In this article we study the existence of almost periodic solutions for distributed parameters biochemical system, with time delay when the input Sin is time dependent. This study is motivated by the input begin time dependent in many applications, and by the importance of almost periodically varying environments. Using the semigroup method, we prove that if the input is almost periodic then th...

Assessing and estimating essential parameters for a metabolic pathway by using a mathematical model is a significant step in Systems Biology. However, estimating process often faces numerous obstacles, for example when the number of unknown parameters escalates or data has noise, gets trapped in local minima and or having repeated exploration of poor solution during search process. Thus, this s...

The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the region in the parameter space in which the system is functional. In this paper, we show that, in addition to volume, the geometry of this region has important consequences for the robustness and the fra...

Iron deficiency anemia is the most prevalent nutritional disorder in the world. Information on the metabolism of hepcidin and its possible significance as a biochemical parameter in iron deficiency anemia is reported in this review, which was based on a survey of the databases PubMed and LILACS for articles published between 2006 and 2010 on hepcidin as a biomarker for the regulation of iron me...

Parameter sensitivity analysis is a powerful tool in the building and analysis of biochemical network models. For stochastic simulations, parameter sensitivity analysis can be computationally expensive, requiring multiple simulations for perturbed values of the parameters. Here, we use trajectory reweighting to derive a method for computing sensitivity coefficients in stochastic simulations wit...

We describe a novel biochemical sensing method and its potential new biosensing applications. A light-sensitive complementary metal oxide semiconductor (CMOS) chip prepared through a standard 0.5m CMOS process was developed for measuring biochemical reactions. A light producing enzymatic reaction catalyzed by horseradish peroxidase (HRP) was designed as a platform reaction to determine the conc...

MOTIVATION Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses. RESULTS Here we present a flexible and widely applicable noise decompo...

SUMMARY SPSens is a software package for the efficient computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity analysis is a valuable tool that can be used to study robustness properties, for drug targeting, and many other purposes. However its application to stochastic models has been limited when Monte Carlo methods are required due to extreme...

MOTIVATION The simulation of biochemical kinetic systems is a powerful approach that can be used for: (i) checking the consistency of a postulated model with a set of experimental measurements, (ii) answering 'what if?' questions and (iii) exploring possible behaviours of a model. Here we describe a generic approach to combine numerical optimization methods with biochemical kinetic simulations,...

Early detection of crop injury from herbicide glyphosate is of significant importance in crop management. In this paper, we attempt to detect glyphosate-induced crop injury by PROSPECT (leaf optical PROperty SPECTra model) inversion through leaf hyperspectral reflectance measurements for non-GlyphosateResistant (non-GR) soybean and non-GR cotton leaves. The PROSPECT model was inverted to retrie...