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Register a new userParallelization of Markov chain generation and its application to the multicanonical method
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Added by
Takanori Sugihara Dr.
Publication date
2009
fields
Physics
and research's language is
English
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We develop a simple algorithm to parallelize generation processes of Markov chains. In this algorithm, multiple Markov chains are generated in parallel and jointed together to make a longer Markov chain. The joints between the constituent Markov chains are processed using the detailed balance. We apply the parallelization algorithm to multicanonical calculations of the two-dimensional Ising model and demonstrate accurate estimation of multicanonical weights.
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We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. These new algorithms are particularly useful for studying the protein folding problem.
The cavity method is a well established technique for solving classical spin models on sparse random graphs (mean-field models with finite connectivity). Laumann et al. [arXiv:0706.4391] proposed recently an extension of this method to quantum spin-1/2 models in a transverse field, using a discretized Suzuki-Trotter imaginary time formalism. Here we show how to take analytically the continuous imaginary time limit. Our main technical contribution is an explicit procedure to generate the spin trajectories in a path integral representation of the imaginary time dynamics. As a side result we also show how this procedure can be used in simple heat-bath like Monte Carlo simulations of generic quantum spin models. The replica symmetric continuous time quantum cavity method is formulated for a wide class of models, and applied as a simple example on the Bethe lattice ferromagnet in a transverse field. The results of the methods are confronted with various approximation schemes in this particular case. On this system we performed quantum Monte Carlo simulations that confirm the exactness of the cavity method in the thermodynamic limit.
We introduce an efficient nonreversible Markov chain Monte Carlo algorithm to generate self-avoiding walks with a variable endpoint. In two dimensions, the new algorithm slightly outperforms the two-move nonreversible Berretti-Sokal algorithm introduced by H.~Hu, X.~Chen, and Y.~Deng in cite{old}, while for three-dimensional walks, it is 3--5 times faster. The new algorithm introduces nonreversible Markov chains that obey global balance and allows for three types of elementary moves on the existing self-avoiding walk: shorten, extend or alter conformation without changing the walks length.
Biological systems use energy to maintain non-equilibrium distributions for long times, e.g. of chemical concentrations or protein conformations. What are the fundamental limits of the power used to hold a stochastic system in a desired distribution over states? We study the setting of an uncontrolled Markov chain $Q$ altered into a controlled chain $P$ having a desired stationary distribution. Thermodynamics considerations lead to an appropriately defined Kullback-Leibler (KL) divergence rate $D(P||Q)$ as the cost of control, a setting introduced by Todorov, corresponding to a Markov decision process with mean log loss action cost. The optimal controlled chain $P^*$ minimizes the KL divergence rate $D(cdot||Q)$ subject to a stationary distribution constraint, and the minimal KL divergence rate lower bounds the power used. While this optimization problem is familiar from the large deviations literature, we offer a novel interpretation as a minimum holding cost and compute the minimizer $P^*$ more explicitly than previously available. We state a version of our results for both discrete- and continuous-time Markov chains, and find nice expressions for the important case of a reversible uncontrolled chain $Q$, for a two-state chain, and for birth-and-death processes.
We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment and detachment of monomers. Exact solutions are obtained for these kinetic equations in the steady regimes of multicomponent copolymerization and depolymerization. Thermodynamic equilibrium is identified as the state at which the growth velocity is vanishing on average and where detailed balance is satisfied. Away from equilibrium, the analytical expression of the thermodynamic entropy production is deduced in terms of the Shannon disorder per monomer in the copolymer sequence. The Mayo-Lewis equation is recovered in the fully irreversible growth regime. The theory also applies to Bernoullian chains in the case where the attachment and detachment rates only depend on the reacting monomer.
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