Related papers: Simulating the Entropic Collapse of Coarse-Grained…
With suitably designed Monte Carlo simulations we have investigated the properties of mobile, impenetrable, yet deformable particles that are immersed into a porous matrix, the latter one realized via a frozen configuration of spherical…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
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…
Depletion forces and macromolecular crowding govern the structure and function of biopolymers in biological cells and the properties of polymer nanocomposite materials. To isolate and analyze the influence of polymer shape fluctuations and…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
We have studied the breakup and subsequent fluid flow in very thin films of partially wetting liquid on solid substrates, using molecular dynamics simulations. The liquid is made of short chain molecules interacting with Lennard-Jones…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling:…
We present a numerical model for a two dimensional (2D) granular assembly, falling in a rectangular container when the bottom is removed. We observe the occurrence of cracks splitting the initial pile into pieces, like in experiments. We…
We experimentally study the condensed phases of repelling core-softened spheres in two dimensions. The dipolar pair repulsion between superparamagnetic spheres trapped in a thin cell is induced by a transverse magnetic field and softened by…
A crystal lattice, when confined to the surface of a cylinder, must have a periodic structure that is commensurate with the cylinder circumference. This constraint can frustrate the system, leading to oblique crystal lattices or to…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
A simple and computationally efficient parameterization of the deleptonization, the entropy changes, and the neutrino stress is presented for numerical simulations of stellar core collapse. The parameterization of the neutrino physics is…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
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…
The collapse kinetics of strongly charged polyelectrolytes in poor solvents is investigated by Langevin simulations and scaling arguments. The rate of collapse increases sharply as the valence of counterions, z, increases from one to four.…