Related papers: Long Range Moves for High Density Polymer Simulati…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
Single three dimensional polymers confined to a slab, i.e. to the region between two parallel plane walls, are studied by Monte Carlo simulations. They are described by $N$-step walks on a simple cubic lattice confined to the region $1 \le…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete…
While general quantum many-body systems require exponential resources to be simulated on a classical computer, systems of non-interacting fermions can be simulated exactly using polynomially scaling resources. Such systems may be of…
Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Scaling up datasets is highly effective in improving the performance of deep learning models, including in the field of robot learning. However, data collection still proves to be a bottleneck. Approaches relying on collecting human…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers,…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
We use an efficient method that eases the daunting task of simulating dynamics in spin systems with long-range interaction. Our Monte Carlo simulations of the long-range Ising model for the nonequilibrium phase ordering dynamics in two…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
Quadrupedal locomotion over complex terrain has been a long-standing research topic in robotics. While recent reinforcement learning-based locomotion methods improve generalizability and foot-placement precision, they rely on implicit…
A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with…
We present the ground state extension of the efficient quantum Monte Carlo algorithm for lattice fermions of arXiv:1411.0683. Based on continuous-time expansion of imaginary-time projection operator, the algorithm is free of systematic…