Related papers: A Universal Method for Analysing Copolymer Growth
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
The impact of polymer-polymer interactions of various types on the thermodynamics, structure, and accommodation of topological constraints is addressed for systems comprising many directed polymers in two spatial dimensions. The approach is…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
A brief review of our recent studies aiming at a better understanding of the scaling behaviour of polymers in disordered environments is given. The main emphasis is on a simple generic model where the polymers are represented by…
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…
We outline a theoretical framework for estimating the evolution of the particle size distribution in colloid and nanoparticle synthesis, when the primary growth mode is by externally controlled addition of singlet building blocks. The…
We solve the Chapman-Kolmogorov equation and study the exact splitting probabilities of the general stochastic process which describes polymer translocation through membrane pores within the broad class of Markov chains. Transition…
We study the dynamics of a polymer that is pulled by a constant force through a viscoelastic medium. This is a model for a polymer being pulled through a cell by an external force, or for an active biopolymer moving due to a self generated…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the…
Experimental mechanisms that yield the growth of homochiral copolymers over their heterochiral counterparts have been advocated by Lahav and co-workers. These chiral amplification mechanisms proceed through racemic {\beta}-sheet-controlled…
Emergence and maintenance of polymers with complex sequences is a major question in the study of origins of life. To answer this, we studied a model polymerization reaction, where polymers are synthesized by stepwise ligation from two types…
We develop a simple recursive approach to treat reversible condensation polymerization with cyclization. Based upon a minimum set of balance equations, the law of mass action, Gaussian chain statistics, and the assumption of independent…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler,…
A first-principle multiscale modeling approach is presented, which is derived from the solution of the Ornstein-Zernike equation for the coarse-grained representation of polymer liquids. The approach is analytical, and for this reason is…
We define a Markov process on the partitions of $[n]=\{1,\ldots,n\}$ by drawing a sample in $[n]$ at each time of a Poisson process, by merging blocks that contain one of these points and by leaving all other blocks unchanged. This…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…