Set-free Markov state model building

Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations.

Obtaining absolute binding free energies from unbiased ligand diffusion has attracted a significant amount of attention due to its implications in drug design. Several studies have used special purpose computers and software to achieve microsecond molecular dynamics which, combined with a Markov state model analysis, are capable of providing absolute binding free energies. We have recently deve...

Stochastic Model Building of Photophysics using Hidden Markov Model

Model-Free Bootstrap for Markov processes

Consider time series data X1, . . . , Xn that arise as a (partial) sample path of a stationary Markov process of order p ≥ 1. Under this general context, there are (at least) two resampling mechanisms available in the literature, namely: (a) bootstrap based on kernel estimates of the transition density of the Markov processes of Rajarshi (1990), and the Local Bootstrap for Markov processes of P...

INFAMY: An Infinite-State Markov Model Checker

The design of complex concurrent systems often involves intricate performance and dependability considerations. Continuous-time Markov chains (CTMCs) are a widely used modeling formalism, where performance and dependability properties are analyzable by model checking. We present INFAMY, a model checker for arbitrarily structured infinite-state CTMCs. It checks probabilistic timing properties ex...

Model Checking Infinite-State Markov Chains

In this paper algorithms for model checking CSL (continuous stochastic logic) against infinite-state continuous-time Markov chains of so-called quasi birth-death type are developed. In doing so we extend the applicability of CSL model checking beyond the recently proposed case for finite-state continuous-time Markov chains, to an important class of infinite-state Markov chains. We present synta...