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Cancer is the second leading cause of death in the United States. It is believed that many people develop cancers in their lifetime but the immune system kills these cells without the need for outside treatments. In cancer progression, however, tumor cells may evade the immune system by a mechanism that is not fully understood. Soluble fibrin (sFn), a marker for disseminated intravascular coagulation,...
Protein structure prediction, known as an NP-complete problem, is one of the basic problems in computational biology. To get an efficiency approach of protein structure prediction with Toy model, a new algorithm structure based on quantum-behaved particle swarm optimization (QPSO) structure is suggested, which is named as multiple-layer QPSO (MLQPSO). In this structure, population of each generation...
A hysteresis model is proposed to describe the calcium-regulated Cilia Beat Frequency (CBF) in airway epithelial cells. In this dynamic model, the kinetics of coupling between [Ca2+]i and CBF is considered as a two-step process. First, Ca2+ directly binds to or indirectly influences the axonemal proteins to induce the conformational changes in axonemal proteins. This process can be modeled by a Hill...
This paper addresses robust stability of genetic regulatory networks (GRNs) with stochastic perturbation and discrete and distributed time-varying delays. Aside from discrete delays, there are few results about stability of GRNs with distributed delay. In this paper, noise perturbation and delays have been considered in both mRNA and protein dynamics. Based on Lyapunov functional approach and linear...
Gene regulatory networks are highly complex dynamical systems of biomolecular components - genes, mRNA, proteins. These components interact with each other and through those interactions determine gene expression levels, i.e., determine the rate of gene transcription to mRNA and, consequently, the rate of mRNA translation to proteins. In this paper, a particle filter with MCMC move step is employed...
Macromolecular transport across the vessel wall, apparently the earliest pre-atherosclerotic event, is known to occur due to advection by transmural pressure driven water transport, characterized by the hydraulic conductivity (Lp). Our group's discovery of the presence of aquaporin-1 (AQP) in aortic endothelial cells suggests a new possibility of water transport across the endothelial cell (EC), alongside...
In this paper we study the asymptotic stability of neutral functional differential equation (NFDE) model of genetic regulatory networks (GRNs) with time-varying delays. It is assumed that time varying delays belong to the predefined intervals. SUM regulatory logic was used for the modeling of the effects from other genes. We consider not only time delayed concentration of messenger ribonucleic acid...
Early patterning in the Drosophila melanogaster embryo occurs through a complicated network of interactions involving transcription factor proteins and the mRNA of their target genes. One such system is the pattern of hunchback mRNA and its regulation by Bicoid and Kru??ppel proteins. This system is well-studied, but there is disagreement amongst biologists on how exactly hunchback expression is regulated...
In this paper we describe a new maximum likelihood approach to infer kinetic rate constants from time-course data and apply it to estimate the rate constants of the synthesis and degradation of the mRNA of Cdc20 protein, and the rate constant of the transcription of the cdc20 gene into Cdc20 protein. The Cdc20 protein plays a crucial role in eukaryotic cell cycle, as it codes for the cyclin antagonist...
Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few...
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