Related papers: Long Range Moves for High Density Polymer Simulati…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…
As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length…
The paper presents a short overview of the theoretical, numerical and experimental works on the critical behavior of a dilute polymer solution of long-flexible polymer chains confined in semi-infinite space restricted by a surface or in a…
A quantum Monte Carlo simulation of a system of hard rods in one dimension is presented and discussed. The calculation is exact since the analytical form of the wavefunction is known, and is in excellent agreement with predictions obtained…
We study the interplay of intrinsic-electronic and environmental factors on long-range charge transport across molecular chains with up to $N\sim 80$ monomers. We describe the molecular electronic structure of the chain with a tight-binding…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models…
Computing stabilizing and optimal control actions for legged locomotion in real time is difficult due to the nonlinear, hybrid, and high dimensional nature of these robots. The hybrid nature of the system introduces a combination of…
High-quality random samples of quantum states are needed for a variety of tasks in quantum information and quantum computation. Searching the high-dimensional quantum state space for a global maximum of an objective function with many local…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…
Monte Carlo (MC) simulations are essential computational approaches with widespread use throughout all areas of science. We present a method for accelerating lattice MC simulations using fully connected and convolutional artificial neural…
Lattice models are valuable tools to gain insight into the statistical physics of heteropolymers. We rigorously map the partition function of these models into a vacuum expectation value of a $\mathbb{Z}_2$ lattice gauge theory (LGT), with…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up…
We propose a new quantum Monte Carlo algorithm to compute fermion ground-state properties. The ground state is projected from an initial wavefunction by a branching random walk in an over-complete basis space of Slater determinants. By…
We present a novel and rigorous approach to the Langevin dynamics of ideal polymer chains subject to internal distance constraints. The permanent constraints are modelled by harmonic potentials in the limit when the strength of the…
This paper presents a motion planning algorithm for quadruped locomotion based on density functions. We decompose the locomotion problem into a high-level density planner and a model predictive controller (MPC). Due to density functions…