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1

Symplectic Numerical Integrators in Constrained Hamiltonian Systems

Benedict J. Leimkuhler, Robert D. Skeel

Journal:

Journal of Computational Physics

Year:

1994

File:

PDF, 351 KB

1994

2

Symplectic splitting methods for rigid body molecular dynamics

Dullweber, Andreas, Leimkuhler, Benedict, McLachlan, Robert

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 560 KB

english, 1997

3

[Lecture Notes in Computational Science and Engineering] Computational Molecular Dynamics: Challenges, Methods, Ideas Volume 4 ||

Deuflhard, Peter, Hermans, Jan, Leimkuhler, Benedict, Mark, Alan E., Reich, Sebastian, Skeel, Robert D.

Year:

1999

Language:

english

File:

PDF, 88.55 MB

english, 1999

4

[Lecture Notes in Computational Science and Engineering] Computational Molecular Dynamics: Challenges, Methods, Ideas Volume 4 || Molecular Dynamics Simulations: The Limits and Beyond

Deuflhard, Peter, Hermans, Jan, Leimkuhler, Benedict, Mark, Alan E., Reich, Sebastian, Skeel, Robert D.

Year:

1999

Language:

english

File:

PDF, 6.62 MB

english, 1999

5

Hypocoercivity Properties of Adaptive Langevin Dynamics

Leimkuhler, Benedict, Sachs, Matthias, Stoltz, Gabriel

Journal:

SIAM Journal on Applied Mathematics

Year:

2020

File:

PDF, 862 KB

2020

6

On the approximation of Feynman–Kac path integrals

Stephen D. Bond, Brian B. Laird, Benedict J. Leimkuhler

Journal:

Journal of Computational Physics

Year:

2003

Language:

english

File:

PDF, 337 KB

english, 2003

7

A Hamiltonian Formulation for Recursive Multiple Thermostats in a Common Timescale

Leimkuhler, Benedict J., Sweet, Christopher R.

Journal:

SIAM Journal on Applied Dynamical Systems

Year:

2005

Language:

english

File:

PDF, 1.04 MB

english, 2005

8

Geometric Integration: Numerical Solution of Differential Equations on Manifolds || Reversible Adaptive Regularization: Perturbed Kepler Motion and Classical Atomic Trajectories

Benedict Leimkuhler

Journal:

Philosophical Transactions Mathematical Physical & Engineering Sciences

Year:

1999

Language:

english

File:

PDF, 2.52 MB

english, 1999

9

Robust and efficient configurational molecular sampling via Langevin dynamics

Leimkuhler, Benedict, Matthews, Charles

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.53 MB

english, 2013

10

A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces

Di Pierro, Michele, Elber, Ron, Leimkuhler, Benedict

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

11

A Metropolis adjusted Nosé-Hoover thermostat

Leimkuhler, Benedict, Reich, Sebastian

Journal:

ESAIM Mathematical Modelling and Numerical Analysis

Year:

2009

Language:

english

File:

PDF, 1004 KB

english, 2009

12

Algorithms for constrained molecular dynamics

Eric Barth, Krzysztof Kuczera, Benedict Leimkuhler, Robert D. Skeel

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 1.46 MB

english, 1995

13

Geometric Integrators for Classical Spin Systems

Jason Frank, Weizhang Huang, Benedict Leimkuhler

Journal:

Journal of Computational Physics

Year:

1997

Language:

english

File:

PDF, 500 KB

english, 1997

14

The Nosé–Poincaré Method for Constant Temperature Molecular Dynamics

Stephen D Bond, Benedict J Leimkuhler, Brian B Laird

Journal:

Journal of Computational Physics

Year:

1999

Language:

english

File:

PDF, 154 KB

english, 1999

15

Reversible adaptive regularization methods for atomic N-body problems in applied fields

Benedict Leimkuhler

Journal:

Applied Numerical Mathematics

Year:

1999

Language:

english

File:

PDF, 689 KB

english, 1999

16

Orthosymplectic integration of linear Hamiltonian systems

Benedict J. Leimkuhler, Erik S. Van Vleck

Journal:

Numerische Mathematik

Year:

1997

Language:

english

File:

PDF, 113 KB

english, 1997

17

Preface

Graeme Fairweather, Ian Gladwell, Benedict Leimkuhler, Erik Van Vleck

Journal:

Applied Numerical Mathematics

Year:

1999

Language:

english

File:

PDF, 66 KB

english, 1999

18

Time-transformations for reversible variable stepsize integration

Stephen D. Bond, Benedict J. Leimkuhler

Journal:

Numerical Algorithms

Year:

1998

Language:

english

File:

PDF, 190 KB

english, 1998

19

Asymptotic Error Analysis of the Adaptive Verlet Method

Stéphane Cirilli, Ernst Hairer, Benedict Leimkuhler

Journal:

BIT Numerical Mathematics

Year:

1999

Language:

english

File:

PDF, 189 KB

english, 1999

20

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || Free Energy Calculations in Biological Systems. How Useful Are They in Practice?

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 556 KB

english, 2006

21

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || Replica-Exchange-Based Free-Energy Methods

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 482 KB

english, 2006

22

The Adaptive Verlet Method

Huang, Weizhang, Leimkuhler, Benedict

Journal:

SIAM Journal on Scientific Computing

Year:

1997

Language:

english

File:

PDF, 1.85 MB

english, 1997

23

A Time-Reversible Variable-Stepsize Integrator for Constrained Dynamics

Barth, Eric, Leimkuhler, Benedict, Reich, Sebastian

Journal:

SIAM Journal on Scientific Computing

Year:

1999

Language:

english

File:

PDF, 603 KB

english, 1999

24

Stabilized Integration of Hamiltonian Systems with Hard-Sphere Inequality Constraints

Bond, Stephen D., Leimkuhler, Benedict J.

Journal:

SIAM Journal on Scientific Computing

Year:

2008

Language:

english

File:

PDF, 236 KB

english, 2008

25

A symplectic method for rigid-body molecular simulation

Kol, Ayla, Laird, Brian B., Leimkuhler, Benedict J.

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 481 KB

english, 1997

26

Dimensional Reductions for the Computation of Time–Dependent Quantum Expectations

Mazzi, Giacomo, Leimkuhler, Benedict J.

Journal:

SIAM Journal on Scientific Computing

Year:

2011

Language:

english

File:

PDF, 335 KB

english, 2011

27

[Lecture Notes in Computational Science and Engineering] Computational Molecular Dynamics: Challenges, Methods, Ideas Volume 4 || Conformational Dynamics Simulations of Proteins

Deuflhard, Peter, Hermans, Jan, Leimkuhler, Benedict, Mark, Alan E., Reich, Sebastian, Skeel, Robert D.

Year:

1999

Language:

english

File:

PDF, 3.81 MB

english, 1999

28

A Projective Thermostatting Dynamics Technique

Jia, Zhidong, Leimkuhler, Benedict J.

Journal:

Multiscale Modeling and Simulation

Year:

2005

Language:

english

File:

PDF, 718 KB

english, 2005

29

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 ||

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 4.75 MB

english, 2006

30

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || Numerical Methods for Calculating the Potential of Mean Force

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 445 KB

english, 2006

31

The canonical ensemble via symplectic integrators using Nosé and Nosé–Poincaré chains

Leimkuhler, Benedict J., Sweet, Christopher R.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 354 KB

english, 2004

32

Generating generalized distributions from dynamical simulation

Barth, Eric J., Laird, Brian B., Leimkuhler, Benedict J.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 351 KB

english, 2003

33

Generalized dynamical thermostating technique

Laird, Brian B., Leimkuhler, Benedict J.

Journal:

Physical Review E

Year:

2003

Language:

english

File:

PDF, 66 KB

english, 2003

34

Generalized Bulgac-Kusnezov methods for sampling of the Gibbs-Boltzmann measure

Leimkuhler, Benedict

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 544 KB

english, 2010

35

On the numerical treatment of dissipative particle dynamics and related systems

Leimkuhler, Benedict, Shang, Xiaocheng

Journal:

Journal of Computational Physics

Year:

2015

Language:

english

File:

PDF, 880 KB

english, 2015

36

A molecular dynamics algorithm for mixed hard-core/continuous potentials

HOUNDONOUGBO, YAO A., LAIRD, BRIAN B., LEIMKUHLER, BENEDICT J.

Journal:

Molecular Physics

Year:

2000

Language:

english

File:

PDF, 643 KB

english, 2000

37

Simulating Hamiltonian Dynamics || Rigid body dynamics

Leimkuhler, Benedict, Reich, Sebastian

Year:

2005

Language:

english

File:

PDF, 890 KB

english, 2005

38

Simulating Hamiltonian Dynamics || Molecular dynamics

Leimkuhler, Benedict, Reich, Sebastian

Year:

2005

Language:

english

File:

PDF, 841 KB

english, 2005

39

Simulating Hamiltonian Dynamics || Constrained mechanical systems

Leimkuhler, Benedict, Reich, Sebastian

Year:

2005

Language:

english

File:

PDF, 491 KB

english, 2005

40

Simulating Hamiltonian Dynamics || Higher-order methods

Leimkuhler, Benedict, Reich, Sebastian

Year:

2005

Language:

english

File:

PDF, 572 KB

english, 2005

41

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 299 KB

english, 2006

42

Nonlinear propagating localized modes in a 2D hexagonal crystal lattice

Bajars, Janis, Eilbeck, J. Chris, Leimkuhler, Benedict

Journal:

Physica D: Nonlinear Phenomena

Year:

2015

Language:

english

File:

PDF, 1.73 MB

english, 2015

43

[Lecture Notes in Computational Science and Engineering] Computational Molecular Dynamics: Challenges, Methods, Ideas Volume 4 || Steered Molecular Dynamics

Deuflhard, Peter, Hermans, Jan, Leimkuhler, Benedict, Mark, Alan E., Reich, Sebastian, Skeel, Robert D.

Year:

1999

Language:

english

File:

PDF, 5.52 MB

english, 1999

44

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || The Langevin Equation for Generalized Coordinates

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 172 KB

english, 2006

45

Molecular dynamics and the accuracy of numerically computed averages

Bond, Stephen D., Leimkuhler, Benedict J.

Journal:

Year:

2007

Language:

english

File:

PDF, 980 KB

english, 2007

46

Extended Hamiltonian approach to continuous tempering

Gobbo, Gianpaolo, Leimkuhler, Benedict J.

Journal:

Physical Review E

Year:

2015

Language:

english

File:

PDF, 1.22 MB

english, 2015

47

Direct control of the small-scale energy balance in two-dimensional fluid dynamics

Frank, Jason, Leimkuhler, Benedict, Myerscough, Keith W.

Journal:

Journal of Fluid Mechanics

Year:

2015

Language:

english

File:

PDF, 20.97 MB

english, 2015

48

Adaptive Thermostats for Noisy Gradient Systems

Leimkuhler, Benedict, Shang, Xiaocheng

Journal:

SIAM Journal on Scientific Computing

Year:

2016

Language:

english

File:

PDF, 317 KB

english, 2016

49

Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamics

Leimkuhler, Benedict, Shang, Xiaocheng

Journal:

Journal of Computational Physics

Year:

2016

Language:

english

File:

PDF, 736 KB

english, 2016

50

Simulating Hamiltonian Dynamics || The modified equations

Leimkuhler, Benedict, Reich, Sebastian

Year:

2005

Language:

english

File:

PDF, 621 KB

english, 2005