Related papers: Efficient simulation of semiflexible polymers
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
Motivated by decentralized approaches to machine learning, we propose a collaborative Bayesian learning algorithm taking the form of decentralized Langevin dynamics in a non-convex setting. Our analysis show that the initial KL-divergence…
By means of Brownian dynamics simulations we study the steady-state dynamic properties of a flexible active polymer in a poor solvent condition. Our results show that the effective diffusion constant of the polymer $D_{\rm eff}$ gets…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
For "large" class $\mathcal{C}$ of continuous probability density functions (p.d.f.), we demonstrate that for every $w\in\mathcal{C}$ there is mixture of discrete Binomial distributions (MDBD) with $T\geq N\sqrt{\phi_{w}/\delta}$ distinct…
We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler…
The dynamics of flexible filaments entrained in flow, important for understanding many biological and industrial processes, are computationally expensive to model with full-physics simulations. This work describes a data-driven technique to…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular…
This paper extends a field-theoretical dynamical networking formalism for mesoscopic polymer dynamics to explicitly include dedicated cross-linker particles. Cross-linkers are represented within a Martin-Siggia-Rose generating functional…
Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
We developed and applied a machine-learned discretization for one-dimensional (1-D) horizontal passive scalar advection, which is an operator component common to all chemical transport models (CTMs). Our learned advection scheme resembles a…
Modeling of turbulent flows is still challenging. One way to deal with the large scale separation due to turbulence is to simulate only the large scales and model the unresolved contributions as done in large-eddy simulation (LES). This…
We define a discrete-time Markov chain for abstract polymer models and show that under sufficient decay of the polymer weights, this chain mixes rapidly. We apply this Markov chain to polymer models derived from the hard-core and…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
We consider the motion of semiflexible polymers in double-well potentials. We calculate shape, energy, and effective diffusion constant of kink excitations, and in particular their dependence on the bending rigidity of the semiflexible…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…