Recent research in experimental and computational biology has revealed the necessity of using stochastic modeling and simulation to investigate the functionality and dynamics of gene networks. However, there is no sophisticated stochastic modeling techniques and efficient stochastic simulation algorithms SSA) for analyzing and simulating gene networks. Therefore, the objective of this research is to design …
Tag Archive: Biology
Mar
12
Design of large scale kinetic metabolic models: Applications in mammalian and algae metabolism
The modeling of cellular metabolism has always been a popular topic among researchers. The existing examples are usually confined to a particular pathway or cellular process. However, the massive research efforts in genetic annotation of the last decade have expanded the field to incorporate genome scale models GSMs), which include the entire cellular metabolism. Due …
Mar
11
MDCT-based dynamic, subject-specific lung models via image registration for CFD-based interrogation of regional lung function
Computational fluid dynamics (CFD) has become an attractive tool in understanding the characteristic of air flow in the human lungs. Due to inter-subject variations, subject-specific simulations are essential for understanding structure-function relationship, assessing lung function and improving drug delivery. However, currently the subject-specific CFD analysis remains challenging due, in large part to, two issues: construction …
Mar
10
Ionic mechanisms of action potential rate dependence, conduction and block in normal epicardium and in remodeled epicardium post-infarction
In this work, detailed computational models are used to study the electrophysiology of normal epicardium and the arrhythmogenic effects of epicardial cell remodeling post-infarction. The canine epicardial myocyte model described here reproduces a wide range of experimentally observed rate dependent phenomena in cell and tissue. Model behavior depends on updated formulations for the 4-AP sensitive …
Mar
10
Scientific and institutional complexities of managing surface water for beneficial human and ecosystem uses under a seasonally variable flow regime in Mediterranean climate northern California
In mediterranean-climate northern California, agricultural water needs are almost exclusively met locally. Grape growers in this region, including Napa, Sonoma, and Mendocino Counties, have diverted surface water from streams under appropriative and riparian doctrines throughout the 20th Century. Increased diversion requests from the Russian River drainage network Sonoma and Mendocino Counties), along with protections extended …
Mar
09
Mitral Valve Organ Culture Provides a Novel Experimental Paradigm
Mitral valve diseases and disorders affect tens of thousands of Americans each year, but understanding of the disease processes has yet to be fully developed. The behavior and characteristics of valve cells and tissue are highly dependent on their surrounding environment, including neighboring cells, extracellular matrix composition and 3D structure, mechanical forces, and signaling molecules …
Mar
08
Statistical methods for interpretation of high resolution mass spectra
Mass spectrometry is a powerful analytical technique used to characterize various compounds. A mass spectrum is a graph of ion intensity as a function of mass-to-charge ratio. Protein study experiments generate thousands of mass spectra, generating an overload of data that necessitates the development of sophisticated data analysis methods. Our work aims at developing the …
Feb
19
Systems theory for pharmaceutical drug discovery
Biological networks are comprised of thousands of interacting components, and these networks have complicated patterns of feedback and feed-forward motifs. It is practically impossible to use intuition to determine whether simultaneously modifying multiple pharmaceutical targets has a good therapeutic response. Even when a drug is discovered which is safe in humans and highly-effective against its …
Feb
16
Robust Stability Analysis for a Class of Extended Linearization Systems
We consider analysis of nonlinear systems that can be brought into a state dependent representation known as extended linearization. Under this formulation, conventional linear analysis techniques may be adapted to study the stability, optimality, and robustness properties of nonlinear systems. When subject to system uncertainty, estimating the radius of stability for systems under extended linearization …
Feb
16
Probabilistic computational methods for structural alignment of RNA sequences
In this thesis, the problem of structural alignment of homologous RNA sequences is addressed. The structural alignment of a given set of RNA sequences is a secondary structure for each sequence, such that the structures are similar to each other, and a sequence alignment between the sequences that is conforming with the secondary structures. A …