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A Computational Framework to Assess the Efficacy of Cytotoxic Molecules and Vascular Disrupting Agents against Solid Tumours

M. Pons-Salort, B. van der Sanden, A. Juhem, A. Popov, A. Stéphanou (2012)

Mathematical Modelling of Natural Phenomena

A computational framework for testing the effects of cytotoxic molecules, specific to a given phase of the cell cycle, and vascular disrupting agents (VDAs) is presented. The model is based on a cellular automaton to describe tumour cell states transitions from proliferation to death. It is coupled with a model describing the tumour vasculature and its adaptation to the blood rheological constraints when alterations are induced by VDAs treatment....

A hyperbolic model of chemotaxis on a network: a numerical study

G. Bretti, R. Natalini, M. Ribot (2014)

ESAIM: Mathematical Modelling and Numerical Analysis - Modélisation Mathématique et Analyse Numérique

In this paper we deal with a semilinear hyperbolic chemotaxis model in one space dimension evolving on a network, with suitable transmission conditions at nodes. This framework is motivated by tissue-engineering scaffolds used for improving wound healing. We introduce a numerical scheme, which guarantees global mass densities conservation. Moreover our scheme is able to yield a correct approximation of the effects of the source term at equilibrium. Several numerical tests are presented to show the...

Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells

G. Pinna, A. Zinovyev, N. Araujo, N. Morozova, A. Harel-Bellan (2012)

Mathematical Modelling of Natural Phenomena

Many cancer-associated genes and pathways remain to be identified in order to clarify the molecular mechanisms underlying cancer progression. In this area, genome-wide loss-of-function screens appear to be powerful biological tools, allowing the accumulation of large amounts of data. However, this approach currently lacks analytical tools to exploit the data with maximum efficiency, for which systems biology methods analyzing complex cellular networks...

Analyzing the dynamics of deterministic systems from a hypergraph theoretical point of view

Luis M. Torres, Annegret K. Wagler (2013)

RAIRO - Operations Research - Recherche Opérationnelle

To model the dynamics of discrete deterministic systems, we extend the Petri nets framework by a priority relation between conflicting transitions, which is encoded by orienting the edges of a transition conflict graph. The aim of this paper is to gain some insight into the structure of this conflict graph and to characterize a class of suitable orientations by an analysis in the context of hypergraph theory.

Enumerated type semantics for the calculus of looping sequences

Livio Bioglio (2011)

RAIRO - Theoretical Informatics and Applications

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. In this paper we enrich this calculus with a type discipline which preserves some biological properties depending on the minimum and the maximum number of elements of some type requested by the present elements. The type system enforces these properties and typed reductions guarantee that evolution preserves them. As an example, we model the hemoglobin structure...

Enumerated type semantics for the calculus of looping sequences

Livio Bioglio (2011)

RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. In this paper we enrich this calculus with a type discipline which preserves some biological properties depending on the minimum and the maximum number of elements of some type requested by the present elements. The type system enforces these properties and typed reductions guarantee that evolution preserves them. As an example, we model the hemoglobin structure and...

Human Immunodeficiency Virus Infection : from Biological Observations to Mechanistic Mathematical Modelling

G. Bocharov, V. Chereshnev, I. Gainova, S. Bazhan, B. Bachmetyev, J. Argilaguet, J. Martinez, A. Meyerhans (2012)

Mathematical Modelling of Natural Phenomena

HIV infection is multi-faceted and a multi-step process. The virus-induced pathogenic mechanisms are manifold and mediated through a range of positive and negative feedback regulations of immune and physiological processes engaged in virus-host interactions. The fundamental questions towards understanding the pathogenesis of HIV infection are now shifting to ‘dynamic’ categories: (i) why is the HIV-immune response equilibrium finally disrupted? (ii)...

Model based analysis of signaling pathways

Jarosław Smieja (2008)

International Journal of Applied Mathematics and Computer Science

The paper is concerned with application of mathematical modeling to the analysis of signaling pathways. Two issues, deterministic modeling of gene transcription and model-driven discovery of regulatory elements, are dealt with. First, the biological background is given and the importance of the stochastic nature of biological processes is addressed. The assumptions underlying deterministic modeling are presented. Special emphasis is put on describing gene transcription. A framework for including...

Modeling Morphogenesis in silico and in vitro: Towards Quantitative, Predictive, Cell-based Modeling

R. M. H. Merks, P. Koolwijk (2009)

Mathematical Modelling of Natural Phenomena

Cell-based, mathematical models help make sense of morphogenesis—i.e. cells organizing into shape and pattern—by capturing cell behavior in simple, purely descriptive models. Cell-based models then predict the tissue-level patterns the cells produce collectively. The first step in a cell-based modeling approach is to isolate sub-processes, e.g. the patterning capabilities of one or a few cell types in cell cultures. Cell-based models can then identify the mechanisms responsible for patterning in...

Modelling the Spread of Infectious Diseases in Complex Metapopulations

J. Saldaña (2010)

Mathematical Modelling of Natural Phenomena

Two main approaches have been considered for modelling the dynamics of the SIS model on complex metapopulations, i.e, networks of populations connected by migratory flows whose configurations are described in terms of the connectivity distribution of nodes (patches) and the conditional probabilities of connections among classes of nodes sharing the same degree. In the first approach migration and transmission/recovery process alternate sequentially,...

Nonlinear stabilizing control of an uncertain bioprocess model

Neli Dimitrova, Mikhail Krastanov (2009)

International Journal of Applied Mathematics and Computer Science

In this paper we consider a nonlinear model of a biological wastewater treatment process, based on two microbial populations and two substrates. The model, described by a four-dimensional dynamic system, is known to be practically verified and reliable. First we study the equilibrium points of the open-loop system, their stability and local bifurcations with respect to the control variable. Further we propose a feedback control law for asymptotic stabilization of the closed-loop system towards a...

On the Use of the Hill Functions in Mathematical Models of Gene Regulatory Networks

M. Santillán (2008)

Mathematical Modelling of Natural Phenomena

Hill functions follow from the equilibrium state of the reaction in which n ligands simultaneously bind a single receptor. This result if often employed to interpret the Hill coefficient as the number of ligand binding sites in all kinds of reaction schemes. Here, we study the equilibrium states of the reactions in which n ligand bind a receptor sequentially, both non-cooperatively and in a cooperative fashion. The main outcomes of such analysis are that: n is not a good estimate, but only an upper...

Reaction-Diffusion Modelling of Interferon Distribution in Secondary Lymphoid Organs

G. Bocharov, A. Danilov, Yu. Vassilevski, G.I. Marchuk, V.A. Chereshnev, B. Ludewig (2011)

Mathematical Modelling of Natural Phenomena

This paper proposes a quantitative model of the reaction-diffusion type to examine the distribution of interferon-α (IFNα) in a lymph node (LN). The numerical treatment of the model is based on using an original unstructured mesh generation software Ani3D and nonlinear finite volume method for diffusion equations. The study results in suggestion that due to the variations in hydraulic conductivity of various zones of the secondary lymphoid organs...

Some necessary and sufficient conditions for the output controllability of temporal Boolean control networks

Yang Liu, Jianquan Lu, Bo Wu (2014)

ESAIM: Control, Optimisation and Calculus of Variations

This paper investigates the output controllability problem of temporal Boolean networks with inputs (control nodes) and outputs (controlled nodes). A temporal Boolean network is a logical dynamic system describing cellular networks with time delays. Using semi-tensor product of matrices, the temporal Boolean networks can be converted into discrete time linear dynamic systems. Some necessary and sufficient conditions on the output controllability via two kinds of inputs are obtained by providing...

Using R to Build and Assess Network Models in Biology

G. Hartvigsen (2011)

Mathematical Modelling of Natural Phenomena

In this paper we build and analyze networks using the statistical and programming environment R and the igraph package. We investigate random, small-world, and scale-free networks and test a standard problem of connectivity on a random graph. We then develop a method to study how vaccination can alter the structure of a disease transmission network. We also discuss a variety of other uses for networks in biology.

Viability, invariance and reachability for controlled piecewise deterministic Markov processes associated to gene networks

Dan Goreac (2012)

ESAIM: Control, Optimisation and Calculus of Variations

We aim at characterizing viability, invariance and some reachability properties of controlled piecewise deterministic Markov processes (PDMPs). Using analytical methods from the theory of viscosity solutions, we establish criteria for viability and invariance in terms of the first order normal cone. We also investigate reachability of arbitrary open sets. The method is based on viscosity techniques and duality for some associated linearized problem. The theoretical results are applied to general...

Viability, invariance and reachability for controlled piecewise deterministic Markov processes associated to gene networks

Dan Goreac (2012)

ESAIM: Control, Optimisation and Calculus of Variations

We aim at characterizing viability, invariance and some reachability properties of controlled piecewise deterministic Markov processes (PDMPs). Using analytical methods from the theory of viscosity solutions, we establish criteria for viability and invariance in terms of the first order normal cone. We also investigate reachability of arbitrary open sets. The method is based on viscosity techniques and duality for some associated linearized problem. The theoretical results are applied to general...

Viability, invariance and reachability for controlled piecewise deterministic Markov processes associated to gene networks

Dan Goreac (2012)

ESAIM: Control, Optimisation and Calculus of Variations

We aim at characterizing viability, invariance and some reachability properties of controlled piecewise deterministic Markov processes (PDMPs). Using analytical methods from the theory of viscosity solutions, we establish criteria for viability and invariance in terms of the first order normal cone. We also investigate reachability of arbitrary open sets. The method is based on viscosity techniques and duality for some associated linearized problem. The theoretical results are applied to general...

Weighted Elastic Net Model for Mass Spectrometry Imaging Processing

D. Hong, F. Zhang (2010)

Mathematical Modelling of Natural Phenomena

In proteomics study, Imaging Mass Spectrometry (IMS) is an emerging and very promising new technique for protein analysis from intact biological tissues. Though it has shown great potential and is very promising for rapid mapping of protein localization and the detection of sizeable differences in protein expression, challenges remain in data processing due to the difficulty of high dimensionality and the fact that the number of input variables in...

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