Search results for "Modeling and Simulation"
showing 10 items of 1561 documents
LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: Theory and validation by QSARs
2019
Abstract Novel 3D protein descriptors based on bilinear, quadratic and linear algebraic maps in R n are proposed. The latter employs the kth 2-tuple (dis) similarity matrix to codify information related to covalent and non-covalent interactions in these biopolymers. The calculation of the inter-amino acid distances is generalized by using several dis-similarity coefficients, where normalization procedures based on the simple stochastic and mutual probability schemes are applied. A new local-fragment approach based on amino acid-types and amino acid-groups is proposed to characterize regions of interest in proteins. Topological and geometric macromolecular cutoffs are defined using local and…
A topological look at human trabecular bone tissue
2017
Bone quality is affected by trabecular architecture at microscopic level. Various abnormalities of bone tissue lead to altered strength and to an increased susceptibility to fracture, such as Osteoporosis and Osteoarthritis, two major health burdens of our society. These are two complex musculoskeletal diseases that mainly concern bone tissue. In the last twenty years, there has been a growing interest in finding an appropriate topological model for the micro-architecture of trabecular bone tissue. In particular, we prove that these models involve general topological spaces. The appropriate notion to deal with is that of CW-complex.
Viral replication modes in single-peak fitness landscapes: A dynamical systems analysis
2017
Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidence from distributions of mutations and from viral RNA amplification suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) mode. Although previous theoretical work has focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, little is known in terms of the bifurcations and transitions involving the so-called error threshold (mutation-induced dominance of mutants) and lethal mutagenesis (extinction of all sequences du…
Sustained oscillations in the MAP kinase cascade.
2016
Abstract The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This paper focuses on the existence of parameters for which Hopf bifurcations occur and generate periodic orbits. Furthermore it is explained how geometric singular perturbation theory allows to generalize results from simple models to more complex ones.
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …
On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory
2017
Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a v…
Evolutionary distances corrected for purifying selection and ancestral polymorphisms.
2019
Abstract Evolutionary distance formulas that take into account effects due to ancestral polymorphisms and purifying selection are obtained on the basis of the full solution of Jukes–Cantor and Kimura DNA substitution models. In the case of purifying selection two different methods are developed. It is shown that avoiding the dimensional reduction implicitly carried out in the conventional model solving is instrumental to incorporate the quoted effects into the formalism. The problem of estimating the numerical values of the model parameters, as well as those of the correction terms, is not addressed.
Identification of control targets in Boolean molecular network models via computational algebra
2015
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The pot…
Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening
2020
Cross-sectional studies conducted with obese and control subjects have suggested associations between gut microbiota alterations and obesity, but the links with specific disease phenotypes and proofs of causality are still scarce. The present study aimed to profile the gut microbiota of lean and obese children with and without insulin resistance to characterize associations with specific obesity-related complications and understand the role played in metabolic inflammation. Through massive sequencing of 16S rRNA gene amplicons and data analysis using a novel permutation approach, we have detected decreased incidence of Blautia species, especially Blautia luti and B. wexlerae, in the gut mic…
Some personal views on the current state and the future of locational analysis
1998
In this paper a group of participants of the 12th European Summer Institute which took place in Tenerife, Spain in June 1995 present their views on the state of the art and the future trends in Locational Analysis. The issues discussed include modeling aspects in discrete Location Theory, the influence of the distance function, the relation between discrete, network and continuous location, heuristic techniques, the state of technology and undesirable facility location. Some general questions are stated regarding the applicability of location models, promising research directions and the way technology affects the development of solution techniques.