Adaptive stochastic methods for sampling driven molecular systems.

Keywords

Ergodicity, A priori and a posteriori, Statistical physics, Brownian motion, Nonlinear system

References

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• Origin of the structural phase transition in Li7La3Zr2O12.Noam Bernstein, M. D. Johannes, Khang Hoang — 2012
• cp2k: atomistic simulations of condensed matter systemsJürg Hutter, Marcella Iannuzzi, Florian Schiffmann — 2014
• Covariance-Controlled Adaptive Langevin Thermostat for Large-Scale Bayesian SamplingXiaocheng Shang, Zhanxing Zhu, Benedict Leimkuhler — 2015
• Electronically coarse-grained molecular dynamics using quantum Drude oscillatorsAndy Jones, Jason Crain, Flaviu Cipcigan — 2013
• Hamiltonian thermostats fail to promote heat flowWm. G. Hoover, Carol G. Hoover — 2013
• Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.Csilla Várnai, Noam Bernstein, Letif Mones — 2013
• Direct control of the small-scale energy balance in two-dimensional fluid dynamicsJason Frank, Benedict Leimkuhler, Keith W. Myerscough — 2014
• Geometric integration and thermostat methods for Hamiltonian systemsJānis Bajārs — 2012
• Adaptive Thermostats for Noisy Gradient SystemsBenedict Leimkuhler, Xiaocheng Shang — 2015
• The Adaptive Buffered Force QM/MM method in the CP2K and AMBER software packagesLetif Mones, Andrew Jones, Andreas W. Götz — 2014
• Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.Geoffrey P. F. Wood, Alavattam Sreedhara, Jamie Moore — 2016
• Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamicsBenedict Leimkuhler, Xiaocheng Shang — 2016
• Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressedFlaviu Cipcigan, V. P. Sokhan, Jason Crain — 2016
• Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking, molecular dynamics, and charge density analysisSaravanan Kandasamy, Chinnasamy Kalaiarasi, P. Kumaradhas — 2017
• Non-Ergodicity of Nosé-Hoover Chain DynamicsPuneet Kumar Patra, Baidurya Bhattacharya — 2014
• Accurate interatomic force fields via machine learning with covariant kernelsAldo Glielmo, Peter Sollich, Alessandro De Vita — 2016
• Integrating local information for inference and optimization in machine learningZhanxing Zhu — 2016
• Extended stochastic dynamics: theory, algorithms, and applications in multiscale modelling and data scienceXiaocheng Shang — 2016
• Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density studyMagudeeswaran Sivanandam, Saravanan Kandasamy, P. Kumaradhas — 2018
• Assessing numerical methods for molecular and particle simulation.Xiaocheng Shang, Martin Kröger, Benedict Leimkuhler — 2017

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