1,490 research outputs found
Emergence of foams from the breakdown of the phase field crystal model
The phase field crystal (PFC) model captures the elastic and topological
properties of crystals with a single scalar field at small undercooling. At
large undercooling, new foam-like behavior emerges. We characterize this foam
phase of the PFC equation and propose a modified PFC equation that may be used
for the simulation of foam dynamics. This minimal model reproduces von
Neumann's rule for two-dimensional dry foams, and Lifshitz-Slyozov coarsening
for wet foams. We also measure the coordination number distribution and find
that its second moment is larger than previously-reported experimental and
theoretical studies of soap froths, a finding that we attribute to the wetness
of the foam increasing with time.Comment: 4 pages, 4 figure
Equilibrium spherically curved 2D Lennard-Jones systems
To learn about basic aspects of nano-scale spherical molecular shells during
their formation, spherically curved two-dimensional N-particle Lennard-Jones
systems are simulated, studying curvature evolution paths at zero-temperature.
For many N-values (N<800) equilibrium configurations are traced as a function
of the curvature radius R. Sharp jumps for tiny changes in R between
trajectories with major differences in topological structure correspond to
avalanche-like transitions. For a typical case, N=25, equilibrium
configurations fall on smooth trajectories in state space which can be traced
in the E-R plane. The trajectories show-up with local energy minima, from which
growth in N at steady curvature can develop.Comment: 10 pages, 2 figures, to be published in Journal of Chemical Physic
Use of genetic algorithms and gradient based optimization techniques for calcium phosphate precipitation
Phase equilibrium computations constitute an important problem for designing and optimizing crystallization processes. The Gibbs free
energy is generally used as an objective function to find phase amount and composition at equilibrium. In such problems, the Gibbs free
energy may be a quite complex function, with several local minima. This paper presents a contribution to handle this kind of problems by
implementation of an optimization technique based on the successive use of a genetic algorithm (GA) and of a classical sequential quadratic
programming (SQP) method: the GA is used to perform a preliminary search in the solution space for locating the neighborhood of the
solution. Then, the SQP method is employed to refine the best solution provided by the GA. The basic operations involved in the design of
the GA developed in this study (encoding with binary representation of real values, evaluation function, adaptive plan) are presented. Several
test problems are first presented to demonstrate the validity of the approach. Then, calcium phosphate precipitation which is of major interest
for P-recovery from wastewater, has been chosen as an illustration of the implemented algorithm
On the role of confinement on solidification in pure materials and binary alloys
We use a phase-field model to study the effect of confinement on dendritic
growth, in a pure material solidifying in an undercooled melt, and in the
directional solidification of a dilute binary alloy. Specifically, we observe
the effect of varying the vertical domain extent () on tip selection,
by quantifying the dendrite tip velocity and curvature as a function of
, and other process parameters. As decreases, we find that the
operating state of the dendrite tips becomes significantly affected by the
presence of finite boundaries. For particular boundary conditions, we observe a
switching of the growth state from 3-D to 2-D at very small , in both
the pure material and alloy. We demonstrate that results from the alloy model
compare favorably with those from an experimental study investigating this
effect.Comment: 13 pages, 9 figures, 3 table
Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism
It is shown that the dual to the linear programming problem that arises in
constraint-based models of metabolism can be given a thermodynamic
interpretation in which the shadow prices are chemical potential analogues, and
the objective is to minimise free energy consumption given a free energy drain
corresponding to growth. The interpretation is distinct from conventional
non-equilibrium thermodynamics, although it does satisfy a minimum entropy
production principle. It can be used to motivate extensions of constraint-based
modelling, for example to microbial ecosystems.Comment: 4 pages, 2 figures, 1 table, RevTeX 4, final accepted versio
Nonclassicality of pure two-qutrit entangled states
We report an exhaustive numerical analysis of violations of local realism by
two qutrits in all possible pure entangled states. In Bell type experiments we
allow any pairs of local unitary U(3) transformations to define the measurement
bases. Surprisingly, Schmidt rank-2 states, resembling pairs of maximally
entangled qubits, lead to the most noise-robust violations of local realism.
The phenomenon seems to be even more pronounced for four and five dimensional
systems, for which we tested a few interesting examples.Comment: 6 pages, journal versio
On the Axiomatics of the 5-dimensional Projective Unified Field Theory of Schmutzer
For more than 40 years E.Schmutzer has developed a new approach to the
(5-dimensional) projective relativistic theory which he later called Projective
Unified Field Theory (PUFT). In the present paper we introduce a new axiomatics
for Schmutzer's theory. By means of this axiomatics we can give a new
geometrical interpretation of the physical concept of the PUFT.Comment: 32 pages, 1 figure, LaTeX 2e, will be submitted to Genaral Relativity
and Gravitatio
Phase Field Model for Three-Dimensional Dendritic Growth with Fluid Flow
We study the effect of fluid flow on three-dimensional (3D) dendrite growth
using a phase-field model on an adaptive finite element grid. In order to
simulate 3D fluid flow, we use an averaging method for the flow problem coupled
to the phase-field method and the Semi-Implicit Approximated Projection Method
(SIAPM). We describe a parallel implementation for the algorithm, using Charm++
FEM framework, and demonstrate its efficiency. We introduce an improved method
for extracting dendrite tip position and tip radius, facilitating accurate
comparison to theory. We benchmark our results for two-dimensional (2D)
dendrite growth with solvability theory and previous results, finding them to
be in good agreement. The physics of dendritic growth with fluid flow in three
dimensions is very different from that in two dimensions, and we discuss the
origin of this behavior
Flux networks in metabolic graphs
A metabolic model can be represented as bipartite graph comprising linked
reaction and metabolite nodes. Here it is shown how a network of conserved
fluxes can be assigned to the edges of such a graph by combining the reaction
fluxes with a conserved metabolite property such as molecular weight. A similar
flux network can be constructed by combining the primal and dual solutions to
the linear programming problem that typically arises in constraint-based
modelling. Such constructions may help with the visualisation of flux
distributions in complex metabolic networks. The analysis also explains the
strong correlation observed between metabolite shadow prices (the dual linear
programming variables) and conserved metabolite properties. The methods were
applied to recent metabolic models for Escherichia coli, Saccharomyces
cerevisiae, and Methanosarcina barkeri. Detailed results are reported for E.
coli; similar results were found for the other organisms.Comment: 9 pages, 4 figures, RevTeX 4.0, supplementary data available (excel
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