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Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
We calculate the magnetization of a two-dimensional superconductor in a perpendicular magnetic field near its Kosterlitz-Thouless transition and at lower temperatures. We find that the critical behavior is more complex than assumed in the…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
A coarsened model for a binary system with limited miscibility of components is proposed; the system is described in terms of structural states in small parts of the material. The material is assumed to have two alternative types of…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Phase transitions and their associated crossovers are imprinted in the behavior of fluctuations. Motivated by recent experiments on ultracold atoms in optical lattices, we compute the thermodynamic density fluctuations $\delta N^2$ of the…
We consider the dynamics of a periodic chain of N coupled overdamped particles under the influence of noise, in the limit of large N. Each particle is subjected to a bistable local potential, to a linear coupling with its nearest…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
We perform molecular dynamics and Monte Carlo simulations of two-dimensional melting with dipole-dipole interactions. Both static and dynamic behaviors are examined. In the isotropic liquid phase, the bond orientational correlation length 6…
Particle transport through an open, discrete 1-D channel against a mechanical or chemical bias is analyzed within a master equation approach. The channel, externally driven by time dependent site energies, allows multiple occupation due to…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible…
The study of interdependent networks has recently experienced a boost with the development of experimentally testable materials that physically realize their critical behaviors, calling for systematic studies that go beyond the percolation…
The competition among reaction processes of a weakly-bound projectile at intermediate times of a slow collision has been unraveled. This has been done using a two-center molecular continuum within a semiclassical, time-dependent…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
Depletion interactions between colloidal particles dispersed in a fluid medium are effective interactions induced by the presence of other types of colloid. They are not instantaneous but build up in time. We show by means Brownian dynamics…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
The formation of molecules and supramolecular structures results from bonding by conservative forces acting among electrons and nuclei and giving rise to equilibrium configurations defined by minima of the interaction potential. Here we…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. The problem is…