Kagan Tuncay

Learn More
The Poisson-Boltzmann (PB) equation has been extensively used to analyze the energetics and structure of proteins and other significant biomolecules immersed in electrolyte media. A new highly efficient approach for solving PB-type equations that allows for the modeling of many-atoms structures such as encountered in cell biology, virology, and(More)
Transcriptional regulatory network (TRN) discovery using information from a single source does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. A methodology, TRND, that integrates a preliminary TRN, gene expression data and gene ontology is developed to discover TRNs. The method is(More)
Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present a computational string model for simulating the dynamics of Escherichia coli chromosome segregation. A novel thermal-average force field accounting for stretching, bending, volume(More)
Gene expression microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, refined diagnoses and the discovery of well-targeted treatments. A new approach to the construction and quantification of transcriptional regulatory networks (TRNs) is presented that integrates gene expression microarray data and cell(More)
Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and(More)
Flow and nutrient dynamics in a subterranean estuary (Waquoit Bay, MA, 1 USA): field data and reactive transport modeling 2 3 Claudette Spiteri, Caroline P. Slomp, Matthew. A. Charette, Kagan Tuncay 4 and Christof Meile 5 (1) Department of Earth Sciences – Geochemistry, Faculty of Geosciences, Utrecht 6 University, P.O. Box 80021, 3508 TA Utrecht, The(More)
It is hypothesized that the many human cell types corresponding to multiple states is supported by an underlying nonlinear dynamical system (NDS) of transcriptional regulatory network (TRN) processes. This hypothesis is validated for epithelial cells whose TRN is found to support an extremely complex array of states that we term a "bifurcation nexus", for(More)
In one-dimensional (1D) early diagenetic models, bioirrigation is typically represented by a nonlocal mass transfer or bioirrigation coefficient, . Usually, all pore water species are assigned the same . Here, we show that this assumption can lead to significant errors in estimates of bioirrigation intensities. Using a simplified early diagenetic reaction(More)
Prediction of the fate and environmental impacts of groundwater contaminants requires the identification of relevant biogeochemical processes and necessitates the macroscopic representation of microbial activity occurring at the microscale. Using a well-studied sandy aquifer environment, we evaluate the importance of pore distribution on organic matter(More)