-
1
-
-
0003451443
-
-
(Clarendon Press, New York, NY, USA)
-
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon Press, New York, NY, USA, 1987);
-
(1987)
Computer Simulation of Liquids
-
-
Allen, M.P.1
Tildesley, D.J.2
-
4
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. Salmon, Y. Shan, and W. Wriggers, " Atomic-level characterization of the structural dynamics of proteins," Science 330 (6002), 341-346 (2010). 10.1126/science.1187409
-
(2010)
Science
, vol.330
, Issue.6002
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.5
Eastwood, M.P.6
Bank, J.A.7
Jumper, J.M.8
Salmon, J.9
Shan, Y.10
Wriggers, W.11
-
5
-
-
70349918314
-
Coarse-grained polymer melts based on isolated atomistic chains: Simulation of polystyrene of different tacticities
-
D. Fritz, V. A. Harmandaris, K. Kremer, and N. Van der Vegt, " Coarse-grained polymer melts based on isolated atomistic chains: Simulation of polystyrene of different tacticities," Macromolecules 42 (19), 7579-7588 (2009). 10.1021/ma901242h
-
(2009)
Macromolecules
, vol.42
, Issue.19
, pp. 7579-7588
-
-
Fritz, D.1
Harmandaris, V.A.2
Kremer, K.3
Van Der Vegt, N.4
-
6
-
-
84880013233
-
Hierarchical simulations of hybrid polymer/solid materials
-
V. Johnston and V. Harmandaris, " Hierarchical simulations of hybrid polymer/solid materials," Soft Matter 9, 6696-6710 (2013). 10.1039/c3sm50330e
-
(2013)
Soft Matter
, vol.9
, pp. 6696-6710
-
-
Johnston, V.1
Harmandaris, V.2
-
7
-
-
84880237535
-
Uncertainty quantification in multiscale simulation of materials: A prospective
-
A. Chernatynskiy, S. Phillpot, and R. LeSar, " Uncertainty quantification in multiscale simulation of materials: A prospective," Annu. Rev. Mater. Res. 43, 157-182 (2013). 10.1146/annurev-matsci-071312-121708
-
(2013)
Annu. Rev. Mater. Res.
, vol.43
, pp. 157-182
-
-
Chernatynskiy, A.1
Phillpot, S.2
Lesar, R.3
-
8
-
-
84867533253
-
Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework
-
P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, " Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework," J. Chem. Phys. 137 (14), 144103 (2012). 10.1063/1.4757266
-
(2012)
J. Chem. Phys.
, vol.137
, Issue.14
-
-
Angelikopoulos, P.1
Papadimitriou, C.2
Koumoutsakos, P.3
-
9
-
-
33645906277
-
Relative entropy based method for probabilistic sensitivity analysis in engineering design
-
H. Liu, A. Sudjianto, and W. Chen, " Relative entropy based method for probabilistic sensitivity analysis in engineering design," J. Mech. Des. 128 (2), 326-336 (2005). 10.1115/1.2159025
-
(2005)
J. Mech. Des.
, vol.128
, Issue.2
, pp. 326-336
-
-
Liu, H.1
Sudjianto, A.2
Chen, W.3
-
10
-
-
79951535155
-
Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation
-
F. Cailliez and P. Pernot, " Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation," J. Chem. Phys. 134 (5), 054124 (2011). 10.1063/1.3545069
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.5
-
-
Cailliez, F.1
Pernot, P.2
-
11
-
-
84871838673
-
Uncertainty quantification in md simulations. Part i: Forward propagation
-
F. Rizzi, H. N. Najm, B. J. Debusschere, K. Sargsyan, M. Salloum, H. Adalsteinsson, and O. M. Knio, " Uncertainty quantification in md simulations. Part i: Forward propagation," Multiscale Model. Simul. 10 (4), 1428-1459 (2012). 10.1137/110853169
-
(2012)
Multiscale Model. Simul.
, vol.10
, Issue.4
, pp. 1428-1459
-
-
Rizzi, F.1
Najm, H.N.2
Debusschere, B.J.3
Sargsyan, K.4
Salloum, M.5
Adalsteinsson, H.6
Knio, O.M.7
-
12
-
-
65249095357
-
Sensitivity analysis and kinetic parameter estimation in a three way catalytic converter
-
S. K. Rao, R. Imam, K. Ramanathan, and S. Pushpavanam, " Sensitivity analysis and kinetic parameter estimation in a three way catalytic converter," Ind. Eng. Chem. Res. 48, 3779-3790 (2009). 10.1021/ie801244w
-
(2009)
Ind. Eng. Chem. Res.
, vol.48
, pp. 3779-3790
-
-
Rao, S.K.1
Imam, R.2
Ramanathan, K.3
Pushpavanam, S.4
-
13
-
-
84873673530
-
A relative entropy rate method for path space sensitivity analysis of stationary complex stochastic dynamics
-
Y. Pantazis and M. A. Katsoulakis, " A relative entropy rate method for path space sensitivity analysis of stationary complex stochastic dynamics," J. Chem. Phys. 138, 054115 (2013). 10.1063/1.4789612
-
(2013)
J. Chem. Phys.
, vol.138
-
-
Pantazis, Y.1
Katsoulakis, M.A.2
-
14
-
-
0032094950
-
Optimal experiment design
-
A. F. Emery and A. V. Nenarokomov, " Optimal experiment design," Meas. Sci. Technol. 9 (6), 864 (1998). 10.1088/0957-0233/9/6/003
-
(1998)
Meas. Sci. Technol.
, vol.9
, Issue.6
, pp. 864
-
-
Emery, A.F.1
Nenarokomov, A.V.2
-
15
-
-
58149293678
-
Statistical prediction and molecular dynamics simulation
-
B. Cooke and S. C. Schmidler, " Statistical prediction and molecular dynamics simulation," Biophys. J. 95, 4497-4511 (2008). 10.1529/biophysj.108.131623
-
(2008)
Biophys. J.
, vol.95
, pp. 4497-4511
-
-
Cooke, B.1
Schmidler, S.C.2
-
16
-
-
28244449320
-
Perspectives on the design and control of multiscale systems
-
R. D. Braatz, R. C. Alkire, E. Seebauer, E. Rusli, R. Gunawan, T. O. Drews, X. Li, and Y. He, " Perspectives on the design and control of multiscale systems," J. Process Control 16, 193-204 (2006). 10.1016/j.jprocont.2005.06.001
-
(2006)
J. Process Control
, vol.16
, pp. 193-204
-
-
Braatz, R.D.1
Alkire, R.C.2
Seebauer, E.3
Rusli, E.4
Gunawan, R.5
Drews, T.O.6
Li, X.7
He, Y.8
-
17
-
-
22144498043
-
Sensitivity analysis of discrete stochastic systems
-
R. Gunawan, Y. Cao, L. Petzold III, and F. J. Doyle, " Sensitivity analysis of discrete stochastic systems," Biophys. J. 88, 2530-2540 (2005). 10.1529/biophysj.104.053405
-
(2005)
Biophys. J.
, vol.88
, pp. 2530-2540
-
-
Gunawan, R.1
Cao, Y.2
Petzold, L.3
Doyle, F.J.4
-
18
-
-
77949884150
-
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks
-
M. Rathinam, P. W. Sheppard, and M. Khammash, " Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks," J. Chem. Phys. 132, 034103 (2010). 10.1063/1.3280166
-
(2010)
J. Chem. Phys.
, vol.132
-
-
Rathinam, M.1
Sheppard, P.W.2
Khammash, M.3
-
19
-
-
84868348853
-
An efficient finite difference method for parameter sensitivities of continuous-time Markov chains
-
D. F. Anderson, " An efficient finite difference method for parameter sensitivities of continuous-time Markov chains," SIAM J. Numer. Anal. 50 (5), 2237-2258 (2012). 10.1137/110849079
-
(2012)
SIAM J. Numer. Anal.
, vol.50
, Issue.5
, pp. 2237-2258
-
-
Anderson, D.F.1
-
20
-
-
84897488302
-
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations
-
G. Arampatzis and M. A. Katsoulakis, " Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations," J. Chem. Phys. 140 (12), 124108 (2014). 10.1063/1.4868649
-
(2014)
J. Chem. Phys.
, vol.140
, Issue.12
-
-
Arampatzis, G.1
Katsoulakis, M.A.2
-
21
-
-
84976859194
-
Likelihood ratio gradient estimation for stochastic systems
-
P. W. Glynn, " Likelihood ratio gradient estimation for stochastic systems," Commun. ACM 33 (10), 75-84 (1990). 10.1145/84537.84552
-
(1990)
Commun. ACM
, vol.33
, Issue.10
, pp. 75-84
-
-
Glynn, P.W.1
-
22
-
-
33846498355
-
Efficient stochastic sensitivity analysis of discrete event systems
-
S. Plyasunov and A. P. Arkin, " Efficient stochastic sensitivity analysis of discrete event systems," J. Comput. Phys. 221 (2), 724-738 (2007). 10.1016/j.jcp.2006.06.047
-
(2007)
J. Comput. Phys.
, vol.221
, Issue.2
, pp. 724-738
-
-
Plyasunov, S.1
Arkin, A.P.2
-
23
-
-
84858964221
-
Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting
-
P. B. Warren and R. J. Allen, " Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting," J. Chem. Phys. 136 (10), 104106 (2012). 10.1063/1.3690092
-
(2012)
J. Chem. Phys.
, vol.136
, Issue.10
-
-
Warren, P.B.1
Allen, R.J.2
-
24
-
-
31544449433
-
Sensitivity analysis of thermodynamic properties of liquid water: A general approach to improve empirical potentials
-
T. Iordanov, G. Schenter, and B. Garret, " Sensitivity analysis of thermodynamic properties of liquid water: A general approach to improve empirical potentials," J. Phys. Chem. A 110, 762-771 (2006). 10.1021/jp0538868
-
(2006)
J. Phys. Chem. A
, vol.110
, pp. 762-771
-
-
Iordanov, T.1
Schenter, G.2
Garret, B.3
-
25
-
-
77957005765
-
Quantifying uncertainty in climate change science through empirical information theory
-
A. Majda and B. Gershgorin, " Quantifying uncertainty in climate change science through empirical information theory," Proc. Natl. Acad. Sci. U. S. A. 107 (34), 14958-14963 (2010). 10.1073/pnas.1007009107
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, Issue.34
, pp. 14958-14963
-
-
Majda, A.1
Gershgorin, B.2
-
26
-
-
77951578683
-
Quantitative analysis on the validity of a coarse-grained model for nonequilibrium polymeric liquids under flow
-
C. Baig and V. Harmandaris, " Quantitative analysis on the validity of a coarse-grained model for nonequilibrium polymeric liquids under flow," Macromolecules 43, 3156-3160 (2010). 10.1021/ma100070p
-
(2010)
Macromolecules
, vol.43
, pp. 3156-3160
-
-
Baig, C.1
Harmandaris, V.2
-
27
-
-
84885461154
-
Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics
-
K. R. Haas, H. Yang, and J.-W. Chu, " Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics," J. Chem. Phys. 139 (12), 121931 (2013). 10.1063/1.4820491
-
(2013)
J. Chem. Phys.
, vol.139
, Issue.12
-
-
Haas, K.R.1
Yang, H.2
Chu, J.-W.3
-
28
-
-
84880678415
-
Hierarchical multiscale modeling of polymer-solid interfaces: Atomistic to coarse-grained description and structural and conformational properties of polystyrene-gold systems
-
V. Johnston and V. Harmandaris, " Hierarchical multiscale modeling of polymer-solid interfaces: Atomistic to coarse-grained description and structural and conformational properties of polystyrene-gold systems," Macromolecules 46, 5741-5750 (2013). 10.1021/ma400357r
-
(2013)
Macromolecules
, vol.46
, pp. 5741-5750
-
-
Johnston, V.1
Harmandaris, V.2
-
29
-
-
84897044092
-
Dynamics of various polymer/graphene interfacial systems through atomistic molecular dynamics simulations
-
A. Rissanou and V. Harmandaris, " Dynamics of various polymer/graphene interfacial systems through atomistic molecular dynamics simulations," Soft Matter 42 (10), 2876-2888 (2014). 10.1039/c3sm52688g
-
(2014)
Soft Matter
, vol.42
, Issue.10
, pp. 2876-2888
-
-
Rissanou, A.1
Harmandaris, V.2
-
30
-
-
84897819416
-
Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations
-
V. Harmandaris, " Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations," Korea-Aust. Rheol. J. 26, 15-28 (2014). 10.1007/s13367-014-0003-7
-
(2014)
Korea-Aust. Rheol. J.
, vol.26
, pp. 15-28
-
-
Harmandaris, V.1
-
31
-
-
0001317269
-
Phase diagrams of Lennard-Jones fluids
-
B. Smit, " Phase diagrams of Lennard-Jones fluids," J. Chem. Phys. 96 (11), 6 (1992). 10.1021/j100180a003
-
(1992)
J. Chem. Phys.
, vol.96
, Issue.11
, pp. 6
-
-
Smit, B.1
-
32
-
-
9144240095
-
Dreiding: A generic force field for molecular simulations
-
S. Mayo, B. Olafson, and W. Goddard, " Dreiding: A generic force field for molecular simulations," J. Phys. Chem. 94 (26), 8897-8909 (1990). 10.1021/j100389a010
-
(1990)
J. Phys. Chem.
, vol.94
, Issue.26
, pp. 8897-8909
-
-
Mayo, S.1
Olafson, B.2
Goddard, W.3
-
36
-
-
0010519502
-
Atomistic molecular dynamics simulation of stress relaxation upon cessation of steady-state uniaxial elongational flow
-
V. Harmandaris, V. Mavrantzas, and D. Theodorou, " Atomistic molecular dynamics simulation of stress relaxation upon cessation of steady-state uniaxial elongational flow," Macromolecules 33 (21), 8062-8076 (2000). 10.1021/ma9918598
-
(2000)
Macromolecules
, vol.33
, Issue.21
, pp. 8062-8076
-
-
Harmandaris, V.1
Mavrantzas, V.2
Theodorou, D.3
-
37
-
-
84877787427
-
Robust and efficient configurational molecular sampling via Langevin dynamics
-
B. Leimkuhler and C. Matthews, " Robust and efficient configurational molecular sampling via Langevin dynamics," J. Chem. Phys. 138 (17), 174102 (2013). 10.1063/1.4802990
-
(2013)
J. Chem. Phys.
, vol.138
, Issue.17
-
-
Leimkuhler, B.1
Matthews, C.2
-
38
-
-
0030560429
-
The law of the Euler scheme for stochastic differential equations. I. Convergence rate of the distribution function
-
V. Bally and D. Talay, " The law of the Euler scheme for stochastic differential equations. I. Convergence rate of the distribution function," Probab. Theory Relat. Fields 104, 43-60 (1996). 10.1007/BF01303802
-
(1996)
Probab. Theory Relat. Fields
, vol.104
, pp. 43-60
-
-
Bally, V.1
Talay, D.2
-
39
-
-
0002308425
-
The law of the Euler scheme for stochastic differential equations. II. Convergence rate of the density
-
V. Bally and D. Talay, " The law of the Euler scheme for stochastic differential equations. II. Convergence rate of the density," Monte Carlo Methods Appl. 2, 93-128 (1996). 10.1515/mcma.1996.2.2.93
-
(1996)
Monte Carlo Methods Appl.
, vol.2
, pp. 93-128
-
-
Bally, V.1
Talay, D.2
-
40
-
-
77950857322
-
Convergence of numerical time-averaging and stationary measures via Poisson equations
-
J. C. Mattingly, A. M. Stuart, and M. V. Tretyakov, " Convergence of numerical time-averaging and stationary measures via Poisson equations," SIAM J. Numer. Anal. 48, 552-577 (2010). 10.1137/090770527
-
(2010)
SIAM J. Numer. Anal.
, vol.48
, pp. 552-577
-
-
Mattingly, J.C.1
Stuart, A.M.2
Tretyakov, M.V.3
-
44
-
-
0000471729
-
Sensitivity analysis of a polarizable water model
-
S. B. Zhu and C. F. Wong, " Sensitivity analysis of a polarizable water model," J. Chem. Phys. 98, 4695-4701 (1994). 10.1021/j100068a034
-
(1994)
J. Chem. Phys.
, vol.98
, pp. 4695-4701
-
-
Zhu, S.B.1
Wong, C.F.2
-
45
-
-
33244478266
-
Calculation of local pressure tensors in systems with many-body interactions
-
H. Heinz, W. Paul, and K. Binder, " Calculation of local pressure tensors in systems with many-body interactions," Phys. Rev. E 72 (6), 066704 (2005). 10.1103/PhysRevE.72.066704
-
(2005)
Phys. Rev. e
, vol.72
, Issue.6
-
-
Heinz, H.1
Paul, W.2
Binder, K.3
-
46
-
-
84865785650
-
Systematic coarse-graining of potential energy landscapes and dynamics in liquids
-
M. S. Shell, " Systematic coarse-graining of potential energy landscapes and dynamics in liquids," J. Chem. Phys. 137 (8), 084503 (2012). 10.1063/1.4746391
-
(2012)
J. Chem. Phys.
, vol.137
, Issue.8
-
-
Shell, M.S.1
-
47
-
-
34547938134
-
Coarse-graining schemes and a posteriori error estimates for stochastic lattice systems
-
M. A. Katsoulakis, P. Plecháč, L. Rey-Bellet, and D. K. Tsagkarogiannis, " Coarse-graining schemes and a posteriori error estimates for stochastic lattice systems," ESAIM: Math. Modell. Numer. Anal. 41, 627-660 (2007). 10.1051/m2an:2007032
-
(2007)
ESAIM: Math. Modell. Numer. Anal.
, vol.41
, pp. 627-660
-
-
Katsoulakis, M.A.1
Plecháč, P.2
Rey-Bellet, L.3
Tsagkarogiannis, D.K.4
-
48
-
-
0037417955
-
Coarse-grained stochastic processes for microscopic lattice systems
-
M. A. Katsoulakis, A. J. Majda, and D. G. Vlachos, " Coarse-grained stochastic processes for microscopic lattice systems," Proc. Natl. Acad. Sci. U. S. A. 100 (3), 782-787 (2003). 10.1073/pnas.242741499
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, Issue.3
, pp. 782-787
-
-
Katsoulakis, M.A.1
Majda, A.J.2
Vlachos, D.G.3
-
49
-
-
0037456891
-
Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems
-
M. A. Katsoulakis, A. J. Majda, and D. G. Vlachos, " Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems," J. Comput. Phys. 112, 250-278 (2003). 10.1016/S0021-9991(03)00051-2
-
(2003)
J. Comput. Phys.
, vol.112
, pp. 250-278
-
-
Katsoulakis, M.A.1
Majda, A.J.2
Vlachos, D.G.3
-
50
-
-
43649102194
-
Mathematical strategies in the coarse-graining of extensive systems: Error quantification and adaptivity
-
M. A. Katsoulakis, L. Rey-Bellet, P. Plecháč, and D. K. Tsagkarogiannis, " Mathematical strategies in the coarse-graining of extensive systems: Error quantification and adaptivity," J. Non-Newtonian Fluid Mech. 152, 101 (2008). 10.1016/j.jnnfm.2007.05.005
-
(2008)
J. Non-Newtonian Fluid Mech.
, vol.152
, pp. 101
-
-
Katsoulakis, M.A.1
Rey-Bellet, L.2
Plecháč, P.3
Tsagkarogiannis, D.K.4
-
51
-
-
84903362489
-
Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems
-
M. A. Katsoulakis and P. Plecháč, " Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems," J. Chem. Phys. 139, 074115 (2013); e-print arXiv:1304.7700. 10.1063/1.4818534
-
(2013)
J. Chem. Phys.
, vol.139
-
-
Katsoulakis, M.A.1
Plecháč, P.2
-
52
-
-
84876469199
-
Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides
-
A. Rissanou, E. Georgilis, M. Kasotaskis, A. Mitraki, and V. Harmandaris, " Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides," J. Phys. Chem. B 117, 3962-3975 (2013). 10.1021/jp311795b
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 3962-3975
-
-
Rissanou, A.1
Georgilis, E.2
Kasotaskis, M.3
Mitraki, A.4
Harmandaris, V.5
-
55
-
-
67349094280
-
A gentle stochastic thermostat for molecular dynamics
-
B. Leimkuhler, E. Noorizadeh, and F. Theil, " A gentle stochastic thermostat for molecular dynamics," J. Stat. Phys. 135 (2), 261-277 (2009). 10.1007/s10955-009-9734-0
-
(2009)
J. Stat. Phys.
, vol.135
, Issue.2
, pp. 261-277
-
-
Leimkuhler, B.1
Noorizadeh, E.2
Theil, F.3
-
56
-
-
84936850319
-
-
See supplementary material at E-JCPSA6-143-021525 for detailed derivation of some expressions presented, as well as for some additional figures.
-
See supplementary material at http://dx.doi.org/10.1063/1.4922924 E-JCPSA6-143-021525 for detailed derivation of some expressions presented, as well as for some additional figures.
-
-
-
-
57
-
-
67650760503
-
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
-
A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, and J. Timmer, " Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood," Bioinformatics 25, 1923 (2009). 10.1093/bioinformatics/btp358
-
(2009)
Bioinformatics
, vol.25
, pp. 1923
-
-
Raue, A.1
Kreutz, C.2
Maiwald, T.3
Bachmann, J.4
Schilling, M.5
Klingmüller, U.6
Timmer, J.7
|