Related papers: Dynamics of polymer chain collapse into compact st…
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
In the present paper we revisit, theoretical and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing to explore the…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…
A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case,…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
We study the structural and dynamical mechanisms of reinforcement of a polymer nanocomposite (PNC) via coarse-grained molecular dynamics simulations. In a regime of strong polymer-filler interactions, the stress at failure of the PNC is…
In this article, a novel cluster analysis algorithm was employed in the study of polymer coil to globule transition via single chain Monte Carlo simulations. The algorithm, which has been recently applied in Molecular Dynamics simulations…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
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…
Advanced chain-growth computer simulation methodologies have been employed for a systematic statistical analysis of the critical behavior of a polymer adsorbing at a substrate. We use finitesize scaling techniques to investigate the…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We investigate, using numerical simulations and analytical arguments, a simple one dimensional model for the swelling or the collapse of a closed polymer chain of size N, representing the dynamical evolution of a polymer in a \Theta-solvent…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…