Biomedical subjects

Ivan Saika-Voivod

Publications and source records attributed to Ivan Saika-Voivod.

5 recordsLinked to original sources

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

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↗

PubMed2002

Evaluating the impact of population bottlenecks in experimental evolution.

Experimental evolution involves severe, periodic reductions in population size when fresh media are inoculated during serial transfer. These bottlenecks affect the dynamics of evolution, reducing the probability that a beneficial mutation will reach fixation. We quantify the impact of these bottlenecks on the evolutionary dynamics, for populations that grow exponentially between transfers and for populations in which growth is curbed by a resource-limited environment. We find that in both cases, mutations that survive bottlenecks are equally likely to occur, per unit time, at all times during the growth phase. We estimate the total fraction of beneficial mutations that are lost due to bottlenecks during experimental evolution protocols and derive the "optimal" dilution ratio, the ratio that maximizes the number of surviving beneficial mutations. Although more severe dilution ratios are often used in the literature, we find that a ratio of 0.1-0.2 minimizes the chances that rare beneficial mutations are lost. Finally, we provide a number of useful approximate results and illustrate our approach with applications to experimental evolution protocols in the literature.

Biological Evolution↗