Publication List.

Publication List

Some Publications.

Pattern Formation and Lattice Gas Automata
A. Lawniczak and R. Kapral, eds., Fields Institute Communications, (American Mathematical Society, Providence, Rhode Island, 1996).
Chemical Waves and Patterns
R. Kapral and K. Showalter, eds., (Kluwer, Dordrecht, 1995).
Dynamics of Self-Organized and Self-Assembled Structures
R. C. Desai and R. Kapral, (Cambridge UP, 2009).
Lattice Gas Automata for Reactive Systems
J. P. Boon, D. Dab, R. Kapral and A. Lawniczak, Phys. Repts. 273, 55-148 (1996).
Links, Knots and Knotted Labyrinths in Bistable Systems
A. Malevanets and R. Kapral, Phys. Rev. Lett. 77, 767 (1996).
Microscopic Model for FitzHugh-Nagumo Dynamics
A. Malevanets and R. Kapral, Phys. Rev. E 55, 5657 (1997).
Knots in Bistable Systems
A. Malevanets and R. Kapral, in Ideal Knots, eds. L. H. Kaufmann, V. Katritch and A. Stasiak (World Scientific, 1998).
Reactive lattice-gas Model for FitzHugh-Nagumo Dynamics
A. Malevanets and R. Kapral, Nonlinear Science Today, (1997).
Simulation of Classical and Quantum Activated Process in the Condensed Phase
G. Ciccotti, M. Ferrario, D. Laria and R. Kapral, in Progress of Computational Physics of Matter: Methods, Software and Applications, eds. L. Reatto and F. Manghi, (World Scientific, New Jersey, 1995), pp. 150-190.
Chemical Rate Laws and Rate Constants
R. Kapral, S. Consta and L. McWhirter, 1998, in {\em Classical and Quantum Dynamics in Condensed Phase Simulations}, eds. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, Singapore), pp.583-616.
Perturbation Theory for the Breakdown of Mean-Field Kinetics in Oscillatory Reaction-Diffusion System
M. Velikanov and R. Kapral, J. Chem. Phys. 109, 281 (1998).
Coloring a Lorentz Gas
S. Nielsen and R. Kapral, J. Chem. Phys., 109, 6460 (1998).
Continuous-Velocity Lattice-Gas model for Fluid Flow
A. Malevanets and R. Kapral, Europhys. Lett., 44, 552 (1998).
Fluctuation Effects on Quadratic Autocatalysis Fronts
M. Velikanov and R. Kapral, J. Chem. Phys., 110, 109 (1998).
Mixing and Segregation in Binary Polar Molecule Clusters
V. Molinero, D. Laria and R. Kapral, J. Chem. Phys., 109, 6844 (1998).
Synchronization Defects and Broken Symmetry in Spiral Waves
A. Goryachev, H. Chate and R. Kapral, Phys. Rev. Lett. 80, 873 (1998).
Coiling and Supercoiling of Vortex Filaments in Oscillatory Media
G. Rousseau, H. Chate and R. Kapral , Phys. Rev. Lett. 80, 5671 (1998).
Transitions to Line Defect Turbulence in Complex-Oscillatory Media
A. Goryachev, H. Chate and R. Kapral , Phys. Rev. Lett. 83, 1878 (1999).
Spiral Waves in Media with Complex-Excitable Dynamics
A. Goryachev and R. Kapral, Int. J. Bif. and Chaos., 9, 2243 (1999).
Mixed Quantum-Classical Dynamics
R. Kapral and G. Ciccotti, J. Chem. Phys., 110, 8919 (1999).
Mesoscopic Model for Solvent Dynamics
A. Malevanets and R. Kapral, J. Chem. Phys., 110, 8605 (1999).
Polymerase Chain Reaction: A Markov Process Approach
M. Velikanov and R. Kapral, J. Theor. Bio., 201, 239 (1999).
Ionization Reactions of Ion Complexes in Mesoscopic Water Clusters
S. Consta and R. Kapral, J. Chem. Phys., 111, 10183 (1999).
Synchronization Line Defects in Oscillatory and Excitable Media
A. Goryachev and R. Kapral, in Stochastic Dynamics and Pattern Formation in Bioloigical and Complex Systems, eds. S. Kim, K. J. Lee and W. Sung, (AIP Conference Proceedings, AIP, NewYork, 2000), p. 23.
Resonantly-Forced Inhomogeneous Reaction-Diffusion Systems
C. Hemming and R. Kapral, Chaos., 10, 720 (2000).
Synchronization Defect Lines
A. Goryachev, R. Kapral and H. Chate, Int. J. Bif. and Chaos., 10, 1537 (2000).
Solute Dynamics in Mesoscale Solvent
A. Malevanets and R. Kapral, J. Chem. Phys., 112, 7260 (2000).
Mixed Quantum-Classical Surface Hopping Dynamics
S. Nielsen, R. Kapral and G. Ciccotti, J. Chem. Phys., 112, 6543 (2000).
Dynamics of Solvation_induced Structural Transitions in Mesoscopic Binary Clusters
V. Molinero, D. Laria and R. Kapral, Phys. Rev. Lett., 84, 455 (2000).
Non-Adiabatic Dynamics in Mixed Quantum-Classical Systems
S. Nielsen, R. Kapral and G. Ciccotti, J. Stat. Phys., 101, 225 (2000).
Compartmentalized Reaction-Diffusion Systems
F. Chavez and R. Kapral, Phys. Rev. E, 63, 016211 (2000).
Asynchronous Algorithm for the Integration of Reaction-Diffusion Equations for Inhomogeneous Excitable Media
G. Rousseau and R. Kapral, Chaos, 10, 812 (2000).
Chaos and Complexity in Chemical Systems
R. Kapral and S. J. Fraser, in Encyclopedia of Chemical Physics and Physical Chemistry, eds. J. H. Moore and N. D. Spencer, (IoP, Philadelphia, 2001), Vol. III, p. 2737.
Subsystem Dynamics in Mixed Quantum-Classical Systems
M. Toutounji and R. Kapral, Chem. Phys., 268, 79 (2001).
Statistical Mechanics of Quantum-Classical Systems
S. Nielsen, R. Kapral and G. Ciccotti, J. Chem. Phys., 115, 5805 (2001).
Quantum-Classical Dynamics in a Classical Bath
R. Kapral , J. Phys. Chem., 105, 2885 (2001).
Cluster Structure and Dynamics in a Mesoscopic Solvent
S.-H. Lee and R. Kapral , Physica A, 298, 56 (2001).
Scroll Waves in Spherical Shell Geometries
F. Chavez, R. Kapral, G. Rousseau and L. Glass, Chaos, 11, 757 (2001).
Turbulent Fronts in Resonantly Forced Oscillatory Systems
C. Hemming and R. Kapral, Faraday Discussions, 120, 371 (2001).
Surface Hopping Dynamics in a Spin Boson System
D. Mac Kernan, G. Ciccotti and R. Kapral , J. Chem. Phys. 116, 2346 (2002).
A Statistical Mechanical Theory of Quantum Dynamics in Classical Environments
R. Kapral and G. Ciccotti, (Springer-Verlag, 2002).
Electron Solvation in Aqueous Reverse Micelles: Equilibrium Properties
D. Laria and R. Kapral , J. Chem. Phys. 117, 7712 (2002).
Emergence of Quantum-Classical Dynamics in an Open Quantum Environment
K. Shiokawa and R. Kapral , J. Chem. Phys. 117, 7852 (2002).
Sequential Short-Time Propagation of Quantum-Classical Dynamics
D. Mac Kernan, R. Kapral and G. Ciccotti, J. Phys.: Condens. Matter 14, 9069 (2002).
Front Explosion in a Resonantly Forced Complex Ginzburg-Landau System
C. Hemming and R. Kapral, Physica D, 168, 10 (2002).
Phase Front Dynamics in Inhomogeneously Forced Oscillatory Systems
C. Hemming and R. Kapral, Physica A, 306, 199 (2002).
Oscillatory and Chaotic Dynamics in Compartmentalized Geometries
F. Chavez and R. Kapral, Phys. Rev. E, 65, 056203 (2002).
Phase Synchronization and Topological Defects in Inhomogeneous Media
J. Davidsen and R. Kapral, Phys. Rev. E, 66, 055202(R) (2002).
Quantum-Classical Dynamics of Nonadiabatic Chemical Reactions
A. Sergi and R. Kapral , J. Chem. Phys. 118, 8566 (2003).
Nonadiabatic Reaction Rates for Dissipative Quantum-Classical Systems
A. Sergi and R. Kapral , J. Chem. Phys. 119, 12776 (2003).
Simulating Quantum Dynamics in Classical Environments
A. Sergi, D. MacKernan, G. Ciccotti and R. Kapral , Theor. Chem. Accts. 110, 49 (2003).
Defect-Mediated Turbulence in Systems with Local Deterministic Chaos
J. Davidsen and R. Kapral, Phys. Rev. Lett. 91, 058303 (2003).
Rapid Convergence of Time-Averaged Frequency in Phase Synchronized Systems
J. Davidsen, I. Z. Kiss, J. L. Hudson and R. Kapral, Phys. Rev. E, 68, 026217 (2003).
Front Explosions in Three-Dimensional Resonantly-Forced Oscillatory Systems
C. Hemming and R. Kapral, Phys. Rev. E, 68, 026203 (2003).
Mesoscopic Multi-Particle Collision Model for Fluid Flow and Molecular Dynamics
A. Malevanets and R. Kapral, SoftSimu2002, Lecture Notes in Physics, (Springer, 2004).
Quantum-Classical Limit of Quantum Correlation Functions
A. Sergi and R. Kapral , J. Chem. Phys. 121, 7565 (2004).
Mesoscopic Model for Diffusion-Influenced Reaction Dynamics
K. Tucci and R. Kapral , J. Chem. Phys. 120, 8262 (2004).
Friction and Diffusion of a Brownian Particle in a Mesoscopic Solvent
S. H. Lee and R. Kapral , J. Chem. Phys. 121, 11163 (2004).
From Ballistic to Brownian Motion in Complex Oscillatory Media
J. Davidsen, R. Erichsen, R. Kapral and H. Chate, Phys. Rev. Lett. 93, 018305 (2004).
Topological Constraints on Spiral Wave Dynamics in Spherical Geometries with Inhomogeneous Excitability
J. Davidsen, L. Glass and R. Kapral, Phys. Rev. E 70, 056203 (2004).
Molecular Dynamics: An Account of its Evolution
R. Kapral and G. Ciccotti, "Theory and applications of Computational Chemistry. The First Fory Years", Eds., C. Dykstra, G. Frenking, K. S. Kim and G. Scuseria (Elsevier, 2005), p. 425.
Quantum-Classical Wigner-Liouville Equation
R. Kapral and A. Sergi, Ukranian J. Math. 57, 749 (2005).
Nonadiabatic Chemical Reactions
A. Sergi and R. Kapral, Computer Phys. Commun., 169, 400 (2005).
Quantum-Classical Liouville Dynamics of Nonadiabatic Proton Transfer
G. Hanna and R. Kapral, J. Chem. Phys. 122, 244505 (2005).
Transport Properties of Quantum-Classical Systems
H. Kim and R. Kapral, J. Chem. Phys. 122, 214105 (2005).
Nonadiabatic Quantum-Classical Reaction Rates with Quantum Equilibrium Structure
H. Kim and R. Kapral, J. Chem. Phys. 123, 194108 (2005).
Two-Particle Friction in a Mesoscopic Solvent
S. H. Lee and R. Kapral, J. Chem. Phys. 122, 214916 (2005).
Blue Moon Sampling, Vectorial Reaction Coordinates and Unbiased Constrained Dynamics
G. Ciccotti, E. Vanden-Eijnden and R. Kapral, ChemPhysChem, 200S, 1809 (2005).
Non-Equilibrium Molecular Dynamics
G. Ciccotti, R. Kapral and A. Sergi, "Handbook of Materials Modeling. Volume I: Methods and Models", Ed., S. Yip (Springer, 2005).
Simulating Reactions That Occur Once in a Blue Moon
G. Ciccotti, R. Kapral and A. Sergi, "Handbook of Materials Modeling. Volume I: Methods and Models", Ed., S. Yip (Springer, 2005).
Model for Line Defects in Complex-Oscillatory Spiral Waves
M. Zhan and R. Kapral, Phys. Rev. E 70, 046221 (2005).
Front Explosion in a Periodically Forced Surface Reaction
J. Davidsen, A. S. Mikhailov and R. Kapral, Phys. Rev. E 72, 046214 (2005).
Mesoscopic Multiparticle Collision Model for Reaction-Diffusion Fronts
K. Tucci and R. Kapral, J. Phys. Chem. B, 109, 21300 (2005).
Dynamics of Condensed Phase Proton and Electron Transfer Processes
R. Kapral and A. Sergi, Handbook of Theoretical and Computational Nanotechnology, eds. M. Rieth and W. Schommers, American Scientific Publishers, vol. 5 (2006), p. 61.
Transport Coefficients of Quantum-Classical Systems
R. Kapral and G. Ciccotti, Lect. Notes Phys., 703, 519 (2006).
Spiral Wave Dynamics in Excitable Media with Spherical Geometries
K. Rohlf, L. Glass and R. Kapral, Chaos, 16, 037115 (2006).
Destruction of Spiral Waves in Chaotic Media
M. Zhan and R. Kapral, Phys. Rev. E, 73, 026224 (2006).
Analysis of Kinetic Isotope Effects for Nonadiabatic Reactions
H. Kim, G. Hanna and R. Kapral, J. Chem. Phys., 125, 084509 (2006).
Quantum Bath Effects on Nonadiabatic Reaction Rates
H. Kim and R. Kapral, Chem. Phys. Lett., 423, 76 (2006).
Simulation of Quantum-Classical Dynamics by Surface-Hopping Trajectories
H. Kim and R. Kapral, CRM Proceedings and Lecture Notes, Am. Math. Soc., 41, (2006).
Nonadiabatic Dynamics of Condensed Phase Rate Processes
G. Hanna and R. Kapral, Acc. Chem. Res., 39, 21 (2006).
Progress in the Theory of Mixed Quantum-Classical Dynamics
R. Kapral, Annu. Rev. Phys. Chem., 57, 1239 (2006).
Mesoscopic Description of Solvent Effects on Polymer Dynamics
S. H. Lee and R. Kapral, J. Chem. Phys., 124, 124901 (2006).
Solvation and Proton Transfer in Polar Molecule Nanoclusters
H. Kim and R. Kapral, J. Chem. Phys., 125, 234309 (2006).
Quantum Statistical Mechanics with Trajectories
G. Ciccotti, D. Coker and R. Kapral, "Quantum Dynamics of Complex Molecular Systems", Eds., D. A. Micha and I. Burghardt (Springer, 2007), p. 275.
Quantum-Classical Reaction Rate Theory
G. Hanna, H. Kim and R. Kapral, "Quantum Dynamics of Complex Molecular Systems", Eds., D. A. Micha and I. Burghardt (Springer, 2007), p. 295.
Quantum Reaction Rates and Sampling of Quantum Equilibrium Structure
H. Kim and R. Kapral, J. Chem. Phys., 127, 226101 (2007).
Decoherence and Quantum-Classical Master Equation Dynamics
R. Grunwald and R. Kapral, J. Chem. Phys., 126, 114109 (2007).
Diffusion and Reaction in Crowded Environments
C. Echeveria, K. Tucci and R. Kapral, J. Phys.: Condens. Matter, 19, 065146 (2007).
Chemically Powered Nanodimers
G. Rueckner and R. Kapral, Phys. Rev. Lett, 98, 150603 (2007).
Proton and Deuteron Transfer Reactions in Molecular Nanoclusters
H. Kim and R. Kapral, ChemPhysChem, 9, 470 (2008).
Trotter-Based Simulation of Quantum-Classical Dynamics
D. MacKernan, G. Ciccotti and R. Kapral, J. Phys. Chem. B, 112, 424 (2008).
Quantum-Classical Liouville Dynamics of Proton and Deuteron Transfer Rates in a Solvated Hydrogen-Bonded Complex
G. Hanna and R. Kapral, J. Chem. Phys., 128, 164520 (2008).
Surface Hopping and Decoherence with Quantum Equilibrium Structure
R. Grunwald, H. Kim and R. Kapral, J. Chem. Phys., 128, 164110 (2008).
Mesoscale Modeling of Molecular Machines: Cyclic Dynamics and Hydrodynamical Fluctuations
A. Cressman, Y. Togashi, A. Mikhailov and R. Kapral, Phys. Rev. E, 77, 050901(R) (2008).
Design Of Chemically Propelled Nanodimer Motors
Yu-Guo Tao and R. Kapral, J. Chem. Phys., 128, 164518 (2008).
Reactive Multiparticle Collision Dynamics
K. Rohlf, S. Fraser and R. Kapral, Comp. Phys. Commun., 98, 150603 (2008).
Twisted Vortex Filaments in the Three-Dimensional Complex Ginzburg-Landau Equation
G. Rousseau, H. Chate and R. Kapral, Chaos, 16, 037115 (2008).
Multiparticle Collision Dynamics: Simulation of Complex Systems on Mesoscales
R. Kapral, Adv. Chem. Phys., 140, 89-146 (2008).
Quantum-Classical Liouville Dynamics in the Mapping Basis
H. Kim, A. Nassimi and R. Kapral, J. Chem. Phys., 129, 084102 (2008).
Filament-Induced Surface Spiral Turbulence in Three-Dimensional Excitable Media
J. Davidsen, M. Zhan and R. Kapral, Phys. Rev.Lett., 101, 208302 (2008).
Mapping Approach for Quantum-Classical Time Correlation Functions
A. Nassimi and R. Kapral, Can. J. Chem. 87, 880 (2009).
Self-Propelled Polymer Nanomotors
Y. Tao and R. Kapral, ChemPhysChem, (2009).
Dynamics of Chemically Powered Nanodimer Motors Subject to an External Force
Y. Tao and R. Kapral, J. Chem. Phys., 131, 024113 (2009).
Effective Medium Theory for Reaction Rates and Diffusion Coefficients of Heterogeneous Media
S. Alonso, R. Kapral and M. Baer, Phys. Rev. Lett., 102, 238302 (2009).
Effective Medium approach for Heterogeneous Reaction-Diffusion Media
S. Alonso, M. Baer and R. Kapral, J. Chem. Phys., 131, 214102 (2009).
Quantum Dynamics in Almost Classical Environments
R. Grunwald, A. Kelly and R. Kapral, "Energy Transfer Dynamics in Biomaterial Systems", Eds., I. Burghardt, et al., (Springer, 2009).
Trajectory Based Simulations of Quantum-Classical Systems
S. Bonella, D. Coker, D. MacKernan, R. Kapral and G. Ciccotti, "Energy Transfer Dynamics in Biomaterial Systems", Eds., I. Burghardt, et al., (Springer, 2009).
Nanoscale Swimmers: Hydrodynamic Interactions and Propulsion of Molecular Machines
T. Sakaue, R. Kapral and A. S. Mikhailov, Euro. Phys. J., 75, 381 (2010).
Linearization Approximations and Liouville Quantum-Classical Dynamics
S. Bonella, G. Ciccotti and R. Kapral, Chem. Phys. Lett., 484, 399 (2010).
Decoherence and Quantum-Classical Dynamics in a Dissipative Bath
J.-P. Rank and R. Kapral, J. Chem. Phys., 132, 074106 (2010).
Quantum-classical description of environmental effects on electronic dynamics at conical intersections
A. Kelly and R. Kapral, J. Chem. Phys., 133, 084502 (2010).
Swimming Upstream: Self-Propelled Nanodimer Motors in a Flow
Y.-G. Tao and R. Kapral, Soft Matter, 6, 756 (2010).
Catalytic Nanomotors: Self-Propelled Sphere Dimers
L. F. Valadares, Y.-G. Tao, N. S. Zacharia, V. Kitaev, F. Galembeck, R. Kapral and G. A. Ozin, Small, 7, 565(2010).
Macromolecular Dynamics in Crowded Environments
C. Echeverria and R. Kapral, J. Chem. Phys., 132, 104902(2010).
Analysis of the quantum-classical Liouville equation in the mapping basis
A. Nassimi, S. Bonella and R. Kapral, J. Chem. Phys., 133, 134115 (2010).
Autocatalytic Reaction Dynamics in Systems Crowded by Catalytic Obstacles
C. Echeverria and R. Kapral, Physica D, 239, 791(2010).
Mesoscopic dynamics of diffusion-influenced enzyme kinetics
J.-X. Chen and R. Kapral, J. Chem. Phys., 134, 044503 (2011).
Dynamics of self-propelled nanomotors in chemically active media
S. Thakur and R. Kapral, J. Chem. Phys., 135, 024509 (2011).
Interaction of a Chemically Propelled Nanomotor with a Chemical Wave
S. Thakur and R. Kapral, Angew. Chem. Int. Ed., 50, 10165 (2011).
A mesoscopic model for protein enzymatic dynamics in solution
C. Echeverria, Y. Togashi, A. S. Mikhailov and R. Kapral, Phys. Chem. Chem. Phys., 13, 10527 (2011).