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Modeling and targeting an essential metabolic pathway of Plasmodium falciparum in apicoplast using Petri nets
Petri net (PN) is one of the promising computational and mathematical formalisms used to represent and study the behavior of complex metabolic...
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Exact distributions for stochastic models of gene expression with arbitrary regulation
Stochasticity in gene expression can result in uctuations in gene product levels. Recent experiments indicated that feedback regulation plays an...
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Local convergence of the Levenberg–Marquardt method under Hölder metric subregularity
We describe and analyse Levenberg–Marquardt methods for solving systems of nonlinear equations. More specifically, we propose an adaptive formula for...
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Infection Time in Multistable Gene Networks. A Backward Stochastic Variational Inequality with Nonconvex Switch-Dependent Reflection Approach
We investigate a mathematical model associated to the infection time in multistable gene networks. The mathematical processes are of hybrid switch...
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Ordered dynamics in biased and cooperative Boolean networks
This paper contributes to the theoretical analysis of the qualitative behavior of two types of Boolean networks: biased and cooperative ones. A...
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Complex Adaptive Systems Modeling: A multidisciplinary Roadmap
PAC Codes07.05.Tp, 89.75.-k, 89.75.Fb
Mathematics Subject Classification (2010)05C82, 68T42, 00A72, 92C42
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Neural field theory with variance dynamics
Previous neural field models have mostly been concerned with prediction of mean neural activity and with second order quantities such as its...
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Inverse problems from biomedicine
Many complex diseases that are difficult to treat cannot be mapped onto a single cause, but arise from the interplay of multiple contributing...
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Reconstruction of extended Petri nets from time-series data by using logical control functions
The aim of this work is to extend a previously presented algorithm (Durzinsky et al.
2008b in Computational methods in systems biology, LNCS, vol... -
Variable elimination in post-translational modification reaction networks with mass-action kinetics
We define a subclass of chemical reaction networks called post-translational modification systems. Important biological examples of such systems...
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A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development
Colon rectal cancers (CRC) are the result of sequences of mutations which lead the intestinal tissue to develop in a carcinoma following a...
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Stable periodicity and negative circuits in differential systems
We provide a counter-example to a conjecture of René Thomas on the relationship between negative feedback circuits and stable periodicity in ordinary...
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The interaction graph structure of mass-action reaction networks
Behaviour of chemical networks that are described by systems of ordinary differential equations can be analysed via the associated graph structures....
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On the impact of the distance between two genes on their interaction curve
We analyze a basic building block of gene regulatory networks using a stochastic/geometric model in search of a mathematical backing for the discrete...
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Hybrid simulation of autoregulation within transcription and translation
We analyse a simple gene regulatory system where a protein enhances its own rate of mRNA transcription. For the integer-valued, chemical master...
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Multistationarity in mass action networks with applications to ERK activation
Ordinary Differential Equations (ODEs) are an important tool in many areas of Quantitative Biology. For many ODE systems multistationarity (i.e. the...
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Efficient simulation of discrete stochastic reaction systems with a splitting method
Stochastic reaction systems with discrete particle numbers are usually described by a continuous-time Markov process. Realizations of this process...