Biomedical subjects

Francesco Sciortino

Publications and source records attributed to Francesco Sciortino.

At least 19 recordsLinked to original sources

PubMed2006

Slow dynamics in a primitive tetrahedral network model.

We report extensive Monte Carlo and event-driven molecular dynamics simulations of the fluid and liquid phase of a primitive model for silica recently introduced by Ford et al. [J. Chem. Phys. 121, 8415 (2004)]. We evaluate the isodiffusivity lines in the temperature-density plane to provide an indication of the shape of the glass transition line. Except for large densities, arrest is driven by the onset of the tetrahedral bonding pattern and the resulting dynamics is strong in Angell's classification scheme [J. Non-Cryst. Solids 131-133, 13 (1991)]. We compare structural and dynamic properties with corresponding results of two recently studied primitive models of network forming liquids-a primitive model for water and an angular-constraint-free model of four-coordinated particles-to pin down the role of the geometric constraints associated with bonding. Eventually we discuss the similarities between "glass" formation in network forming liquids and "gel" formation in colloidal dispersions of patchy particles.

Journal Article↗

PubMed2006

Phase diagram of patchy colloids: towards empty liquids.

We report theoretical and numerical evaluations of the phase diagram for patchy colloidal particles of new generation. We show that the reduction of the number of bonded nearest neighbors offers the possibility of generating liquid states (i.e., states with temperature T lower than the liquid-gas critical temperature) with a vanishing occupied packing fraction (phi), a case which can not be realized with spherically interacting particles. Theoretical results suggest that such reduction is accompanied by an increase of the region of stability of the liquid phase in the (T-phi) plane, possibly favoring the establishment of homogeneous disordered materials at small phi, i.e., stable equilibrium gels.

Chemical Phenomena↗

PubMed2006

Dynamics in the presence of attractive patchy interactions.

We report extensive Monte Carlo and event-driven molecular dynamics simulations of a liquid composed of particles interacting via hard-sphere interactions complemented by four tetrahedrally coordinated short-range attractive ("sticky") spots, a model introduced several years ago by Kolafa and Nezbeda (Kolafa, J.; Nezbeda, I. Mol. Phys. 1987, 87, 161). To access the dynamic properties of the model, we introduce and implement a new event-driven molecular dynamics algorithm suited to study the evolution of hard bodies interacting, beside the repulsive hard-core, with a short-ranged interpatch square well potential. We evaluate the thermodynamic properties of the model in deep supercooled states, where the bond network is fully developed, providing evidence of density anomalies. Different from models of spherically symmetric interacting particles, the liquid can be supercooled without encountering the gas-liquid spinodal in a wide region of packing fractions phi. Around an optimal phi, a stable fully connected tetrahedral network of bonds develops. By analyzing the dynamics of the model we find evidence of anomalous behavior: around the optimal packing, dynamics accelerate on both increasing and decreasing phi. We locate the shape of the isodiffusivity lines in the (phi - T) plane and establish the shape of the dynamic arrest line in the phase diagram of the model. Results are discussed in connection with colloidal dispersions of sticky particles and gel-forming proteins and their ability to form dynamically arrested states.

Journal Article↗

PubMed2006

Molecular correlation functions for uniaxial ellipsoids in the isotropic state.

We perform event-driven molecular dynamics simulations of a system composed by uniaxial hard ellipsoids for different values of the aspect ratio and packing fraction. We compare the molecular orientational-dependent structure factors previously calculated within the Percus-Yevick approximation with the numerical results. The agreement between theoretical and numerical results is rather satisfactory. We also show that, for specific orientational quantities, the molecular structure factors are sensitive to the particle shape and can be used to distinguish prolate from oblate ellipsoids. A first order theoretical expansion around the spherical shape and a geometrical analysis of the configurations confirms and explains such an observation.

Journal Article↗

PubMed2005

Dynamic arrest in a liquid of symmetric dumbbells: reorientational hopping for small molecular elongations.

We present extensive equilibrium and out-of-equilibrium molecular-dynamics simulations of a liquid of symmetric dumbbell molecules, for constant packing fraction, as a function of temperature and molecular elongation. We compute diffusion constants as well as odd and even orientational correlators. The notations odd and even refer to the parity of the order l of the corresponding Legendre l polynomial, evaluated for the orientation of the molecular axis relative to its initial position. Rotational degrees of freedom of order l are arrested if, in the long-time limit, the corresponding orientational l correlator does not decay to zero. It is found that for large elongations translational and rotational degrees of freedom freeze at the same temperature. For small elongations only the even rotational degrees of freedom remain coupled to translational motions and arrest at a finite common temperature. On the contrary, the odd rotational degrees of freedom remain ergodic at all investigated temperatures. Hence, in the translationally arrested state, each molecule remains trapped in the cage formed by its neighboring molecules, but is able to perform 180 degrees rotations, which lead to relaxation only for the odd orientational correlators. The temperature dependence of the characteristic time of these residual rotations is well described by an Arrhenius law. Finally, we discuss the evidence in favor of the presence of the type-A transition for the odd rotational degrees of freedom, as predicted by mode-coupling theory for small molecular elongations. This transition is distinct from the type-B transition, associated with the arrest of the translational and even rotational degrees of freedom for small elongations, and with all degrees of freedom for large elongations. Odd orientational correlators are computed for small elongations at very low temperatures in the translationally arrested state. The obtained results suggest that hopping events restore the ergodicity of the odd rotational degrees of freedom at temperatures far below the A transition.

Journal Article↗

PubMed2005

Phase diagram of amorphous solid water: low-density, high-density, and very-high-density amorphous ices.

We calculate the phase diagram of amorphous solid water by performing molecular dynamics simulations using the extended simple point charge (SPC/E) model. Our simulations follow different paths in the phase diagram: isothermal compression/decompression, isochoric cooling/heating, and isobaric cooling/heating. We are able to identify low-density amorphous (LDA), high-density amorphous (HDA), and very-high density amorphous (VHDA) ices. The density rho of these glasses at different pressure P and temperature T agree well with experimental values. We also study the radial distribution functions of glassy water. In agreement with experiments, we find that LDA, HDA, and VHDA are characterized by a tetrahedral hydrogen-bonded network and that, as compared to LDA, HDA has an extra interstitial molecule between the first and second shell. VHDA appears to have two such extra molecules. We obtain VHDA, as in experiment, by isobaric heating of HDA. We also find that "other forms" of glassy water can be obtained upon isobaric heating of LDA, as well as amorphous ices formed during the transformation of LDA to HDA. We argue that these other forms of amorphous ices, as well as VHDA, are not altogether new glasses but rather are the result of aging induced by heating. Samples of HDA and VHDA with different densities are recovered at normal P, showing that there is a continuum of glasses. Furthermore, the two ranges of densities of recovered HDA and recovered VHDA overlap at ambient P. Our simulations reproduce the experimental findings of HDA --> LDA and VHDA --> LDA transformations. We do not observe a VHDA --> HDA transformation, and our final phase diagram of glassy water together with equilibrium liquid data suggests that for the SPC/E model the VHDA --> HDA transformation cannot be observed with the present heating rates accessible in simulations. Finally, we discuss the consequences of our findings for the understanding of the transformation between the different amorphous ices and the two hypothesized phases of liquid water.

Journal Article↗

PubMed2005

Static and dynamic anomalies in a repulsive spherical ramp liquid: theory and simulation.

We compare theoretical and simulation results for static and dynamic properties for a model of particles interacting via a spherically symmetric repulsive ramp potential. The model displays anomalies similar to those found in liquid water, namely, expansion upon cooling and an increase of diffusivity upon compression. In particular, we calculate the state points P (rho,T) from the simulation and successfully compare it with the state points P (rho,T) obtained using the Rogers-Young (RY) closure for the Ornstein-Zernike (OZ) equation. Both the theoretical and the numerical calculations confirm the presence of a line of isobaric density maxima, and lines of compressibility minima and maxima. Indirect evidence of a liquid-liquid critical point is found. Dynamic properties also show anomalies. Along constant temperature paths, as the density increases, the dynamics alternate between slowing down and speeding up, and we associate this behavior with the progressive structuring and destructuring of the liquid. Finally we confirm that mode coupling theory successfully predicts the nonmonotonic behavior of dynamics and the presence of multiple glass phases, providing strong evidence that structure (the only input of mode coupling theory) controls dynamics.

Journal Article↗

PubMed2005

Structural relaxation in the glass transition region of water.

We perform molecular dynamics (MD) simulations using the extended simple-point-charge (SPC/E) model for water to study the structural relaxation through the glass transition region. We follow the same standard protocol used in differential scanning calorimetry experiments. Specifically, we cool liquid configurations at different cooling rates to produce a glass, and then we heat the glass back to the liquid state. We also study aging effects in the glass before heating. We find that MD simulations can reproduce the phenomenology observed in experiments. We review the Tool-Narayanaswamy-Moynihan (TNM) phenomenological approach, introduced to describe the behavior of the specific heat upon heating glass to the liquid phase. The TNM approach requires, as an ansatz, an expression for the temperature dependence of the relaxation time. We compare the simulation results with the prediction of the TNM approach supplemented with two well-known expressions for the relaxation time: the Narayanaswamy-Moynihan (NM) and the Adam-Gibbs-Scherer (AGS) expressions. We find that, in the case of slow cooling rates, our simulations are well represented by the TNM approach, but only if the AGS expression is adopted. We also find that the TNM approach fails in the case of fast cooling rates for both NM and AGS expressions. Several attempts to provide more freedom to the fitting procedure by allowing the fitting parameters to depend on temperature, cooling, and/or heating rates do not improve the agreement between the simulation data and the TNM predictions.

Journal Article↗

PubMed2005

Structural order in glassy water.

We investigate structural order in glassy water by performing classical molecular dynamics simulations using the extended simple point charge (SPC/E) model of water. We perform isochoric cooling simulations across the glass transition temperature at different cooling rates and densities. We quantify structural order by orientational and translational order metrics. Upon cooling the liquid into the glassy state, both the orientational order parameter Q and translational order parameter tau increase. At T=0 K, the glasses fall on a line in the Q-tau plane or order map. The position of this line depends only on density and coincides with the location in the order map of the inherent structures (IS) sampled upon cooling. We evaluate the energy of the IS, eIS(T), and find that both order parameters for the IS are proportional to eIS. We also study the structural order during the transformation of low-density amorphous ice (LDA) to high-density amorphous ice (HDA) upon isothermal compression and are able to identify distinct regions in the order map corresponding to these glasses. Comparison of the order parameters for LDA and HDA with those obtained upon isochoric cooling indicates major structural differences between glasses obtained by cooling and glasses obtained by compression. These structural differences are only weakly reflected in the pair correlation function. We also characterize the evolution of structural order upon isobaric annealing, leading at high pressure to very-high density amorphous ice (VHDA).

Journal Article↗

PubMed2005

Evidence for the weak steric hindrance scenario in the supercooled-state reorientational dynamics.

We use molecular-dynamics computer simulations to study the translational and reorientational dynamics of a glass-forming liquid of dumbbells. For sufficiently elongated molecules the standard strong steric hindrance scenario for the rotational dynamics is found. However, for small elongations we find a different scenario--the weak steric hindrance scenario--caused by a new type of glass transition in which the orientational dynamics of the molecule's axis undergoes a dynamical transition with a continuous increase of the nonergodicity parameter. These results are in agreement with the theoretical predictions by the mode-coupling theory for the glass transition.

Journal Article↗

PubMed2005

Relation between the high density phase and the very-high density phase of amorphous solid water.

It has been suggested that high-density amorphous (HDA) ice is a structurally arrested form of high-density liquid (HDL) water, while low-density amorphous ice is a structurally arrested form of low-density liquid (LDL) water. Recent experiments and simulations have been interpreted to support the possibility of a second distinct high-density structural state, named very high-density amorphous (VHDA) ice, questioning the LDL-HDL hypothesis. We test this interpretation using extensive computer simulations and find that VHDA is a more stable form of HDA and that, in fact, VHDA should be considered as the amorphous ice of the quenched HDL.

Journal Article↗

PubMed2005

Simulated silica.

We review how molecular dynamics computer simulations are providing a comprehensive picture of the behaviour of silica, as modelled by the van Beest-Kramer-van Santen (BKS) potential. We have recently evaluated a number of key properties of this model system: the phase diagram, including melting lines of three crystal phases; the equation of state and free energy of the liquid phase; the dynamical equation of state; the average energy of inherent structures, and configurational entropy, associated with the potential energy landscape of the liquid; and a characterization of the local coordination environments in the supercooled liquid. The results reveal the interplay among a number of phenomena, in particular, the relationship between the energy landscape and the fragile-to-strong crossover of the liquid dynamics; and the relation of both of these to the possibility of a liquid-liquid phase transition in the supercooled liquid.

Computer Simulation↗

PubMed2004

Phase diagram of silica from computer simulation.

We evaluate the phase diagram of the "BKS" potential [Phys. Rev. Lett. 64, 1955 (1990)]], a model of silica widely used in molecular dynamics (MD) simulations. We conduct MD simulations of the liquid, and three crystals ( beta -quartz, coesite, and stishovite) over wide ranges of temperature and density, and evaluate the total Gibbs free energy of each phase. The phase boundaries are determined by the intersection of these free energy surfaces. Not unexpectedly for a classical pair potential, our results reveal quantitative discrepancies between the locations of the BKS and real silica phase boundaries. At the same time, we find that the topology of the real phase diagram is reproduced, confirming that the BKS model provides a satisfactory qualitative description of a silicalike material. We also compare the phase boundaries with the locations of liquid-state thermodynamic anomalies identified in previous studies of the BKS model.

Journal Article↗

PubMed2004

Distributions of inherent structure energies during aging.

We perform extensive simulations of a binary mixture Lennard-Jones system subjected to a temperature jump in order to study the time evolution of fluctuations during aging. Analyzing data from 1500 different aging realizations, we calculate distributions of inherent structure energies for different aging times and contrast them with equilibrium. We find that the distributions initially become narrower and then widen as the system equilibrates. For deep quenches, fluctuations in the glassy system differ significantly from those observed in equilibrium. Simulation results are partially captured by theoretical predictions only when the final temperature is higher than the mode coupling temperature.

Journal Article↗

PubMed2004

Equilibrium cluster phases and low-density arrested disordered states: the role of short-range attraction and long-range repulsion.

We study a model in which particles interact with short-ranged attractive and long-ranged repulsive interactions, in an attempt to model the equilibrium cluster phase recently discovered in sterically stabilized colloidal systems in the presence of depletion interactions. At low packing fractions, particles form stable equilibrium clusters which act as building blocks of a cluster fluid. We study the possibility that cluster fluids generate a low-density disordered arrested phase, a gel, via a glass transition driven by the repulsive interaction. In this model the gel formation is formally described with the same physics of the glass formation.

Journal Article↗

PubMed2004

Glass-transition temperature of water: a simulation study.

We report a computer simulation study of the glass transition for water using the extended simple point charge potential. To mimic the difference between standard and hyperquenched glass, we generate glassy configurations with different cooling rates, and we calculate the temperature dependence of the specific heat on heating. The absence of crystallization phenomena allows us, for properly annealed samples, to detect in the specific heat the simultaneous presence of a weak prepeak ("shadow transition") and an intense glass transition peak at higher temperature. Our results support the view-point that the glass transition temperature is higher than the conventionally accepted value 136 K. We also compare our simulation results with the Tool-Narayanaswamy-Moynihan phenomenological model.

Journal Article↗

PubMed2004

Cooling rate, heating rate, and aging effects in glassy water.

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.

Journal Article↗

PubMed2004

Free energy and configurational entropy of liquid silica: fragile-to-strong crossover and polyamorphism.

Recent molecular dynamics (MD) simulations of liquid silica, using the "BKS" model [Phys. Rev. Lett. 64, 1955 (1990)]], have demonstrated that the liquid undergoes a dynamical crossover from super-Arrhenius, or "fragile" behavior, to Arrhenius, or "strong" behavior, as temperature T is decreased. From extensive MD simulations, we show that this fragile-to-strong crossover (FSC) can be connected to changes in the properties of the potential energy landscape, or surface (PES), of the liquid. To achieve this, we use thermodynamic integration to evaluate the absolute free energy of the liquid over a wide range of density and T. We use this free energy data, along with the concept of "inherent structures" of the PES, to evaluate the absolute configurational entropy S(c) of the liquid. We find that the temperature dependence of the diffusion coefficient and of S(c) are consistent with the prediction of Adam and Gibbs, including in the region where we observe the FSC to occur. We find that the FSC is related to a change in the properties of the PES explored by the liquid, specifically an inflection in the T dependence of the average inherent structure energy. In addition, we find that the high T behavior of S(c) suggests that the liquid entropy might approach zero at finite T, behavior associated with the so-called Kauzmann paradox. However, we find that the change in the PES that underlies the FSC is associated with a change in the T dependence of S(c) that elucidates how the Kauzmann paradox is avoided in this system. Finally, we also explore the relation of the observed PES changes to the recently discussed possibility that BKS silica exhibits a liquid-liquid phase transition, a behavior that has been proposed to underlie the observed polyamorphism of amorphous solid silica.

Journal Article↗