No Arabic abstract
We present a new model of sequential adsorption in which the adsorbing particles experience dipolar interactions. We show that in the presence of these long-range interactions, highly ordered structures in the adsorbed layer may be induced at low temperatures. The new phenomenology manifests through significant variations of the pair correlation function and the jamming limit, with respect to the case of noninteracting particles. Our study could be relevant in understanding the adsorption of magnetic colloidal particles in presence of a magnetic field.
A class of non-local contact processes is introduced and studied using mean-field approximation and numerical simulations. In these processes particles are created at a rate which decays algebraically with the distance from the nearest particle. It is found that the transition into the absorbing state is continuous and is characterized by continuously varying critical exponents. This model differs from the previously studied non-local directed percolation model, where particles are created by unrestricted Levy flights. It is motivated by recent studies of non-equilibrium wetting indicating that this type of non-local processes play a role in the unbinding transition. Other non-local processes which have been suggested to exist within the context of wetting are considered as well.
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes - we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e., communication between CPUs is possible by directly reading from or writing to other CPUs local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.
We study the stochastic dynamics of an electrolyte driven by a uniform external electric field and show that it exhibits generic scale invariance despite the presence of Debye screening. The resulting long-range correlations give rise to a Casimir-like fluctuation-induced force between neutral boundaries that confine the ions; this force is controlled by the external electric field, and it can be both attractive and repulsive with similar boundary conditions, unlike other long-range fluctuation-induced forces. This work highlights the importance of nonequilibrium correlations in electrolytes and shows how they can be used to tune interactions between uncharged biological or synthetic structures at large separations.
We use a computational model to investigate the emergence of interaction forces between pairs of intruders in a horizontally vibrated granular fluid. The time evolution of a pair of particles shows a maximum of the likelihood to find the pair at contact in the direction of shaking. This relative interaction is further studied by fixing the intruders in the simulation box where we identify effective mechanical forces, and torques between particles and quantify an emergent long range attractive force as a function of the shaking relative angle, amplitude, and the packing density of grains. We determine the local density and kinetic energy profiles of granular particles along the axis of the dimer to find no gradients in the density fields and additive gradients in the kinetic energies.
Many-body localization (MBL) behavior is analyzed {in an extended Bose-Hubbard model with quasiperiodic infinite-range interactions. No additional disorder is present. Examining level statistics and entanglement entropy of eigenstates we show that a significant fraction of eigenstates of the system is localized in the presence of strong interactions. In spite of this, our results suggest that the system becomes ergodic in the standard thermodynamic limit in which the energy of the system is extensive. At the same time, the MBL regime seems to be stable if one allows for a super-extensive scaling of the energy. We show that our findings can be experimentally verified by studies of time dynamics in many-body cavity quantum electrodynamics setups. The quench spectroscopy is a particularly effective tool that allows us to systematically study energy dependence of time dynamics and to investigate a mobility edge in our system.