Search results for "Modeling and simulation"

An alternative formulation of the boundary element method

1982

Abstract The paper suggests an alternative formulation of the Boundary Element Method, in which singular solutions generated by unit dislocations are required and moreover the stresses at the interior points of the body are directly computed from the boundary quantities, without passing through the displacements. Relationships between the singular solutions for unit dislocation and unit force are derived.

A stochastic model of mutant growth

1987

Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin.

2012

Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all as…

Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes

2015

In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝn space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝn space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragme…

Nucleotide's bilinear indices: Novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affin…

2009

A new set of nucleotide-based bio-macromolecular descriptors are presented. This novel approach to bio-macromolecular design from a linear algebra point of view is relevant to nucleic acids quantitative structure-activity relationship (QSAR) studies. These bio-macromolecular indices are based on the calculus of bilinear maps on Re(n)[b(mk)(x (m),y (m)):Re(n) x Re(n)--Re] in canonical basis. Nucleic acid's bilinear indices are calculated from kth power of non-stochastic and stochastic nucleotide's graph-theoretic electronic-contact matrices, M(m)(k) and (s)M(m)(k), respectively. That is to say, the kth non-stochastic and stochastic nucleic acid's bilinear indices are calculated using M(m)(k)…

Scatter Search—Wellsprings and Challenges

2006

I came up with the idea of editing this volume in the summer of 2002 while working on the book "Scatter search methodologies and implementations in C" with Manuel Laguna in the University of Colorado at Boulder. There, Fred Glover kindly let me use his office, where I found a copy of the "Tabu Search Methods for Optimization" special issue that he edited in 1988 for the European Journal of Operational Research. This encounter made me realize that Scatter Search has reached a level of maturity as an optimization method that has parallels with what Tabu Search was experiencing in the late eighties. So I thought that the moment was perfect to embark on this project, which has been supported en…

Multiple-attribute decision support system based on fuzzy logic for performance assessment

2005

Abstract This paper deals with the problem of assessing the performance of a set of production units, simultaneously considering different kinds of information, yielded by a Data Envelopment Analysis, a qualitative data analysis and an expert assessment. The tool for integrating heterogeneous data is a model that applies fuzzy logic to decision support systems. The results obtained are a holistic performance assessment of each unit of the set and a ranking order of the units.

Response determination of linear dynamical systems with singular matrices: A polynomial matrix theory approach

2017

Abstract An approach is developed based on polynomial matrix theory for formulating the equations of motion and for determining the response of multi-degree-of-freedom (MDOF) linear dynamical systems with singular matrices and subject to linear constraints. This system modeling may appear for reasons such as utilizing redundant DOFs, and can be advantageous from a computational cost perspective, especially for complex (multi-body) systems. The herein developed approach can be construed as an alternative to the recently proposed methodology by Udwadia and coworkers, and has the significant advantage that it circumvents the use of pseudoinverses in determining the system response. In fact, ba…

The analytic hierarchy process with stochastic judgements

2014

The analytic hierarchy process (AHP) is a widely-used method for multicriteria decision support based on the hierarchical decomposition of objectives, evaluation of preferences through pairwise comparisons, and a subsequent aggregation into global evaluations. The current paper integrates the AHP with stochastic multicriteria acceptability analysis (SMAA), an inverse-preference method, to allow the pairwise comparisons to be uncertain. A simulation experiment is used to assess how the consistency of judgements and the ability of the SMAA-AHP model to discern the best alternative deteriorates as uncertainty increases. Across a range of simulated problems results indicate that, according to c…

Demyelination patterns in a mathematical model of multiple sclerosis.

2016

In this paper we derive a reaction-diffusion-chemotaxis model for the dynamics of multiple sclerosis. We focus on the early inflammatory phase of the disease characterized by activated local microglia, with the recruitment of a systemically activated immune response, and by oligodendrocyte apoptosis. The model consists of three equations describing the evolution of macrophages, cytokine and apoptotic oligodendrocytes. The main driving mechanism is the chemotactic motion of macrophages in response to a chemical gradient provided by the cytokines. Our model generalizes the system proposed by Calvez and Khonsari (Math Comput Model 47(7–8):726–742, 2008) and Khonsari and Calvez (PLos ONE 2(1):e…