Test of molecular mode coupling theory for general rigid molecules

We report recent progress on the test of mode coupling theory for molecular liquids (MMCT) for molecules of arbitrary shape. The MMCT equations in the long time limit are solved for supercooled water including all molecular degrees of freedom. In contrast to our earlier treatment of water as a linear molecule, we find that the glass-transition temperature ${T}_{c}$ is overestimated by the theory as was found in the case of simple liquids. The nonergodicity parameters are calculated from the ``full'' set of MMCT equations truncated at ${l}_{\mathrm{co}}=2.$ These results are compared (i) with the nonergodicity parameters from MMCT with ${l}_{\mathrm{co}}=2$ in the ``dipole'' approximation ${…

Nucleation and accretion of bioelastomeric fibers at biological temperatures and low concentrations.

Quasi-elastic light scattering (QELS) studies are reported, which address the early stages of aggregation of the polypentamer poly(VPGVG). This reflects the major primary structural feature of native elastin. The study is focused on the region of the phase diagram which in both its temperature and concentration range is closest to the state of affairs occurring in the course of bioelastogenesis by progressive synthesis of the precursor protein. Results here reported allow for the first time a self-consistent view of the physics of elastogenesis, and specify the role of the region of metastability and of that of instability of the phase diagram in the non-chaotic, orderly formation of elasto…

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 configura…

Valutazione dell'empowerment nei percorsi integrati di riabilitazione psichiatrica: il contributo dell'autovalutazione della quality of life nell'esperienza del Gruppo Albatros

Aging as dynamics in configuration space

The relaxation dynamics of many disordered systems, such as structural glasses, proteins, granular materials or spin glasses, is not completely frozen even at very low temperatures. This residual motion leads to a change of the properties of the material, a process commonly called aging. Despite recent advances in the theoretical description of such aging processes, the microscopic mechanisms leading to the aging dynamics are still a matter of dispute. In this Letter we investigate the aging dynamics of a simple glass former by means of molecular dynamics computer simulation. Using the concept of the inherent structure we give evidence that aging dynamics can be understood as a decrease of …

Self-assembly of bioelastomeric structures from solutions: Mean-field critical behavior and Flory-Huggins free energy of interactions

Elastic and quasi-elastic light scattering studies were performed on aqueous solutions of poly (Val-Pro-Gly-Gly), a representative synthetic bioelastomer that differs from the previously studied poly (Val-Pro-Gly-Val-Gly) by the deletion of the hydrophobic Val in position four. When the spinodal line was approached from the region of thermodynamic stability, the intensity of light scattered by fluctuations, and the related lifetime and correlation length, were observed to diverge with mean-field critical exponents for both systems. Fitting of the experimental data allowed determining the spinodal and binodal (coexistence) lines that characterize the phase diagrams of the two systems, and it…

Inherent structure entropy of supercooled liquids

We present a quantitative description of the thermodynamics in a supercooled binary Lennard Jones liquid via the evaluation of the degeneracy of the inherent structures, i.e. of the number of potential energy basins in configuration space. We find that for supercooled states, the contribution of the inherent structures to the free energy of the liquid almost completely decouples from the vibrational contribution. An important byproduct of the presented analysis is the determination of the Kauzmann temperature for the studied system. The resulting quantitative picture of the thermodynamics of the inherent structures offers new suggestions for the description of equilibrium and out-of-equilib…

Quantitative tests of mode-coupling theory for fragile and strong glass-formers

We calculate for a binary mixture of Lennard-Jones particles the time dependence of the solution of the mode-coupling equations in which the full wave vector dependence is taken into account. In addition we also take into account the short time dynamics, which we model with a simple memory kernel. We find that the so obtained solution agrees very well with the time and wave vector dependence of the coherent and incoherent intermediate scattering functions as determined from molecular dynamics computer simulations. Furthermore we calculate the wave vector dependence of the Debye-Waller factor for a realistic model of silica and compare these results with the ones obtained from a simulation o…

Event-Driven Simulation of the Dynamics of Hard Ellipsoids

We introduce a novel algorithm to perform event-driven simulations of hard rigid bodies of arbitrary shape, that relies on the evaluation of the geometric distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we perform molecular dynamics simulations varying the aspect-ratio X0 and the packing fraction phi. We evaluate the translational Dtrans and the rotational Drot diffusion coefficient and the associated isodiffusivity lines in the phi-X0 plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the Dtrans and Drot isodiffusivity lines. While the self intermediate scattering function exhibits stret…

Molecular mode-coupling theory for supercooled liquids: application to water.

We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple atomic liquids, and then extended to the analysis of liquids composed by linear molecules, is here generalized to systems of arbitrarily shaped, rigid molecules. We compare the predictions of the theory for the $q$-vector dependence of the molecular nonergodicity parameters, calculated by solving numerically the molecular MCT equations in two different approximation schemes, with ``exact'' results calculated from a molecular dynamics simulation of superc…

Test of the semischematic model for a liquid of linear molecules

We apply to a liquid of linear molecules the semischematic mode-coupling model, previously introduced to describe the center of mass (COM) slow dynamics of a network-forming molecular liquid. We compare the theoretical predictions and numerical results from a molecular dynamics simulation, both for the time and the wave-vector dependence of the COM density-density correlation function. We discuss the relationship between the presented analysis and the results from an approximate solution of the equations from molecular mode-coupling theory [R. Schilling and T. Scheidsteger, Phys. Rev. E 56 2932 (1997)].

Simulation of the dynamics of hard ellipsoids

We study a system of uniaxial hard ellipsoids by molecular dynamics simulations, changing both the aspect-ratio X-0 (X-0 = a/b, where a is the length of the revolution axis and b is the length of the two other axes) and the packing fraction phi. We calculate the translational and rotational mean squared displacements, the translational D-trans and the rotational D-rot diffusion coefficients and the associated isodiffusivity lines in the phi - X-0 plane. For the first time, we characterize the cage effect through the logarithmic time derivative of log and log . These quantities exhibit a minimum if the system is supercooled and we show that, consistently with our previous findings, for large…

Solute-induced Water Structure: Computer Simulation on a Model System

Abstract Two series of Monte Carlo simulations have been carried out on a system consisting of 125 water molecules, one of which is kept fixed to simulate a water molecule whose mobility is restricted by a solute. The results are checked against similar simulations without restrictions, used as a control, and they show how the blocked molecule helps increase both the structural order and the connectivity of the hydrogen bond network. Cooperativity originating from proton polarizability of H-bonds and/or from many-body terms of interaction potentials cannot be involved since we use a rigid water model and ab initio pair potentials. The present findings are interpreted as indicative of a moti…

An algorithm to find all paths between two nodes in a graph

Thermodynamics of supercooled liquids in the inherent structure formalism: a case study

In this article we review the thermodynamics of liquids in the framework of the inherent structure formalism. We then present calculations of the distribution of the basins in the potential energy of a binary Lennard-Jones mixture as a function of temperature. The comparison between the numerical data and the theoretical formalism allows us to evaluate the degeneracy of the inherent structures in a bulk system and to estimate the energy of the lowest energy disordered state (the Kauzmann energy). We find that, around the mode-coupling temperature, the partition function of the liquid is approximated well by the product of two loosely coupled partition functions, one depending on the inheren…

Molecular correlations in a supercooled liquid

We present static and dynamic properties of molecular correlation functions S_{lmn,l'm'n'}(q,t) in a simulated supercooled liquid of water molecules, as a preliminary effort in the direction of solving the molecular mode coupling theory (MMCT) equations for supercooled molecular liquids. The temperature and time dependence of various molecular correlation functions, calculated from 250 ns long molecular dynamics simulations, show the characteristic patterns predicted by MMCT and shed light on the driving mechanism responsible for the slowing down of the molecular dynamics. We also discuss the symmetry properties of the molecular correlation functions which can be predicted on the basis of t…

Dynamics of Uniaxial Hard Ellipsoids

We study the dynamics of monodisperse hard ellipsoids via a new event-driven molecular dynamics algorithm as a function of volume fraction $\phi$ and aspect ratio $X_0$. We evaluate the translational $D_{trans}$ and the rotational $D_{rot}$ diffusion coefficient and the associated isodiffusivity lines in the $\phi-X_0$ plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the $D_{trans}$ and $D_{rot}$ isodiffusivity lines. While the self intermediate scattering function exhibits stretched relaxation, i.e. glassy dynamics, only for large $\phi$ and $X_0 \approx 1$, the second order orientational correlator $C_2(t)$ sho…