Search Results - "Wagoner, Jason A"

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA by Cubuk, Jasmine, Alston, Jhullian J., Incicco, J. Jeremías, Singh, Sukrit, Stuchell-Brereton, Melissa D., Ward, Michael D., Zimmerman, Maxwell I., Vithani, Neha, Griffith, Daniel, Wagoner, Jason A., Bowman, Gregory R., Hall, Kathleen B., Soranno, Andrea, Holehouse, Alex S.

“…The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this…”
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Molecular Motors: Power Strokes Outperform Brownian Ratchets by Wagoner, Jason A, Dill, Ken A

“…Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Their actions are often described in terms of…”
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Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines by Wagoner, Jason A, Dill, Ken A

“…Abstract Many biomolecular machines need to be both fast and efficient. How has evolution optimized these machines along the tradeoff between speed and…”
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Assessing Implicit Models for Nonpolar Mean Solvation Forces: The Importance of Dispersion and Volume Terms by Wagoner, Jason A., Baker, Nathan A.

“…Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating…”
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Mechanisms for achieving high speed and efficiency in biomolecular machines by Wagoner, Jason A., Dill, Ken A.

“…How does a biomolecular machine achieve high speed at high efficiency?We explore optimization principles using a simple two-state dynamical model. With this…”
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Evolution of mechanical cooperativity among myosin II motors by Wagoner, Jason A., Dill, Ken A.

“…Myosin II is a biomolecular machine that is responsible for muscle contraction. Myosin II motors act cooperatively: during muscle contraction, multiple motors…”
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Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets by Wagoner, Jason A, Pande, Vijay S

“…We extend the theory of hybrid explicit/implicit solvent models to include an explicit domain that grows and shrinks in response to a solute's evolving…”
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Reducing the effect of Metropolization on mixing times in molecular dynamics simulations by Wagoner, Jason A, Pande, Vijay S

“…Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by…”
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A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent by Wagoner, Jason A, Pande, Vijay S

“…A common theme of studies using molecular simulation is a necessary compromise between computational efficiency and resolution of the forcefield that is used…”
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Assessing the performance of implicit solvation models at a nucleic acid surface by Dong, Feng, Wagoner, Jason A, Baker, Nathan A

“…Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need…”
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Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions by Swanson, Jessica M. J, Wagoner, Jason A, Baker, Nathan A, McCammon, J. A

“…Accurate implicit solvent models require parameters that have been optimized in a system- or atom-specific manner on the basis of experimental data or more…”
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A Catch Bond Suppresses Fluctuations in the Coordinated Actions of Myosin II Motors by Wagoner, Jason A.

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Evolutionary Tradeoffs in Efficiency and Turnover Rate for F0F1-ATPase by Wagoner, Jason A., Dill, Ken

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Molecular Motors have Evolved to Optimize Thermodynamic Performance by Wagoner, Jason A., Dill, Ken

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The Nonequilibrium Statistical Thermodynamics of Biological Cycles by Wagoner, Jason A., Dill, Ken

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Adaptive Boundaries in Multi-Resolution Simulations by Wagoner, Jason A., Dill, Ken, Pande, Vijay

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Finite Representation of an Infinite Molecular System: Algorithms and Applications by Wagoner, Jason A

“…The utility of molecular simulation techniques relies on the ability to accurately and efficiently explore the appropriate distribution of configurations. For…”
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Adaptive Boundaries in Multiscale Simulations by Wagoner, Jason A, Pande, Vijay S

“…Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit…”
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Reducing the effect of Metropolization on mixing times in molecular dynamics simulations by Wagoner, Jason A, Pande, Vijay S

“…Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by…”
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