LEADER 04347nam 2200517 450 001 9910830048103321 005 20200614100252.0 010 $a1-119-17679-4 010 $a1-119-17678-6 010 $a1-119-17680-8 035 $a(CKB)4330000000009103 035 $a(MiAaPQ)EBC5986240 035 $a(MiAaPQ)EBC7076144 035 $a(Au-PeEL)EBL7076144 035 $a(PPN)248343254 035 $a(OCoLC)1139536156 035 $a(EXLCZ)994330000000009103 100 $a20191219d2020 uy 0 101 0 $aeng 135 $aurcnu|||||||| 181 $ctxt$2rdacontent 182 $cc$2rdamedia 183 $acr$2rdacarrier 200 10$aMolecular kinetics in condensed phases $etheory, simulation, and analysis /$fRon Elber, Dmitrii E. Makarov, Henri Orland 210 1$aHoboken, NJ :$cJohn Wiley & Sons Ltd.,$d2020 215 $a1 online resource (292 pages) $cillustrations 311 $a1-119-17677-8 327 $aThe Langevin equation and stochastic processes -- The Fokker-Planck equation -- The Schro?dinger representation -- Discrete systems : the master equation and kinetic Monte Carlo -- Path integrals -- Barrier crossing -- Sampling transition paths -- The rate of conformational change : definition and computation -- Zwanzig-Caldeiga-Leggett model for low-dimensional dynamics -- Escape from a potential well in the case of dynamics obeying the generalized Langevin equation : general solution based on the Zwanzig-Caldeira-Leggett Hamiltonian -- Diffusive dynamics on a multidimensional energy landscape -- Quantum effects in chemical kinetics -- Computer simulations of molecular kinetics : foundation -- The master equation as a model for transitions between macrostates -- Direct calculation of rate coefficients with computer simulations -- A simple numerical example of rate calculations -- Rare events and reaction coordinates -- Celling -- An example of the use of cells : alanine dipeptide. 330 $a"Modern approaches to the study of kinetics routinely combine the use of computer simulations with analytic analysis. This book is focused on the theory, algorithms, simulations methods, and analysis of molecular kinetics in condensed phases. It provides a detailed and comprehensive description of modern theories and simulation methods to model molecular events. Emphasis is placed on rigorous stochastic modeling of molecular processes and the use of the mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times, and transition times. Simulations focus on atomically detailed modeling of molecules in action and the connections of these simulations to theory and experiment. Applications are described that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. The book is divided into five sections and topics covered include: Introduction: Langevin dynamics, Fokker Planck equation, path integrals, generalized Langevin equation, generalized master equation, theory of optimal pathways. Kinetic Theory: Transition state theory, transmission coefficient, duration of transition path, Kramers theory, Grote-Hynes theory, generalized Langevin equation and transition state theory, diffusion controlled reactions, quantum effects on reaction rates. Simulations: Molecular dynamics simulations, Monte Carlo method, accelerated dynamics approaches for kinetics, calculations of reaction pathways. Analysis: Committors, transition path theory, kinetic networks, Markov state models. Examples: One and two-dimensional models, simulations of biological macromolecules, models of protein folding, molecular machines, transport processes"--$cProvided by publisher. 606 $aChemical kinetics$xMathematical models 606 $aStochastic processes$xMathematical models 606 $aMolecular structure 615 0$aChemical kinetics$xMathematical models. 615 0$aStochastic processes$xMathematical models. 615 0$aMolecular structure. 676 $a541.394 700 $aElber$b Ron$01680467 702 $aMakarov$b Dmitrii E. 702 $aOrland$b Henri 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9910830048103321 996 $aMolecular kinetics in condensed phases$94049187 997 $aUNINA