In this work, we revisit the electron-transfer rate theory, with particular interests in the distinct quantum solvation effect and the characterizations of adiabatic/nonadiabatic and Markovian/non-Markovian rate processes. We first present a full account for the quantum solvation effect on the electron transfer in Debye solvents, addressed previously in J. Theor. Comput. Chem. 2006, 5, 685. Dis...

We construct a strongly minimal set which is not a finite cover of one with DMP. We also prove that for a strongly minimal theory T generic automorphisms exist iff T has DMP, thus proving a conjecture of Kikyo and

A classical random walk (St, t ∈ N) is defined by St := t ∑ n=0 Xn, where (Xn) are i.i.d. When the increments (Xn)n∈N are a one-order Markov chain, a short memory is introduced in the dynamics of (St). This so-called “persistent” random walk is nolonger Markovian and, under suitable conditions, the rescaled process converges towards the integrated telegraph noise (ITN) as the time-scale and spa...

Since the advent of Markovian Process Algebras, users have requested the ability to employ a greater variety of action distribution. We present a conservative extension to the popular Markovian process algebra, PEPA, which incorporates generally distributed sojourn-times for action duration. Just as a PEPA model generates a Markov chain for analysis purposes, so semi-Markov PEPA produces a semi...

Firstly, the Markovian stochastic Schrödinger equations are presented, together with their connections with the theory of measurements in continuous time. Moreover, the stochastic evolution equations are translated into a simulation algorithm, which is illustrated by two concrete examples — the damped harmonic oscillator and a two-level atom with homodyne photodetection. Then, we consider how t...

A state estimator design is described for discrete time systems having observably intermittent measurements. A stationary Markov process is used to model probabilistic measurement losses. The stationarity of the Markov process suggests an analagous stationary estimator design related to the Markov states. A precomputable time-varying state estimator is proposed as an alternative to Kalman’s opt...

Over the years, there have been claims that evolution proceeds according to systematically different processes over different timescales and that protein evolution behaves in a non-Markovian manner. On the other hand, Markov models are fundamental to many applications in evolutionary studies. Apparent non-Markovian or time-dependent behavior has been attributed to influence of the genetic code ...

Why some strains of a species exhibit a certain phenotype (e.g. drug resistant) but not the other strains of the same species is a critical question to answer. Studying the metabolism of the two groups of strains may discover the corresponding pathways that are conserved in the first group but not in the second group. However, only a few tools provide functions to compare two groups of metaboli...

A generalization of the Reversed Compound Agent Theorem of Markovian process algebra is derived that yields separable, but non-product-form solutions for collections of interacting processes such as arise in multi-class queueing networks with Processor Sharing servers. It is based on an analysis of the minimal cycles in the state space of a multi-agent cooperation, which can be simply identifie...

We derive novel upper and lower finite-length bounds of the error probability in joint source-channel coding when the source obeys the ergodic Markov process and the channel is a Markovian additive channel or a Markovian conditional additive channel. These bounds achieve the tight bounds in the large and moderate deviation regimes. Index Terms Markov chain, joint source-channel coding, finite-l...