Current Research Projects

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
Circadian oscillations in gene expression are an important biological adaptation to life in a periodic environment. These rhythms are generated through cellular genetic feedback loops, and are subject to significant stochastic variation. It is only through intercellular communication, and signaling from the suprachiasmatic nucleus (SCN) master clock in the brain that circadian rhythms are coordinated across the body and entrain to daily light cycles. The Petzold group studies circadian rhythm generation at cellular and network levels. Research focuses on the development and structure of... 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
Post-traumatic stress disorder (PTSD) is a severe anxiety disorder that affects a substantial portion of combat veterans and poses serious consequences to long-term health. Left untreated, PTSD can be life-threatening, as it is often linked with substance abuse and severe depression. Consequently, the identification of PTSD indicators (“biomarkers”) that can be detected in the blood or non-invasively is of great interest. Using both a social defeat mouse model of PTSD and minimally invasive data taken from U.S. Army veterans, we aim to identify biomarkers that aid in both the diagnosis and... More
Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to the worldwide decline and extinction of populations of numerous amphibian species. In particular we have observed invasion of this pathogen and the resulting local population extinctions of the mountain yellow-legged frog, Rana muscosa. A number of attempts have been made to save frog populations from being driven extinct by this disease, including anti-fungal treatments, and reducing the infectious zoospore density in the... 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
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
In mechanical engineering and material science, there has been a longstanding interest in materials with both high strength (resistance to applied force in the absence of macroscopic flaws) and high toughness (resistance to fracture), since these two properties are often at odds. Recently there has been increased interest in synthetics that mimic natural structures such as nacre. Nacre, shown in the figure below, is a material that consists of calcium carbonate and organic protein, but it has a toughness that is three orders of magnitude higher than calcium carbonate. The microstructure of... More
Electrodeposition is a very fast and economical way for depositing thin metal films. The commercial applications of electrodeposition range from solar cells and batteries to semiconductors and high density storage devices, just to name a few. The thin films are grown from individual nuclei on a substrate surface that grow into larger crystals by capturing adsorbed atoms (adatoms) that diffuse around on the surface. The growth rate of the thin films is limited by how quickly adatoms can diffuse and attach to the growth sites of the nuclei. This project examines the different modes of... More