Search results for " Simulation"
showing 10 items of 4034 documents
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot
2018
Abstract Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of …
Tabu search for the dynamic Bipartite Drawing Problem
2018
Abstract Drawings of graphs have many applications and they are nowadays well-established tools in computer science in general, and optimization in particular. Project scheduling is one of the many areas in which representation of graphs constitutes an important instrument. The experience shows that the main quality desired for drawings of graphs is readability, and crossing reduction is a fundamental aesthetic criterion to achieve it. Incremental or dynamic graph drawing is an emerging topic in this context, where we seek to preserve the layout of a graph over successive drawings. In this paper, we target the edge crossing reduction in the context of incremental graph drawing. Specifically…
On enhancing the object migration automaton using the Pursuit paradigm
2017
Abstract One of the most difficult problems that is all-pervasive in computing is that of partitioning. It has applications in the partitioning of databases into relations, the realization of the relations themselves into sub-relations based on the partitioning of the attributes, the assignment of processes to processors, graph partitioning, and the task assignment problem, etc. The problem is known to be NP-hard. The benchmark solution for this for the Equi-Partitioning Problem (EPP) has involved the classic field of Learning Automata (LA), and the corresponding algorithm, the Object Migrating Automata (OMA) has been used in all of these application domains. While the OMA is a fixed struct…
nalysis, Modeling and Simulation of Mechatronic Systems using the Bond Graph Method
2011
The Bond Graph is the proper choice of physical system used for: (i) Modeling which can be applied to systems combining multidisciplinary energy domains, (ii) Analysis to provide a great value proposition for finding the algebraic loops within the system enabling the process of troubleshooting and eliminating the defects by using the proper component(s) to fix the causality conflict even without being acquainted in the proper system, and (iii) Simulation facilitated through derived state space equations from the Bond Graph model is solved using industrial simulation software, such as 20-Sim. The Bond Graph technique is a graphical language of modeling, in which component energy ports are co…
Heuristics for the Constrained Incremental Graph Drawing Problem
2019
Abstract Visualization of information is a relevant topic in Computer Science, where graphs have become a standard representation model, and graph drawing is now a well-established area. Within this context, edge crossing minimization is a widely studied problem given its importance in obtaining readable representations of graphs. In this paper, we focus on the so-called incremental graph drawing problem, in which we try to preserve the user’s mental map when obtaining successive drawings of the same graph. In particular, we minimize the number of edge crossings while satisfying some constraints required to preserve the position of vertices with respect to previous drawings. We propose heur…
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
2015
This is a post-peer-review, pre-copyedit version of an article published in Journal of Computational Science. The final authenticated version is available online at: https://doi.org/10.1016/j.jocs.2015.04.001 [Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting epistasis, i.e. interactions among k markers (k ≥ 2), is an important but time consuming operation since statistical computations have to be performed for each k-tuple of measured markers. Efficient exhaustive methods have been proposed for k = 2, but exhaustive thi…
Diagrammatic approach to cellular automata and the emergence of form with inner structure
2018
We present a diagrammatic method to build up sophisticated cellular automata (CAs) as models of complex physical systems. The diagrams complement the mathematical approach to CA modeling, whose details are also presented here, and allow CAs in rule space to be classified according to their hierarchy of layers. Since the method is valid for any discrete operator and only depends on the alphabet size, the resulting conclusions, of general validity, apply to CAs in any dimension or order in time, arbitrary neighborhood ranges and topology. We provide several examples of the method, illustrating how it can be applied to the mathematical modeling of the emergence of order out of disorder. Specif…
Analogical Modeling and Numerical Simulation for Sintering Phenomena
2013
In this paper the authors propose an approach for analogical modeling and numerical simulation of the phenomena of sintering, taking into account different cases depending on the type of energy used in the process of aggregation and the nature of the material powder, using a software which simulates the propagation and the control of the temperature. Many physical phenomena encountered in science and engineering can be described mathematically through partial differential equations (PDE) and ordinary differential equations (ODE) such as propagation phenomena, engineering applications, hydrotechnics, chemistry, pollution a.s.o. There may be situations when the exact establish of the analytic…
Analytical design of nonlinear optical loop mirrors for fiber-optic communication systems
2006
International audience; We propose an easy and efficient method for analytically designing nonlinear optical loop mirrors (NOLMs) for fiber-optic communication systems. This analytical design is based on a Taylor series expansion of the transfer function of the NOLM, from which highly stable dynamical regimes can be readily obtained for any desired pulse parameters. We present numerical simulations showing dramatically improved performances in a 160 Gb/s transmission system that incorporates the NOLMs designed analytically.
New QM/MM implementation of the DFTB3 method in the gromacs package.
2015
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…