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Marcello Sega

Publications and source records attributed to Marcello Sega.

35 records · Page 2Linked to original sources
arXiv2019

Atomistic simulation of PDADMAC/PSS oligoelectrolyte multilayers: overall comparison of tri- and tetra-layer systems

By employing large-scale molecular dynamics simulations of atomistically resolved oligoelectrolytes in aqueous solutions, we study in detail the first four layer-by-layer deposition cycles of an oligoelectrolyte multilayer made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS). The multilayers are grown on a silica substrate in 0.1M {NaCl} electrolyte solutions and the swollen structures are then subsequently exposed to varying added salt concentration. We investigated the microscopic properties of the films, analyzing in detail the differences between three- and four-layers systems. Our simulations provide insights on the early stages of growth of a multilayer, which are particularly challenging for experimental observations. We found a rather strong entanglement of the oligoelectrolytes, with a fuzzy layering of the film structure. The main charge compensation mechanism is for all cases intrinsic, whereas extrinsic compensation is relatively ehanced for the layer of the last deposition cycle. In addition, we quantified other fundamental observables of these systems, as the film thickness, water uptake, and overcharge fractions for each deposition layer.

cond-mat.soft↗
arXiv2018

A simple approximation for the distribution of ions between charged plates in the weak coupling regime

The solution of the Poisson--Boltzmann equation for counterions confined between two charged plates is known analytically up to a constant, namely, the ion density in the middle of the channel. This quantity is relevant also because it gives access, through the contact theorem, to the osmotic pressure of the system. Here we compare the values of the ion density obtained by numerical and simulation approaches, and report a useful analytic approximation for the weak coupling regime in the absence of added salt, which predicts the value of the ion density in the worst case within 5%. The inclusion of higher order terms in a Laurent expansion can further improve the accuracy, at the expense of simplicity.

physics.comp-ph↗
arXiv2017

Pressure Profile Calculation with Mesh Ewald Methods

The importance of calculating pressure profiles across liquid interfaces is increasingly gaining recognition, and efficient methods for the calculation of long-range contributions are fundamental in addressing systems with a large number of charges. Here, we show how to compute the local pressure contribution for mesh-based Ewald methods, retaining the typical N log N scaling as a function of the lattice nodes N. This is a considerable improvement on existing methods, which include approximating the electrostatic contribution using a large cut-off and the, much slower, Ewald calculation. As an application, we calculate the contribution to the pressure profile across the water/vapour interface, coming from different molecular layers, both including and removing the effect of thermal capillary waves. We compare the total pressure profile with the one obtained using the cutoff approximation for the calculation of the stresses, showing that the stress distribution obtained by the Harasima and Irving-Kirkwood are quite similar and shifted with respect to each other at most 0.05~nm.

cond-mat.soft↗
arXiv2016

Long-range dispersion effects on the water/vapor interface simulated using the most common models

The long-range contribution to dispersion forces is known to have a major impact on the properties of inhomogeneous fluids, and its correct treatment is increasingly recognized as being a necessary requirement to avoid cutoff-related artefacts. Although analytical corrections for quantities like the surface tension are known, these can not take into account the structural changes induced by the long-range contributions. Here, we analyze the interfacial properties of seven popular water models, comparing the results with the cut-off version of the dispersion potential. The differences in surface tension estimates are in all cases found to be less than 2 mN/m.

cond-mat.soft↗
arXiv2015

The importance of chemical potential in the determination of water slip in nanochannels

We investigate the slip properties of water confined in graphite-like nano-channels by non-equilibrium molecular dynamics simulations, with the aim of identifying and analyze separately the influence of different physical quantities on the slip length. In a system under confinement but connected to a reservoir of fluid, the chemical potential is the natural control parameter: we show that two nanochannels characterized by the same macroscopic contact angle -- but a different microscopic surface potential -- do not exhibit the same slip length unless the chemical potential of water in the two channels is matched. Some methodological issues related to the preparation of samples for the comparative analysis in confined geometries are also discussed.

cond-mat.mes-hall↗
arXiv2014

Kinetic dielectric decrement revisited: phenomenology of finite ion concentrations

With the help of a recently developed non-equilibrium approach, we investigate the ionic strength dependence of the Hubbard--Onsager dielectric decrement. We compute the depolarization of water molecules caused by the motion of ions in sodium chloride solutions from the dilute regime (0.035 M) up close to the saturation concentration (4.24 M), and find that the kinetic decrement displays a strong nonmonotonic behavior, in contrast to the prediction of available models. We introduce a phenomenological modification of the Hubbard--Onsager continuum theory, that takes into account the screening due to the ionic cloud at mean field level, and, is able to describe the kinetic decrement at high concentrations including the presence of a pronounced minimum.

cond-mat.soft↗
arXiv2014

Layer-by-layer formation of oligoelectrolyte multilayers: a combined experimental and computational study

For the first time, the combination of experimental preparation and results of fully atomistic simulations of an oligoelectrolyte multilayer (OEM) made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS) is presented. The layer-by-layer growth was carried out by dipping silica substrates in oligoelectrolyte solutions and was modeled by means of atomistic molecular dynamics simulations with a protocol that mimics the experimental procedure up to the assembly of four layers. Measurements of OEM thickness, surface roughness and amount of adsorbed oligoelectrolyte chains obtained from both approaches are compared. A good agreement between simulated and experimental results was found, with some deviations due to intrinsic limitations of both methods. However, the combination of information extracted from simulations to support the analysis of experimental data can overcome such restrictions and improve the interpretation of experimental results. On the other hand, processes dominated by slower kinetics, like the destabilization of adsorbed layers upon equilibration with the surrounding environment, are out of reach for the simulation modeling approach, but they can be investigated by monitoring in situ the oligoelectrolyte adsorption during the assembly process. This demonstrates how the synergistic use of simulation and experiments improves the knowledge of OEM properties down to the molecular scale.

cond-mat.soft↗
arXiv2014

Kinetic and ion pairing contributions in the dielectric spectra of electrolyte aqueous solutions

Understanding dielectric spectra can reveal important information about the dynamics of solvents and solutes from the dipolar relaxation times down to electronic ones. In the late 1970s, Hubbard and Onsager predicted that adding salt ions to a polar solution would result in a reduced dielectric permittivity that arises from the unexpected tendency of solvent dipoles to align opposite to the applied field. So far, this effect has escaped an experimental verification, mainly because of the concomitant appearance of dielectric saturation from which the Hubbard-Onsager decrement cannot be easily separated. Here we develop a novel non-equilibrium molecular dynamics simulation approach to determine this decrement accurately for the first time. Using a thermodynamic consistent all-atom force field we show that for an aqueous solution containing sodium chloride around 4.8 Mol/l, this effect accounts for 12\% of the total dielectric permittivity. The dielectric decrement can be strikingly different if a less accurate force field for the ions is used. Using the widespread GROMOS parameters, we observe in fact an {\it increment} of the dielectric permittivity rather than a decrement. We can show that this increment is caused by ion pairing, introduced by a too low dispersion force, and clarify the microscopic connection between long-living ion pairs and the appearance of specific features in the dielectric spectrum of the solution.

cond-mat.soft↗
arXiv2014

Regularization of the slip length divergence in water nanoflows by inhomogeneities at the Angstrom scale

We performed non-equilibrium Molecular Dynamics simulations of water flow in nano-channels with the aim of discriminating {\it static} from {\it dynamic} contributions of the solid surface to the slip length of the molecular flow. We show that the regularization of the slip length divergence at high shear rates, formerly attributed to the wall dynamics, is controlled instead by its static properties. Surprisingly, we find that atomic displacements at the Angstrom scale are sufficient to remove the divergence of the slip length and realize the no-slip condition. Since surface thermal fluctuations at room temperature are enough to generate these displacements, we argue that the no-slip condition for water can be achieved also for ideal surfaces, which do not present any surface roughness.

cond-mat.soft↗
arXiv2014

Mesoscale Structures at Complex Fluid-Fluid Interfaces: a Novel Lattice Boltzmann / Molecular Dynamics Coupling

Complex fluid-fluid interfaces featuring mesoscale structures with adsorbed particles are key components of newly designed materials which are continuously enriching the field of soft matter. Simulation tools which are able to cope with the different scales characterizing these systems are fundamental requirements for efficient theoretical investigations. In this paper we present a novel simulation method, based on the approach of Ahlrichs and Dünweg [Ahlrichs and Dünweg, Int. J. Mod. Phys. C, 1998, 9, 1429], that couples the "Shan-Chen" multicomponent Lattice Boltzmann technique to off-lattice molecular dynamics to simulate efficiently complex fluid-fluid interfaces. We demonstrate how this approach can be used to study a wide class of challenging problems. Several examples are given, with an accent on bicontinuous phases formation in polyelectrolyte solutions and ferrofluid emulsions. We also show that the introduction of solvation free energies in the particle-fluid interaction unveils the hidden, multiscale nature of the particle-fluid coupling, allowing to treat symmetrically (and interchangeably) the on-lattice and off-lattice components of the system.

cond-mat.soft↗
arXiv2012

Identifying interfacial molecules in nonplanar interfaces: the generalized ITIM algorithm

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the alpha-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a DPC and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface

cond-mat.soft↗
arXiv2010

Puckering Free Energy of Pyranoses: an NMR and Metadynamics--Umbrella Sampling Investigation

We present the results of a combined metadynamics--umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer--Pople puckering coordinates has been calculated for the whole series of alpha and beta aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the gromos 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformers populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

physics.chem-ph↗
arXiv2010

Influence of pore dielectric boundaries on the translocation barrier of DNA

We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model DNA segment by evaluating the potential of mean force in absence and presence of polarization effects by means of coarse-grained molecular dynamics simulations. The effect of induced polarization charges has been taken into account by employing ICC*, a recently developed algorithm that can efficiently compute induced polarization charges induced on suitably discretized dielectric boundaries. Since water has a higher dielectric constant than the pore walls, polarization effects repel charged objects in the vicinity of the interface, with the effect of significantly increasing the free energy barrier. Another investigated side effect is the change of the counterion distribution around the charged polymer in presence of the induced pore charges. Furthermore we investigate the influence of adding salt to the solution.

cond-mat.soft↗
arXiv2009

Mesoscopic simulations of the counterion-induced electroosmotic flow - a comparative study

We present mesoscopic simulations of the counterion-induced electroosmotic flow in different electrostatic coupling regimes. Two simulation methods are compared, Dissipative Particle Dynamics (DPD) and coupled Lattice-Boltzmann/Molecular Dynamics (LB/MD). A general mapping scheme to match DPD to LB/MD is developed. For the weak-coupling regime, analytic expressions for the flow profiles in the presence of partial-slip as well as no-slip boundary conditions are derived from the Poisson-Boltzmann and Stokes equations, which are in good agreement with the numerical results. The influence of electrofriction and partial slip on the flow profiles is discussed.

cond-mat.other↗
arXiv2009

On the Calculation of Puckering Free Energy Surfaces

Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds, and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artefacts that are generated when a wrong parametrization is used.

physics.chem-ph↗
arXiv2008

Kramers Theory for Conformational Transitions of Macromolecules

We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space. We present a method which identifies the transition state along the most probable reaction pathway. It is then possible to microscopically compute the activation energy, the damping coefficient, the eigenfrequencies at the transition state and obtain the rate, without any a-priori choice of a reaction coordinate. Our theoretical results are tested against the results of Molecular Dynamics simulations for transitions in a 2-dimensional double well and for the cis-trans isomerization of a linear molecule.

q-bio.BM↗