All Department Publications

Found 117 results
Author Title Type [ Year(Asc)]
Filters: Author is A Yethiraj  [Clear All Filters]
2012
Park S, Zhu X, Yethiraj A. Atomistic Simulations of Dilute Polyelectrolyte Solutions. Journal of Physical Chemistry B. 2012;116:4319-4327.
Mondal J, Yethiraj A. Effect of secondary structure on the self-assembly of amphiphilic molecules: A multiscale simulation study. Journal of Chemical Physics. 2012;136.
2011
Kim JS, Yethiraj A. Crowding Effects on Protein Association: Effect of Interactions between Crowding Agents. Journal of Physical Chemistry B. 2011;115:347-353.
Mondal J, Yethiraj A. Driving Force for the Association of Amphiphilic Molecules. Journal of Physical Chemistry Letters. 2011;2:2391-2395.
Wu Z, Cui Q, Yethiraj A. Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. Journal of Physical Chemistry Letters. 2011;2:1794-1798.
Mondal J, Bratton BP, Li Y, Yethiraj A, Weisshaar JC. Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells. Biophysical Journal. 2011;100:2605-2613.
Jung HT, Sung BJ, Yethiraj A. The Influence of the Polymer Chain Stiffness on Tracer Diffusion in Polymeric Matrices. Journal of Polymer Science Part B-Polymer Physics. 2011;49:818-825.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Force Field for Membrane-Peptide Simulations. Journal of Chemical Theory and Computation. 2011;7:3793-3802.
Frischknecht AL, Yethiraj A. Two- and three-body interactions among nanoparticles in a polymer melt. Journal of Chemical Physics. 2011;134.
2010
Kim JS, Yethiraj A. Crowding Effects on Association Reactions at Membranes. Biophysical Journal. 2010;98:951-958.
Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for beta- and alpha/beta-Peptides. III. Molecular Mechanical Model for Acyclic beta-Amino Acids. Journal of Computational Chemistry. 2010;31:2063-2077.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. Journal of Physical Chemistry B. 2010;114:10524-10529.
Mondal J, Zhu X, Cui Q, Yethiraj A. Self-Assembly of beta-Peptides: Insight from the Pair and Many-Body Free Energy of Association. Journal of Physical Chemistry C. 2010;114:13551-13556.
Mondal J, Sung BJ, Yethiraj A. Sequence dependent self-assembly of beta-peptides: Insights from a coarse-grained model. Journal of Chemical Physics. 2010;132.
Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent Interaction of beta-Peptides with Membranes. Journal of Physical Chemistry B. 2010;114:13585-13592.
Reddy G, Yethiraj A. Solvent effects in polyelectrolyte adsorption: Computer simulations with explicit and implicit solvent. Journal of Chemical Physics. 2010;132.
Sung BJ, Yethiraj A. Structure of void space in polymer solutions. Physical Review E. 2010;81.
2009
Ma L, Yethiraj A, Chen X, Cui Q. A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability. Biophysical Journal. 2009;96:3543-3554.
Sung BJ, Yethiraj A. Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes. Biophysical Journal. 2009;97:472-479.
Kim JS, Yethiraj A. Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study. Biophysical Journal. 2009;96:1333-1340.
Yethiraj A. Liquid State Theory of Polyelectrolyte Solutions. Journal of Physical Chemistry B. 2009;113:1539-1551.
Tang Y, Chen X, Yoo J, Yethiraj A, Cui Q. Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli. Experimental Mechanics. 2009;49:35-46.
Kim JS, Damodaran S, Yethiraj A. Retardation of Ice Crystallization by Short Peptides. Journal of Physical Chemistry A. 2009;113:4403-4407.
Mondal J, Sung BJ, Yethiraj A. Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers. Journal of Physical Chemistry B. 2009;113:9379-9385.
Sung BJ, Chang RW, Yethiraj A. Swelling of polymers in porous media. Journal of Chemical Physics. 2009;130.
2008
Pizzey CL, Pomerantz WC, Sung B-J, Yuwono VM, Gellman SH, Hartgerink JD, Yethiraj A, Abbott NL. Characterization of nanofibers formed by self-assembly of beta-peptide oligomers using small angle x-ray scattering. Journal of Chemical Physics. 2008;129.
Kim JS, Yethiraj A. A diffusive anomaly of water in aqueous sodium chloride solutions at low temperatures. Journal of Physical Chemistry B. 2008;112:1729-1735.
Sung BJ, Yethiraj A. The effect of matrix structure on the diffusion of fluids in porous media. Journal of Chemical Physics. 2008;128.
Kim JS, Yethiraj A. The effect of salt on the melting of ice: A molecular dynamics simulation study. Journal of Chemical Physics. 2008;129.
Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Peptides. II. Molecular Mechanical (MM) Model for a Cyclic β-Residue. The Journal of Physical Chemistry B [Internet]. 2008;112:5439-5448. Available from: http://pubs.acs.org/doi/abs/10.1021/jp077601y
Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating mechanisms of mechanosensitive channels of large conductance, I: A continuum mechanics-based hierarchical framework. Biophysical Journal. 2008;95:563-580.
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating mechanisms of mechanosensitive channels of large conductance, II: Systematic study of conformational transitions. Biophysical Journal. 2008;95:581-596.
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating Mechanisms of Mechanosensitive Channels of Large Conductance, II: Systematic Study of Conformational Transitions. Biophysical Journal. 2008;95:581 - 596.
Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework. Biophysical Journal. 2008;95:563 - 580.
Sung BJ, Yethiraj A. Lateral diffusion of proteins in the plasma membrane: Spatial tessellation and percolation theory. Journal of Physical Chemistry B. 2008;112:143-149.
Tang YY, Yoo J, Yethiraj A, Cui Q, Chen X. Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochemistry and Biophysics. 2008;52:1-18.
Padmanabhan V, Kumar SK, Yethiraj A. Phase behavior of semiflexible polymer chains. Journal of Chemical Physics. 2008;128.
Chang W-S, Link S, Yethiraj A, Barbara PF. Single molecule spectroscopy of conjugated polymer chains in an electric field-aligned liquid crystal. Journal of Physical Chemistry B. 2008;112:448-453.
2007
Zhu X, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-mixed peptides. I. QM and QM/MM models. Journal of Chemical Theory and Computation. 2007;3:1538-1549.
Moorthy J, Burgess R, Yethiraj A, Beebe D. Microfluidic based platform for characterization of protein interactions in hydrogel nanoenvironments. Analytical Chemistry. 2007;79:5322-5327.
Sung BJ, Yethiraj A. Permeation of a hard sphere fluid into a quenched matrix. Journal of Chemical Physics. 2007;126.
Barbara PF, Chang WS, Link S, Scholes GD, Yethiraj A. Structure and dynamics of conjugated polymers in liquid crystalline solvents. Annual Review of Physical Chemistry. 2007;58:565-584.
Chang R, Yethiraj A. Structure and dynamics of short chain molecules in disordered porous materials: A molecular dynamics simulation study. Journal of Chemical Physics. 2007;126.
Yethiraj A, Weisshaar JC. Why are lipid rafts not observed in vivo?. Biophys J. 2007;93(9):3113-9.
2006
Reddy G, Chang RW, Yethiraj A. Adsorption and dynamics of a single polyelectrolyte chain near a planar charged surface: Molecular dynamics simulations with explicit solvent. Journal of Chemical Theory & Computation. 2006;2:630-636.
Link S, Chang WS, Yethiraj A, Barbara PF. Anisotropic diffusion of elongated and aligned polymer chains in a nematic solvent. Journal of Physical Chemistry B. 2006;110:19799.
Chang RW, Yethiraj A. Dynamics of chain molecules in disordered materials. Physical Review Letters. 2006;9610.
Jagannathan K, Sung BJ, Yethiraj A. Dynamics of probes in model glassy matrices. Physical Review Letters. 2006;97.
Tang Y, Cao G, Chen X, Yoo J, Yethiraj A, Cui Q. A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J. 2006;91(4):1248-63.
Reddy G, Yethiraj A. Implicit and explicit solvent models for the simulation of dilute polymer solutions. Macromolecules. 2006;39:8536.

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