The immune system provides an intricate, balanced response to combat the effects of inflammatory stimuli. It incorporates both positive and negative feedback from multiple physiological systems such as cardiovascular endocrine including mechanisms functioning on a variety time scales. They have been studied individually via scientific experiments using mathematical modeling. However, more analy...

Bacteria can form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth a complex process affected by several variables, insights into formation could be obtained studying simple schematic models. In this manuscript, we describe hybrid molecular dynamics and Monte Car...

clostridium botulinum type a (bont/a) produces a neurotoxin recently found to be useful as an injectable drug for the treatment of abnormal muscle contractions. the catalytic domain of this toxin which is responsible for the main toxin activity is a zinc metalloprotease that inhibits the release of neurotransmitter mediators in neuromuscular junctions. a cell penetrating cationic peptide, tat, ...

The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellular processes. The analysis of reconstructed metabolic networks as systems leads to the development of an in silico or computer representation of collections of cellular metabolic constituents, their interaction...

The past two decades have seen impressive success for reductionist biologic science, generating new experimental data at an unprecedented rate. The list of organisms with completely sequenced genomes is growing each month. In June, the completion of a draft sequence of the entire human genome was announced amid much fanfare. Molecular mechanisms for fundamental processes such as ligand-receptor...

Stent intervention is a recommended therapy to reduce the pressure gradient and restore blood flow for patients with coarctation of aorta (CoA). In this work, we developed framework personalized stent in CoA using silico modeling, combining computational fluid dynamics (CFD) image-based prediction geometry after intervention. Firstly, aorta, whose was reconstructed from magnetic resonance imagi...

ChIP sequencing (ChIP-seq) is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the o...