Related papers: Efficient simulation of semiflexible polymers
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
This paper deals with the formulation, calibration, and validation of a Lattice Discrete Particle Model (LDPM) for the simulation of the pressure-dependent inelastic response of granular rocks. LDPM is formulated in the framework of…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…
Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the…
Polymer translocation has long been a topic of interest in the field of biological physics given its relevance in both biological (protein and DNA/RNA translocation through nuclear and cell membranes) and technological processes (nanopore…
We investigate the static and dynamic properties of dendrimers diffusing through a network of linear associative polymers using coarse-grained Brownian dynamics simulations. Both dendrimers and network chains are modelled as bead-spring…
The exact estimation of latent variable models with big data is known to be challenging. The latents have to be integrated out numerically, and the dimension of the latent variables increases with the sample size. This paper develops a…
We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at…
Polymers exposed to shear flow exhibit a rich tumbling dynamics. While rigid rods rotate on Jeffery orbits, flexible polymers stretch and coil up during tumbling. Theoretical results show that in both of these asymptotic regimes the…
Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
We present a model for semiflexible polymers in Hamiltonian formulation which interpolates between a Rouse chain and worm-like chain. Both models are realized as limits for the parameters. The model parameters can also be chosen to match…
Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…
This article provides next step towards solving speed bottleneck of any system that intensively uses convolutions operations (e.g. CNN). Method described in the article is applied on deformable part models (DPM) algorithm. Method described…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
Real-time simulation of elastic structures is essential in many applications, from computer-guided surgical interventions to interactive design in mechanical engineering. The Finite Element Method is often used as the numerical method of…
Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual…
The inverse Langevin function is a fundamental part of the statistical chain models used to describe the behavior of polymeric-like materials, appearing also in other fields such as magnetism, molecular dynamics and even biomechanics. In…
We study the dynamics and conformations of a single active semiflexible polymer whose monomers experience a propulsion force perpendicular to the local tangent, with the end beads being different from the inner beads ("end-tailored"). Using…