http://hdl.handle.net/1803/64 Mon, 13 May 2013 01:37:52 GMT 2013-05-13T01:37:52Z http://hdl.handle.net/1803/1222 Title: Viral flight data recorder for systems biology applications Authors: Boczko, Erik M. Abstract: The paper briefly describes the construction of self organizing nanoparticles that can be designed to detect and record arbitrary intracellular events. The basic design captures nucleic acids. The design utilizes a single viral coat protein to nucleate a capsid if and only if a quantum of specific intracellular events occur. Wed, 13 Aug 2008 05:00:00 GMT http://hdl.handle.net/1803/1222 2008-08-13T05:00:00Z http://hdl.handle.net/1803/1166 Title: Age distribution formulas for budding yeast Authors: Boczko, Erik M.; Ban, Hyunju Abstract: Yeast are an important eukaryotic model system in the study of aging. Replicative age in budding yeast can be quantitatively determined by visualizing chitanous bud scars. The dynamics of the process of growth and division effects the distribution of replicative age. How much physiological information is encoded in experimental age distributions is not fully understood. Formulas relating the stationary age distribution to the spectrum of generational and culture doubling times have been proposed by several authors over the past four decades. We discuss the assumptions upon which they rest and some natural extensions. We describe the replicative age distribution of a population growing exponentially in terms of generational flux residence times. We demonstrate the utility of this description and show that it produces excellent agreement with experimental data, and describe how it compares with previous work. We demonstrate that the age distribution in a variety of strains can be predicted by a realistic population model, and we indicate how the age distribution is altered by perturbations and control. Tue, 05 Aug 2008 18:15:41 GMT http://hdl.handle.net/1803/1166 2008-08-05T18:15:41Z http://hdl.handle.net/1803/185 Title: Next-generation quantitative measurements to validate a model for yeast nitrogen catabolite repression in Saccharomyces cerevisiae Authors: Stowers, Chris; Boczko, Erik M. Abstract: Our work is motivated by the desire to quantitatively measure biological dynamical systems. Our agenda is to describe and understand emergent behavior and to explain the observed super robustness of biological dynamics. The specific system that provides the focus for our work is an ostensibly simple stress response circuit in baker's yeast, Saccharomyces cerevisiae, that regulates the organisms' genetic response to nitrogen limitation called nitrogen catabolite repression (NCR). The circuitry of the network has been well studied for the last 40 years and comparatively much is known about its function, however, little is known about its dynamics. In order to study the dynamics at the same level of sophistication at which we formulate and reason with mathematical models, we require quantitative biophysical and biochemical techniques that are accurate at molecular dimensions on physiological timescales. Such techniques are currently in their infancy. The overall goal is to further develop the tools and techniques to measure the quantitative biological behavior of the NCR circuit well enough to refine a current NCR model and understand how to apply the model to other regulatory networks leading to advances in biology, control theory and beyond. The broader impact of our effort reaches far beyond understanding the molecular physiology of a simple fungal stress response towards a deeper understanding of the underpinnings of why some circuits persist while others do not. Mon, 12 Feb 2007 14:10:02 GMT http://hdl.handle.net/1803/185 2007-02-12T14:10:02Z http://hdl.handle.net/1803/153 Title: Molecular Seismology: An inverse problem in nanobiology. Authors: Boczko, Erik M.; Hinow, Peter Abstract: The density profile of an elastic fiber like DNA will change in space and time as ligands associate with it. This observation affords a new direction in single molecule studies provided that density profiles can be measured in space and time. In fact, this is precisely the objective of seismology, where the mathematics of inverse problems have been employed with success. We argue that inverse problems in elastic media can be directly applied to biophysical problems of fiber-ligand association, and demonstrate that robust algorithms exist to perform density reconstruction in the condensed phase. Tue, 12 Sep 2006 19:44:22 GMT http://hdl.handle.net/1803/153 2006-09-12T19:44:22Z