Related papers: Deconstructing the energy landscape: new algorithm…
We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each…
In this paper we present simulations of a surface-adsorbed polymer subject to an elongation force. The polymer is modelled by a self-avoiding walk on a regular lattice. It is confined to a half-space by an adsorbing surface with attractions…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is…
We consider the problem of undirected polymers (tied at the endpoints) in random environment, also known as the unoriented first passage percolation on the hypercube, in the limit of large dimensions. By means of the multiscale refinement…
We present a theory for the reverse analysis on the sequence information of a single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z) curves during quasi static stretching. Upon stretching of a self-assembled RHP, it…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
We investigate the phase diagram of disordered copolymers at the interface between two selective solvents, and in particular its weak-coupling behavior, encoded in the slope $m_c$ of the critical line at the origin. In mathematical terms,…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free energy landscape of such…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
Using a mapping of compact polymers on the Manhattan lattice to spanning trees, we calculate exactly the average number of bends at infinite temperature. We then find, in a high temperature approximation, the energy of the system as a…
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…
The problem of phase retrieval has been intriguing researchers for decades due to its appearance in a wide range of applications. The task of a phase retrieval algorithm is typically to recover a signal from linear phase-less measurements.…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
Joint ground states of two directed polymers in a random medium are investigated. Using exact min-cost flow optimization the true two-line ground-state is compared with the single line ground state plus its first excited state. It is found…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We investigate the solution landscapes of the confined diblock copolymer and homopolymer in two-dimensional domain by using the extended Ohta--Kawasaki model. The projected saddle dynamics method is developed to compute the saddle points…
Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and…