Related papers: Deconstructing the energy landscape: new algorithm…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…
A novel numerical approach to analyze the mechanical behavior within composite materials including the inelastic regime up to final failure is presented. Therefore, a second-gradient theory is combined with phase-field methods to fracture.…
Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers…
The problem of phase retrieval is revisited and studied from a fresh perspective. In particular, we establish a connection between the phase retrieval problem and the sensor network localization problem, which allows us to utilize the vast…
We present new linear energy-stable numerical schemes for numerical simulation of complex polymer-solvent mixtures. The mathematical model proposed by Zhou, Zhang and E (Physical Review E 73, 2006) consists of the Cahn-Hilliard equation…
Photoluminescence (PL) is a ubiquitous proxy for material quality in optoelectronic devices, widely used for high-throughput materials discovery. However, we demonstrate that in the presence of charge-selective contacts, PL loses its…
We propose a field-theoretical approach to a polymer system immersed in an ideal mixture of clustering centers. The system contains several species of these clustering centers with different functionality, each of which connects a fixed…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
Since constraints hinder the application of numerical algorithms, phase diagrams of quantum dimer models are still controversial, even on the square lattice. The core controversy is whether the mixed state exists. In this article, we give…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
We investigate a lattice model of polymers where the nearest-neighbour monomer-monomer interaction strengths differ according to whether the local configurations have so-called ``hydrogen-like'' formations or not. If the interaction…
The dynamics of polymer decompression, i.e., a process from compressed, compact state to the relaxed swoll en conformation, can be formally described as a {\it nonlinear diffusion}. We discuss here two basic examples: (i) the expansion, or…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
The recently proposed excitonic renormalization framework presents an alternative ansatz to elec- tronic structure theory of weakly interacting fragments. It makes use of absolutely localized orbitals and correlated states evaluated on…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…
The kinetic behavior of a phase field model of electrochemistry is explored for advancing (electrodeposition) and receding (electrodissolution) conditions in one dimension. We described the equilibrium behavior of this model in [J. E.…
The phase diagram of the quantum dimer model on the hexagonal (honeycomb) lattice is computed numerically, extending on earlier work by Moessner, Sondhi, and Chandra. The different ground state phases are studied in detail using several…