Related papers: Folding Kinetics of a Polymer
We analyze the freezing and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in…
Investigating thermodynamic properties of liquid-solid transitions of flexible homopolymers with elastic bonds by means of multicanonical Monte Carlo simulations, we find crystalline conformations that resemble ground-state structures of…
We investigate - with Monte Carlo computer simulations - the phase behaviour of dimeric colloidal molecules on periodic substrates with square symmetry. The molecules are formed in a two-dimensional suspension of like charged colloids…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
In this paper we describe a version of London Langevin molecular dynamics simulations that allows for investigations of the vortex lattice melting transition in the highly anisotropic high-temperature superconductor material…
Combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, we report the observation of a protein-like dynamical transition in linear chains of Poly(N-isopropylacrylamide). We…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
We present Monte Carlo simulations on a lattice system that displays a first order phase transition between a disordered phase (liquid) and an ordered phase (crystal). The model is augmented by an interaction that simulates the effect of…
We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedback-optimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
The mechanical properties of thermally excited two-dimensional crystalline membranes can depend dramatically on their geometry and topology. A particularly relevant example is the effect on the crumpling transition of holes in the membrane.…
Vitrimers are a special class of polymers that undergo dynamic cross-linking under thermal stimuli. Their ability to exchange covalent bonds can be harnessed to mitigate damage in a composite or to achieve recyclable aerospace composites.…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…