Related papers: Molecular dynamics simulation of polymer helix for…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By…
Molecular process of crystallization from an oriented amorphous state was reproduced by molecular dynamics simulation for a realistic polyethylene model. Initial oriented amorphous state was obtained by uniaxial drawing an isotropic glassy…
A method for the discrete particle simulation of of almost rigid, sharply edged frictional particles, such as railway ballast is proposed. In difference to Molecular Dynamics algorithms, the method does not require knowledge about the…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical…
Surface tension-driven flow techniques have recently emerged as an efficient means of shedding light into the rheology of thin polymer films. Motivated by experimental and theoretical approaches in films bearing a varying surface…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
Molecular dynamics simulations (mds) were carried out to investigate the reorientational motion of a rigid (fixed bond length), asymmetric diatomic molecule in the liquid and glassy states. In the latter the molecule reorients via…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
A large-scale molecular dynamics simulation is performed on a glass-forming Lennard-Jones mixture to determine the nature of dynamical heterogeneities which arise in this model fragile liquid. We observe that the most mobile particles…