Publications
201 results found
Lee S, Brekke-Svaland G, Bresme F, 2017, Plastic deformation and twinning mechanisms in magnesian calcites: a non-equilibrium computer simulation study, Physical Chemistry Chemical Physics, Vol: 20, Pages: 1794-1799, ISSN: 1463-9076
Deformation twinning provides a mechanism for energy dissipation in crystalline structures, with important implications on the mechanical response of carbonate biogenic materials. Carbonate crystals can incorporate magnesium, e.g. in the sea, modifying their elastic response significantly. We present a full atom computational investigation of the dependence of the twinning response of calcite with magnesium content, covering compositions compatible with three main structures, calcite, dolomite and magnesite. We find, in agreement with experiments that the incorporation of magnesium disfavors twinning as a dissipation mechanism in ordered structures (dolomite, magnesite), however the response is strongly dependent on the arrangement of the magnesium ions in the crystal structure. We show that structures with a high content of magnesium (>33%) in a disordered arrangement, lead to plastic response before twinning or fracturing. We demonstrate that the position of the magnesium ions plays a key role in the determination of the crystal deformation mode. This observation is correlated with the formation of percolation clusters of magnesium in magnesian calcites.
Niether D, Di Lecce S, Bresme F, et al., 2017, Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation., Physical Chemistry Chemical Physics, Vol: 20, Pages: 1012-1020, ISSN: 1463-9076
Urea is widely used as a protein denaturant in aqueous solutions. Experimental and computer simulation studies have shown that it dissolves in water almost ideally at high concentrations, introducing little disruption in the water hydrogen bonded structure. However, at concentrations of the order of 5 M or higher, urea induces denaturation in a wide range of proteins. The origin of this behaviour is not completely understood, but it is believed to stem from a balance between urea-protein and urea-water interactions, with urea becoming possibly hydrophobic at a specific concentration range. The small changes observed in the water structure make it difficult to connect the denaturation effects to the solvation properties. Here we show that the exquisite sensitivity of thermodiffusion to solute-water interactions allows the identification of the onset of hydrophobicity of urea-water mixtures. The hydrophobic behaviour is reflected in a sign reversal of the temperature dependent slope of the Soret coefficient, which is observed, both in experiments and non-equilibrium computer simulations at ∼5 M concentration of urea in water. This concentration regime corresponds to the one where abrupt changes in the denaturation of proteins are commonly observed. We show that the onset of hydrophobicity is intrinsically connected to the urea-water interactions. Our results allow us to identify correlations between the Soret coefficient and the partition coefficient, log P, hence establishing the thermodiffusion technique as a powerful approach to study hydrophobicity.
Wang S, Bresme F, 2017, Simulation Studies on the Lipid Interaction and Conformation of Novel Drug-Delivery Pseudopeptidic Polymers, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 121, Pages: 9113-9125, ISSN: 1520-6106
Pseudopeptides based on poly(l-lysine isophthalamide) backbone have emerged as promising drug delivery candidates due to their pH-activated membrane disruption ability. To gain molecular understanding on these novel polymeric species, we have constructed force-field parameters and simulated the behaviors of polymers with and without phenylalanine grafted as side chains under conditions compatible with different pHs. The free energy changes upon polymer permeation through membrane were calculated using the umbrella sampling technique. We show that both polymers with and without grafts interact better with the membrane under conditions compatible with lower pH. The conformational states of the polymers were investigated in water and at a water–membrane interface. On the basis of Markov state modeling results, we propose a possible advantage of the grafted polymer over the ungrafted polymer for membrane rupture because of its quicker conformational rearrangement kinetics.
Muscatello J, Chacon E, Tarazona P, et al., 2017, Deconstructing Temperature Gradients across Fluid Interfaces: The Structural Origin of the Thermal Resistance of Liquid-Vapor Interfaces, PHYSICAL REVIEW LETTERS, Vol: 119, ISSN: 0031-9007
The interfacial thermal resistance determines condensation-evaporation processes and thermal transport across material-fluid interfaces. Despite its importance in transport processes, the interfacial structure responsible for the thermal resistance is still unknown. By combining nonequilibrium molecular dynamics simulations and interfacial analyses that remove the interfacial thermal fluctuations we show that the thermal resistance of liquid-vapor interfaces is connected to a low density fluid layer that is adsorbed at the liquid surface. This thermal resistance layer (TRL) defines the boundary where the thermal transport mechanism changes from that of gases (ballistic) to that characteristic of dense liquids, dominated by frequent particle collisions involving very short mean free paths. We show that the thermal conductance is proportional to the number of atoms adsorbed in the TRL, and hence we explain the structural origin of the thermal resistance in liquid-vapor interfaces.
Tascini AS, Chen R, Seddon JM, et al., 2017, How wettable is the skin surface?, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S232-S232, ISSN: 0175-7571
Fajardo OY, Bresme F, Kornyshev AA, et al., 2017, Water in Ionic Liquid Lubricants: Friend and Foe, ACS NANO, Vol: 11, Pages: 6825-6831, ISSN: 1936-0851
To a greater or lesser extent, most room-temperature ionic liquids (RTILs) absorb water from humid air. Penetration of water into the lubricating nanoscale film may affect its equilibrium structure and dynamic properties and thus influence the ability of RTILs as lubricants to reduce friction between solid surfaces. Here we investigate the impact of hydration on lubrication using nonequilibrium molecular dynamics simulations. Water adsorption changes both the ionic liquid molecules’ orientation and the slip conditions at the solid–liquid interfaces, resulting in a reduced resistance against squeezing-out of the lubricant by an external load. For the same normal load, the film becomes thinner when water is present. We show that even small amounts of water can screen the electrostatic interactions between the ions, making RTILs more “fluid” and compressible and hence less resistant to external stress. The impact that screening has on friction involves several aspects that are systematically analyzed in this paper.
Di Lecce S, Albrecht T, Bresme F, 2017, A computational approach to calculate the heat of transport of aqueous solutions, Scientific Reports, Vol: 7, ISSN: 2045-2322
Thermal gradients induce concentration gradients in alkali halide solutions, and the salt migrates towards hot or cold regionsdepending on the average temperature of the solution. This effect has been interpreted using the heat of transport, whichprovides a route to rationalize thermophoretic phenomena. Early theories provide estimates of the heat of transport at infinitedilution. These values are used to interpret thermodiffusion (Soret) and thermoelectric (Seebeck) effects. However, accessingheats of transport of individual ions at finite concentration remains an outstanding question both theoretically and experimentally.Here we discuss a computational approach to calculate heats of transport of aqueous solutions at finite concentrations, andapply our method to study lithium chloride solutions at concentrations>0.5M. The heats of transport are significantly differentfor Li+and Cl−ions, unlike what is expected at infinite dilution. We find theoretical evidence for the existence of minima in theSoret coefficient of LiCl, where the magnitude of the heat of transport is maximized. The Seebeck coefficient obtained from theionic heats of transport varies significantly with temperature and concentration. We identify thermodynamic conditions leadingto a maximization of the thermoelectric response of aqueous solutions.
Gonzalez MA, Barriga HMG, Richens JL, et al., 2017, How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 19, Pages: 9199-9209, ISSN: 1463-9076
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems. It is well recognised that lanthanide salts can influence the behaviour of both lipid and protein systems, however a full molecular level description of lipid–lanthanide interactions is still outstanding. Here we present a study of lanthanide–bilayer interactions, using molecular dynamics computer simulations, fluorescence electrostatic potential experiments and nuclear magnetic resonance. Computer simulations reveal the microscopic structure of DMPC lipid bilayers in the presence of Yb3+, and a surprising ability of the membranes to adsorb significant concentrations of Yb3+ without disrupting the overall membrane structure. At concentrations commonly used in NMR experiments, Yb3+ ions bind strongly to 5 lipids, inducing a small decrease of the area per lipid and a slight increase of the ordering of the aliphatic chains and the bilayer thickness. The area compressibility modulus increases by a factor of two, with respect to the free-salt case, showing that Yb3+ ions make the bilayer more rigid. These modifications of the bilayer properties should be taken into account in the interpretation of NMR experiments.
Di Lecce S, Albrecht T, Bresme F, 2017, The role of ion-water interactions in determining the Soret coefficient of LiCl aqueous solutions, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 19, Pages: 9575-9583, ISSN: 1463-9076
The application of a thermal gradient to an aqueous electrolyte solution induces the Soret effect, and the salt migrates towards hot (thermophilic) or cold regions (thermophobic). Experimental studies of LiCl reported changes in the sign of the Soret coefficient as well as a minimum in this coefficient at specific salt concentrations and temperatures. At the minimum the thermodiffusive response of the solution is enhanced significantly. We have performed non-equilibrium molecular dynamics simulations of LiCl solutions to quantify the dependence of the sign change and minimum of the Soret coefficient with salt concentration and temperature. We find that the ion mass plays a secondary role in determining the magnitude of the Soret coefficient, while the diameter of the cation has a significant impact on the coefficient and on the observation of the minimum. Our simulations show that the ordering of water around Li+ plays a key role in determining the Soret coefficient of LiCl salts.
Law BM, McBride SP, Wang JY, et al., 2017, Line tension and its influence on droplets and particles at surfaces, Progress in Surface Science, Vol: 92, Pages: 1-39, ISSN: 0079-6816
In this review we examine the influence of the line tension τ on droplets and particles at surfaces. The line tension influences the nucleation behavior and contact angle of liquid droplets at both liquid and solid surfaces and alters the attachment energetics of solid particles to liquid surfaces. Many factors, occurring over a wide range of length scales, contribute to the line tension. On atomic scales, atomic rearrangements and reorientations of submolecular components give rise to an atomic line tension contribution τatom (∼1 nN), which depends on the similarity/dissimilarity of the droplet/particle surface composition compared with the surface upon which it resides. At nanometer length scales, an integration over the van der Waals interfacial potential gives rise to a mesoscale contribution |τvdW| ∼ 1–100 pN while, at millimeter length scales, the gravitational potential provides a gravitational contribution τgrav ∼ +1–10 μN. τgrav is always positive, whereas, τvdW can have either sign. Near wetting, for very small contact angle droplets, a negative line tension may give rise to a contact line instability. We examine these and other issues in this review.
David A, Fajardo OY, Kornyshev AA, et al., 2017, Electrotunable lubricity with ionic liquids: the influence of nanoscale roughness, Faraday Discuss, Vol: 199, Pages: 279-297, ISSN: 1359-6640
The properties of ionic liquids can be modified by applying an external electrostatic potential, providing a route to control their performance in nanolubrication applications. Most computational studies to date have focused on the investigation of smooth surfaces. Real surfaces are generally inhomogeneous and feature roughness of different length scales. We report here a study of the possible effects that surface roughness may have on electrotunable lubricity with ionic liquids, performed here by means of non-equilibrium molecular dynamics simulations. In order to advance our understanding of the interplay of friction and substrate structure we investigate coarse grained models of ionic liquids confined in model surfaces with nanometer roughness. The friction is shown to depend on the roughness of the substrate and the direction of shear. For the investigated systems, the friction coefficient is found to increase with roughness. These results are in contrast with previous studies, where roughness induced reduction of friction was reported, and they highlight the strong sensitivity of the friction process to the structure of the surfaces. The friction force features a maximum at a specific surface charge density. This behaviour is reminiscent of the one reported in ionic liquids confined by flat surfaces, showing the generality of this physical effect in confined ionic liquids. We find that an increase of the substrate-liquid dispersion interactions shifts the maximum to lower surface charges. This effect opens a route to control electrotunable friction phenomena by tuning both the electrostatic potential and the composition of the confining surfaces.
Tascini AS, Armstrong J, Chiavazzo E, et al., 2017, Thermal transport across nanoparticle-fluid interfaces, ISSN: 2578-5486
Tascini AS, Armstrong J, Chiavazzo E, et al., 2016, Thermal transport across nanoparticle-fluid interfaces: the interplay of interfacial curvature and nanoparticle-fluid interactions, Physical Chemistry Chemical Physics, Vol: 19, Pages: 3244-3253, ISSN: 1463-9084
We investigate the general dependence of the thermal transport across nanoparticle–fluid interfaces using molecular dynamics computations. We show that the thermal conductance depends strongly both on the wetting characteristics of the nanoparticle–fluid interface and on the nanoparticle size. Strong nanoparticle–fluid interactions, leading to full wetting states in the host fluid, result in high thermal conductances and efficient interfacial transport of heat. Weak interactions result in partial drying or full drying states, and low thermal conductances. The variation of the thermal conductance with particle size is found to depend on the fluid–nanoparticle interactions. Strong interactions coupled with large interfacial curvatures lead to optimum interfacial heat transport. This complex dependence can be modelled using an equation that includes the interfacial curvature as a parameter. In this way, we rationalise the existing experimental and computer simulation results and show that the thermal transport across nanoscale interfaces is determined by the correlations of both interfacial curvature and nanoparticle–fluid interactions.
Daub CD, Astrand P-O, Bresme F, 2016, Polarisation of polar dumbbell fluids in thermal gradients: the importance of the treatment of electrostatic interactions, Molecular Physics, Vol: 114, Pages: 3249-3254, ISSN: 0026-8976
We use non-equilibrium molecular dynamics simulations to study dipolar dumbbell fluids in a thermal gradient. We study the relative orientation of size asymmetric molecules with respect to the thermal gradient, and the sensitivity of the orientation to whether the Wolf method or Ewald summation is employed to compute the electrostatic interactions. For these systems, we find that the Wolf method overestimates the degree of molecular orientation. We also present new data on fluids with very small dipole moments which give novel insight into how the molecular asymmetry influences the polarisation response in the thermal gradient.
Iriarte-Carretero I, Gonzalez MA, Armstrong J, et al., 2016, The rich phase behavior of the thermopolarization of water: from a reversal in the polarization, to enhancement near criticality conditions, Physical Chemistry Chemical Physics, Vol: 18, Pages: 19894-19901, ISSN: 1463-9084
We investigate using non-equilibrium molecular dynamics simulations the polarization of water induced by thermal gradients using the accurate TIP4P/2005 water model. The full dependence of the polarization covering a wide range of thermodynamic states, from near supercritical to ambient conditions, is reported. Our results show a strong dependence of the thermo-polarization field with the thermodynamic state. The field features a strong enhancement near the critical point, which can be rationalized in terms of the large increase and ultimately the divergence of the thermal expansion of the fluid at the critical temperature. We also show that the TIP4P/2005 model features a reversal in the sign of the thermal polarization at densities ∼1 g cm−3. The latter result is consistent with the recent observation of this reversal phenomenon in SPC/E water and points the existence of this general physical phenomenon in water.
Jackson N, Miguel Rubi J, Bresme F, 2016, Non-equilibrium molecular dynamics simulations of the thermal transport properties of Lennard-Jones fluids using configurational temperatures, Molecular Simulation, Vol: 42, Pages: 1214-1222, ISSN: 1029-0435
We investigate the accuracy of two expressions for configurational temperature when calculating thermal transport properties in non-equilibrium systems under thermal gradients. The temperature, introduced by Jepps et al. [Phys. Rev. E. 62;2000:4757] is found to give results in almost exact agreement with the equipartition temperature for the thermal conductivity of the Lennard-Jones fluid, and for the temperature profile across a solid–liquid interface. Measurements of are, however, less precise than those of the equipartition temperature, which results in less accurate measurements of the interfacial thermal conductance across a liquid–vapour interface. The approximate expression , which depends strongly on the number of sampled atoms, predicts unphysical negative thermal conductances in liquid–vapour interfaces, highlighting the limitations of some definitions of the configurational temperature in the computation of thermal transport properties via non-equilibrium simulations.
Armstrong J, Mukhopadhyay S, Bresme F, et al., 2016, Heads or tails: how do chemically substituted fullerenes melt?, Physical Chemistry Chemical Physics, Vol: 18, Pages: 17202-17209, ISSN: 1463-9084
We address the question as to whether the melting of chemically substituted fullerenes is driven by the dynamics of the fullerene moiety (the head) or the substituted sub-unit (the tail). To this end, we have performed quasielastic neutron-scattering experiments and classical molecular-dynamics simulations as a function of temperature on the prototypical fullerene derivative phenyl-C61-butyric acid methyl ester. To enable a direct and quantitative comparison between experimental and simulation data, dynamic structure factors for the latter have been calculated from atomic trajectories and further convolved with the known instrument response. A detailed analysis of the energy- and momentum-transfer dependence of this observable in the quasielastic regime shows that melting is entirely driven by temperature-activated tail motions. We also provide quantitative estimates of the activation energy for this process as the material first enters a plastic-crystalline phase, followed by the emergence of a genuine liquid at higher temperatures.
Daub CD, Tafjord J, Kjelstrup S, et al., 2016, Molecular alignment in molecular fluids induced by coupling between density and thermal gradients, Physical Chemistry Chemical Physics, Vol: 18, Pages: 12213-12220, ISSN: 1463-9084
Mohammad-Aghaie D, Bresme F, 2016, Force-field dependence on the liquid-expanded to liquid-condensed transition in DPPC monolayers, MOLECULAR SIMULATION, Vol: 42, Pages: 391-397, ISSN: 0892-7022
Zhang Y, Carter JW, Lervik A, et al., 2016, Structural organization of sterol molecules in DPPC bilayers: a coarse-grained molecular dynamics investigation, Soft Matter, Vol: 12, Pages: 2108-2117, ISSN: 1744-6848
Bresme F, Lervik A, Armstrong J, 2016, Non-equilibrium Molecular Dynamics, EXPERIMENTAL THERMODYNAMICS, VOL X: NON-EQUILIBRIUM THERMODYNAMICS WITH APPLICATIONS, Editors: Bedeaux, Kjelstrup, Sengers, Publisher: ROYAL SOC CHEMISTRY, Pages: 105-133, ISBN: 978-1-78262-024-2
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- Citations: 2
Armstrong J, Bresme F, 2015, Temperature inversion of the thermal polarization of water, Physical Review E, Vol: 92, ISSN: 1539-3755
Temperature gradients polarize water, a nonequilibrium effect that may result in significant electrostatic fields for strong thermal gradients. Using nonequilibrium molecular dynamics simulations, we show that the thermal polarization features a significant dependence with temperature that ultimately leads to an inversion phenomenon, whereby the polarization field reverses its sign at a specific temperature. Temperature inversion effects have been reported before in the Soret coefficient of aqueous solutions, where the solution changes from thermophobic to thermophilic at specific temperatures. We show that a similar inversion behavior is observed in pure water. Microscopically, the inversion is the result of a balance of dipolar and quadrupolar contributions and the strong temperature dependence of the quadrupolar contribution, which is determined by the thermal expansion of the liquid.
Fajardo OY, Bresme F, Kornyshev AA, et al., 2015, Electrotunable friction with ionic liquid lubricants: How important is the molecular structure of the ions?, Journal of Physical Chemistry Letters, Vol: 6, Pages: 3998-4004, ISSN: 1948-7185
Using nonequilibrium molecular dynamics simulations and a coarse-grained model of ionic liquids, we have investigated the impact that the shape and the intramolecular charge distribution of the ions have on the electrotunable friction with ionic liquid nanoscale films. We show that the electric field induces significant structural changes in the film, leading to dramatic modifications of the friction force. Comparison of the present work with previous studies using different models of ionic liquids indicate that the phenomenology presented here applies to a wide range of ionic liquids. In particular, the electric-field-induced shift of the slippage plane from the solid–liquid interface to the interior of the film and the nonmonotonic variation of the friction force are common features of ionic lubricants under strong confinement. We also demonstrate that the molecular structure of the ions plays an important role in determining the electrostriction and electroswelling of the confined film, hence showing the importance of ion-specific effects in electrotunable friction.
Chacon E, Tarazona P, Bresme F, 2015, A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes, JOURNAL OF CHEMICAL PHYSICS, Vol: 143, ISSN: 0021-9606
Armstrong J, Daub CD, Bresme F, 2015, Note: How does the treatment of electrostatic interactions influence the magnitude of thermal polarization of water? The SPC/E model, Journal of Chemical Physics, Vol: 143, ISSN: 1089-7690
We investigate how the treatment of electrostatic interactions influences the magnitude of the thermal polarization of water. We performed non-equilibrium molecular dynamics simulations of the extended simple point charge model of water under a thermal gradient, using two different systems: a water droplet confined in a spherical wall where the interactions are computed exactly using the Coulombic potential and a periodic prismatic box using the Wolf and 3D Ewald methods. All the methods reproduce the thermal polarization (TP) of water as well as the direction of the TP field, but the standard implementation of the Wolf method overestimates the strength of the TP field by one order of magnitude, showing that this method might be problematic in simulations involving temperature and/or density gradients.
Perez de la Luz A, Arlette Mendez-Maldonado G, Nunez-Rojas E, et al., 2015, A New Force Field of Formamide and the Effect of the Dielectric Constant on Miscibility, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol: 11, Pages: 2792-2800, ISSN: 1549-9618
Daub CD, Astrand P-O, Bresme F, 2015, Lithium Ion-Water Clusters in Strong Electric Fields: A Quantum Chemical Study, Journal of Physical Chemistry A, Vol: 119, Pages: 4983-4992, ISSN: 1520-5215
We use density functional theory to investigate the impact that strong electric fields have on the structure and energetics of small lithium ion–water clusters, Li+·nH2O, with n = 4 or 6. We find that electric field strengths of ∼0.5 V/Å are sufficient to break the symmetry of the n = 4 tetrahedral energy minimum structure, which undergoes a transformation to an asymmetric cluster consisting of three water molecules bound to lithium and one additional molecule in the second solvation shell. Interestingly, this cluster remains the global minimum configuration at field strengths ≳0.15 V/Å. The 6-coordinated cluster, Li+·6H2O, features a similar transition to 5- and 4-coordinated clusters at field strengths of ∼0.2 and ∼0.3 V/Å, respectively, with the tetra-coordinated structure being the global minimum even in the absence of the field. Our findings are relevant to understanding the behavior of the Li+ ion in aqueous environments under strong electric fields and in interfacial regions where field gradients are significant.
Gonzalez MA, Abascal JLF, Valeriani C, et al., 2015, Bubble nucleation in simple and molecular liquids via the largest spherical cavity method, JOURNAL OF CHEMICAL PHYSICS, Vol: 142, ISSN: 0021-9606
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- Citations: 15
Bringas G, Navarro-Santos P, Lopez-Rendon R, et al., 2015, Molecular Dynamics Simulations of 2-(Dimethylamino)ethanol (DMEA), JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 119, Pages: 5035-5046, ISSN: 1520-6106
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Fajardo OY, Bresme F, Kornyshev AA, et al., 2015, Electrotunable Lubricity with Ionic Liquid Nanoscale Films, Scientific Reports, Vol: 5, ISSN: 2045-2322
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