular Science and Technology; Institute for Theoretical Chemistry; Texas Materials Institute

Theory and computer simulation of the dynamics of biomolecules

Single molecule dynamics

Our work in single molecules theory is motivated by the recent developments in scanning tunneling microscopy, atomic force microscopy, and single molecule optical spectroscopy, which enable experimenters to observe and manipulate individual molecules. For example, by monitoring fluorescence, one photon at a time, from a dye molecule planted on a single protein, one can record a "movie" of the protein's dynamics. Understanding the information contained in such a "movie" requires theoretical insight into the relationship between the emission process and the molecule's dynamics. Our research involves the development and use of simulation methods in order to study quantum dynamics of single molecules and to understand how these dynamics are manifested in the properties of the molecules' emission.

Mechanical properties of single protein molecules

Some proteins have load-bearing functions in living organisms and are unique materials. We use atomistic simulations as well as simple theoretical models to study the mechanical resistance of individual protein molecules subject to stretching forces. Our goal here is to understand the atomic force microscopy pulling experiments performed on single proteins and to learn how the mechanical properties of proteins depend on their structure.

Protein translocation

Protein translocation across certain membranes and protein degradation by ATP-dependent proteases involve the threading of proteins though narrow pores whose dimensions cannot accommodate folded domains. We are using computer simulations to understand these processes at the molecular level. This work is done in close collaboration with experimentalists and, besides simulations, involves development of new computational methods for estimating entropies and equilibrium constants from molecular dynamics or Monte Carlo data.

 

Representative Publications

Ryan R. Cheng and Dmitrii E. Makarov, Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: A case study of polymer cyclization, J. Chem. Phys. 134 (2011) 085104

 

Reza Soheilifard, Dmitrii E. Makarov, and Gregory J. Rodin, Rigorous coarse graining for the dynamics of linear systems with application to relaxation dynamics in proteins, J. Chem. Phys. 135 (2011) 054107

 

Srabanti Chaudhury and Dmitrii E. Makarov, A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements, J. Chem. Phys. 133 (2010) 034118

 

Takanori Uzawa, Ryan R. Cheng, Ryan J. White, Dmitrii E. Makarov, and Kevin W. Plaxco, A Mechanistic Study of Electron Transfer from the Distal Termini of Electrode-Bound, Single-Stranded DNAs, JACS 132 (2010), 16120-16126

 

Ryan R. Cheng, Takanori Uzawa, Kevin W. Plaxco, and Dmitrii E. Makarov, Universality in the Timescales of Internal Loop Formation in Unfolded Proteins and Single-Stranded Oligonucleotides, Biophysical Journal, 99 (2010), 3959-3968

 

Dmitrii E. Makarov, Computer simulations and theory of protein translocation, Accounts of Chemical Research 42 (2009) 281-289.