Related papers: A Macromolecule in a Solvent: Adaptive Resolution …
In recent years, fluorescence correlation spectroscopy has been increasingly applied for the study of polymer dynamics on the nanometer scale. The core idea is to extract, from a measured autocorrelation curve, an effective mean-square…
This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief…
Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
A coarse-grained multi-blob description of polymer solutions is presented, based on soft, transferable effective interactions between bonded and non-bonded blobs. The number of blobs is chosen such that the blob density does not exceed…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of active force on the polymer adsorption behavior and the combined effect of chain mobility, length N,…
Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a…
The dynamics of a heteropolymer chain in solution is studied in the limit of long chain length. Using functional integral representation we derive an effective equation of motion, in which the heterogeneity of the chain manifests itself as…
Machine learning techniques including neural networks are popular tools for materials and chemical scientists with applications that may provide viable alternative methods in the analysis of structure and energetics of systems ranging from…
Although medium chain length insoluble amphiphiles are well known to form gaseous and liquid expanded phases on an air/water interface, the situation for the soluble case is less clear. We perform molecular dynamics simulations of model…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
The surface of a molecule determines much of its chemical and physical property, and is of great interest and importance. In this Letter, we introduce the concept of molecular multiresolution surfaces as a new paradigm of multiscale…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
Under the local plasmonic excitation, the Raman images of a single molecule can now reach sub-nanometer resolution. We report here a theoretical description of the interaction between a molecule and a highly confined plasmonic field. It is…