Center for Multiscale Theory and Simulation

NSF CENTER for CHEMICAL INNOVATION

Anton Sinitskiy

Graduate Student
Voth Group
Department of Chemistry
University of Chicago
sinitskiy@uchicago.edu

Anton Sinitskiy graduated from the Chemistry Department of Moscow State University in 2002 with M.S. degree (highest honors) in Theoretical and Physical Chemistry. He then joined the Economics Department of MSU and five years later obtained the degree of Cand. Econ. Sci. (a Russian analogue of Ph.D. in Theoretical Economics) in 2007. In 2009, Anton became a graduate student at the University of Chicago, Chemistry Department, and joined the laboratory of Prof. Voth in 2010. He is currently working on the methodology of coarse-graining biomolecules in the NSF-funded Center for Multiscale Theory and Simulation.

Research Interests:

In general, I am interested in strict mathematical description of emergent phenomena. Coarse-graining of biomolecules represents an important particular case of this problem, where lower-level laws acting on the atomistic scale are utilized to derive higher-level ones related to the subcellular scale. How to define coarse-grained (CG) variables? How many CG variables to take? What are the dynamical equations governing CG degrees of freedom? How long should the atomistic MD trajectories be in order to build a reliable CG model? These and other similar questions are of fundamental importance for integrating Molecular Biology and Computational Chemistry.

Physically justified CG models can be used as a computational microscope, enabling us to see what is going on in living cells on those space- and timescales that are too small to be seen by traditional experimental techniques (such as electron or optical microscopy), but too large to be studied by standard computational methods (such as quantum mechanics or molecular dynamics). Practical applications of CG methodology involve design of new medicines, materials and better understanding of how the complicated machinery of life may go wrong, and how to fix it.

Publications:

  1. Dama, J. F., Sinitskiy, A. V., McCullagh, M., Weare, J., Roux, B., Dinner, A. R. & Voth, G. A. (2013). Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. Submitted.
  2. Sinitskiy, A. V. & Voth G. A. (2013). Coarse-Graining of Proteins Based on Elastic Network Models. Chem. Phys. Accepted.
  3. Sinitskiy, A. V., Saunders, M. G. & Voth, G. A. (2012). Optimal number of coarse-grained sites in different components of large biomolecular complexes. J. Phys. Chem. B., 116, 8363–8374.
  4. Sinitskiy, A. V., Tchougréeff, A. L. & Dronskowski, R. (2011). Phenomenological model of spin crossover in molecular crystals as derived from atom–atom potentials. Phys. Chem. Chem. Phys.13, 13238-13246.
  5. Sinitskiy, A. V., Greenman, L. & Mazziotti, D. A. (2010). Strong correlation in hydrogen chains and lattices using the variational two-electron reduced density matrix method. J. Chem. Phys.133, 014104.
  6. Sinitskiy, A. V., Tchougréeff, A. L., Tokmachev, A. M. & Dronskowski, R. (2009). Modeling molecular crystals formed by spin-active metal complexes by atom–atom potentials. Phys. Chem. Chem. Phys.11, 10983-10993.
  7. Sinitsky, A. V., Darhovskii, M. B., Tchougréeff, A. L. & Misurkin, I. A. (2002). Effective crystal field for trivalent first transition row ions. Int. J. Quant. Chem.88, 370-379.
  8. Pushkar, Yu. N, Sinitsky, A., Parenago, O. O., Kharlanov, A. N. & Lunina E. V. (2000). Structure and Lewis acid properties of gallia–alumina catalysts. Appl. Surf. Sci.167, 69-78.

Current project:

  •  Unifying Markov state models and coarse-grained models of biomolecules