Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes

Recent studies have shown the possibility of water transport across carbon nanotubes, even in the case of nanotubes with small diameter (0.822 nm). In this case, water shows subcontinuum transport following an ordered 1D structure stabilized by hydrogen bonds. In this work, we report MD simulations describing the effect of a perpendicular electric field in this single-file water transport in carbon nanotubes. We show that water permeation is substantially reduced for field intensities of 2-3 V/nm and it is no longer possible under perpendicular fields of 4 V/nm.Comment: Accepted in Molecular Simulatio

Computer Simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.This work was supported by the Spanish Ministry of Science and Innovation through grant RTI2018-096273-B-I00 and the “Severo Ochoa” Grant SEV-2015-0496 for Centres of Excellence in R&D awarded to ICMAB. We thank the CESGA supercomputing center for computer time and technical support at the Finisterrae supercomputer. D. C. Malaspina is supported by the European Union Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No. 6655919.Peer reviewe

Computer simulation study of irreversible adsorption : coverage fluctuations

In this paper, we develop a cellular automata model to study the coverage fluctuations in monolayers of irreversible adsorbed particles. The effect of bulk diffusion and excluded volume interactions between adsorbed and incoming particles on coverage fluctuations is analyzed by simulations and analytically. We also show that the macroscopic boundary and initial conditions imposed at the system (open or closed cell) determine the effect of these factors on coverage fluctuations. In fact, under certain conditions, the excluded volume interactions only influence fluctuations near the jamming limit

Ion transport through biological channels

The transport of ions across single-molecule protein nanochannels is important both in the biological context and in proposed nanotechnological applications. Here we discuss these systems from the perspective of non-equilibrium physics, and in particular, whether the concepts underlying the physics of diffusive and electrokinetic transport can be employed to predict and understand these systems.This work was supported by the Spanish Government (grant FIS2011-1305 1-E) and of University Jaume I grant P1·1B2012-16

Molecular Dynamics simulations of concentrated aqueous electrolyte solutions

Transport properties of concentrated electrolytes have been analyzed using classical molecular dynamics simulations with the algorithms and parameters typical of simulations describing complex electrokinetic phenomena. The electrical conductivity and transport numbers of electrolytes containing monovalent (KCl), divalent (MgCl$_2$), a mixture of both (KCl + MgCl$_2$), and trivalent (LaCl$_3$) cations have been obtained from simulations of the electrolytes in electric fields of different magnitude. The results obtained for different simulation parameters have been discussed and compared with experimental measurements of our own and from the literature. The electroosmotic flow of water molecules induced by the ionic current in the different cases has been calculated and interpreted with the help of the hydration properties extracted from the simulations

On-the-fly coarse-graining methodology for the simulation of chain formation of superparamagnetic colloids in strong magnetic fields

The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG) model. Within this approach, the coarse grain objects of the simulation are not fixed a priori at the beginning of the simulation but rather redefined on the fly. The motion of the CG objects (single particles or aggregates) is described by an anisotropic diffusion model and the magnetic dipole-dipole interaction is replaced by an effective short range interaction between CG objects. The new methodology correctly reproduces previous results from detailed Langevin Dynamics simulations of dispersions of superparamagnetic colloids under strong fields whilst requiring an amount of CPU time orders of magnitude smaller. This substantial improvement in the computational requirements allows the simulation of problems in which the relevant phenomena extends to time scales inaccessible with previous simulation techniques. A relevant example is the waiting time dependence of the relaxation time T_2 of water protons observed in Magnetic Resonance experiments containing dispersions of superparamagnetic colloids, which is correctly predicted by our simulations. Future applications may include other popular real-world applications of superparamagnetic colloids such as the magnetophoretic separation processes.Comment: 12 pages, 12 figure

Dispersions Superparamagnètiques: una visió de Física Estadística d'una nanotecnologia emergent

Els avenços en la fabricació de nous materials que presenten superparamagnetisme -un fenòmen físic que només apareix en la nanoescala- han permés el desenvolupament de noves i prometedores aplicacions en camps com ara la biotecnologia o la nanomedicina. Tot i això, les bases físiques de molts dels comportaments observats són encara poc enteses. Presentem aquí alguns avenços recents que permeten entendre millor aspectes físics bàsics d'aquests sistemes que poden ser rellevants per a dissenyar-ne més racionalment les seves aplicacions

Interaction-Limited Aggregation: Fine-Tuning the Size of pNIPAM Particles by Association with Hydrophobic Ions

We have investigated the formation of stable clusters of poly(N-isopropylacrylamide) (pNIPAM) chains in water at temperatures above the lower critical solution temperature (LCST), induced by the presence of sodium tetraphenylborate, NaPh4B. The hydrophobic Ph4B– ions interact strongly with the pNIPAM chains, providing them with a net effective negative charge, which leads to the stabilization of pNIPAM clusters for temperatures above the LCST, with a mean cluster size that depends non-monotonically on salt concentration. Combining experiments with physical modeling at the mesoscopic level and atomistic molecular dynamic simulations, we show that this effect is caused by the interplay between the hydrophobic attraction between pNIPAM chains and the electrostatic repulsion induced by the associated Ph4B– ions. These results provide insight on the significance of weak associative anion–polymer interaction driven by hydrophobic interaction and how this anionic binding can prevent macroscopic phase separation. Harvesting the competition between attractive hydrophobic and repulsive electrostatic interaction opens avenues for the dynamic control of the formation of well-calibrated polymer microparticles.Junta de AndaluciaEuropean Regional Development Fund - Consejeria de Conocimiento, Investigacion y Universidad PY20-00241Agencia de Gestio D'Ajuts Universitaris de Recerca Agaur (AGAUR) Generalitat de Catalunya PID2021- 124297NB-C33Spanish GovernmentSpanish Government through the "Severo Ochoa" Program for Centers of Excellence in RDMCIN/AEI/10.13039/501100011033 2021 SGR 01519 CEX2019-000917-