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Discrete Groups and Internal Symmetries of Icosahedral Viral Capsids

Richard Kerner (2014)

Molecular Based Mathematical Biology

A classification of all possible icosahedral viral capsids is proposed. It takes into account the diversity of hexamers’ compositions, leading to definite capsid size.We showhowthe self-organization of observed capsids during their production results from definite symmetries of constituting hexamers. The division of all icosahedral capsids into four symmetry classes is given. New subclasses implementing the action of symmetry groups Z2, Z3 and S3 are found and described. They concern special cases...

From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology

E. Domingo, C. Perales (2012)

Mathematical Modelling of Natural Phenomena

RNA viruses replicate as complex and dynamic mutant distributions. They are termed viral quasispecies, in recognition of the fundamental contribution of quasispecies theory in our understanding of error-prone replicative entities. Viral quasispecies have launched a fertile field of transdiciplinary research, both experimental and theoretical. Here we review the origin and some implications of the quasispecies concept, with emphasis on internal interactions...

Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation

Weihua Geng, Shan Zhao (2013)

Molecular Based Mathematical Biology

The Poisson-Boltzmann (PB) model is an effective approach for the electrostatics analysis of solvated biomolecules. The nonlinearity associated with the PB equation is critical when the underlying electrostatic potential is strong, but is extremely difficult to solve numerically. In this paper, we construct two operator splitting alternating direction implicit (ADI) schemes to efficiently and stably solve the nonlinear PB equation in a pseudo-transient continuation approach. The operator splitting...

Genetic and Tabu search algorithms for peptide assembly problem

Jacek Błażewicz, Marcin Borowski, Piotr Formanowicz, Tomasz Głowacki (2010)

RAIRO - Operations Research

Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented....

High-order WENO scheme for polymerization-type equations*

Pierre Gabriel, Léon Matar Tine (2010)

ESAIM: Proceedings

Polymerization of proteins is a biochemical process involved in different diseases. Mathematically, it is generally modeled by aggregation-fragmentation-type equations. In this paper we consider a general polymerization model and propose a high-order numerical scheme to investigate the behavior of the solution. An important property of the equation is the mass conservation. The WENO scheme is built to preserve the total mass of proteins along time....

Homogeneous Systems with a Quiescent Phase

K. P. Hadeler (2008)

Mathematical Modelling of Natural Phenomena

Recently the effect of a quiescent phase (or dormant/resting phase in applications) on the dynamics of a system of differential equations has been investigated, in particular with respect to stability properties of stationary points. It has been shown that there is a general phenomenon of stabilization against oscillations which can be cast in rigorous form. Here we investigate, for homogeneous systems, the effect of a quiescent phase, and more generally, a phase with slower dynamics. We show that...

Host Factors in Viral Life Cycles

G. Pérez-Vilaró, J. Jungfleisch, V. Saludes, N. Scheller, M. Giménez-Barcons, J. Díez (2012)

Mathematical Modelling of Natural Phenomena

Viruses are obligate intracellular parasites that rely on the host cell for expansion. With the development of global analyses techniques like transcriptomics, proteomics and siRNA library screening of complete cellular gene sets, a large range of host cell factors have been discovered that either support or restrict virus growth. Here we summarize some of the recent findings and focus our discussion on the hepatitis C virus and the human immunodeficiency...

Intracellular Modelling of Cell-Matrix Adhesion during Cancer Cell Invasion

V. Andasari, M.A.J. Chaplain (2012)

Mathematical Modelling of Natural Phenomena

When invading the tissue, malignant tumour cells (i.e. cancer cells) need to detach from neighbouring cells, degrade the basement membrane, and migrate through the extracellular matrix. These processes require loss of cell-cell adhesion and enhancement of cell-matrix adhesion. In this paper we present a mathematical model of an intracellular pathway for the interactions between a cancer cell and the extracellular matrix. Cancer cells use similar...

Kendall's tau-type rank statistics in genome data

Moonsu Kang, Pranab Kumar Sen (2008)

Applications of Mathematics

High-dimensional data models abound in genomics studies, where often inadequately small sample sizes create impasses for incorporation of standard statistical tools. Conventional assumptions of linearity of regression, homoscedasticity and (multi-) normality of errors may not be tenable in many such interdisciplinary setups. In this study, Kendall's tau-type rank statistics are employed for statistical inference, avoiding most of parametric assumptions to a greater extent. The proposed procedures...

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