Water shapes and defines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biological systems is of primary importance for a proper assessment of biological activity and the development of new drugs and vaccines. A handy way to characterize the interactions between biological systems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is well established that water bulk density and dynamical properties are recovered at distances in the order of $\sim1$~nm from the surface of biological systems. Such evidence led to the definition of \emph{hydration} water as the thin layer of water covering the surface of biological systems and affecting-defining their properties and functionality. Here, we review some of our latest contributions showing that phospholipid membranes affect the structural properties and the hydrogen bond network of water at greater distances than the commonly evoked $\sim1$~nm from the membrane surface. Our results imply that the concept of hydration water should be revised or extended, and pave the way to a deeper understanding of the mutual interactions between water and biological systems.
Graphene nanochannels are relevant for their possible applications, as in water purification, and for the challenge of understanding how they change the properties of confined liquids. Here, we use all-atom molecular dynamics simulations to investigate water confined in an open graphene slit-pore as a function of its width $w$, down to sub-nm scale. We find that the water translational and rotational dynamics exhibits an oscillatory dependence on $w$, due to water layering. The oscillations in dynamics correlate with those in hydration pressure, which can be negative (hydrophobic attraction), …
Using heterodyne-detected optical Kerr effect (HD-OKE) measurements, we investigate the vibrational dynamics and the structural relaxation of water nanoconfined in Vycor porous silica samples (pore size $\simeq~4~nm$ ) at different levels of hydration and temperatures. At low level of hydration, corresponding to two complete superficial water layers, no freezing occurs and water remains mobile at all the investigated temperatures with dynamic features similar, but not equal, to the bulk water. The fully hydrated sample shows formation of ice at about 248 K, this process does not involve all th…
A water structure indicator suitable for generic contexts: two-liquid behavior at hydration and nanoconfinement conditions and a molecular approach to hydrophobicity and wetting
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to the presence of a hydrophilic surface, the dynamic behaviour of the liquid appears to be strongly dependent on the hydration level. On lowering temperature and/or hydration level the intermediate scattering function displays a double-step relaxation behaviour whose long time tail is strongly non-exponential. At higher hydrations two quite distinct subsets of …
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at av…
We present results of molecular dynamics simulations of water confined in a silica pore. A cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass. The simulations are performed at different hydration levels. At all hydration levels water adsorbs strongly on the Vycor surface; a double layer structure is evident at higher hydrations. At almost full hydration the modifications of the confinement-induced site-site pair distribution functions are in qualitative agreement with neutron diffraction experiment. A decrease in the numb…
Fluid-induced alteration of rocks and mineral-based materials often starts at confined mineral interfaces where nm-thick water films can persist even at high overburden pressures and at low vapor pressures. These films enable transport of reactants and affect forces acting between mineral surfaces. However, the feedback between the surface forces and reactivity of confined solids is not fully understood. We used the surface forces apparatus (SFA) to follow surface reactivity in confinement and measure nm-range forces between two rough calcite surfaces in NaCl, CaCl$_2$, or MgCl$_2$ solutions w…
The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We use forward flux sampling, a molecular simulation technique, to compute the rate of capillary evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of gap, surface size and temperature. Over the range of conditions investigated (gaps between 9 and 14 Å and surface areas between 1 and 9 nm^2) the free energ…
The low frequency vibrational spectra of hydrated porous silica are specifically sensitive to the hydrogen bond interactions and provides a wealth of information on the structural and dynamical properties of the water contained in the pores of the matrix. We investigate systematically this spectral region of Vycor porous silica (pore size about 4 nm) for a series of samples at different levels of hydration, from the dry matrix to completely filled pores. The spectra are obtained as the Fourier transforms of time-resolved heterodyne detected optical Kerr effect (HD- OKE) measurements. The compa…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of water at bio-interfaces (e.g., proteins or membranes) and nano-interfaces (e.g., nanoparticles or graphene sheets) and coarse-grain models of hydration water for protein folding and protein design. We study protein self-assembly and crystallization, in bulk or under confinement, and the kinetics of protein adsorption onto nanoparticles, verify- ing our predict…
Ion specificity and related Hofmeister effects, ubiquitous in aqueous systems, can have spectacular consequences in hydrated clays, where ion-specific nanoscale surface forces can determine large scale cohesive, swelling and shrinkage behaviors of soil and sediments. We have used a semi-atomistic computational approach and examined sodium, calcium and aluminum counterions confined with water between charged surfaces representative of clay materials, to show that ion-water structuring in nanoscale confinement is at the origin of surface forces between clay particles which are intrinsically ion-…
This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement between graphene sheets. By means of molecular dynamics simulations, an adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The conf…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, lambda, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity, kappa. For infinitely long cylinders, F is a maximum at lambda=0, and decreases with lambda until the polymers are no longer in contact. For flexible cha…
Confinement effects on protein stability in a freezing water environment
University of Pamplona（潘普洛纳大学）；Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP)（液体与生物系统物理研究所 (CONICET-UNLP)）；Universidad Nacional Arturo Jauretche（阿图罗·豪雷切国立大学）；Universidad Nacional de La Plata（拉普拉塔国立大学）；Universidad Tecnológica Nacional, Facultad Regional La Plata（国家技术大学，拉普拉塔地区学院）
Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement has remained elusive. As expected, water in contact with biological membranes recovers its bulk density and dynamics at $\sim 1$ nm from phospholipid headgroups but surprisingly enhances its intermediate-range order (IRO) over a distance, at least, twice as large. Here, we explore how the IRO is related to the water's hydrogen bond network (HBN) and its coo…
We derive a Kinetic Monte Carlo model for studying how contacts form between confined surfaces in an ideal solution. The model incorporates repulsive and attractive surface-surface forces between a periodic (2+1)-dimensional solid-on-solid (SOS) crystal surface and a confining flat surface. The repulsive interaction is derived from the theory of electric double-layers, and the attractive interactions are Van der Waals interactions between particles on the SOS surface and the confining surface. The confinement is induced by a constant external pressure normal to the surfaces which is in mechani…
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface a…
Colloidal patchy particles with divalent attractive interaction can self-assemble into linear polymer chains. Their equilibrium properties in 2D and 3D are well described by Wertheim's thermodynamic perturbation theory which predicts a well-defined exponentially decaying equilibrium chain length distribution. In experimental realizations, due to gravity, particles sediment to the bottom of the suspension forming a monolayer of particles with a gravitational height smaller than the particle diameter. In accordance with experiments, an anomalously high monomer concentration is observed in simula…
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes, and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvat…
Dielectric permittivity of water confined in stacks of charged lipid layers: extracting profiles from molecular dynamics simulations using a modified Poisson-Boltzmann equation
Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière（里昂第一大学，法国国家科学研究中心，光物质研究所）；UPR 22/CNRS, Institut Charles Sadron, Université de Strasbourg（斯特拉斯堡大学，法国国家科学研究中心查尔斯·萨德龙研究所）
