Robert D. Skeel - Publications

Affiliations: 
University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
Computer Science

65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Skeel RD, Zhao R, Post CB. A minimization principle for transition paths of maximum flux for collective variables. Theoretical Chemistry Accounts. 136. PMID 29225509 DOI: 10.1007/S00214-016-2041-3  0.339
2017 Skeel R, Fang Y. Comparing Markov Chain Samplers for Molecular Simulation Entropy. 19: 561. DOI: 10.3390/E19100561  0.396
2016 Hardy DJ, Wolff MA, Xia J, Schulten K, Skeel RD. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. The Journal of Chemical Physics. 144: 114112. PMID 27004867 DOI: 10.1063/1.4943868  0.434
2016 Skeel RD. An alternative construction of the Ewald sum Molecular Physics. 114: 3166-3170. DOI: 10.1080/00268976.2016.1222455  0.359
2015 Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. Multilevel Summation Method for Electrostatic Force Evaluation. Journal of Chemical Theory and Computation. 11: 766-779. PMID 25691833 DOI: 10.1021/Ct5009075  0.371
2014 Fang Y, Sanz-Serna JM, Skeel RD. Compressible generalized hybrid Monte Carlo. The Journal of Chemical Physics. 140: 174108. PMID 24811626 DOI: 10.1063/1.4874000  0.41
2011 Skeel RD, Reich S. Corrected potential energy functions for constrained molecular dynamics European Physical Journal: Special Topics. 200: 55-72. DOI: 10.1140/Epjst/E2011-01518-8  0.404
2010 Zhao R, Shen J, Skeel RD. Maximum Flux Transition Paths of Conformational Change. Journal of Chemical Theory and Computation. 6: 2411-2423. PMID 20890401 DOI: 10.1021/Ct900689M  0.342
2009 Hairer E, McLachlan RI, Skeel RD. ON ENERGY CONSERVATION OF THE SIMPLIFIED TAKAHASHI-IMADA METHOD. Esaim. Mathematical Modelling and Numerical Analysis = Esaim. Modelisation Mathematique Et Analyse Numerique : M=2an. 43: 631-644. PMID 20539750 DOI: 10.1051/M2An/2009019  0.404
2009 Skeel RD. WHAT MAKES MOLECULAR DYNAMICS WORK? Siam Journal On Scientific Computing : a Publication of the Society For Industrial and Applied Mathematics. 31: 1363-1378. PMID 20084278 DOI: 10.1137/070683660  0.415
2009 Sweet CR, Hampton SS, Skeel RD, Izaguirre JA. A separable shadow Hamiltonian hybrid Monte Carlo method. The Journal of Chemical Physics. 131: 174106. PMID 19894997 DOI: 10.1063/1.3253687  0.426
2007 Skeel RD, Hardy DJ, Phillips JC. Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations. Journal of Computational Physics. 225: 1-5. PMID 18591998 DOI: 10.1016/J.Jcp.2007.03.010  0.367
2005 Wang W, Skeel RD. Fast evaluation of polarizable forces. The Journal of Chemical Physics. 123: 164107. PMID 16268681 DOI: 10.1063/1.2056544  0.401
2005 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26: 1781-802. PMID 16222654 DOI: 10.1002/Jcc.20289  0.382
2005 Engle RD, Skeel RD, Drees M. Monitoring energy drift with shadow Hamiltonians Journal of Computational Physics. 206: 432-452. DOI: 10.1016/J.Jcp.2004.12.009  0.404
2004 Zou G, Skeel RD. Robust variance reduction for random walk methods Siam Journal On Scientific Computing. 25: 1964-1981. DOI: 10.1137/S1064827503424025  0.568
2003 Zou G, Skeel RD. Robust biased Brownian dynamics for rate constant calculation. Biophysical Journal. 85: 2147-57. PMID 14507681 DOI: 10.1016/S0006-3495(03)74641-4  0.547
2003 Ma Q, Izaguirre JA, Skeel RD. Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities Siam Journal On Scientific Computing. 24: 1951-1973. DOI: 10.1137/S1064827501399833  0.367
2003 Wang W, Skeel RD. Analysis of a few numerical integration methods for the Langevin equation Molecular Physics. 101: 2149-2156. DOI: 10.1080/0026897031000135825  0.38
2002 Skeel RD, Tezcan I, Hardy DJ. Multiple grid methods for classical molecular dynamics. Journal of Computational Chemistry. 23: 673-84. PMID 11939600 DOI: 10.1002/Jcc.10072  0.413
2002 Skeel RD, Hardy DJ. Practical construction of modified Hamiltonians Siam Journal On Scientific Computing. 23: 1172-1188. DOI: 10.1137/S106482750138318X  0.393
2002 Skeel RD, Izaguirre JA. An impulse integrator for Langevin dynamics Molecular Physics. 100: 3885-3891. DOI: 10.1080/0026897021000018321  0.395
2001 Skeel RD, Srinivas K. Nonlinear stability analysis of area-preserving integrators Siam Journal On Numerical Analysis. 38: 129-148. DOI: 10.1137/S0036142998349527  0.315
2001 Lzaguirre JA, Catarello DP, Wozniak JM, Skeel RD. Langevin stabilization of molecular dynamics Journal of Chemical Physics. 114: 2090-2098. DOI: 10.1063/1.1332996  0.374
2000 Zou G, Skeel RD, Subramaniam S. Biased Brownian dynamics for rate constant calculation. Biophysical Journal. 79: 638-45. PMID 10919998 DOI: 10.1016/S0006-3495(00)76322-3  0.519
1999 Izaguirre JA, Reich S, Skeel RD. Longer time steps for molecular dynamics Journal of Chemical Physics. 110: 9853-9864. DOI: 10.1063/1.478995  0.326
1999 Skeel RD. Symplectic integration with floating-point arithmetic and other approximations Applied Numerical Mathematics. 29: 3-18. DOI: 10.1016/S0168-9274(98)00033-6  0.377
1999 Hardy DJ, Okunbor DI, Skeel RD. Symplectic variable step size integration for N-body problems Applied Numerical Mathematics. 29: 19-30. DOI: 10.1016/S0168-9274(98)00031-2  0.376
1999 Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: Greater Scalability for Parallel Molecular Dynamics Journal of Computational Physics. 151: 283-312. DOI: 10.1006/Jcph.1999.6201  0.342
1999 Schlick T, Skeel RD, Brunger AT, Kalé LV, Board JA, Hermans J, Schulten K. Algorithmic Challenges in Computational Molecular Biophysics Journal of Computational Physics. 151: 9-48. DOI: 10.1006/Jcph.1998.6182  0.324
1998 Garcia-Archilla B, Sanz-Serna JM, Skeel RD. Long-time-step methods for oscillatory differential equations Siam Journal On Scientific Computing. 20: 930-963. DOI: 10.1137/S1064827596313851  0.399
1998 Schlick T, Mandziuk M, Skeel RD, Srinivas K. Nonlinear Resonance Artifacts in Molecular Dynamics Simulations Journal of Computational Physics. 140: 1-29. DOI: 10.1006/Jcph.1998.5879  0.381
1997 López-Marcos MA, Sanz-Serna JM, Skeel RD. Explicit symplectic integrators using Hessian-vector products Siam Journal On Scientific Computing. 18: 223-238. DOI: 10.1137/S1064827595288085  0.413
1997 Skeel RD, Zhang G, Schlick T. A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications Siam Journal On Scientific Computing. 18: 203-222. DOI: 10.1137/S1064827595282350  0.413
1997 Littell TR, Skeel RD, Zhang M. Error analysis of symplectic multiple time stepping Siam Journal On Numerical Analysis. 34: 1792-1807. DOI: 10.1137/S0036142995287094  0.436
1997 Zhang M, Skeel RD. Cheap implicit symplectic integrators Applied Numerical Mathematics. 25: 297-302. DOI: 10.1016/S0168-9274(97)00066-4  0.384
1997 Bishop TC, Skeel RD, Schulten K. Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics Journal of Computational Chemistry. 18: 1785-1791. DOI: 10.1002/(Sici)1096-987X(19971115)18:14<1785::Aid-Jcc7>3.0.Co;2-G  0.36
1995 Barth E, Kuczera K, Leimkuhler B, Skeel RD. Algorithms for constrained molecular dynamics Journal of Computational Chemistry. 16: 1192-1209. DOI: 10.1002/Jcc.540161003  0.433
1995 Zhang M, Skeel RD. Symplectic integrators and the conservation of angular momentum Journal of Computational Chemistry. 16: 365-369. DOI: 10.1002/Jcc.540160309  0.349
1994 Okunbor DI, Skeel RD. Canonical Runge-Kutta-Nyström methods of orders five and six Journal of Computational and Applied Mathematics. 51: 375-382. DOI: 10.1016/0377-0427(92)00119-T  0.347
1994 Okunbor DI, Skeel RD. Canonical numerical methods for molecular dynamics simulations Journal of Computational Chemistry. 15: 72-79. DOI: 10.1002/Jcc.540150109  0.441
1993 Tam H, Skeel RD. Stability of Parallel Explicit ODE Methods Siam Journal On Numerical Analysis. 30: 1179-1192. DOI: 10.1137/0730061  0.356
1993 Skeel RD. Variable step size destabilizes the Störmer/leapfrog/verlet method Bit. 33: 172-175. DOI: 10.1007/Bf01990352  0.328
1993 Biesiadecki JJ, Skeel RD. Dangers of Multiple Time Step Methods Journal of Computational Physics. 109: 318-328. DOI: 10.1006/Jcph.1993.1220  0.447
1992 Okunbor D, Skeel RD. An Explicit Runge–Kutta–Nyström Method is Canonical If and Only If Its Adjoint is Explicit Siam Journal On Numerical Analysis. 29: 521-527. DOI: 10.1137/0729032  0.409
1992 Okunbor D, Skeel RD. Explicit canonical methods for hamiltonian systems Mathematics of Computation. 59: 439-455. DOI: 10.1090/S0025-5718-1992-1136225-3  0.361
1992 Guo R, Skeel RD. An algebraic hierarchical basis preconditioner Applied Numerical Mathematics. 9: 21-32. DOI: 10.1016/0168-9274(92)90064-K  0.343
1992 Skeel RD, Gear CW. Does variable step size ruin a symplectic integrator? Physica D: Nonlinear Phenomena. 60: 311-313. DOI: 10.1016/0167-2789(92)90247-K  0.337
1992 Skeel RD, Tam HW. Limits of parallelism in explicit ODE methods Numerical Algorithms. 2: 337-349. DOI: 10.1007/Bf02139473  0.41
1991 Skeel RD. Macromolecular dynamics on a shared-memory multiprocessor Journal of Computational Chemistry. 12: 175-179. DOI: 10.1002/Jcc.540120206  0.362
1990 Skeel RD, Berzins M. A Method for the Spatial Discretization of Parabolic Equations in One Space Variable Siam Journal On Scientific and Statistical Computing. 11: 1-32. DOI: 10.1137/0911001  0.372
1989 Skeel RD. Waveform Iteration and the Shifted Picard Splitting Siam Journal On Scientific and Statistical Computing. 10: 756-776. DOI: 10.1137/0910046  0.416
1989 Skeel RD. The second-order backward differentiation formula is unconditionally zero-stable Applied Numerical Mathematics. 5: 145-149. DOI: 10.1016/0168-9274(89)90030-5  0.393
1986 Skeel RD. Construction of variable-stepsize multistep formulas Mathematics of Computation. 47: 503-510. DOI: 10.2307/2008169  0.33
1986 Skeel RD, Vu TV. Note on Blended Linear Multistep Formulas Acm Transactions On Mathematical Software (Toms). 12: 223-224. DOI: 10.1145/7921.7925  0.324
1986 Skeel RD. The Order of Accuracy for Deferred Corrections Using Uncentered End Formulas Siam Journal On Numerical Analysis. 23: 393-402. DOI: 10.1137/0723026  0.374
1986 Skeel RD. Thirteen ways to estimate global error Numerische Mathematik. 48: 1-20. DOI: 10.1007/Bf01389440  0.319
1982 Skeel RD. A Theoretical Framework for Proving Accuracy Results for Deferred Corrections Siam Journal On Numerical Analysis. 19: 171-196. DOI: 10.1137/0719009  0.346
1981 Skeel RD. Accuracy of point cyclic reductions for poisson's equation Journal of Computational Physics. 44: 198-205. DOI: 10.1016/0021-9991(81)90045-0  0.348
1980 Skeel RD. Iterative refinement implies numerical stability for gaussian elimination Mathematics of Computation. 35: 817-832. DOI: 10.1090/S0025-5718-1980-0572859-4  0.335
1979 Skeel RD. Scaling for Numerical Stability in Gaussian Elimination Journal of the Acm (Jacm). 26: 494-526. DOI: 10.1145/322139.322148  0.312
1979 Skeel RD. Equivalent forms of multistep formulas Mathematics of Computation. 33: 1229-1250. DOI: 10.1090/S0025-5718-1979-0537967-4  0.315
1977 Skeel RD, Kong AK. Blended Linear Multistep Methods Acm Transactions On Mathematical Software (Toms). 3: 326-345. DOI: 10.1145/355759.355762  0.37
1977 Skeel RD, Jackson LW. Consistency of Nordsieck Methods Siam Journal On Numerical Analysis. 14: 910-924. DOI: 10.1137/0714061  0.32
1976 Skeel R. Analysis of Fixed-Stepsize Methods Siam Journal On Numerical Analysis. 13: 664-685. DOI: 10.1137/0713055  0.371
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