67 research outputs found
Modeling Bacterial Metabolism and Genetic Regulation
No full textA number of methods have been proposed to incorporate gene expression data to improve metabolic modeling with Flux Balance Analysis (FBA). With the idea of using probabilities of specific genes to be on or off which are computed from gene expression data, one of such methods, PROM (the Probabilistic Regulation of Metabolism) is known to produce better results than traditional methods. However, it suffers from the lack of biological explanation why it uses such probabilities to limit fluxes of reactions instead of setting genes to be on or off. In our method, we use the probabilities to penalize inconsistent gene usage by incorporating gene use variables into the objective function during FBA. We also decided to implement the method on KBase, an open platform for genomics and systems biology, to utilize existing methods and data, and to make it easier to publish and share our method and results in future
Infrared intensities of methyl fluoride: Determination of the signs of the dipole moment derivatives
No full text
Proposing Genes for Gap Reactions in Metabolic Pathways
No full textA metabolic model is a map of the biochemical reactions that take place in an organism. These reactions are catalyzed by enzymes, which are encoded by genes in the organism’s genome. However, there are reactions that are known to exist and needed to complete the metabolic model, but are not associated with any genes. These are called “gap reactions”. Our goal is to find the genes that encode the enzymes that catalyze these gap reactions. We have researched two approaches: a knowledge-driven approach that focuses on finding a small set of good candidates, and a data-driven approach that focuses on scoring all candidates to rank their plausibility. Identifying the genes that are associated with gap reactions produces better predictive models and directs laboratory experimentation
Silicon based device for smart assessment of cellular stiffness
No full textCellular stiffness plays an important role for several diseases such as atherosclerosis, malaria and cancer. Cellular stiffness can be derived by the velocity of a cell that is squeezed through a constriction channel. For example, a rigid cell will move slowly through the constriction channel and vice versa. In this research a microfluidic device with integrated electrodes was fabricated to detect the cell within the constriction channel. The velocity of the cell can be measured if the cell is detected at two different location. In this thesis the fabrication process of the device based on standard IC process is presented and electrically characterized.Electrical Engineering | Microelectronic
(re)framing the narrative: Storytelling otherwise for a just forest economy in Kampala's city region
No full textKampala is the heartbeat of Uganda’s economy and has driven rural-urban migration over the years as people travel in search of better opportunities (Namwanje, 2022). This has led to rapid urbanisation and unprecedented growth of the informal sector that extends beyond the geographical confines of the city. Rural areas, acting as spatial extensions of the city, have served as productive landscapes, supporting Kampala’s bustling informal economy and the livelihoods of city dwellers. Over the years, large expanses of uncultivated land in rural areas and natural forests in some cases, have been replaced with monocultural commercial forests causing socio-ecological degradation in Kampala’s city region. While studying past and current trends in Uganda’s forest governance, as well as the socio-cultural relations between people and forests, the study brings to light the social and epistemic injustices of past and current exclusionary forestry policies and practices. Storytelling is used not only as an investigative tool to understand the lives of the Batwa indigenous forest peoples, but also as an approach to document local knowledges and envision an alternative future outside the realm of western technocratic approaches. Counter-storytelling operates as activism, transcending oppression while fostering emanicipation and transformation of the Batwa people. In so doing, the project seeks to achieve self-determination for a just forest economy in Kampala’s city region.Architecture, Urbanism and Building Sciences | Complex Citie
Hierarchy of reaction dynamics in a thermally fluctuating environment
No full textNonlinear dynamics in the passage over rank-one saddle is investigated as a function of temperature in the presence of stochastic, thermal fluctuation. The analyses are based on a framework we developed recently adopting a multidimensional underdamped Langevin equation (without any assumption for the form of the potential of mean force). The framework can in principle provide a single coordinate to enable us to predict the final destination of the reaction in a thermally fluctuating media. At each temperature, the preciseness or the error of the reaction coordinate is evaluated in capturing the true reaction dynamics at different levels of approximations. By using the Müller-Brown potential as an illustrative example, it is found that a hierarchy of dynamical structure exists in the region of rank-one saddle, in which the crossing dynamics qualitatively changes as the temperature increases. We discuss the mechanism of how the reaction coordinate persists, which provides a boundary of the reaction to divide the phase space into the reactive and the nonreactive regions, even in the presence of thermal fluctuation
Dynamic reaction coordinate in thermally fluctuating environment in the framework of the multidimensional generalized Langevin equations
No full textA framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Müller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account the thermally fluctuating environments, the memory effect, and the nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment
Why and how do systems react in thermally fluctuating environments?
No full textMany chemical reactions, including those of biological importance, take place in thermally fluctuating environments. Compared to isolated systems, there arise markedly different features due to the effects of energy dissipation through friction and stochastic driving by random forces reflecting the fluctuation of the environment. Investigation of how robustly the system reacts under the influence of thermal fluctuation, and elucidating the role of thermal fluctuation in the reaction are significant subjects in the study of chemical reactions. In this article, we start with overviewing the generalized Langevin equation (GLE), which has long been used and continues to be a powerful tool to describe a system surrounded by a thermal environment. It has been also generalized further to treat a nonstationary environment, in which the conventional fluctuation-dissipation theorem no longer holds. Then, within the framework of the Langevin equation we present a method recently developed to extract a new reaction coordinate that is decoupled from all the other coordinates in the region of a rank-one saddle linking the reactant and the product. The reaction coordinate is buried in nonlinear couplings among the original coordinates under the influence of stochastic random force. It was ensured that the sign of this new reaction coordinate (= a nonlinear functional of the original coordinates, velocities, friction, and random force) at any instant is sufficient to determine in which region, the reactant or the product, the system finally arrives. We also discuss how one can extend the method to extract such a coordinate from the GLE framework in stationary and nonstationary environments, where memory effects exist in dynamics of the reaction
Nonlinear dynamical effects on reaction rates in thermally fluctuating environments
No full textA framework to calculate the rate constants of condensed phase chemical reactions of manybody systems is presented without relying on the concept of transition state. The theory is based on a framework we developed recently adopting a multidimensional underdamped Langevin equation in the region of rank-one saddle. The theory provides a reaction coordinate expressed as an analytical nonlinear functional of the position coordinates and velocities of the system (solute), the friction constants, and the random force of the environment (solvent). Up to moderately high temperature, the sign of the reaction coordinate can determine the final destination of the reaction in a thermally fluctuating media, irrespective of what values the other (nonreactive) coordinates may take. In this paper, it is shown that the reaction probability is analytically derived as the probability of the reaction coordinate being positive, and that the integration with the Boltzmann distribution of the initial conditions leads to the exact reaction rate constant when the local equilibrium holds and the quantum effect is negligible. Because of analytical nature of the theory taking into account all nonlinear effects and their combination with fluctuation and dissipation, the theory naturally provides us with the firm mathematical foundation of the origin of the reactivity of the reaction in a fluctuating media
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