arXiv subjects

Giancarlo Franzese

Publications and source records attributed to Giancarlo Franzese.

At least 37 records · Page 2Linked to original sources

arXiv2021

Network Topology in Water Nanoconfined between Phospholipid Membranes

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 coordination defects. We characterize the increased IRO by an alteration of the HBN up to more than eight coordination shells of hydration water. The HBN analysis emphasizes the existence of a bound-unbound water interface at $\sim 0.8$ nm from the membrane. The unbound water has a distribution of defects intermediate between bound and bulk water, but with density and dynamics similar to bulk, while bound water has reduced thermal energy and much more HBN defects than low-temperature water. This observation could be fundamental for developing nanoscale models of biological interactions and for understanding how alteration of the water structure and topology, for example, due to changes in extracellular ions concentration, could affect diseases and signaling. More generally, it gives us a different perspective to study nanoconfined water.

cond-mat.soft↗

arXiv2020

The Franzese-Stanley Coarse Grained Model for Hydration Water

Water modeling is a challenging problem. Its anomalies are difficult to reproduce, promoting the proliferation of a large number of computational models, among which researchers select the most appropriate for the property they study. In this chapter, we introduce a coarse-grained model introduced by Franzese and Stanley (FS) that accounts for the many-body interactions of water. We review mean-field calculations and Monte Carlo simulations on water monolayers for a wide range of pressures and temperatures, including extreme conditions. The results show the presence of two dynamic crossovers and explain the origin of diffusion anomalies. Moreover, the model shows that all the different scenarios, proposed in the last decades as alternative explanations of the experimental anomalies of water, can be related by the fine-tuning of the many-body (cooperative) interaction. Once this parameter is set from the experiments, the FS model predicts a phase transition between two liquids with different densities and energies in the supercooled water region, ending in a liquid-liquid critical point. From this critical point stems a liquid-liquid Widom line, i.e., the locus of maxima of the water correlation length, that in the FS model can be directly calculated. The results are consistent with the extrapolations from experiments. Furthermore, they agree with those from atomistic models but make predictions over a much wider thermodynamic region, allowing for a better interpretation of the available experimental data. All these findings provide a coherent picture of the properties of water and confirm the validity of the FS model that has proved to be useful for large-scale simulations of biological systems.

cond-mat.stat-mech↗

arXiv2019

In silico evidence that protein unfolding is as a precursor of the protein aggregation

We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein-protein interaction.

cond-mat.soft↗

arXiv2019

Hydrogen bond correlated percolation in a supercooled water monolayer as a hallmark of the critical region

Numerical simulations for a number of water models have supported the possibility of a metastable liquid-liquid critical point (LLCP) in the deep super-cooled region. Here we consider a theoretical model for a supercooled liquid water monolayer and its mathematical mapping onto a percolation problem. The mapping allows us to identify the finite-size clusters at any state-point, and the infinite cluster at the critical point, with the regions of correlated hydrogen bonds (HBs). We show that the percolation line coincides with the first-order liquid-liquid phase transition ending at the LLCP. At pressures below the LLCP, the percolation line corresponds to the strong maxima of the thermodynamic response functions and to the locus of maximum correlation length (Widom line). At higher pressures, we find a percolation transition with a positive slope and we discuss its possible relation with the thermodynamics.

cond-mat.soft↗

arXiv2018

Water between membranes: Structure and Dynamics

An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked membranes with hydration from poor to complete, as observed in a number of biological systems. Experiments show that the dynamics of water slows down dramatically when the hydration level is reduced. All-atom molecular dynamics simulations identify three (inner, hydration and outer) regions, within a distance of approximately 1 nm from the membrane, where water molecules exhibit different degrees of slowing down in the dynamics. The slow-down is a consequence of the robustness of the hydrogen bonds between water and lipids and the long lifetime of the hydrogen bonds between water molecules near the membrane. The interaction with the interface, therefore, induces a structural change in the water that can be emphasized by calculating its intermediate range order. Surprisingly, at distances as far as ~ 2.5 nm from the interface, although the bulk-like dynamics is recovered, the intermediate range order of water is still slightly higher than that in the bulk at the same thermodynamic conditions. Therefore, the water-membrane interface has a structural effect at ambient conditions that propagates further than the often-invoked 1 nm length scale. Membrane fluctuations smear out this effect macroscopically, but an analysis performed by considering local distances and instantaneous configurations is able to reveal it, possibly contributing to our understanding of the role of water at biomembrane interfaces.

cond-mat.soft↗

arXiv2018

Nonequilibrium Phenomena in Confined Systems

Keywords: nonequilibirum phenomena; diffusion in confined systems; dynamics and relaxation in confined systems; entropic transport in confined systems; ion and polymer translocation; forces induced by fluctuations; confined active mater; macromolecular crowding.

cond-mat.stat-mech↗

arXiv2017

Multi-scale approach for self-Assembly and protein folding

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 predictions in collaboration with several experimental groups. We try to find answers for fundamental questions (Why water is so important for life? Which properties make water unique for biological processes?) and applications (Can we design better drugs? Can we limit protein- aggregations causing Alzheimer? How to implement nanotheranostic?). Here we focus only on the two larger scales of our approach: (i) The coarse-grain description of hydrated proteins and protein folding at sub-nanometric length-scale and milliseconds-to-seconds time-scales, and (ii) the coarse-grain modeling of protein self-assembly on nanoparticles at 10-to-100 nm length-scale and seconds-to-hours time-scales.

cond-mat.soft↗

arXiv2017

How the stability of a folded protein depends on interfacial water properties and residue-residue interactions

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule is denaturated. It is known that the extension and shape of the SR depend on i) the specific protein residue-residue interactions in the native state of the amino acids sequence and ii) the water properties at the hydration interface. Here we analyze by Monte Carlo simulations of different coarse-grained protein models in explicit water how changes in i) and ii) affect the SR. We show that the solvent properties ii) are essential to rationalize the SR shape at low T and high P and that our finding are robust with respect to parameter changes and with respect to different protein models. These results can help in developing new strategies for the design of novel synthetic biopolymers.

cond-mat.soft↗

arXiv2017

Structural properties of water confined by phospholipid membranes

Biological membranes are essential for the cell life and hydration water provides the driving force for their assembly and stability. Here we study the structural properties of water in a phospholipid membrane. We characterize local structures inspecting the intermediate range order (IRO) adopting a sensitive local order metric, recently proposed by Martelli et al., which measures and grades the degree of overlap of local environments with structures of perfect ice. Close to the membrane, water acquires high IRO and changes its dynamical properties, e.g., slowing down its translational and rotational degrees of freedom in a region that extends over $\simeq 1$ nm from the membrane interface. Surprisingly, we show that at a distance as far as $\simeq 2.5$ nm from the interface, although the bulk-like dynamics is recovered, water's IRO is still slightly higher than in bulk at the same thermodynamic conditions. Therefore, the water-membrane interface has a structural effect at ambient conditions that propagates further than the often-invoked $1$ nm-length scale, a results that should be taken carefully into account when analyzing experimental data of water confined by membranes and could help us understanding the role of water in biological systems.

cond-mat.soft↗

arXiv2016

Effects of confinement between attractive and repulsive walls on the thermodynamics of an anomalous fluid

We study by molecular dynamics simulations the thermodynamics of an anomalous fluid confined in a slit pore with one wall structured and attractive and another unstructured and repulsive. We find that the phase diagram of the homogeneous part of the confined fluid is shifted to higher temperatures, densities and pressures with respect to the bulk, but it can be rescaled on the bulk case. We calculate a moderate increase of mobility of the homogeneous confined fluid that we interpret as a consequence of the layering due to confinement and the collective modes due to long-range correlations. We show that, as in bulk, the confined fluid has structural, diffusion and density anomalies, that order in the water-like hierarchy, and a liquid-liquid critical point (LLCP). The overall anomalous region moves to higher temperatures, densities and pressure and the LLCP displaces to higher temperature compared to bulk. Motivated by experiments, we calculate also the phase diagram not just for the homogeneous part of the confined fluid but for the entire fluid in the pore and show that it is shifted towards higher pressures but preserves the thermodynamics, including the LLCP. Because our model has water-like properties, we argue that in experiments with supercooled water confined in slit pores with a width of > 3 nm if hydrophilic, and of > 1.5 nm if hydrophobic, the existence of the LLCP could be easier to test than in bulk, where it is not directly accessible.

cond-mat.stat-mech↗

arXiv2016

Liquid-Liquid Critical Point in 3D Many-Body Water Model

Many-body interactions can play a relevant role in water properties. Here we study by Monte Carlo simulations a coarse-grained model for bulk water that includes many-body interactions associated to water cooperativity. The model is efficient and allows us to equilibrate water at extreme low temperatures in a wide range of pressures. We find the line of temperatures of maximum density at constant pressure and, at low temperature and high pressure, a phase transition between high-density liquid and low-density liquid phases. The liquid-liquid phase transition ends in a critical point. In the supercritical liquid region we find for each thermodynamic response function a locus of weak maxima at high temperature and a locus of strong maxima at low temperature, with both loci converging at the liquid-liquid critical point where they diverge. Comparing our results with previous works for the phase diagram of a many-body water monolayer, we observe that the weak maxima of the specific heat are less evident in bulk and appear only at negative pressures, while we find those of compressibility and thermal expansion coefficient also at positive pressures in bulk. However, the strong maxima of compressibility and thermal expansion coefficient are very sharp for the bulk case. Our results clarify fundamental properties of bulk water, possibly difficult to detect with atomistic models not accounting for many-body interactions.

cond-mat.stat-mech↗

arXiv2016

Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Increasing Hydration Level: All-Atoms Molecular Dynamics

Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational dynamical properties of water molecules confined in stacked phospholipid membranes at different levels of hydration, from poorly hydrated to a completely hydrated membrane. We find that both the translational and the reorientation dynamics of water are dramatically slowed down as the hydration is reduced. Analyzing in details the structure and dynamics of the hydrogen bond at the interface, we show that both those among water molecules and those between water and lipids slow down by decreasing the hydration, however the latter are always slower than the former. By increasing hydration, water saturates all the possible hydrogen bonds with the lipids and, by further increase of hydration, the hydrogen bonds among waters becomes the majority. However, the dynamics of the water-lipids hydrogen bonds becomes up to one order of magnitude slower than that of the water-water hydrogen bonds, inducing a large slowing down of the dynamics of the entire system even at large hydration level.

cond-mat.soft↗

arXiv2014

Structural behavior and dynamics of an anomalous fluid between solvophilic and solvophobic walls: templating, molding and superdiffusion

Confinement can modify the dynamics, the thermodynamics and the structural properties of liquid water, the prototypical anomalous liquid. By considering a general anomalous liquid, suitable for globular proteins, colloids or liquid metals, we study by molecular dynamics simulations the effect of a solvophilic structured and a solvophobic unstructured wall on the phases, the crystal nucleation and the dynamics of the fluid. We find that at low temperatures the large density of the solvophilic wall induces a high-density, high-energy structure in the first layer ("tempting" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range effect thanks to a sequence of templating, molding and templating effects through the layers. We find dynamical slowing down of the solvent near the solvophilic wall but with largely heterogeneous dynamics near the wall due to superdiffusive liquid veins within a frozen matrix of solvent. Hence, the partial freezing of the first hydration layer does not correspond necessarily to an effective reduction of the channel section in terms of transport properties.

cond-mat.soft↗

arXiv2014

Critical behavior of a water monolayer under hydrophobic confinement

The properties of water can have a strong dependence on the confinement. Here, we consider a water monolayer nanoconfined between hydrophobic parallel walls under conditions that prevent its crystallization. We investigate, by simulations of a many-body coarse-grained water model, how the properties of the liquid are affected by the confinement. We show, by studying the response functions and the correlation length and by performing finite-size scaling of the appropriate order parameter, that at low temperature the monolayer undergoes a liquid-liquid phase transition ending in a critical point in the universality class of the two-dimensional (2D) Ising model. Surprisingly, by reducing the linear size L of the walls, keeping the walls separation h constant, we find a 2D-3D crossover for the universality class of the liquid-liquid critical point for L/h~50, i.e. for a monolayer thickness that is small compared to its extension. This result is drastically different from what is reported for simple liquids, where the crossover occurs for L/h ~ 5, and is consistent with experimental results and atomistic simulations. We shed light on these findings showing that they are a consequence of the strong cooperativity and the low coordination number of the hydrogen bond network that characterizes water.

cond-mat.soft↗

arXiv2013

Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization

The liquid-liquid critical point scenario of water hypothesizes the existence of two metastable liquid phases---low-density liquid (LDL) and high-density liquid (HDL)---deep within the supercooled region. The hypothesis originates from computer simulations of the ST2 water model, but the stability of the LDL phase with respect to the crystal is still being debated. We simulate supercooled ST2 water at constant pressure, constant temperature and constant number of molecules N for N<=729 and times up to 1000 ns. We observe clear differences between the two liquids, both structural and dynamical. Using several methods, including finite-size scaling, we confirm the presence of a liquid-liquid phase transition ending in a critical point. We find that the LDL is stable with respect to the crystal in 98% of our runs (we perform 372 runs for LDL or LDL-like states), and in 100% of our runs for the two largest system sizes (N=512 and 729, for which we perform 136 runs for LDL or LDL-like states). In all these runs tiny crystallites grow and then melt within 1000 ns. Only for N<=343 we observe six events (over 236 runs for LDL or LDL-like states) of spontaneous crystallization after crystallites reach an estimated critical size of about 70+/-10 molecules.

cond-mat.soft↗

arXiv2013

Understanding surface-adsorption of proteins: the Vroman effect

It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamic simulations the competitive protein adsorption on a surface (Vroman effect), i.e. the non-monotonic behavior of the amount of protein adsorbed on a surface in contact with plasma as a function of contact time and plasma concentration. We find a complex behavior, with regimes during which small and large proteins are not necessarily competing between them, but are both competing with others in solution. We show how the effect can be understood, controlled and inverted.

cond-mat.soft↗

arXiv2012

Effect of pressure on the anomalous response functions of a confined water monolayer at low temperature

We study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we calculate three response functions: the isobaric specific heat $C_P$, the isothermal compressibility $K_T$, and the isobaric thermal expansivity $α_P$. At low temperature $T$, we find two distinct maxima in $C_P$, $K_T$ and $|α_P|$, all converging toward a liquid-liquid critical point (LLCP) with increasing pressure $P$. We show that the maximum in $C_P$ at higher $T$ is due to the fluctuations of hydrogen (H) bond formation and that the second maximum at lower $T$ is due to the cooperativity among the H bonds. We discuss a similar effect in $K_T$ and $|α_P|$. If this cooperativity were not taken into account, both the lower-$T$ maximum and the LLCP would disappear. However, comparison with recent experiments on water hydrating protein powders provides evidence for the existence of the lower-$T$ maximum, supporting the hypothesized LLCP at positive $P$ and finite $T$. The model also predicts that when $P$ moves closer to the critical $P$ the $C_P$ maxima move closer in $T$ until they merge at the LLCP. Considering that other scenarios for water are thermodynamically possible, we discuss how an experimental measurement of the changing separation in $T$ between the two maxima of $C_P$ as $P$ increases could determine the best scenario for describing water.

cond-mat.stat-mech↗

arXiv2012

Nanoparticle Confinement in Anomalous Liquids

We investigate using molecular dynamics the effect of the structure of nanoconfinement for liquids with water-like anomalies and liquid-liquid phase transition (LLPT). We find that if the confinement is in an ordered matrix of nanoparticles (NPs) the anomalies are preserved, although the LLPT shifts to lower temperatures, higher pressures and higher densities with respect to bulk. On the contrary, if the NPs matrix is disordered, we find a drastically different phase diagram: the LLPT occurs only in a reduced interval of densities and the anomalies are washed out. To understand this effect we calculate the changes in the system at the microscopic level. In all the different confinements considered here we observe a dramatic increase of density of liquid near the confining NPs. In the disordered case the confinement induces larger heterogeneity in the local density, responsible for the weakening of the LLPT and the disappearance of anomalies.

cond-mat.stat-mech↗