Related papers: Simulating the Entropic Collapse of Coarse-Grained…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Using numerical simulations, we investigate the gravitational evolution of filamentary molecular cloud structures and their condensation into dense protostellar cores. One possible process is the so called 'edge effect', the pile-up of…
Dense suspensions of soft colloidal particles display a broad range of physical and rheological properties which are still far from being fully understood. To elucidate the role of deformability on colloidal flow, we employ computer…
When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here…
A lubrication model can be used to describe the dynamics of a weakly volatile viscous fluid layer on a hydrophobic substrate. Thin layers of the fluid are unstable to perturbations and break up into slowly evolving interacting droplets. A…
We present numerical simulations of the evolution of low-mass, isothermal, molecular cores which are subjected to an increase in external pressure $P\xt$. If $P\xt$ increases very slowly, the core approaches instability quite…
Recent experiments have shown that various structures may be formed during the evaporative dewetting of thin films of colloidal suspensions. Nano-particle deposits of strongly branched `flower-like', labyrinthine and network structures are…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
We study with molecular dynamics simulations of a generic bead-spring model the cyclic crazing behaviour of glassy polymers. The aim is to elucidate the mechanical response of sole fibrillated craze matter as well as its interaction with…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…
A new quantitative theory for polyelectrolytes in salt free dilute solutions is developed. Depending on the electrostatic interaction strength, polyelectrolytes in solutions can undergo strong stretching (with polyelectrolyte dimension…