Current Research Projects

We present StochSS: Stochastic Simulation as-a-Service, an integrated development environment for modeling and simulation of discrete stochastic biochemical systems.  An easy to use GUI enables researchers to quickly develop and simulate biological models on a desktop or laptop, which can then be expanded or combined to incorporate increasing levels of complexity.  As the demand for computational power increases, StochSS is able to seamlessly scale up by deploying cloud computing resources.  The software currently supports simulation of ODE and well-mixed discrete stochastic models, as well... More
The aim of this work is to develop efficient and flexible methods for accurate modeling and simulation of intracellular biochemical processes, with target applications in biology [1] and medicine [2]. Histogram of the Schlögl model [7] based on 10,000 realizations of the SSA (blue) and explicit tau-leaping (red) methods. A deterministic simulation cannot capture the bistability of this model. It has been established that traditional deterministic differential equation-based models may fail to capture important dynamics of biochemical systems due to the inherent randomness of the processes... More
Cell polarization is a fundamental process that underlies many aspects of cell and developmental biology. In the polarization process, cellular components that were previously uniformly distributed become asymmetrically localized to create the complexity of form and function that are the hallmark of biological systems. One of the best-studied examples of cell polarization is the growth of the mating projection (shmoo) during yeast mating. Yeast cells localize specific proteins to the front of the cell in response to a spatial gradient of mating pheromone secreted by the partner. The spatial... More
Trauma-induced coagulopathy is the catastrophic malfunction of blood coagulation after massive injuries. We investigate coagulopathy using a combination of systems biology modeling and analysis of clinical data.   The goal of our systems biology effort is to understand coagulopathy and to use this understanding to be able to predict the effects of possible therapies on patient outcome. To this end we use two approaches--bottom-up and top-down. In the bottom-up approach, we simulate a damaged blood vessel using a partial differential equation model of blood chemistry and flow (Figure 1),... More
StochKit is an efficient, extensible stochastic simulation framework developed in the C++ language that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms. The current version of StochKit includes the popular Gillespie Stochastic Simulation Algorithm (SSA) Direct Method, our new Logarithmic Direct Method which is considerably faster than the original Direct Method, slow-scale SSA for multiscale problems, adaptive non-negativity preserving explicit tau-leaping, and core modules for... More