Related papers: Simple Model of Sickle Hemogloblin
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence…
We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis…
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers,…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…
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…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
The Monte Carlo carbyne model is modified to investigate the glass transition of the semi-flexible entangled polymer chains. The stochastic bombardment between monomers are monitored by Metropolis algorithm with help of the consideration of…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
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…