Abstract:Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from

The use of edible coatings on fresh and processed food products as a means of extending shelf life by preventing or delaying spoilage, providing a partial barrier to moisture, oxygen, and carbon dioxide, improving the mechanical handling properties, and even as carriers of many functional ingredients, is rapidly growing. Edible coatings can be applied by different methods such as panning, fluidized bed, dipping, and spraying. This review presents and discusses some aspects of the application of edible coatings on food products using spraying, which is the most commonly used technique for applying food coatings and to obtain uniform layers.

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In this study, we solve the nonexact two-stage two-dimensional guillotine cutting problem considering usable leftovers, in which stock plates remainders of the cutting patterns (nonused material or trim loss) can be used in the future, if they are large enough to fulfill future demands for items (ordered smaller plates). This cutting problem can be characterized as a residual bin-packing problem because of the possibility of putting back into stock residual pieces, as the trim loss of each cutting/packing pattern does not necessarily represent waste of material depending on its size. Two bilevel mathematical programming models to represent this nonexact two-stage two-dimensional residual bin-packing problem are presented. The models basically consist of cutting/packing the ordered items using a set of plates of minimum cost and, among all possible solutions of minimum cost, choosing one that maximizes the value of the generated usable leftovers. Because of special characteristics of these bilevel models, they can be reformulated as one-level mixed integer programming models. Results of some numerical experiments are presented to show that the models represent appropriately the problem and illustrate their performance.

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BackgroundWhat an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied.ResultsSuch relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks.ConclusionsThe results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.Electronic supplementary materialThe online version of this article (doi:10.1186/s13015-016-0087-3) contains supplementary material, which is available to authorized users.

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