Search Results - "McKiernan, Keri A"

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 by Wang, Lee-Ping, McKiernan, Keri A, Gomes, Joseph, Beauchamp, Kyle A, Head-Gordon, Teresa, Rice, Julia E, Swope, William C, Martínez, Todd J, Pande, Vijay S

“…The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical…”
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Modeling the mechanism of CLN025 beta-hairpin formation by McKiernan, Keri A, Husic, Brooke E, Pande, Vijay S

“…Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test…”
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Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating by McKiernan, Keri A, Koster, Anna K, Maduke, Merritt, Pande, Vijay S

“…This work reports a dynamical Markov state model of CLC-2 "fast" (pore) gating, based on 600 microseconds of molecular dynamics (MD) simulation. In the…”
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Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter by Harrigan, Matthew P., McKiernan, Keri A., Shanmugasundaram, Veerabahu, Denny, Rajiah Aldrin, Pande, Vijay S.

“…Two-pore domain potassium (K2P) channel ion conductance is regulated by diverse stimuli that directly or indirectly gate the channel selectivity filter (SF)…”
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Development and validation of a potent and specific inhibitor for the CLC-2 chloride channel by Koster, Anna K., Reese, Austin L., Kuryshev, Yuri, Wen, Xianlan, McKiernan, Keri A., Gray, Erin E., Wu, Caiyun, Huguenard, John R., Maduke, Merritt, Du Bois, J.

“…CLC-2 is a voltage-gated chloride channel that is widely expressed in mammalian tissues. In the central nervous system, CLC-2 appears in neurons and glia…”
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Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field by McKiernan, Keri A, Wang, Lee-Ping, Pande, Vijay S

“…We present a united-atom model (gb-fb15) for the molecular dynamics simulation of hydrated liquid-crystalline dipalmitoylphosphatidylcholine (DPPC)…”
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A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models by Husic, Brooke E, McKiernan, Keri A, Wayment-Steele, Hannah K, Sultan, Mohammad M, Pande, Vijay S

“…Markov state models (MSMs) are a powerful framework for the analysis of molecular dynamics data sets, such as protein folding simulations, because of their…”
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Pressure-induced crystallization of amorphous red phosphorus by Rissi, Erin N., Soignard, Emmanuel, McKiernan, Keri A., Benmore, Chris. J., Yarger, Jeffery L.

“…Structural transitions in amorphous red phosphorus were studied at ambient temperature and pressures up to 12 GPa. Amorphous (red) phosphorus was observed to…”
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Understanding how Beta-Hairpins Fold using Molecular Dynamics Simulations in Multiple Force Fields by Husic, Brooke E., McKiernan, Keri A., Pande, Vijay S.

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Improving and Applying Atomistic Simulation to Study Biophysical Conformational Dynamics by McKiernan, Keri A

“…Models are tools used to interpret and draw conclusions from nature. Molecular dynamics (MD) simulation is a powerful technique for modeling complex atomistic…”
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Classical Quantum Optimization with Neural Network Quantum States by Gomes, Joseph, McKiernan, Keri A, Eastman, Peter, Pande, Vijay S

“…The classical simulation of quantum systems typically requires exponential resources. Recently, the introduction of a machine learning-based wavefunction…”
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Automated quantum programming via reinforcement learning for combinatorial optimization by McKiernan, Keri A, Davis, Erik, Alam, M. Sohaib, Rigetti, Chad

“…We develop a general method for incentive-based programming of hybrid quantum-classical computing systems using reinforcement learning, and apply this to solve…”
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