Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin (2007)
Zong, Chenghang, Wilson, Corey J., Shen, Tongye, Wittung-Stafshede, Pernilla, Mayo, Stephen L., Wolynes, Peter G.
Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting...
Statistical mechanics of a cat's cradle (2006)
Shen, Tongye, Wolynes, Peter G
It is believed that, much like a cat's cradle, the cytoskeleton can be thought of as a network of strings under tension. We show that both regular and random bond-disordered networks having bonds...
Statistical Mechanics of a Cat's Cradle (2006)
Shen, Tongye, Wolynes, Peter G.
It is believed that, much like a cat's cradle, the cytoskeleton can be thought of as a network of strings under tension. We show that both regular and random bond-disordered networks having bonds...
Stability and Dynamics of Crystals and Glasses of Motorized Particles (2004)
Shen, Tongye, Wolynes, Peter G.
Many of the large structures of the cell, such as the cytoskeleton, are assembled and maintained far from equilibrium. We study the stabilities of various structures for a simple model of such a...
Electrostatic Steering of Substrate to Acetylcholinesterase: Analysis of Field Fluctuations (2001)
Stanislaw T. Wlodek, Tongye Shen, J. Andrew Mccammon
Based on previous molecular dynamics simulation results for acetylcholinesterase dimer, we calculate and analyse the electrostatic field fluctuations around the enzyme. The results show that dynamic...
Stability and dynamics of crystals and glasses of motorized particles
Shen, Tongye, Wolynes, Peter G.
Many of the large structures of the cell, such as the cytoskeleton, are assembled and maintained far from equilibrium. We study the stabilities of various structures for a simple model of such a...
Levy, Yaakov, Cho, Samuel S., Shen, Tongye, Onuchic, José N., Wolynes, Peter G.
Protein folding has become one of the best understood biochemical reactions from a kinetic viewpoint. The funneled energy landscape, a consequence of the minimal frustration achieved by evolution in...
Henchman, Richard H, Tai, Kaihsu, Shen, Tongye, McCammon, J Andrew
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may...
Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan A.
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been...
Stability and dynamics of crystals and glasses of motorized particles
Shen, Tongye, Wolynes, Peter G.
Many of the large structures of the cell, such as the cytoskeleton, are assembled and maintained far from equilibrium. We study the stabilities of various structures for a simple model of such a...
Levy, Yaakov, Cho, Samuel S., Shen, Tongye, Onuchic, José N., Wolynes, Peter G.
Protein folding has become one of the best understood biochemical reactions from a kinetic viewpoint. The funneled energy landscape, a consequence of the minimal frustration achieved by evolution in...
Henchman, Richard H, Tai, Kaihsu, Shen, Tongye, McCammon, J Andrew
A 10-ns trajectory from a molecular dynamics simulation is used to examine the structure and dynamics of water in the active site gorge of acetylcholinesterase to determine what influence water may...
Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan A.
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been...
Lu, Ting, Shen, Tongye, Zong, Chenghang, Hasty, Jeff, Wolynes, Peter G.
Cellular signal transduction often involves a reaction network of phosphorylation and transport events arranged with a ladder topology. If we keep track of the location of the phosphate groups...
Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model
Chang, Chia-En, Shen, Tongye, Trylska, Joanna, Tozzini, Valentina, McCammon, J. Andrew
The internal motions of proteins may serve as a “gate” in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to...
Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin
Zong, Chenghang, Wilson, Corey J., Shen, Tongye, Wittung-Stafshede, Pernilla, Mayo, Steven L., Wolynes, Peter G.
Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting...
A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw
Hamelberg, Donald, Shen, Tongye, McCammon, J. Andrew
Phosphorylation of proteins by kinases is the most commonly studied class of posttranslational modification, yet its structural consequences are not well understood. The human SR (serine-arginine)...
Phenotypic variability of growing cellular populations
Lu, Ting, Shen, Tongye, Bennett, Matthew R., Wolynes, Peter G., Hasty, Jeff
The dynamics and diversity of proliferating cellular populations are governed by the interplay between the growth and death rates among the various phenotypes within a colony. In addition, epigenetic...