Related papers: Growth and dissolution of macromolecular Markov ch…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
Using stochastic thermodynamics, the properties of interacting linear chains subject to periodic drivings are investigated. The systems are described by Fokker-Planck-Kramers equation and exact (explicit) solutions are obtained for periodic…
We estimate the probability regarding polymerization of a macromolecule which is made of distinct monomers. The lattice model of the random walk has been used to mimic the conformations of an ideal chain in two and three dimensions. It has…
Numerically optimized reduced descriptions of macromolecular liquids often present thermodynamic inconsistency with atomistic level descriptions even if the total correlation function, i.e. the structure, appears to be in agreement. An…
The structural and thermodynamic properties of mixtures of colloidal spheres and non-adsorbing polymer chains are studied within a novel general two-component macromolecular liquid state approach applicable for all size asymmetry ratios.…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…
The kinetics of ordering and concurrent ordering and clustering is analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. A simplified energy eigenstructure, or…
In classical chaotic systems the entropy, averaged over initial phase space distributions, follows an universal behavior. While approaching thermal equilibrium it passes through a stage where it grows linearly, while the growth rate, the…
We briefly review the recently developed, Markov process based isothermal chemical thermodynamics for nonlinear, driven mesoscopic kinetic systems. Both the instantaneous Shannon entropy {\boldmath $S[p_{\alpha}(t)]$} and relative entropy…
Using molecular dynamics simulations of a tangent-soft-sphere bead-spring polymer model, we examine the degree to which semiflexible polymer melts solidify at isostaticity. Flexible and stiff chains crystallize when they are isostatic as…
Kinetics of steady-state copolymerization has been investigated since 1940s. Irreversible terminal and penultimate models were successfully applied to a number of comonomer systems, but failed for systems where depropagation is significant.…
The stretching of a polymer chain by a large scale chaotic flow is considered. The steady state which emerges as a balance of the turbulent stretching and anharmonic resistance of the chain is quantitatively described, i.e. the dependency…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
We obtain the entropy of flexible linear chains composed of M monomers placed on the square lattice using a transfer matrix approach. An excluded volume interaction is included by considering the chains to be self-and mutually avoiding, and…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Markov chains are a natural and well understood tool for describing one-dimensional patterns in time or space. We show how to infer $k$-th order Markov chains, for arbitrary $k$, from finite data by applying Bayesian methods to both…