3,233 research outputs found
Generating functional analysis of complex formation and dissociation in large protein interaction networks
We analyze large systems of interacting proteins, using techniques from the
non-equilibrium statistical mechanics of disordered many-particle systems.
Apart from protein production and removal, the most relevant microscopic
processes in the proteome are complex formation and dissociation, and the
microscopic degrees of freedom are the evolving concentrations of unbound
proteins (in multiple post-translational states) and of protein complexes. Here
we only include dimer-complexes, for mathematical simplicity, and we draw the
network that describes which proteins are reaction partners from an ensemble of
random graphs with an arbitrary degree distribution. We show how generating
functional analysis methods can be used successfully to derive closed equations
for dynamical order parameters, representing an exact macroscopic description
of the complex formation and dissociation dynamics in the infinite system
limit. We end this paper with a discussion of the possible routes towards
solving the nontrivial order parameter equations, either exactly (in specific
limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of
Phys Conference Series
Towards a Method to Conceptualize Domain Ontologies
This paper presents the suite of principles, designs criteria and verification process used in
the knowledge conceptualization process of a consensuated domain ontology in the domain of
chemicals. To achieve agreement between different development teams we propose the use of
a common and shared conceptual model as starting point. To capture domain knowledge of a
given domain and organize it in a shared and consensuated conceptual model, we recommend
an approach that integrates the following intermediate representation techniques: Data
Dictionary, Concepts Classification Trees, Tables of Instance Attributes, Table of Class
Attributes, Table of Constants, Tables of Formulas, Attributes Classification Trees, and
Tables of Instances. We also provide a set of guidelines to verify the knowledge gathered
inside each intermediate representations and between intermediate representations
Groundwater pollution in quaternary aquifer of Vitoria - Gasteiz (Basque Country, Spain)
As a result of diverse changes in land use and in water-resource management in the high basin of the Zadorra River (Basque Country), an important loss of water resources and an intense contamination by nitrogen compounds has taken place. The purpose of this paper is to detail the land transformations that have taken place on the aquifer since the 1950s: increase of drainage network, change from dry to irrigated farming, and diversion of rivers at the aquifer unit inlet. Furthermore, we analyze the impact of these transformations on the hydrodynamics and water quality of this aquifer system
Reflectionless discrete perfectly matched layers for higher-order finite difference schemes
This paper introduces discrete-holomorphic Perfectly Matched Layers (PMLs)
specifically designed for high-order finite difference (FD) discretizations of
the scalar wave equation. In contrast to standard PDE-based PMLs, the proposed
method achieves the remarkable outcome of completely eliminating numerical
reflections at the PML interface, in practice achieving errors at the level of
machine precision. Our approach builds upon the ideas put forth in a recent
publication [Journal of Computational Physics 381 (2019): 91-109] expanding the
scope from the standard second-order FD method to arbitrary high-order schemes.
This generalization uses additional localized PML variables to accommodate the
larger stencils employed. We establish that the numerical solutions generated
by our proposed schemes exhibit an exponential decay rate as they propagate
within the PML domain. To showcase the effectiveness of our method, we present
a variety of numerical examples, including waveguide problems. These examples
highlight the importance of employing high-order schemes to effectively address
and minimize undesired numerical dispersion errors, emphasizing the practical
advantages and applicability of our approach
The Kuramoto model: A simple paradigm for synchronization phenomena
Synchronization phenomena in large populations of interacting elements are the subject of intense research efforts in physical, biological, chemical, and social systems. A successful approach to the problem of synchronization consists of modeling each member of the population as a phase oscillator. In this review, synchronization is analyzed in one of the most representative models of coupled phase oscillators, the Kuramoto model. A rigorous mathematical treatment, specific numerical methods, and many variations and extensions of the original model that have appeared in the last few years are presented. Relevant applications of the model in different contexts are also included
Evenly convex sets, and evenly quasiconvex functions, revisited
Since its appearance, even convexity has become a remarkable notion in convex analysis. In the fifties, W. Fenchel introduced the evenly convex sets as those sets solving linear systems containing strict inequalities. Later on, in the eighties, evenly quasiconvex functions were introduced as those whose sublevel sets are evenly convex. The significance of even convexity relies on the different areas where it enjoys applications, ranging from convex optimization to microeconomics. In this paper, we review some of the main properties of evenly convex sets and evenly quasiconvex functions, provide further characterizations of evenly convex sets, and present some new results for evenly quasiconvex functions.This research has been partially supported by MINECO of Spain and ERDF of EU, Grants PGC2018-097960-B-C22 and ECO2016-77200-P
Editorial: New insights into adult neurogenesis and neurodegeneration: challenges for brain repair
The formation of new neurons in the brain is probably one of the most controversial topics in the scientific community since in the 1960's Joseph Altman described for the first time that proliferating cells give rise to new neurons in the adult brain of rats and other mammals. This Research Topic includes 1 brief research report, 3 mini review, 4 review and 9 original research papers gathering different contributions highlighting new developments in the field of neurogenesis
Robust solutions to multi-objective linear programs with uncertain data
In this paper we examine multi-objective linear programming problems in the face of data uncertainty both in the objective function and the constraints. First, we derive a formula for the radius of robust feasibility guaranteeing constraint feasibility for all possible scenarios within a specified uncertainty set under affine data parametrization. We then present numerically tractable optimality conditions for minmax robust weakly efficient solutions, i.e., the weakly efficient solutions of the robust counterpart. We also consider highly robust weakly efficient solutions, i.e., robust feasible solutions which are weakly efficient for any possible instance of the objective matrix within a specified uncertainty set, providing lower bounds for the radius of highly robust efficiency guaranteeing the existence of this type of solutions under affine and rank-1 objective data uncertainty. Finally, we provide numerically tractable optimality conditions for highly robust weakly efficient solutions.This research was partially supported by the Australian Research Council, Discovery Project DP120100467, the MICINN of Spain, grant number MTM2011-29064-C03-02, and Generalitat Valenciana, grant number ACOMP/2013/062
WebODE: An integrated workbench for ontology representation, reasoning, and exchange
We present WebODE as a scalable, integrated workbench for ontological engineering that eases the modelling of ontologies, the reasoning with ontologies and the exchange of ontologies with other ontology tools and ontology-based applications. We will first describe the WebODE's knowledge model. We will then describe its extensible architecture, focusing on the set of independent ontology development functionalities that are integrated in this framework, such as the Ontology Editor, the Axiom Builder, the OKBC-based inference engine, and the documentation and interoperability services
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