Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

Tsourtis, Anastasios; Pantazis, Yannis; Katsoulakis, Markos A.; Harmandaris, Vagelis

doi:10.1063/1.4922924

Title: Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

Journal Article · Tue Jul 07 00:00:00 EDT 2015 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4922924· OSTI ID:1228659

Tsourtis, Anastasios ^[1]; Pantazis, Yannis ^[2]; Katsoulakis, Markos A. ^[2]; Harmandaris, Vagelis ^[3]

Department of Mathematics and Applied Mathematics, University of Crete, Crete, Greece
Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003, USA
Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete, Greece

View Accepted Manuscript (Publisher)

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: FG02-13ER26161

OSTI ID:: 1228659

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Vol. 143 Journal Issue: 1; ISSN 0021-9606

Publisher:: American Institute of PhysicsCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 13 works

Citation information provided by
Web of Science

References (45)

Relative Entropy Based Method for Probabilistic Sensitivity Analysis in Engineering Design Liu, Huibin; Chen, Wei; Sudjianto, Agus Journal of Mechanical Design, Vol. 128, Issue 2 https://doi.org/10.1115/1.2159025	journal	January 2006
The law of the Euler scheme for stochastic differential equations: I. Convergence rate of the distribution function Bally, V.; Talay, D. Probability Theory and Related Fields, Vol. 104, Issue 1 https://doi.org/10.1007/BF01303802	journal	March 1996
Atomic-Level Characterization of the Structural Dynamics of Proteins Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K. Science, Vol. 330, Issue 6002 https://doi.org/10.1126/science.1187409	journal	October 2010
Hierarchical Multiscale Modeling of Polymer–Solid Interfaces: Atomistic to Coarse-Grained Description and Structural and Conformational Properties of Polystyrene–Gold Systems Johnston, Karen; Harmandaris, Vagelis Macromolecules, Vol. 46, Issue 14 https://doi.org/10.1021/ma400357r	journal	July 2013
Robust and efficient configurational molecular sampling via Langevin dynamics Leimkuhler, Benedict; Matthews, Charles The Journal of Chemical Physics, Vol. 138, Issue 17 https://doi.org/10.1063/1.4802990	journal	May 2013
DREIDING: a generic force field for molecular simulations Mayo, Stephen L.; Olafson, Barry D.; Goddard, William A. The Journal of Physical Chemistry, Vol. 94, Issue 26, p. 8897-8909 https://doi.org/10.1021/j100389a010	journal	December 1990
Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework Angelikopoulos, Panagiotis; Papadimitriou, Costas; Koumoutsakos, Petros The Journal of Chemical Physics, Vol. 137, Issue 14 https://doi.org/10.1063/1.4757266	journal	October 2012
Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting Warren, Patrick B.; Allen, Rosalind J. The Journal of Chemical Physics, Vol. 136, Issue 10 https://doi.org/10.1063/1.3690092	journal	March 2012
Efficient stochastic sensitivity analysis of discrete event systems Plyasunov, Sergey; Arkin, Adam P. Journal of Computational Physics, Vol. 221, Issue 2 https://doi.org/10.1016/j.jcp.2006.06.047	journal	February 2007
Coarse-graining schemes and a posteriori error estimates for stochastic lattice systems Katsoulakis, Markos A.; Plecháč, Petr; Rey-Bellet, Luc ESAIM: Mathematical Modelling and Numerical Analysis, Vol. 41, Issue 3 https://doi.org/10.1051/m2an:2007032	journal	May 2007
Uncertainty Quantification in Multiscale Simulation of Materials: A Prospective Chernatynskiy, Aleksandr; Phillpot, Simon R.; LeSar, Richard Annual Review of Materials Research, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-matsci-071312-121708	journal	July 2013
Sensitivity Analysis of Thermodynamic Properties of Liquid Water: A General Approach to Improve Empirical Potentials ^† Iordanov, Tzvetelin D.; Schenter, Gregory K.; Garrett, Bruce C. The Journal of Physical Chemistry A, Vol. 110, Issue 2 https://doi.org/10.1021/jp0538868	journal	January 2006
Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations Harmandaris, Vagelis A. Korea-Australia Rheology Journal, Vol. 26, Issue 1 https://doi.org/10.1007/s13367-014-0003-7	journal	February 2014
A relative entropy rate method for path space sensitivity analysis of stationary complex stochastic dynamics Pantazis, Yannis; Katsoulakis, Markos A. The Journal of Chemical Physics, Vol. 138, Issue 5 https://doi.org/10.1063/1.4789612	journal	February 2013
The Law of the Euler Scheme for Stochastic Differential Equations: II. Convergence Rate of the Density Bally, Vlad; Talay, Denis Monte Carlo Methods and Applications, Vol. 2, Issue 2 https://doi.org/10.1515/mcma.1996.2.2.93	journal	January 1996
Quantifying uncertainty in climate change science through empirical information theory Majda, A. J.; Gershgorin, B. Proceedings of the National Academy of Sciences, Vol. 107, Issue 34 https://doi.org/10.1073/pnas.1007009107	journal	August 2010
Hierarchical simulations of hybrid polymer–solid materials Johnston, Karen; Harmandaris, Vagelis Soft Matter, Vol. 9, Issue 29 https://doi.org/10.1039/c3sm50330e	journal	January 2013
Sensitivity Analysis of Discrete Stochastic Systems Gunawan, Rudiyanto; Cao, Yang; Petzold, Linda Biophysical Journal, Vol. 88, Issue 4 https://doi.org/10.1529/biophysj.104.053405	journal	April 2005
Dynamics of various polymer–graphene interfacial systems through atomistic molecular dynamics simulations Rissanou, Anastassia N.; Harmandaris, Vagelis Soft Matter, Vol. 10, Issue 16 https://doi.org/10.1039/c3sm52688g	journal	January 2014
Likelihood ratio gradient estimation for stochastic systems Glynn, Peter W. Communications of the ACM, Vol. 33, Issue 10 https://doi.org/10.1145/84537.84552	journal	October 1990
Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics Haas, Kevin R.; Yang, Haw; Chu, Jhih-Wei The Journal of Chemical Physics, Vol. 139, Issue 12 https://doi.org/10.1063/1.4820491	journal	September 2013
Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems Katsoulakis, Markos A.; Plecháč, Petr The Journal of Chemical Physics, Vol. 139, Issue 7 https://doi.org/10.1063/1.4818534	journal	August 2013
Atomistic Molecular Dynamics Simulation of Stress Relaxation upon Cessation of Steady-State Uniaxial Elongational Flow Harmandaris, Vagelis A.; Mavrantzas, Vlasis G.; Theodorou, Doros N. Macromolecules, Vol. 33, Issue 21 https://doi.org/10.1021/ma9918598	journal	October 2000
Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems Katsoulakis, Markos A.; Majda, Andrew J.; Vlachos, Dionisios G. Journal of Computational Physics, Vol. 186, Issue 1 https://doi.org/10.1016/S0021-9991(03)00051-2	journal	March 2003
Mathematical strategies in the coarse-graining of extensive systems: Error quantification and adaptivity Katsoulakis, Markos A.; Plecháč, Petr; Rey-Bellet, Luc Journal of Non-Newtonian Fluid Mechanics, Vol. 152, Issue 1-3 https://doi.org/10.1016/j.jnnfm.2007.05.005	journal	June 2008
Uncertainty Quantification in MD Simulations. Part I: Forward Propagation Rizzi, F.; Najm, H. N.; Debusschere, B. J. Multiscale Modeling & Simulation, Vol. 10, Issue 4 https://doi.org/10.1137/110853169	journal	January 2012
Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation Cailliez, Fabien; Pernot, Pascal The Journal of Chemical Physics, Vol. 134, Issue 5 https://doi.org/10.1063/1.3545069	journal	February 2011
Perspectives on the design and control of multiscale systems Braatz, R. D.; Alkire, R. C.; Seebauer, E. Journal of Process Control, Vol. 16, Issue 3 https://doi.org/10.1016/j.jprocont.2005.06.001	journal	March 2006
Effect of Solvent on the Self-Assembly of Dialanine and Diphenylalanine Peptides Rissanou, Anastassia N.; Georgilis, Evangelos; Kasotakis, Emmanouil The Journal of Physical Chemistry B, Vol. 117, Issue 15 https://doi.org/10.1021/jp311795b	journal	April 2013
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks Rathinam, Muruhan; Sheppard, Patrick W.; Khammash, Mustafa The Journal of Chemical Physics, Vol. 132, Issue 3 https://doi.org/10.1063/1.3280166	journal	January 2010
Coarse-grained stochastic processes for microscopic lattice systems Katsoulakis, M. A.; Majda, A. J.; Vlachos, D. G. Proceedings of the National Academy of Sciences, Vol. 100, Issue 3 https://doi.org/10.1073/pnas.242741499	journal	January 2003
A Gentle Stochastic Thermostat for Molecular Dynamics Leimkuhler, Ben; Noorizadeh, Emad; Theil, Florian Journal of Statistical Physics, Vol. 135, Issue 2 https://doi.org/10.1007/s10955-009-9734-0	journal	April 2009
Statistical Prediction and Molecular Dynamics Simulation Cooke, Ben; Schmidler, Scott C. Biophysical Journal, Vol. 95, Issue 10 https://doi.org/10.1529/biophysj.108.131623	journal	November 2008
Optimal experiment design Emery, A. F.; Nenarokomov, Aleksey V. Measurement Science and Technology, Vol. 9, Issue 6 https://doi.org/10.1088/0957-0233/9/6/003	journal	June 1998
Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations Arampatzis, Georgios; Katsoulakis, Markos A. The Journal of Chemical Physics, Vol. 140, Issue 12 https://doi.org/10.1063/1.4868649	journal	March 2014
Sensitivity Analysis of a Polarizable Water Model Zhu, Sheng-Bai; Wong, Chung F. The Journal of Physical Chemistry, Vol. 98, Issue 17 https://doi.org/10.1021/j100068a034	journal	April 1994
Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities Fritz, Dominik; Harmandaris, Vagelis A.; Kremer, Kurt Macromolecules, Vol. 42, Issue 19 https://doi.org/10.1021/ma901242h	journal	October 2009
Convergence of Numerical Time-Averaging and Stationary Measures via Poisson Equations Mattingly, Jonathan C.; Stuart, Andrew M.; Tretyakov, M. V. SIAM Journal on Numerical Analysis, Vol. 48, Issue 2 https://doi.org/10.1137/090770527	journal	January 2010
Calculation of local pressure tensors in systems with many-body interactions Heinz, Hendrik; Paul, Wolfgang; Binder, Kurt Physical Review E, Vol. 72, Issue 6 https://doi.org/10.1103/PhysRevE.72.066704	journal	December 2005
Phase equilibria in the system carbon dioxide-water at elevated pressures Mather, Alan E.; Franck, E. Ulrich The Journal of Physical Chemistry, Vol. 96, Issue 1 https://doi.org/10.1021/j100180a003	journal	January 1992
An Efficient Finite Difference Method for Parameter Sensitivities of Continuous Time Markov Chains Anderson, David F. SIAM Journal on Numerical Analysis, Vol. 50, Issue 5 https://doi.org/10.1137/110849079	journal	January 2012
Sensitivity Analysis and Kinetic Parameter Estimation in a Three Way Catalytic Converter Rao, S. Koteswara; Imam, Rayees; Ramanathan, Karthik Industrial & Engineering Chemistry Research, Vol. 48, Issue 8 https://doi.org/10.1021/ie801244w	journal	April 2009
Systematic coarse-graining of potential energy landscapes and dynamics in liquids Shell, M. Scott The Journal of Chemical Physics, Vol. 137, Issue 8 https://doi.org/10.1063/1.4746391	journal	August 2012
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood Raue, A.; Kreutz, C.; Maiwald, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp358	journal	June 2009
Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow Baig, Chunggi; Harmandaris, Vagelis A. Macromolecules, Vol. 43, Issue 7 https://doi.org/10.1021/ma100070p	journal	April 2010

Similar Records

Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

Journal Article · Tue Jul 07 00:00:00 EDT 2015 · Journal of Chemical Physics · OSTI ID:1228659

Tsourtis, Anastasios; Pantazis, Yannis; Harmandaris, Vagelis

Spectral Methods for Parametric Sensitivity in Stochastic Dynamical Systems

Journal Article · Mon Jan 01 00:00:00 EST 2007 · Biophysical Journal · OSTI ID:1228659

Kim, D.; Debusschere, B. J.; Najm, H. N.

Fast variance reduction for steady-state simulation and sensitivity analysis of stochastic chemical systems using shadow function estimators

Journal Article · Mon Jul 14 00:00:00 EDT 2014 · Journal of Chemical Physics · OSTI ID:1228659

Milias-Argeitis, Andreas; Khammash, Mustafa; Lygeros, John

Title: Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

Citation Formats

References (45)

Similar Records

Related Subjects