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Simone Melchionna

Publications and source records attributed to Simone Melchionna.

At least 19 recordsLinked to original sources
arXiv2023

Comparison of effective and stable Langevin dynamics integrators

Langevin and Brownian simulations play a prominent role in computational research, and state of the art integration algorithms provide trajectories with different stability ranges and accuracy in reproducing statistical averages. The practical usability of integrators is an important aspect to allow choosing large time steps while ensuring numerical stability and overall computational efficiency. In this work, different use cases and practical features are selected in order to perform a cumulative comparison of integrators with a focus on evaluating the derived velocity and position autocorrelation functions, a comparison that is often disregarded in the literature. A standard industrial open-source software methodology is suggested to compare systematically the different algorithms.

physics.comp-ph↗
arXiv2021

Three-level multilevel simulation of the neuroreceptor function of NMDA

We present a new multiscale method to study the N-Methyl-D-Aspartate (NMDA) neuroreceptor starting from the reconstruction of its crystallographic structure. Thanks to the combination of homology modelling, Molecular Dynamics and Lattice Boltzmann simulations, we analyse the allosteric transition of NDMA upon ligand binding and compute the receptor response to ionic passage across the membrane.

physics.bio-ph↗
arXiv2019

Entropic Lattice Boltzmann Model for Charged Leaky Dielectric Multiphase Fluids in Electrified Jets

We present a lattice Boltzmann model for charged leaky dielectric multiphase fluids in the context of electrified jet simulations, which are of interest for a number of production technologies including electrospinning. The role of non-linear rheology on the dynamics of electrified jets is considered by exploiting the Carreau model for pseudoplastic fluids. We report exploratory simulations of charged droplets at rest and under a constant electric field, and we provide results for charged jet formation under electrospinning conditions.

physics.comp-ph↗
arXiv2019

Mesoscopic simulations at the physics-chemistry-biology interface

We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale LBPD simulations of biopolymer translocation across cellular membranes, molecular transport in ion channels and amyloid aggregation in cells. We also provide prospects for future LBPD explorations in the direction of cellular organization, the direct simulation of full biological organelles, all the way to up to physiological scales of potential relevance to future precision-medicine applications, such as the accurate description of homeostatic processes. It is argued that, with the advent of Exascale computing, the mesoscale physics approach advocated in this paper, may come to age in the next decade and open up new exciting perspectives for physics-based computational medicine.

physics.comp-ph↗
arXiv2019

Disordered interfaces in soft fluids with suspended colloids

Computer simulations of bi-continuous two-phase fluids with intersparsed dumbbells show that, unlike rigid colloids, soft dumbbells do not lead to arrested coarsening. However, they significantly alter the curvature dynamics of the fluid-fluid interface, whose probability density distributions are shown to exhibit (i) a universal spontaneous transition from an initial broad-shape distribution towards a highly localized one and (ii) super-diffusive dynamics with long-range effects. Both features may prove useful for the design of novel families of soft porous materials.

physics.comp-ph↗
arXiv2018

Simulating Soft-Sphere Margination in Arterioles and Venules

In this paper, we deploy a Lattice Boltzmann - Particle Dynamics (LBPD) method to dissect the transport properties within arterioles and venules. First, the numerical approach is applied to study the transport of Red Blood Cells (RBC) through plasma and validated by means of comparison with the experimental data in the seminal work by Fåhræus and Lindqvist. Then, the presence of micro-scale, soft spheres within the blood flow is considered: the evolution in time of the position of such spheres is studied, in order to highlight the presence of possible \textit{margination} effects. The results of the simulations and the evaluation of the computational eff

physics.comp-ph↗
arXiv2017

Electrokinetic Lattice Boltzmann solver coupled to Molecular Dynamics: application to polymer translocation

We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our approach is based on a multiscale modeling that combines the slow dynamics of the large particles with the fast dynamics of the solvent into a unique framework. The former is numerically solved via Molecular Dynamics and the latter via a multi-component Lattice Boltzmann. The two techniques are coupled together to allow for a seamless exchange of information between the descriptions. Being based on a kinetic multi-component description of the fluid species, the scheme is flexible in modeling charge flow within complex geometries and ranging from large to vanishing salt concentration. The details of the scheme are presented and the method is applied to the problem of translocation of a charged polymer through a nanopores. In the end, we discuss the advantages and complexities of the approach.

cond-mat.soft↗
arXiv2016

Mapping Reactive Flow Patterns in Monolithic Nanoporous Catalysts

The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass transport inside the complex nano-scale architecture of porous catalyst membranes which is a multiscale problem in both the temporal and spatial domain. To address this problem, we developed a multi-scale mass transport computational framework based on the Lattice Boltzmann Method (LBM) that allows us to account for catalytic reactions at the gas-solid interface by introducing a new boundary condition. In good agreement with experiments, the simulations reveal that most catalytic reactions occur near the gas-flow facing side of the catalyst membrane if chemical reactions are fast compared to mass transport within the porous catalyst membrane.

physics.flu-dyn↗
arXiv2016

Pressure and surface tension of an active simple liquid: a comparison between kinetic, mechanical and free-energy based approaches

We discuss different definitions of pressure for a system of active spherical particles driven by a non-thermal coloured noise. We show that mechanical, kinetic and free-energy based approaches lead to the same result up to first order in the non-equilibrium expansion parameter. The first prescription is based on a generalisation of the kinetic mesoscopic virial equation and expresses the pressure exerted on the walls in terms of the average of the virial of the inter-particle forces. In the second approach, the pressure and the surface tension are identified with the volume and area derivatives, respectively, of the partition function associated with the known stationary non-equilibrium distribution of the model. The third method is a mechanical approach and is related to the work necessary to deform the system. The pressure is obtained by comparing the expression of the work in terms of local stress and strain with the corresponding expression in terms of microscopic distribution. This is determined from the force balance encoded in the Born-Green-Yvon equation. Such a method has the advantage of giving a formula for the local pressure tensor and the surface tension even in inhomogeneous situations. By direct inspection, we show that the three procedures lead to the same values of the pressure, and give support to the idea that the partition function, obtained via the unified coloured noise approximation, is more than a formal property of the system, but determines the stationary non-equilibrium thermodynamics of the model.

cond-mat.stat-mech↗
arXiv2015

Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking

The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.

physics.bio-ph↗
arXiv2015

Lattice Boltzmann Method for mixtures at variable Schmidt number

When simulating multicomponent mixtures via the Lattice Boltzmann Method, it is desirable to control the mutual diffusivity between species while maintaining the viscosity of the solution fixed. This goal is herein achieved by a modification of the multicomponent Bhatnagar-Gross-Krook (BGK) evolution equations by introducing two different timescales for mass and momentum diffusion. Diffusivity is thus controlled by an effective drag force acting between species. Numerical simulations confirm the accuracy of the method for neutral binary and charged ternary mixtures in bulk conditions. The simulation of a charged mixture in a charged slit channel show that the conductivity and electro-osmotic mobility exhibit a departure from the Helmholtz-Smoluchowski prediction at high diffusivity.

cond-mat.stat-mech↗
arXiv2015

Electro-osmotic flow in coated nanocapillaries: a theoretical investigation

Motivated by recent experiments, we present a theoretical investigation of how the electro-osmotic flow occurring in a capillary is modified when its charged surfaces are coated by charged polymers. The theoretical treatment is based on a three dimensional model consisting of a ternary fluid-mixture, representing the solvent and two species for the ions, confined between two parallel charged plates decorated by a fixed array of scatterers representing the polymer coating. The electro-osmotic flow, generated by a constant electric field applied in a direction parallel to the plates, is studied numerically by means of Lattice Boltzmann simulations. In order to gain further understanding we performed a simple theoretical analysis by extending the Stokes-Smoluchowski equation to take into account the porosity induced by the polymers in the region adjacent the walls. We discuss the nature of the velocity profiles by focusing on the competing effects of the polymer charges and the frictional forces they exert. We show evidence of the flow reduction and of the flow inversion phenomenon when the polymer charge is opposite to the surface charge. By using the density of polymers and the surface charge as control variables, we propose a phase diagram that discriminates the direct and the reversed flow regimes and determine its dependence on the ionic concentration.

cond-mat.mes-hall↗
arXiv2015

Steric modulation of ionic currents in DNA translocation through nanopores

Ionic currents accompanying DNA translocation strongly depend on molarity of the electrolyte solution and the shape and surface charge of the nanopore. By means of the Poisson-Nernst-Planck equations it is shown how conductance is modulated by the presence of the DNA intruder and as a result of competing electrostatic and confinement factors. The theoretical results reproduce quantitatively the experimental ones and are summarized in a conductance diagram that allows distinguishing the region of reduced conductivity from the region of enhanced conductivity as a function of molarity and the pore dimension.

cond-mat.soft↗
arXiv2015

Kinetic Density Functional Theory: A microscopic approach to fluid mechanics

In the present paper we give a brief summary of some recent theoretical advances in the treatment of inhomogeneous fluids and methods which have applications in the study of dynamical properties of liquids in situations of extreme confinement, such as nanopores, nanodevices, etc. The approach obtained by combining kinetic and density functional methods is microscopic, fully self-consistent and allows to determine both configurational and flow properties of dense fluids. The theory predicts the correct hydrodynamic behavior and provides a practical and numerical tool to determine how the transport properties are modified when the length scales of the confining channels are comparable with the size of the molecules. The applications range from the dynamics of simple fluids under confinement, to that of neutral binary mixtures and electrolytes where the theory in the limit of slow gradients reproduces the known phenomenological equations such as the Planck-Nernst-Poisson and the Smoluchowski equations. The approach here illustrated allows for fast numerical solution of the evolution equations for the one-particle phase-space distributions by means of the weighted density lattice Boltzmann method and is particularly useful when one considers flows in complex geometries.

cond-mat.stat-mech↗
arXiv2013

Weighted density Lattice Boltzmann approach to fluids under confinement

The Enskog-like kinetic approach, recently introduced by us to study strongly inhomogeneous flu- ids, is reconsidered in order to improve the description of the transport coefficients. The approach is based on a separation of the interaction between hydrodynamic and non-hydrodynamic parts. The latter is treated within a simple relaxation approximation. We show that, by considering the non-hydrodynamic part via a weighted density approximation, we obtain a better prediction of the transport coefficients. By virtue of the simplicity of the kinetic equation we are able to solve numer- ically the phase space distribution in the presence of inhomogeneities, such as confining surfaces, via a Lattice Boltzmann method. Analytical estimates of the importance of these corrections to the transport coefficients in bulk conditions is provided. Poiseuille flow of the hard-sphere fluid confined between two parallel smooth walls is studied and their pore-averaged properties are determined.

cond-mat.stat-mech↗
arXiv2012

Charge transport in nanochannels: a molecular theory

We introduce a theoretical and numerical method to investigate the flow of charged fluid mixtures under extreme confinement. We model the electrolyte solution as a ternary mixture, comprising two ionic species of opposite charge and a third uncharged component. The microscopic approach is based on kinetic theory and is fully self-consistent. It allows to determine configurational prop- erties, such as layering near the confining walls, and the flow properties. We show that, under appropriate assumptions, the approach reproduces the phenomenological equations used to describe electrokinetic phenomena, without requiring the introduction of constitutive equations to determine the fluxes. Moreover, we model channels of arbitrary shape and nanometric roughness, features that have important repercussions on the transport properties of these systems. Numerical simulations are obtained by solving the evolution dynamics of the one-particle phase- space distributions of each species by means of a Lattice Boltzmann method for flows in straight and wedged channels. Results are presented for the microscopic density, the velocity profiles and for the volumetric and charge flow-rates. Strong departures from electroneutrality are shown to appear at molecular level.

cond-mat.mes-hall↗
arXiv2012

Stabilized Lattice Boltzmann-Enskog method for compressible flows and its application to one and two-component fluids in nanochannels

A numerically stable method to solve the discretized Boltzmann-Enskog equation describing the behavior of non ideal fluids under inhomogeneous conditions is presented. The algorithm employed uses a Lagrangian finite-difference scheme for the treatment of the convective term and a forcing term to account for the molecular repulsion together with a Bhatnagar-Gross-Krook relaxation term. In order to eliminate the spurious currents induced by the numerical discretization procedure, we use a trapezoidal rule for the time integration together with a version of the two-distribution method of He et al. (J. Comp. Phys 152, 642 (1999)). Numerical tests show that, in the case of one component fluid in the presence of a spherical potential well, the proposed method reduces the numerical error by several orders of magnitude. We conduct another test by considering the flow of a two component fluid in a channel with a bottleneck and provide information about the density and velocity field in this structured geometry.

cond-mat.mes-hall↗