Publications

Found 197 results
2013
Wu Z., Cui Q., Yethiraj A..  2013.  Why Do Arginine and Lysine Organize Lipids Differently? Insights from Coarse-Grained and Atomistic Simulations Journal of Physical Chemistry B. 117:12145-12156.
2012
Park S., Zhu X., Yethiraj A..  2012.  Atomistic Simulations of Dilute Polyelectrolyte Solutions. Journal of Physical Chemistry B. 116:4319-4327.
Cho H.W, Kwon G., Sung B.J, Yethiraj A..  2012.  Effect of Polydispersity on Diffusion in Random Obstacle Matrices. Physical Review Letters. 109
Mondal J., Yethiraj A..  2012.  Effect of secondary structure on the self-assembly of amphiphilic molecules: A multiscale simulation study. Journal of Chemical Physics. 136
Kim J.S, Wu Z., Morrow A.R, Yethiraj A., Yethiraj A..  2012.  Self-Diffusion and Viscosity in Electrolyte Solutions. Journal of Physical Chemistry B. 116:12007-12013.
Mondal J., Zhu X., Cui Q., Yethiraj A..  2012.  Sequence-Dependent pK(a) Shift Induced by Molecular Self-Assembly: Insights from Computer Simulation. Journal of Physical Chemistry B. 116:491-495.
2011
Kim JSoo, Yethiraj A..  2011.  Crowding Effects on Protein Association: Effect of Interactions between Crowding Agents. Journal of Physical Chemistry B. 115:347-353.
Mondal J, Yethiraj A..  2011.  Driving Force for the Association of Amphiphilic Molecules. Journal of Physical Chemistry Letters. 2:2391-2395.
Wu Z, Cui Q., Yethiraj A..  2011.  Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. Journal of Physical Chemistry Letters. 2:1794-1798.
Mondal J, Bratton BP, Li Y, Yethiraj A., Weisshaar J.C.  2011.  Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells. Biophysical Journal. 100:2605-2613.
Jung HTae, Sung BJune, Yethiraj A..  2011.  The Influence of the Polymer Chain Stiffness on Tracer Diffusion in Polymeric Matrices. Journal of Polymer Science Part B-Polymer Physics. 49:818-825.
Wu Z, Cui Q., Yethiraj A..  2011.  A New Coarse-Grained Force Field for Membrane-Peptide Simulations. Journal of Chemical Theory and Computation. 7:3793-3802.
Frischknecht AL, Yethiraj A..  2011.  Two- and three-body interactions among nanoparticles in a polymer melt. Journal of Chemical Physics. 134
2010
Kim JSoo, Yethiraj A..  2010.  Crowding Effects on Association Reactions at Membranes. Biophysical Journal. 98:951-958.
Zhu X, Koenig P, Hoffmann M, Yethiraj A., Cui Q..  2010.  Establishing Effective Simulation Protocols for beta- and alpha/beta-Peptides. III. Molecular Mechanical Model for Acyclic beta-Amino Acids. Journal of Computational Chemistry. 31:2063-2077.
Wu Z, Cui Q., Yethiraj A..  2010.  A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. Journal of Physical Chemistry B. 114:10524-10529.
Mondal J, Zhu X, Cui Q., Yethiraj A..  2010.  Self-Assembly of beta-Peptides: Insight from the Pair and Many-Body Free Energy of Association. Journal of Physical Chemistry C. 114:13551-13556.
Mondal J, Sung BJune, Yethiraj A..  2010.  Sequence dependent self-assembly of beta-peptides: Insights from a coarse-grained model. Journal of Chemical Physics. 132
Mondal J, Zhu X, Cui Q., Yethiraj A..  2010.  Sequence-Dependent Interaction of beta-Peptides with Membranes. Journal of Physical Chemistry B. 114:13585-13592.
Reddy G, Yethiraj A..  2010.  Solvent effects in polyelectrolyte adsorption: Computer simulations with explicit and implicit solvent. Journal of Chemical Physics. 132
Sung BJune, Yethiraj A..  2010.  Structure of void space in polymer solutions. Physical Review E. 81
2009
Ma L., Yethiraj A., Chen X., Cui Q..  2009.  A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability. Biophysical Journal. 96:3543-3554.
Sung B.J, Yethiraj A..  2009.  Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes. Biophysical Journal. 97:472-479.
Kim J.S, Yethiraj A..  2009.  Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study. Biophysical Journal. 96:1333-1340.
Yethiraj A..  2009.  Liquid State Theory of Polyelectrolyte Solutions. Journal of Physical Chemistry B. 113:1539-1551.
Tang Y., Chen X., Yoo J., Yethiraj A., Cui Q..  2009.  Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli. Experimental Mechanics. 49:35-46.
Kim J.S, Damodaran S., Yethiraj A..  2009.  Retardation of Ice Crystallization by Short Peptides. Journal of Physical Chemistry A. 113:4403-4407.
Mondal J., Sung B.J, Yethiraj A..  2009.  Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers. Journal of Physical Chemistry B. 113:9379-9385.
Sung B.J, Chang R.W, Yethiraj A..  2009.  Swelling of polymers in porous media. Journal of Chemical Physics. 130
2008
Pizzey CL, Pomerantz WC, Sung B-J, Yuwono VM, Gellman S.H, Hartgerink JD, Yethiraj A., Abbott NL.  2008.  Characterization of nanofibers formed by self-assembly of β-peptide oligomers using small angle x-ray scattering. Journal of Chemical Physics. 129:095103/1-095103/8.
Kim JSoo, Yethiraj A..  2008.  A diffusive anomaly of water in aqueous sodium chloride solutions at low temperatures. Journal of Physical Chemistry B. 112:1729-1735.
Sung BJune, Yethiraj A..  2008.  The effect of matrix structure on the diffusion of fluids in porous media. Journal of Chemical Physics. 128
Kim J.S, Yethiraj A..  2008.  The effect of salt on the melting of ice: A molecular dynamics simulation study. Journal of Chemical Physics. 129
Zhu X, Koenig P, Gellman S.H, Yethiraj A., Cui Q..  2008.  Establishing Effective Simulation Protocols for β- and α/β-Peptides. II. Molecular Mechanical (MM) Model for a Cyclic β-Residue. Journal of Physical Chemistry B. 112:5439-5448.
Tang Y, Yoo J, Yethiraj A., Cui Q., Chen X.  2008.  Gating mechanisms of mechanosensitive channels of large conductance, II: Systematic study of conformational transitions. Biophysical Journal. 95:581-596.
Chen X, Cui Q., Tang Y, Yoo J, Yethiraj A..  2008.  Gating mechanisms of mechanosensitive channels of large conductance, I: A continuum mechanics-based hierarchical framework. Biophysical Journal. 95:563-580.
Sung BJune, Yethiraj A..  2008.  Lateral diffusion of proteins in the plasma membrane: Spatial tessellation and percolation theory. Journal of Physical Chemistry B. 112:143-149.
Tang Y.Y, Yoo J., Yethiraj A., Cui Q., Chen X..  2008.  Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochemistry and Biophysics. 52:1-18.
Padmanabhan V, Kumar SK, Yethiraj A..  2008.  Phase behavior of semiflexible polymer chains. Journal of Chemical Physics. 128
Chang W-S, Link S, Yethiraj A., Barbara PF.  2008.  Single molecule spectroscopy of conjugated polymer chains in an electric field-aligned liquid crystal. Journal of Physical Chemistry B. 112:448-453.

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