Search results for "Computer Modeling"
showing 10 items of 11 documents
Universal natural shapes: From unifying shape description to simple methods for shape analysis and boundary value problems
2012
Gielis curves and surfaces can describe a wide range of natural shapes and they have been used in various studies in biology and physics as descriptive tool. This has stimulated the generalization of widely used computational methods. Here we show that proper normalization of the Levenberg-Marquardt algorithm allows for efficient and robust reconstruction of Gielis curves, including self-intersecting and asymmetric curves, without increasing the overall complexity of the algorithm. Then, we show how complex curves of k-type can be constructed and how solutions to the Dirichlet problem for the Laplace equation on these complex domains can be derived using a semi-Fourier method. In all three …
Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder.
2014
Background: Mutations in phosphomannomutase2 cause glycosylation disorder, a disease without a cure that will largely benefit from accurate ligand-bound models. Results: We obtained two models of phospomannomutase2 bound to glucose 1,6-bisphosphate and validated them with limited proteolysis. Conclusion: Ligand binding induces a large conformational transition in PMM2. Significance: We produce and validate closed-form models of PMM2 that represent a starting point for rational drug discovery.
Simulating Secularities: Challenges and Opportunities in the Computational Science of (Non)Religion
2021
This article provides scholars of nonreligion and secularism with an introduction to some of the major opportunities and challenges associated with the growing application of computational methods to the phenomena they study. It also illustrates these opportunities and challenges by describing several overlapping research projects and some of the models of (non)religion they have produced. Finally, the article addresses some of the significant philosophical issues surrounding the use of computer modeling and simulation, focusing on the ethical and epistemological concerns that these tools often raise. I invite scholars of nonreligion to consider adding these techniques to their methodologic…
Unreliable predictions about COVID‐19 infections and hospitalizations make people worry: The case of Italy
2021
Simulating multilevel dynamics of antimicrobial resistance in a membrane computing model
2019
Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested “membrane-surrounded entities” able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects…
Human Simulation and Sustainability : Ontological, Epistemological, and Ethical Reflections
2020
This article begins with a brief outline of recent advances in the application of computer modeling to sustainability research, identifying important gaps in coverage and associated limits in methodological capability, particularly in regard to taking account of the tangled human factors that are often impediments to a sustainable future. It then describes some of the ways in which a new transdisciplinary approach within &ldquo
Computer Modeling in Philosophy of Religion
2019
AbstractHow might philosophy of religion be impacted by developments in computational modeling and social simulation? After briefly describing some of the content and context biases that have shaped traditional philosophy of religion, this article provides examples of computational models that illustrate the explanatory power of conceptually clear and empirically validated causal architectures informed by the bio-cultural sciences. It also outlines some of the material implications of these developments for broader metaphysical and metaethical discussions in philosophy. Computer modeling and simulation can contribute to the reformation of the philosophy of religion in at least three ways: b…
Electric conduction in solids: a pedagogical approach supported by laboratory measurements and computer modelling environments
2008
In this paper we present a pedagogic approach aimed at modeling electric conduction in semiconductors, built by using NetLogo, a programmable modeling environment for building and exploring multi‐agent systems. ‘Virtual experiments’ are implemented to confront predictions of different microscopic models with real measurements of electric properties of matter, such as resistivity. The relations between these electric properties and other physical variables, like temperature, are, then, analyzed.
MuTE: a MATLAB toolbox to compare established and novel estimators of the multivariate transfer entropy.
2014
A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different ap…
Mechanics of pericardial effusion: A simulation study
2015
Pericardial effusion is a pathological accumulation of fluid within pericardial cavity, which may compress heart chambers with hemodynamic impairment. We sought to determine the mechanics underlying the physiology of the hemodynamic impairment due to pericardial effusion using patient-specific computational modeling. Computational models of left ventricle and right ventricle were based on magnetic resonance images obtained from patients with pericardial effusion and controls. Myocardial material parameters were adjusted, so that volumes of ventricular chambers and pericardial effusion agreed with magnetic resonance imaging data. End-diastolic and end-systolic pressure–volume relationships …