Related papers: Kinetically driven helix formation during the homo…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
The biopolymers actin and microtubules are often in an ongoing assembling/disassembling state far from thermal equilibrium. Above a critical density this leads to spatially periodic patterns, as shown by a scaling argument and in terms of a…
We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order…
The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The…
We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that…
Using Langevin simulations we examine driven colloids interacting with quenched disorder. For weak substrates the colloids form an ordered state and depin elastically. For increasing substrate strength we find a sharp crossover to…
We study the dynamics of an heteropolymeric chain relaxing toward a new equilibrium configuration after the action of an external perturbation. We compare the results from Monte Carlo simulations with the results of a Langevin normal mode…
When liquid-crystal elastomers are prepared without any alignment, disordered polydomain structures emerge as the materials are cooled into the nematic phase. These polydomain structures have been attributed to quenched disorder in the…
In order to understand the possible sequence of transitions from the disordered columnar phase to the helical phase in hexa(hexylthio)triphenylene (HHTT), we study a three-dimensional planar model with octupolar interactions inscribed on a…
Liquid-liquid crystal phase separation (LLCPS) occurs in many industrial and biological settings. To date the states of the separated condensed liquid crystals have been found to be nematic, columnar, or smectic phases. Interestingly, when…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
Recent (Bose \& Durbin, \textit{Phys. Rev. Fluids}, 1, 073602, 2016) direct numerical simulations (DNS) of adverse- and zero-pressure-gradient boundary layers beneath moderate levels of free stream turbulence ($Tu$ $\le 2\%$) revealed a…
Freestanding tubular crystals offer a general description of crystalline order on deformable surfaces with cylindrical topology, such as single-walled carbon nanotubes, microtubules, and recently reported colloidal assemblies. These systems…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
We consider crystal formation of particles with dipole-dipole interactions that are confined to move in a one-dimensional helical geometry with their dipole moments oriented along the symmetry axis of the confining helix. The stable…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the…
Colloidal particles moving in a fluid interact via the induced velocity field. The collective dynamic state for a class of actively forced colloids, driven by harmonic potentials via a rule that couples forces to configurations, to perform…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…