On the Role of Inherent Structures in Glass-Forming Materials: I. The Vitrification Process

Statistical Inference of Rate Constants in Chemical and Biochemical Reaction Networks Using an "Inverse" Event-Driven Kinetic Monte Carlo Method

The use of rate models for networks of stochastic reactions is frequently used to comprehend the macroscopically observed dynamic properties of finite size reactive systems as well as their relationship to the underlying molecular events. Τhis particular approach usually stumbles on parameter derivation associated with stochastic kinetics, a quite demanding procedure. The present study incorporates a novel algorithm, which infers kinetic parameters from the system's time evolution, manifested as changes in molecular species populations. The proposed methodology reconstructs distributions required to infer kinetic parameters of a stochastic process pertaining to either a simulation or experimental data. The suggested approach accurately replicates rate constants of the stochastic reaction networks, which have evolved over time by event-driven Monte Carlo (MC) simulations using the Gillespie algorithm. Furthermore, our approach has been successfully used to estimate rate constants of association and dissociation events between molecular species developing during molecular dynamics (MD) simulations. We certainly believe that our method will be remarkably helpful for considering the macroscopic characteristic molecular roots related to stochastic physical and biological processes.

The inherent dynamics of isotropic- and nematic-phase liquid crystals

The geodesic (shortest) pathways through the potential energy landscape of a liquid can be thought of as defining what its dynamics would be if thermal noise were removed, revealing what we have called the "inherent dynamics" of the liquid. We show how these inherent paths can be located for a model liquid crystal former, showing, in the process, how the molecular mechanisms of translation and reorientation compare in the isotropic and nematic phases of these systems. These mechanisms turn out to favor the preservation of local orientational order even under macroscopically isotropic conditions (a finding consistent with the experimental observation of pseudonematic domains in these cases), but disfavor the maintenance of macroscopic orientational order, even in the nematic phase. While the most efficient nematic pathways that maintain nematic order are indeed shorter than those that do not, it is apparently difficult for the system to locate these paths, suggesting that molecular motion in liquid-crystal formers is dynamically frustrated, and reinforcing the sense that there are strong analogies between liquid crystals and supercooled liquids.

Computer simulations of glasses: the potential energy landscape

We review the current state of research on glasses, discussing the theoretical background and computational models employed to describe them. This article focuses on the use of the potential energy landscape (PEL) paradigm to account for the phenomenology of glassy systems, and the way in which it can be applied in simulations and the interpretation of their results. This article provides a broad overview of the rich phenomenology of glasses, followed by a summary of the theoretical frameworks developed to describe this phenomonology. We discuss the background of the PEL in detail, the onerous task of how to generate computer models of glasses, various methods of analysing numerical simulations, and the literature on the most commonly used model systems. Finally, we tackle the problem of how to distinguish a good glass former from a good crystal former from an analysis of the PEL. In summarising the state of the potential energy landscape picture, we develop the foundations for new theoretical methods that allow the ab initio prediction of the glass-forming ability of new materials by analysis of the PEL.

Temporal disconnectivity of the energy landscape in glassy systems

An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how--and mainly when--subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011)]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined approaches are compared to an "on the fly" molecular dynamics-based algorithm [D. G. Tsalikis, N. Lempesis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Theory Comput. 6, 1307 (2010)].

On Structure and Properties of Amorphous Materials

Mechanical, optical, magnetic and electronic properties of amorphous materials hold great promise towards current and emergent technologies. We distinguish at least four categories of amorphous (glassy) materials: (i) metallic; (ii) thin films; (iii) organic and inorganic thermoplastics; and (iv) amorphous permanent networks. Some fundamental questions about the atomic arrangements remain unresolved. This paper focuses on the models of atomic arrangements in amorphous materials. The earliest ideas of Bernal on the structure of liquids were followed by experiments and computer models for the packing of spheres. Modern approach is to carry out computer simulations with prediction that can be tested by experiments. A geometrical concept of an ideal amorphous solid is presented as a novel contribution to the understanding of atomic arrangements in amorphous solids.