相关论文: A Rational Approach to Ring Flexibility in Interna…
Weakly coupled Ising chains provide a condensed-matter realization of confinement. In these systems, kinks and antikinks bind into mesons due to an attractive interaction potential that increases linearly with the distance between the…
We analyse the golden rule limit of the recently proposed isomorphic ring polymer (iso-RP) method. This method aims to combine an exact expression for the quantum mechanical partition function of a system with multiple electronic states…
We demonstrate that internal pivot-like defects, arising from rigor mutant motor proteins that bind without stepping, fundamentally reshape the dynamics of semiflexible filaments in two-dimensional motility assays. Using large-scale…
Polymer-related materials exhibit rich glassy behaviors at different length scales due to their various molecular structures and topological constraints. Recent studies have identified transient interpenetration of the long-chain rings…
We present a new non-adiabatic ring polymer molecular dynamics (NRPMD) method based on the spin mapping formalism, which we refer to as the spin-mapping NRPMD (SM-NRPMD) approach. We derive the path-integral partition function expression…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
The magnetic behavior of molecular Single-Chain Magnets is investigated in the framework of a one-dimensional Ising model with single spin-flip Glauber dynamics. Opportune modifications to the original theory are required in order to…
Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and…
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
Intracellular processes often rely on the timely encounter of mobile reaction partners, including intermittently motor-driven organelles. The underlying cytoskeletal network presents a complex landscape that both directs particle movement…
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
This article describes a numerical procedure designed to tune the parameters of periodically-driven dynamical systems to a state in which they exhibit rich dynamical behavior. This is achieved by maximizing the diversity of subharmonic…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between…
Path-integral-based molecular dynamics (MD) simulations are widely used for the calculation of numerically exact quantum Boltzmann properties and approximate dynamical quantities. A nearly universal feature of MD numerical integration…
A ring crystal of ions trapped in a linear multipole trap is studied as a basis for an optical frequency standard. The equilibrium conditions and cooling possibilities are discussed through an analytical model and molecular dynamics…
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as continuous Gaussian polymer exposed to tangential active forces. The analytical solution of…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
We study of the dynamics of ring polymers confined to diffuse in a background gel at low concentrations. We do this in order to probe the inter-play between topology and dynamics in ring polymers. We develop an algorithm that takes into…