Zobrazeno 1 - 10
of 30
pro vyhledávání: '"Ben Leimkuhler"'
Publikováno v:
Trstanova, Z, Leimkuhler, B & Lelievre, T 2020, ' Local and Global Perspectives on Diffusion Maps in the Analysis of Molecular Systems ', Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 476, no. 2233, 20190036 . https://doi.org/10.1098/rspa.2019.0036
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2020, 476 (2233), ⟨10.1098/rspa.2019.0036⟩
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Royal Society, The, 2020, 476 (2233), ⟨10.1098/rspa.2019.0036⟩
Proceedings. Mathematical, Physical, and Engineering Sciences
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2020, 476 (2233), ⟨10.1098/rspa.2019.0036⟩
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Royal Society, The, 2020, 476 (2233), ⟨10.1098/rspa.2019.0036⟩
Proceedings. Mathematical, Physical, and Engineering Sciences
Diffusion maps approximate the generator of Langevin dynamics from simulation data. They afford a means of identifying the slowly evolving principal modes of high-dimensional molecular systems. When combined with a biasing mechanism, diffusion maps c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::10e63b85056f35679c3830efa1e40612
https://www.pure.ed.ac.uk/ws/files/128886956/Local_and_Global_Perspectives_on_Diffusion_Maps_in_the_Analysis_of_Molecular_Systems.pdf
https://www.pure.ed.ac.uk/ws/files/128886956/Local_and_Global_Perspectives_on_Diffusion_Maps_in_the_Analysis_of_Molecular_Systems.pdf
Publikováno v:
Nonlinearity, 26, 1945-1973
Bajars, J, Frank, J E & Leimkuhler, B J 2013, ' Weakly coupled heat bath models for Gibbs-like invariant states in nonlinear wave equations ', Nonlinearity, vol. 26, no. 7, pp. 1945-1973 . https://doi.org/10.1088/0951-7715/26/7/1945
Bajars, J, Frank, J E & Leimkuhler, B J 2013, ' Weakly coupled heat bath models for Gibbs-like invariant states in nonlinear wave equations ', Nonlinearity, vol. 26, no. 7, pp. 1945-1973 . https://doi.org/10.1088/0951-7715/26/7/1945
Thermal bath coupling mechanisms as utilized in molecular dynamics are applied to partial differential equation models. Working from a semi-discrete (Fourier mode) formulation for the Burgers-Hopf or Korteweg-de Vries equation, we introduce auxiliary
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34094391b48231ec244e40c7053d18ba
https://doi.org/10.1088/0951-7715/26/7/1945
https://doi.org/10.1088/0951-7715/26/7/1945
Autor:
Ben Leimkuhler, Charles Matthews
This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern co
Autor:
Zhidong Jia, Ben Leimkuhler
Publikováno v:
ESAIM: Mathematical Modelling and Numerical Analysis. 41:333-350
In this paper, we discuss advanced thermostatting techniques for sampling molecular systems in the canonical ensemble. We first survey work on dynamical thermostatting methods, including the Nose-Poincare method, and generalized bath methods which in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8026f6e83a1c478cb5a0dca15ed66eed
https://doi.org/10.1051/m2an:2007019
https://doi.org/10.1051/m2an:2007019
Autor:
Ben Leimkuhler, Charles Matthews
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
In the previous chapter we described numerical methods for solving the equations of Langevin dynamics, a system of stochastic differential equations that sample the canonical ensemble. The methods allow us to compute averages of the form $$\displayst
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0b8b2f2015ca1995aee7fee137779687
https://doi.org/10.1007/978-3-319-16375-8_8
https://doi.org/10.1007/978-3-319-16375-8_8
Autor:
Charles Matthews, Ben Leimkuhler
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
In this chapter, we discuss principles for the design of algorithms for canonical sampling, based on the numerical discretization of stochastic dynamics models (such as Langevin dynamics) introduced in the previous chapter. Before we begin our discus
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::392224feb2140a26052835f02b8d20a0
https://doi.org/10.1007/978-3-319-16375-8_7
https://doi.org/10.1007/978-3-319-16375-8_7
Autor:
Ben Leimkuhler, Charles Matthews
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7af8ae440a69fc757e584150c753a9f9
https://doi.org/10.1007/978-3-319-16375-8_1
https://doi.org/10.1007/978-3-319-16375-8_1
Autor:
Ben Leimkuhler, Charles Matthews
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
Until now, we have considered molecular models for isolated collections of atoms. We have seen how to derive equations of motion, and studied the properties of the relevant dynamical systems. We have also observed that the chaotic nature of a typical
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3e37169a92ecfe4ea854c18cd49a188d
https://doi.org/10.1007/978-3-319-16375-8_6
https://doi.org/10.1007/978-3-319-16375-8_6
Autor:
Ben Leimkuhler, Charles Matthews
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
In the previous chapters, we considered the approximation of Hamiltonian trajectories. In this chapter we study the paths emanating from the collection of all initial conditions within a given set. This is the starting point for statistical mechanics
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c12711c15d1f5dfda60099851ae0ac48
https://doi.org/10.1007/978-3-319-16375-8_5
https://doi.org/10.1007/978-3-319-16375-8_5
Autor:
Ben Leimkuhler, Charles Matthews
Publikováno v:
Molecular Dynamics ISBN: 9783319163741
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b53c1e17a91d17c876df66c61ab208ca
https://doi.org/10.1007/978-3-319-16375-8_2
https://doi.org/10.1007/978-3-319-16375-8_2