Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models

Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models

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 ...

Local evolution equations for non-Markovian processes

A Fokker-Planck equation approach for the treatment of non-Markovian stochastic processes is proposed. The approach is based on the introduction of fictitious trajectories sharing with the real ones their local structure and initial conditions. Different statistical quantities are generated by different construction rules for the trajectories, which coincide only in the Markovian case. The meri...

Non-Markovian Agent Evolution with EVOLP

Logic Programming Update Languages were proposed as an extension of logic programming, which allow for modelling the dynamics of knowledge bases where both extensional knowledge (facts) as well as intentional knowledge (rules) may change over time due to updates, with important application Multi-Agent Systems (MAS). Despite their generality, these languages do not provide means to directly acce...

Markovian embedding of non-Markovian superdiffusion.

We consider different Markovian embedding schemes of non-Markovian stochastic processes that are described by generalized Langevin equations and obey thermal detailed balance under equilibrium conditions. At thermal equilibrium, superdiffusive behavior can emerge if the total integral of the memory kernel vanishes. Such a situation of vanishing static friction is caused by a super-Ohmic thermal...

Non-discounted Denumerable Markovian Decision Models