TL;DR: The method proposed here is to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.
Abstract: The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous to the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.
TL;DR: In this article, the spectral properties of the Ruelle-Perron-Frobenius operator associated to an Anosov map on classes of functions with high smoothness were studied.
Abstract: We study the spectral properties of the Ruelle-Perron-Frobenius operator associated to an Anosov map on classes of functions with high smoothness. To this end we construct anisotropic Banach spaces of distributions on which the transfer operator has a small essential spectrum. In the C ∞ case, the essential spectral radius is arbitrarily small, which yieldsa descriptionof the correlationswith arbitraryprecision. Moreover,we obtain sharp spectral stability results for deterministic and random perturbations. In particular, we obtain differentiability results for spectral data (which imply differentiability of the Sinai-Ruelle-Bowenmeasure, the variancefor the centrallimit theorem, the rates of decay for smooth observable, etc.).
TL;DR: In this paper, a variational principle based on the maximization of a Rayleigh coefficient is derived for modeling the slow parts of Markov processes by approximating the dominant eigenfunctions and eigenvalues of the propagator.
Abstract: The slow processes of metastable stochastic dynamical systems are difficult to access by direct numerical simulation due to the sampling problems. Here, we suggest an approach for modeling the slow parts of Markov processes by approximating the dominant eigenfunctions and eigenvalues of the propagator. To this end, a variational principle is derived that is based on the maximization of a Rayleigh coefficient. It is shown that this Rayleigh coefficient can be estimated from statistical observables that can be obtained from short distributed simulations starting from different parts of state space. The approach forms a basis for the development of adaptive and efficient computational algorithms for simulating and analyzing metastable Markov processes while avoiding the sampling problem. Since any stochastic process with finite memory can be transformed into a Markov process, the approach is applicable to a wide range of processes relevant for modeling complex real-world phenomena.
TL;DR: In this paper, it was shown that the transfer operator associated with smooth random perturbations of the map is close, in a proper sense, to the unperturbed transfer operator.
Abstract: We extend a number of results from one-dimensional dynamics based on spectral properties of the Ruelle–Perron–Frobenius transfer operator to Anosov diffeomorphisms on compact manifolds. This allows us to develop a direct operator approach to study ergodic properties of these maps. In particular, we show that it is possible to define Banach spaces on which the transfer operator is quasi-compact. (Information on the existence of a Sinai–Ruelle–Bowen measure, its smoothness properties and statistical properties readily follow from such a result.) In dimension d = 2 we show that the transfer operator associated with smooth random perturbations of the map is close, in a proper sense, to the unperturbed transfer operator. This allows us to obtain easily very strong spectral stability results, which, in turn, imply spectral stability results for smooth deterministic perturbations as well. Finally, we are able to implement an Ulam-type finite rank approximation scheme thus reducing the study of the spectral properties of the transfer operator to a finite-dimensional problem.
TL;DR: An exact and explicit ladder-tensor-network ansatz is presented for the nonequilibrium steady state of an anisotropic Heisenberg XXZ spin-1/2 chain which is driven far from equilibrium with a pair of Lindblad operators acting on the edges of the chain only.
Abstract: An exact and explicit ladder-tensor-network ansatz is presented for the nonequilibrium steady state of an anisotropic Heisenberg $XXZ$ spin-$1/2$ chain which is driven far from equilibrium with a pair of Lindblad operators acting on the edges of the chain only. We show that the steady-state density operator of a finite system of size $n$ is---apart from a normalization constant---a polynomial of degree $2n\ensuremath{-}2$ in the coupling constant. Efficient computation of physical observables is facilitated in terms of a transfer operator reminiscent of a classical Markov process. In the isotropic case we find cosine spin profiles, $1/{n}^{2}$ scaling of the spin current, and long-range correlations in the steady state. This is a fully nonperturbative extension of a recent result [Phys. Rev. Lett. 106, 217206 (2011)].