Related papers: Deconstructing the energy landscape: new algorithm…
We present a lattice model for polymer solutions, explicitly incorporating interactions with a bath of solvent and cosolvent molecules. By exploiting the well-known analogy between polymer systems and the $O(n)$-vector spin model in the…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
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 consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
The "folding algorithm"\cite{fold1} is a matrix product state algorithm for simulating quantum systems that involves a spatial evolution of a matrix product state. Hence, the computational effort of this algorithm is controlled by the…
The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
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…
Describing the complex landscape of infinite-dimensional free energy is generally a challenging problem. This difficulty arises from the existence of numerous minimizers and, consequently, a vast number of saddle points. These factors make…
Phase retrieval in optical imaging refers to the recovery of a complex signal from phaseless data acquired in the form of its diffraction patterns. These patterns are acquired through a system with a coherent light source that employs a…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
This paper studies a polymer chain in the vicinity of a linear interface separating two immiscible solvents. The polymer consists of random monomer types, while the interface carries random charges. Both the monomer types and the charges…
Active polymeric systems exhibit a rich spectrum of non-equilibrium phenomena arising from stochastic forces that explicitly break detailed balance. Despite the rapid growth of experimental and numerical studies, analytical progress remains…