240 research outputs found
The relationship between fragility, configurational entropy and the potential energy landscape of glass forming liquids
Glass is a microscopically disordered, solid form of matter that results when
a fluid is cooled or compressed in such a fashion that it does not crystallise.
Almost all types of materials are capable of glass formation -- polymers, metal
alloys, and molten salts, to name a few. Given such diversity, organising
principles which systematise data concerning glass formation are invaluable.
One such principle is the classification of glass formers according to their
fragility\cite{fragility}. Fragility measures the rapidity with which a
liquid's properties such as viscosity change as the glassy state is approached.
Although the relationship between features of the energy landscape of a glass
former, its configurational entropy and fragility have been analysed previously
(e. g.,\cite{speedyfr}), an understanding of the origins of fragility in these
features is far from being well established. Results for a model liquid, whose
fragility depends on its bulk density, are presented in this letter. Analysis
of the relationship between fragility and quantitative measures of the energy
landscape (the complicated dependence of energy on configuration) reveal that
the fragility depends on changes in the vibrational properties of individual
energy basins, in addition to the total number of such basins present, and
their spread in energy. A thermodynamic expression for fragility is derived,
which is in quantitative agreement with {\it kinetic} fragilities obtained from
the liquid's diffusivity.Comment: 8 pages, 3 figure
Spin-Glass Model for Inverse Freezing
We analyze the Blume-Emery-Griffiths model with disordered magnetic
interaction displaying the inverse freezing phenomenon. The behaviour of this
spin-1 model in crystal field is studied throughout the phase diagram and the
transition and spinodal lines for the model are computed using the Full Replica
Symmetry Breaking Ansatz that always yelds a thermodynamically stable phase. We
compare the results both with the quenched disordered model with Ising spins on
lattice gas - where no reentrance takes place - and with the model with
generalized spin variables recently introduced by Schupper and Shnerb [Phys.
Rev. Lett. 93, 037202 (2004)]. The simplest version of all these models, known
as Ghatak-Sherrington model, turns out to hold all the general features
characterizing an inverse transition to an amorphous phase, including the right
thermodynamic behavior.Comment: 6 pages, 4 figures, to appear in the Proceeding for the X
International Workshop on Disordered Systems (2006), Molveno, Ital
Configurational Entropy and Diffusivity of Supercooled Water
We calculate the configurational entropy S_conf for the SPC/E model of water
for state points covering a large region of the (T,rho) plane. We find that (i)
the (T,rho) dependence of S_conf correlates with the diffusion constant and
(ii) that the line of maxima in S_conf tracks the line of density maxima. Our
simulation data indicate that the dynamics are strongly influenced by S_conf
even above the mode-coupling temperature T_MCT(rho).Comment: Significant update of reference
Enumeration of distinct mechanically stable disk packings in small systems
We create mechanically stable (MS) packings of bidisperse disks using an
algorithm in which we successively grow or shrink soft repulsive disks followed
by energy minimization until the overlaps are vanishingly small. We focus on
small systems because this enables us to enumerate nearly all distinct MS
packings. We measure the probability to obtain a MS packing at packing fraction
and find several notable results. First, the probability is highly
nonuniform. When averaged over narrow packing fraction intervals, the most
probable MS packing occurs at the highest and the probability decays
exponentially with decreasing . Even more striking, within each
packing-fraction interval, the probability can vary by many orders of
magnitude. By using two different packing-generation protocols, we show that
these results are robust and the packing frequencies do not change
qualitatively with different protocols.Comment: 4 pages, 3 figures, Conference Proceedings for X International
Workshop on Disordered System
Phase Transitions and Their Interaction with Dislocations in Silicon
In this paper, phase transformations (PTs) in silicon were investigated through molecular dynamics (MD) using Tersoff potential. In the first step, simulations of PTs in single crystal silicon under various stress-controlled loading were carried out. Results shows that all instability points under various stress states are described by criteria, which are linear in the space of normal stresses. There is a region in the stress space in which conditions for direct and reverse PTs coincide and a unique homogeneous phase transition (without nucleation) can be realized. Finally, phase transition in bi-crystalline silicon with a dislocation pileup along the grain boundary (GB) was carried out. Results showed that the phase transition pressure first decreases linearly with the number of dislocation pileups and then reaches a plateau with the accumulation of dislocations in the pileup. The maximum reduction of phase transition pressure is 30% compared to that for perfect single crystalline silicon
3D Protein structure prediction with genetic tabu search algorithm
Abstract Background Protein structure prediction (PSP) has important applications in different fields, such as drug design, disease prediction, and so on. In protein structure prediction, there are two important issues. The first one is the design of the structure model and the second one is the design of the optimization technology. Because of the complexity of the realistic protein structure, the structure model adopted in this paper is a simplified model, which is called off-lattice AB model. After the structure model is assumed, optimization technology is needed for searching the best conformation of a protein sequence based on the assumed structure model. However, PSP is an NP-hard problem even if the simplest model is assumed. Thus, many algorithms have been developed to solve the global optimization problem. In this paper, a hybrid algorithm, which combines genetic algorithm (GA) and tabu search (TS) algorithm, is developed to complete this task. Results In order to develop an efficient optimization algorithm, several improved strategies are developed for the proposed genetic tabu search algorithm. The combined use of these strategies can improve the efficiency of the algorithm. In these strategies, tabu search introduced into the crossover and mutation operators can improve the local search capability, the adoption of variable population size strategy can maintain the diversity of the population, and the ranking selection strategy can improve the possibility of an individual with low energy value entering into next generation. Experiments are performed with Fibonacci sequences and real protein sequences. Experimental results show that the lowest energy obtained by the proposed GATS algorithm is lower than that obtained by previous methods. Conclusions The hybrid algorithm has the advantages from both genetic algorithm and tabu search algorithm. It makes use of the advantage of multiple search points in genetic algorithm, and can overcome poor hill-climbing capability in the conventional genetic algorithm by using the flexible memory functions of TS. Compared with some previous algorithms, GATS algorithm has better performance in global optimization and can predict 3D protein structure more effectively
Generic mechanism for generating a liquid-liquid phase transition
Recent experimental results indicate that phosphorus, a single-component
system, can have two liquid phases: a high-density liquid (HDL) and a
low-density liquid (LDL) phase. A first-order transition between two liquids of
different densities is consistent with experimental data for a variety of
materials, including single-component systems such as water, silica and carbon.
Molecular dynamics simulations of very specific models for supercooled water,
liquid carbon and supercooled silica, predict a LDL-HDL critical point, but a
coherent and general interpretation of the LDL-HDL transition is lacking. Here
we show that the presence of a LDL and a HDL can be directly related to an
interaction potential with an attractive part and two characteristic
short-range repulsive distances. This kind of interaction is common to other
single-component materials in the liquid state (in particular liquid metals),
and such potentials are often used to decribe systems that exhibit a density
anomaly. However, our results show that the LDL and HDL phases can occur in
systems with no density anomaly. Our results therefore present an experimental
challenge to uncover a liquid-liquid transition in systems like liquid metals,
regardless of the presence of the density anomaly.Comment: 5 pages, 3 ps Fig
Coarse-Grained Barrier Trees of Fitness Landscapes
Recent literature suggests that local optima in fitness landscapes are clustered, which offers an explanation of why perturbation-based metaheuristics often fail to find the global optimum: they become trapped in a sub-optimal cluster. We introduce a method to extract and visualize the global organization of these clusters in form of a barrier tree. Barrier trees have been used to visualize the barriers between local optima basins in fitness landscapes. Our method computes a more coarsely grained tree to reveal the barriers between clusters of local optima. The core element is a new variant of the flooding algorithm, applicable to local optima networks, a compressed representation of fitness landscapes. To identify the clusters, we apply a community detection algorithm. A sample of 200 NK fitness landscapes suggests that the depth of their coarse-grained barrier tree is related to their search difficulty
The Shapes of Cooperatively Rearranging Regions in Glass Forming Liquids
The shapes of cooperatively rearranging regions in glassy liquids change from
being compact at low temperatures to fractal or ``stringy'' as the dynamical
crossover temperature from activated to collisional transport is approached
from below. We present a quantitative microscopic treatment of this change of
morphology within the framework of the random first order transition theory of
glasses. We predict a correlation of the ratio of the dynamical crossover
temperature to the laboratory glass transition temperature, and the heat
capacity discontinuity at the glass transition, Delta C_p. The predicted
correlation agrees with experimental results for the 21 materials compiled by
Novikov and Sokolov.Comment: 9 pages, 6 figure
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