 Professor, Born 1963
B. Tech. 1985, Indian Institute of Technology, Bombay India
M.S. 1987, Louisiana State University
Ph.D. 1991, North Carolina State University
Room: 8305b
Phone: 608-262-0258
Email: yethiraj@chem.wisc.edu
Position: Professor
B. J. Sung and A. Yethiraj, “Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes”, Biophysical J. 97, 472-479 (2009). J. Mondal, B. J. Sung, and A. Yethiraj, “Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers”, J. Phys. Chem. B 113, 9379-9385 (2009). J. S. Kim and A. Yethiraj, “The effect of macromolecular crowding on reaction rates: A Brownian dynamics simulations study”, Biophysical J. 96, 1333-1340 (2009). L. Ma, A. Yethiraj, X. Chen, and Q. Cui, “A computational framework for the mechanical response of macromolecules: Application to the salt concentration dependence of DNA bendability”, Biophysical J. 96, 3543-3545 (2009). J. S. Kim and A. Yethiraj, “Retardation of Ice Crystallization by Short Peptides”, J. Phys. Chem. A 113, 4403-4407 (2009). B. J. Sung, R. W. Chang, and A. Yethiraj, “Swelling of polymers in porous media”, J. Chem. Phys. 130, 124908 (2009). A. Yethiraj, “Liquid state theory of polyelectrolyte solutions”, J. Phys. Chem. B 113, 15390-1551 (2009) (feature article). Y. Tang, X. Chen, J. Yoo, A. Yethiraj, and Q. Cui, “Numerical simulation of nanoindentation and patch clamp experiments on mechanosensitive channels of large conductance in Escherichia coli, Experimental Mechanics 49, 35-46 (2009). J. S. Kim and A. Yethiraj, “The effect of salt on the melting of ice: A molecular dynamics simulation study”, J. Chem. Phys. 129, 124504 (2008). C. L. Pizzey, W. C. Pomerantz, B. J. Sung, V. M. Yuwomo, J. D. Hartgerink, A. Yethiraj, S. H. Gellman, and N. L. Abbott, “Characterization of hollow fiber formation in beta-peptide liquid crystals by small angle x-ray scattering”, J. Chem. Phys. 129, 095103 (2008). X. Zhu, P. Koenig, S.H. Gellman, A. Yethiraj and Q. Cui, "Establishing Effective Simulation Protocols for and A/B Mixed Peptides I Molecular Mechanical (MM Model for a Cyclic B-residue", J. Phys. Chem. B, 112 5439-5448 (2008)
B.J. Sung and A. Yethiraj, "The Effect of Matrix Structure on the Diffusion of Fluids in Porous Media", J. Chem. Phys. 128, 054702 (2008)
J.S. Kim and A. Yethiraj, "Diffusive Anamaly of Water in Aqueous Sodium Chloride Solutions at Low Temperatures", J. Phys. Chem. B, 112, 1729-1735 (2008)
B.J. Sung and A. Yethiraj, "Lateral Diffusion of Proteins in the Plasma Membrane: Spatial Tessallation and Percolation Theory", J. Phys. Chem B, 112, 143-149 (2008) A. Yethiraj and J.C. Weisshaar, "Why Are Lipids Not Observed in vivo", Biophysical J., 93, 3113-3119 (2007) X. Zhu, a. Yethiraj, and Q. Cui, "Establishing Effective Simulation Protocols for B and A/B Mixed Peptides. I. QM and QM/MM Models", J. Chem. Theor. and Comput. 3, 1538-1549 (2007) R. Chang and A. Yethiraj, "Structure and Dynamics of Chain Molecules in Disordered Porous Marterials: A Molecular Dynamics Simulation Study", J. Chem. Phys., 126, 174906 (2007) B.J. Sung and A. Yethiraj, "Laterail Diffusion and Percolationin Membranes", Phys. Rev. Lett. 96, 228103 (2006) K. Jagannathan, B.J. Sung, and A. Yethiraj, "Dynamics of Probes in Model Glassy Matrices", Phys. Rev. Lett. 97, 145503 (2006) G. Reddy and A. Yethiraj, "Implicit and Explicit Solvent Models for the Computer Simulation of Dilute Polymer Solutions", Macromolecules, 39, 8536-8542 (2006)
| Research Description
Our research focuses on theoretical studies of soft condensed matter. While it is clear that the short-range structure of complex fluids plays an important role in determining the physical and chemical propreties, the complexity of these systems precludes modeling them on an atomistic level. A judicious choice of coarse-grained models that hopefully capture the essential features without incorporating much of the detail is therefore a crucial step in the theoretical study of these systems. We are interested in constructing such models, and then employing theory and computer simulation to investigate their properties, with the final aim of predicting experimental observables. Our research has two components: the development of methods, and the application of these methods to understand the structure and dynamics of condensed phases. Some areas of current interest are:
Dynamics in complex media. The dynamics of in disordered materials is of importance in a number of phenomena including separation processes, drug delivery, electrophoresis, and transport in cells. Fascinating transport processes arise in many of these areas of nano-scale research. In living cells, for example, transport plays an important role in neurotransmission and protein secretion. We are studying the dynamics of macromolecules in complex environments via computer simulations. The goal is to obtain an understanding of the mechanism of molecular motion. It is hoped that we will obtain an understanding of these dynamic phenomena that will provide us with a theoretical standard against which experimental data, e.g., the diffusion of proteins in E. coli, may be compared.
Macromolecular solutions. The conformational properties and phase behavior of solutions of macromolecules is of interest from a basic scientific standpoint because they are extremely sensitive to the solution conditions. We are interested in two classes of macromolecules: polyelectrolytes and β-peptides. Our understanding of solutions of polyelectrolytes and peptides is in its infancy, and there are many issues that are far from resolved. These include the conformational properties, self-diffusion, viscosity, and adsorption behavior. We are using computer simulation and liquid state theory to establish the importance of solvent effects, counterion correlations, and polymer architecture on the behavior of polyelectrolytes in solution. The methods we develop and the knowledge we obtain should be useful in the study of other complex fluids including surfactants, biological macromolecules, and gels.
Membrane biophysics. The cell membrane is a very heterogeneous environment with several types of lipids and peripheral and integral membrane proteins. We are using simple models to study three different aspects of membrane biophysics: the diffusion of membrane components, the self-assembly of lipids (rafts), and the self-assembly of proteins. The lateral diffusion of proteins and lipid molecules in cell membranes is essential to many physiological processes including diffusion-controlled reactions, such as in the electron transfer reactions involving cytochromes in the mitochondria, and the binding of hormones. We are using a combination of computer simulation, geometric analyses, and percolation theory to elucidate the effect of obstacles (integral membrane proteins) on the diffusion of lipids and GPI anchored proteins.
Effect of peptides on crystallization. The effect of peptides on the nucleation and growth of ice crystals under super-cooled conditions is important for a number of reasons including a fundamental understanding of the hardiness of plants in extreme conditions, the survival of artic fish, and the preservation of ice-cream. The freeze-thaw cycle in most freezers results in the nucleation of crystals in ice-cream with undesirable textural consquences. Peptide oligomers have been suggested as additives that might inhibit crystallization while not affecting the taste of the ice-cream. We are using atomistic simulations to study the crystallization of water with added salt and small peptides. We hope to learn the mechanism by which crystallization is affected by additives.
Senior Editor, The Journal of Physical Chemistry, 2007 to present Vilas Associate Award, 2006 Fellow, American Physical Society, 2001 Alexander von Humboldt Research Fellowship, 1999 Samuel C. Johnson Distinguished Fellowship, 1998 Alfred P. Sloan Fellow, 1997-1999 National Science Foundation, CAREER award, 1995 National Science Foundation, Research Initiation Award, 1994 - Edward M. Schoenborn Award for Outstanding Ph.D. Candidate in Chemical Engineering, North Carolina State University, 1991
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