Yukawa potentials in systems with partial periodic boundary conditions II : Lekner sums for quasi-two dimensional systems

Yukawa potentials may be long ranged when the Debye screening length is large. In computer simulations, such long ranged potentials have to be taken into account with convenient algorithms to avoid systematic bias in the sampling of the phase space. Recently, we have provided Ewald sums for quasi-two dimensional systems with Yukawa interaction potentials [M. Mazars, {\it J. Chem. Phys.}, {\bf 126}, 056101 (2007) and M. Mazars, {\it Mol. Phys.}, Paper I]. Sometimes, Lekner sums are used as an alternative to Ewald sums for Coulomb systems. In the present work, we derive the Lekner sums for quasi-two dimensional systems with Yukawa interaction potentials and we give some numerical tests for pratical implementations. The main result of this paper is to outline that Lekner sums cannot be considered as an alternative to Ewald sums for Yukawa potentials. As a conclusion to this work : Lekner sums should not be used for quasi-two dimensional systems with Yukawa interaction potentials.Comment: 25 pages, 5 figures and 1 tabl

Holonomic constraints : an analytical result

Systems subjected to holonomic constraints follow quite complicated dynamics that could not be described easily with Hamiltonian or Lagrangian dynamics. The influence of holonomic constraints in equations of motions is taken into account by using Lagrange multipliers. Finding the value of the Lagrange multipliers allows to compute the forces induced by the constraints and therefore, to integrate the equations of motions of the system. Computing analytically the Lagrange multipliers for a constrained system may be a difficult task that is depending on the complexity of systems. For complex systems, it is most of the time impossible to achieve. In computer simulations, some algorithms using iterative procedures estimate numerically Lagrange multipliers or constraint forces by correcting the unconstrained trajectory. In this work, we provide an analytical computation of the Lagrange multipliers for a set of linear holonomic constraints with an arbitrary number of bonds of constant length. In the appendix of the paper, one would find explicit formulas for Lagrange multipliers for systems having 1, 2, 3, 4 and 5 bonds of constant length, linearly connected.Comment: 13 pages, no figures. To appear in J. Phys. A : Math. The

Bond Orientational Order Parameters in the Crystalline Phases of the Classical Yukawa-Wigner Bilayers

We present a study of the structural properties of the crystalline phases for a planar bilayer of particles interacting via repulsive Yukawa potentials in the weak screening region. The study is done with Monte Carlo computations and the long ranged contributions to energy are taken into account with the Ewald method for quasi-two dimensional systems. Two first order phase transitions (fluid-solid and solid-solid) and one second order transition (solid-solid) are found when the surface density is varied at constant temperature. A particular attention is pay to the characteristics of the crystalline phases by the analysis of bond orientational order parameters and center-to-center correlations functions.Comment: 6 pages, 6 figures, 2 table

Yukawa potentials in systems with partial periodic boundary conditions I : Ewald sums for quasi-two dimensional systems

Yukawa potentials are often used as effective potentials for systems as colloids, plasmas, etc. When the Debye screening length is large, the Yukawa potential tends to the non-screened Coulomb potential ; in this small screening limit, or Coulomb limit, the potential is long ranged. As it is well known in computer simulation, a simple truncation of the long ranged potential and the minimum image convention are insufficient to obtain accurate numerical data on systems. The Ewald method for bulk systems, i.e. with periodic boundary conditions in all three directions of the space, has already been derived for Yukawa potential [cf. Y., Rosenfeld, {\it Mol. Phys.}, \bm{88}, 1357, (1996) and G., Salin and J.-M., Caillol, {\it J. Chem. Phys.}, \bm{113}, 10459, (2000)], but for systems with partial periodic boundary conditions, the Ewald sums have only recently been obtained [M., Mazars, {\it J. Chem. Phys.}, {\bf 126}, 056101 (2007)]. In this paper, we provide a closed derivation of the Ewald sums for Yukawa potentials in systems with periodic boundary conditions in only two directions and for any value of the Debye length. A special attention is paid to the Coulomb limit and its relation with the electroneutrality of systems.Comment: 40 pages, 5 figures and 4 table

Structure and thermodynamics of a ferrofluid bilayer

We present extensive Monte Carlo simulations for the thermodynamic and structural properties of a planar bilayer of dipolar hard spheres for a wide range of densities, dipole moments and layer separations. Expressions for the stress and pressure tensors of the bilayer system are derived. For all thermodynamic states considered the interlayer energy is shown to be attractive and much smaller than the intralayer contribution to the energy. It vanishes at layer separations of the order of two hard sphere diameters. The normal pressure is negative and decays as a function of layer separation $h$ as $-1/h^5$. Intralayer and interlayer pair distribution functions and angular correlation functions are presented. Despite the weak interlayer energy strong positional and orientational correlations exist between particles in the two layers.Comment: 45 pages, 4 Tables, 9 Figure

Antiviral and Anti-Inflammatory Activities of Fluoxetine in a SARS-CoV-2 Infection Mouse Model

Introduction The coronavirus disease 2019 (COVID-19) pandemic continues to cause significant morbidity and mortality worldwide. Since a large portion of the world’s population is currently unvaccinated or incompletely vaccinated and has limited access to approved treatments against COVID-19, there is an urgent need to continue research on treatment options, especially those at low cost and which are immediately available to patients, particularly in low- and middle-income countries. Prior in vitro and observational studies have shown that fluoxetine, possibly through its inhibitory effect on the acid sphingomyelinase/ceramide system, could be a promising antiviral and anti-inflammatory treatment against COVID-19. Objectives The aim of this sudy was to test the potential antiviral and anti-inflammatory activities of fluoxetine against SARS-CoV-2 in a K18-hACE2 mouse model of infection, and against several variants of concern in vitro, and test the hypothesis of the implication of ceramides and/or their derivatives hexosylceramides. Methods We evaluated the potential antiviral and anti-inflammatory activities of fluoxetine in a K18-hACE2 mouse model of SARS-CoV-2 infection, and against variants of concern in vitro, i.e., SARS-CoV-2 ancestral strain, Alpha B.1.1.7, Gamma P1, Delta B1.617 and Omicron BA.5. Results Fluoxetine, administrated after SARS-CoV-2 infection, significantly reduced lung tissue viral titres (Figure 1) and expression of several inflammatory markers (i.e., IL-6, TNFα, CCL2 and CXCL10) (Figure 2). It also inhibited the replication of all variants of concern in vitro. A modulation of the ceramide system in the lung tissues, as reflected by the increase in the ratio HexCer 16:0/Cer 16:0 in fluoxetine-treated mice, may contribute to explain these effects (Figure 3). Conclusions Our findings demonstrate the antiviral and anti-inflammatory properties of fluoxetine in a K18-hACE2 mouse model of SARS-CoV-2 infection, and its in vitro antiviral activity against variants of concern, establishing fluoxetine as a very promising candidate for the prevention and treatment of SARS-CoV-2 infection and disease pathogenesis

Finite group actions on reductive groups and buildings and tamely-ramified descent in Bruhat-Tits theory

The purpose of the paper is to give a new approach to tamely-ramified descent in Bruhat-Tits theory. This descent was first studied by Guy Rousseau in his thesis.Comment: 28 pages. arXiv admin note: text overlap with arXiv:1611.0743

Linearly scaling direct method for accurately inverting sparse banded matrices

In many problems in Computational Physics and Chemistry, one finds a special kind of sparse matrices, termed "banded matrices". These matrices, which are defined as having non-zero entries only within a given distance from the main diagonal, need often to be inverted in order to solve the associated linear system of equations. In this work, we introduce a new O(n) algorithm for solving such a system, being n X n the size of the matrix. We produce the analytical recursive expressions that allow to directly obtain the solution, as well as the pseudocode for its computer implementation. Moreover, we review the different options for possibly parallelizing the method, we describe the extension to deal with matrices that are banded plus a small number of non-zero entries outside the band, and we use the same ideas to produce a method for obtaining the full inverse matrix. Finally, we show that the New Algorithm is competitive, both in accuracy and in numerical efficiency, when compared to a standard method based in Gaussian elimination. We do this using sets of large random banded matrices, as well as the ones that appear when one tries to solve the 1D Poisson equation by finite differences.Comment: 24 pages, 5 figures, submitted to J. Comp. Phy

Efficient and reliable nonlocal damage models

We present an efficient and reliable approach for the numerical modelling of failure with nonlocal damage models. The two major numerical challenges––the strongly nonlinear, highly localized and parameter-dependent structural response of quasi-brittle materials, and the interaction between nonadjacent finite elements associated to nonlocality––are addressed in detail. Reliability of the numerical results is ensured by an h-adaptive strategy based on error estimation. We use a residual-type error estimator for nonlinear FE analysis based on local computations, which, at the same time, accounts for the nonlocality of the damage model. Efficiency is achieved by a proper combination of load-stepping control technique and iterative solver for the nonlinear equilibrium equations. A major issue is the computation of the consistent tangent matrix, which is nontrivial due to nonlocal interaction between Gauss points. With computational efficiency in mind, we also present a new nonlocal damage model based on the nonlocal average of displacements. For this new model, the consistent tangent matrix is considerably simpler to compute than for current models. The various ideas discussed in the paper are illustrated by means of three application examples: the uniaxial tension test, the three-point bending test and the single-edge notched beam test.Peer ReviewedPostprint (author’s final draft