Using statistical physics principles to solve problems in biology is one of the most promising directions due to the complexity and non-equilibrium fluctuations in biological systems. In this work, we try to describe the dynamics at both cellular and molecular levels. Microtubule dynamics and dynamic disorder of enzyme proteins are two of the examples we investigated. The dynamics of microtubules and the mechanical properties of these polymers are essential for many key cellular processes. However, critical discrepancies between experimental observations and existing models need to be resolved before further progress towards a complete model can be made. We carried out computational studies to compare the mechanical properties of two alternative models, one corresponding to the existing, conventional model, and the other considering an additional type of tubulin lateral interaction described in a cryo-EM structure of a proposed trapped intermediate in the microtubule assembly process. Our work indicates that a class of sheet structures is transiently trapped as an intermediate during the assembly process in physiological conditions. In the second part of the work, we analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can serve as a basic functional motif with properties normally discussed with larger networks in the field of systems biology. The work on slow enzyme dynamics fills the missing gap between studies on intramolecular and network dynamics. We also showed that enzyme fluctuations could be amplified into fluctuations in phosphorylation networks. This can be used as a novel biochemical "reporter" for measuring single enzyme conformational fluctuation rates. / Ph. D.

Agronomic and water quality impacts of urea particle size were evaluated through field and laboratory experiments and mathematical modeling. In a two-year field study, corn silage yield, corn nitrogen (N) removal, and nitrate-N (NO₃⁻-N) leaching from urea pellets (1.5 g each) and granules (0.01-0.02 g each) applied at 184 kg-N/ha were compared. A control treatment (no N) and two other N application rates (110 and 258 kg-N/ha) were also included. Urea particle size impact on dissolution rate, dissolved urea movement, mineralization, and N0³-N leaching were evaluated in the laboratory. A two-dimensional (2-D) mathematical model was developed to simulate the fate of subsurface-banded urea and its transformation products, ammonium (NH₄⁺)and NO₃⁻. With 184 kg-N/ha, corn silage yield was 15% higher (p = 0.02) and corn N removal was 19% higher (p = 0.07) with pellets than granules in the second year of the field study. In the absence of yield response at 110 kg-N/ha, reason for higher yield at 184 kg-N/ha with pellets was unclear. Greater N removal reduced NO₃⁻-N leaching potential from pellets compared to granules during the over-winter period. No urea form response to yield or corn N removal was observed in the first year. In 23 of 27 sampling events, granules had higher NO₃⁻-N concentration in the root zone than pellets, with average nitrate-N concentrations of 2.6 and 2.2 mg-N/L, respectively. However, statistically, NO₃⁻-N leaching from the root zone was unaffected by urea form, probably due to high variability within treatments masking the treatment effects. In October 1997, pellets retained 16% more (p = 0.04) inorganic-N in the top half of the root zone than granules, due to slower nitrification in pellets as was determined in the mineralization study. Slower NO₃⁻-N leaching allowed for greater N extraction by plants. Pellets had lower dissolution, urea hydrolysis, and nitrification rates than granules; however, nitrification inhibition was the dominant mechanism controlling N fate. The model took into account high substrate concentration effects on N transformations, important for simulating the fate of band-applied N. The model exhibited good mass conservative properties, robustness, and expected moisture and N distribution profiles. Differences in measured field data and model outputs were likely due to uncertainties and errors in measured data and input parameters. Model calibration results indicated that moisture-related parameters greatly affected N fate simulation. Sensitivity analyses indicated the importance of nitrification-related parameters in N simulation, particularly, their possible multiplicative effects. Need for extensive model testing and validation was recognized. The validated 2-D N model could be incorporated into a management model for better management of subsurface-banded granular N. However, the 2-D model is not appropriate for simulating the three dimensional N movement from pellets. / Ph. D.

<i>Caulobacter crescentus</i> is an important model organism for studying regulation of cell growth, division and differentiation in prokaryotes. <i>C. crescentus</i> undergoes asymmetric division producing two progeny cells with identical genome but different developmental programs: the "swarmer" cell is flagellated and motile, and the "stalked" cell is sessile (attached to a surface by its stalk and holdfast). Only stalked cells undergo chromosome replication and cell division. A swarmer cell must shed its flagellum and grow a stalk before it can enter the replication-division cycle. Based on published experimental evidence, we propose a molecular mechanism controlling the cell division cycle in this bacterium. Our quantitative model of the mechanism illustrates detailed temporal dynamics of regulatory proteins and corresponding physiological changes during the process of cell cycle progression and differentiation of wild-type cells (both stalked cells and swarmer cells) and of a number of known and novel mutant strains. Our model presents a unified view of temporal regulation of protein activities during the asymmetric cell division cycle of <i>C. crescentus</i> and provides an opportunity to study and analyze the system dynamics of the <i>Caulobacter</i> cell cycle (as opposed to the dynamics of individual steps). The model can serve as a starting point for investigating molecular regulations of cell division and differentiation in other genera of alpha-proteobacteria, such as <i>Brucella</i> and <i>Rhizobium</i>, because recent experimental data suggest that these alpha-proteobacteria share similar genetic mechanisms for cell cycle control. / Ph. D.

In the post-"omic" era the analysis of high-throughput data is regarded as one of the major challenges faced by researchers. One focus of this data analysis is uncovering biological network topologies and dynamics. It is believed that this kind of research will allow the development of new mathematical models of biological systems as well as aid in the improvement of already existing ones. The work that is presented in this dissertation addresses the problem of the analysis of highly complex data sets with the aim of developing a methodology that will enable the reconstruction of a biological network from time series data through an iterative process. The first part of this dissertation relates to the analysis of existing methodologies that aim at inferring network structures from experimental data. This spans the use of statistical tools such as correlations analysis (presented in Chapter 2) to more complex mathematical frameworks (presented in Chapter 3). A novel methodology that focuses on the inference of biological networks from time series data by least squares fitting will then be introduced. Using a set of carefully designed inference rules one can gain important information about the system which can aid in the inference process. The application of the method to a data set from the response of the yeast Saccharomyces cerevisiae to cumene hydroperoxide is explored in Chapter 5. The results show that this method can be used to generate a coarse-level mathematical model of the biological system at hand. Possible developments of this method are discussed in Chapter 6. / Ph. D.

Vector-borne diseases (VBDs) cause significant harm to humans, plants, and animals worldwide. For instance, VBDs are very difficult to manage, as they are governed by complex interactions. VBD transmission depends on the pathogen itself, vector-host movement, and environmental conditions. Mosquito-borne diseases are a perfect example of how all these factors contribute to changes in VBD dynamics. Although vectors are highly sensitive to climate, modeling studies tend to ignore climate effects. Here, I am interested in the arthropod small vectors that are sensitive to climate factors such as temperature, precipitation, and drought. In particular, I am looking at the effect of temperature on vector traits for two VBDs, namely, dengue, caused by a virus that infects humans and bluetongue disease, caused by a virus that infects ruminants. First, I collect data on mosquito traits' response to temperature changes, this includes adult traits as well as juvenile traits. Next, I use these traits to model mosquito density, and then I incorporate the density into our mathematical models to investigate the effect it has on the basic reproductive ratio R0, a measure of how contagious the disease is. I use R0 to determine disease risk. For dengue, my results show that using mosquito life stage traits response to temperature improves our vector density approximation and disease risk estimates. For bluetongue, I use midge traits response to temperature to show that the suitable temperature for bluetongue risk is between 21.5 °C and 30.7 °C. These results can inform future control and prevention strategies. / Doctor of Philosophy / Infectious diseases are a type of illness that occurs when microorganisms spread between hosts. Some infectious diseases are directly transmitted and some require indirect transmission such as vector-borne diseases (VBDs). Each VBD requires the presence of a vector for the disease to be transmitted. For example, dengue that puts 40% of the world population at risk, requires mosquitoes to transmit the disease between humans. My research aims to investigate how the main climate factor, temperature, influences the spread of VBDs. I develop mathematical and statistical models that explain the effect of temperature on vector traits of a mosquito-borne disease (dengue) and a midge-borne disease (bluetongue) and investigate modeling formulas to improve our estimates for dengue mosquito densities. My results can be used to inform future prevention and control strategies.

The quorum sensing signaling system based on intercellular exchange of N-acyl-homoserine lactones is used by many proteobacteria to regulate the transcription of essential genes in a signal density-dependent manner. It is involved in a number of processes including the development of highly organized bacterial communities, e.g., biofilms, the regulation of expression of virulence factors, production of antibiotics, and bioluminescence. The extensive genetic and biochemical data available on the quorum sensing system in Vibrio fischeri allows the development of a systems biology approach to undertake a spatial and dynamical analysis of the regulation throughout the population. The quorum sensing regulated lux genes are organized in two divergent transcriptional units: luxR and luxICDABEG. The latter contains the genes required for luminescence and the luxI gene necessary for synthesis of an N-acyl-homoserine lactone commonly called autoinducer (AI). The luxR gene codes for a transcriptional regulatory protein that activates the transcription of both operons at a threshold concentration of AI. The positive feedback loop induces a rapid increase of transcription level of the lux genes when a critical population density is reached (reflected by the concentration of AI in the environment). With a combination of molecular biology tools, physiological analysis, and mathematical modeling we identified critical characteristics of the system and expect to assign parameter values in order to achieve a comprehensive understanding of the dynamics. An ordinary differential equation mathematical model is used to investigate the dynamics of the system and derive parameter values. In parallel a novel microfluidic cell culture experimental set-up is used to carefully control environmental parameters as well as to achieve chemostatic conditions for high-density cell populations. An unstable variant of the green fluorescent protein was used as a reporter to follow the time response at a single cell level. Thus spatial organization and noise across the population can be analyzed. Plasmids carrying different genetic constructs were transformed in a recombinant Escherichia coli strain to specifically identify genetic and biochemical elements involved in the regulation of the lux genes under diverse conditions. Then the quantitative data extracted from batch culture and microfluidic assays were used to assign parameter values in the models. The particular question being investigated first is the nature of the regulation to increasing concentration of the signal. The hypothesis tested is that the regulation of the production of the signal by individual cells is biphasic and, therefore, quorum sensing should be robust to global and local variations in cell density. / Master of Science

Systems biology is an interdisciplinary field that focuses on elucidating complex biological processes (systems) by investigating the interactions among its components through an iterative cycle composed of data generation, data analysis and mathematical modeling. Our contributions to systems biology revolve around the following two axes: - Data analysis: Two data analysis projects, which were initiated when I was a co-op at GlaxoSmithKline, are discussed in this thesis. First, next generation sequencing data generated for a phase I clinical trial is analyzed to determine the altered microbial community in human gut before and after antibiotic usage (Chapter 2). To our knowledge, there have not been similar comparative studies in humans on the impacts on the gut microbiome of an antibiotic when administered by different modes. Second, publicly available gene expression data is analyzed to investigate human immune response to tuberculosis (TB) infection (Chapter 3). The novel feature of this study is systematic drug repositioning for the prevention, control and treatment of TB using the Connectivity map. - Mathematical modeling: Polynomial dynamical systems, a state- and time- discrete logical modeling framework, is used to model two biological processes. First, a denitrification pathway in Pseudomonas aeruginosa is modeled to shed light on the reason of greenhouse gas nitrous oxide accumulation (Chapter 4). It is the first mathematical model of denitrification that can predict the effect of phosphate on the denitrification performance of this bacterium. Second, an iron homeostasis pathway linked to iron utilization, oxidative stress response and oncogenic pathways is constructed to investigate how normal breast cells become cancerous (Chapter 5). To date, our intracellular model is the only expanded core iron model that can capture a breast cancer phenotype by overexpression and knockout simulations. / Ph. D.

Yes / The coupling of thermal (Multi Stage Flash, MSF) and membrane processes (Reverse Osmosis, RO) in desalination systems has been widely presented in the literature to achieve an improvement of performance compared to an individual process. However, very little study has been made to the combined Multi Effect Distillation (MED) and Reverse Osmosis (RO) processes. Therefore, this research investigates several design options of MED with thermal vapor compression (MED_TVC) coupled with RO system. To achieve this aim, detailed mathematical models for the two processes are developed, which are independently validated against the literature. Then, the integrated model is used to investigate the performance of several configurations of the MED_TVC and RO processes in the hybrid system. The performance indicators include the fresh water productivity, energy consumption, fresh water purity, and recovery ratio. Basically, the sensitivity analysis for each configuration is conducted with respect to seawater conditions and steam supply variation. Most importantly, placing the RO membrane process upstream in the hybrid system generates the overall best configuration in terms of the quantity and quality of fresh water produced. This is attributed to acquiring the best recovery ratio and lower energy consumption over a wide range of seawater salinity.

Yes / Adequate drug distribution through tumours is essential for treatment to be effective. Palbociclib is a cyclin-dependent kinase (CDK) 4/6 inhibitor approved for use in patients with hormone receptor (HR) positive, HER2 negative metastatic breast cancer (BC). It has unusual physicochemical properties, which may significantly influence its distribution in tumour tissue. We studied the penetration and distribution of palbociclib in vitro, including the use of multicellular three-dimensional models and mathematical modelling. MCF-7 and DLD-1 cell lines were grown as single cell suspensions (SCS) and spheroids; palbociclib uptake and efflux were studied using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Intracellular concentrations of palbociclib for MCF-7 SCS (Cmax 3.22 µM) and spheroids (Cmax 2.91 µM) were 32 and 29 fold higher and in DLD-1, 13 and 7 fold higher, respectively than the media concentration (0.1 µM). Total palbociclib uptake was lower in DLD-1 cells than MCF-7 cells both in SCS and in spheroids. Both uptake and efflux of palbociclib were slower in spheroids than SCS. These data were used to develop a mathematical model of palbociclib transport that quantifies key parameters determining drug penetration and distribution. The model reproduced qualitatively most features of the experimental data and distinguished between SCS and spheroids, providing additional support for hypotheses derived from the experimental data. Mathematical modelling has the potential for translating in vitro data into clinically relevant estimates of tumour drug concentrations. / Grant for Translational Research and a grant from Leeds NHS Charitable Trustees.

Conventional desalination plant, municipal water supply and wastewater treatment system are among the most electricity-intensive facilities. Microbial Desalination Cell (MDC) has emerged as a promising technique to capture the chemical energy stored in wastewater directly for desalination, which has the potential to solve the high energy consumption issue in desalination industry as well as wastewater treatment system. The MDC is composed of two critical components, the electrodes (anode and cathode), and the ion-exchange membranes separating the two electrodes which drive anions migrate towards the anode, and cations migrate towards the cathode. The multiple components allow us to manipulate the configuration to achieve most efficient desalination performance. By coupling with Donnan Dialysis or Microbial Fuel Cell, the device can effectively achieve boron removal which has been a critical issue in desalination plants. The uncertainty of water quality of the final desalinated water caused by contaminant back diffusion from the wastewater side can be theoretically explained by two mechanisms, Donnan exchange and molecule transport which are controlled by bioelectricity and concentration gradient. Scaling and fouling is also a factor needs to be taken into consideration when operating the MDC system in real world. With mathematical modeling, we can provide insight to bridge the gap between lab-scale experiments and industrial applications. This study is expected to provide guidance to enhance the efficiency as well as the reliability and controllability of MDC for desalination. / Ph. D. / Water and energy are the world’s most valuable resources. The recent emerging technology, Microbial Desalination Cell (MDC), however, can achieve wastewater treatment, desalination for fresh water production, and energy generation simultaneously. Owing to the anodophilic microorganisms working as organic matter consumer and electron generator, the wastewater can be cleaned and the device can generate electricity through electron flow to drive ion separation for salt removal in the solution. The MDC can be constructed in versatile configurations. Decoupled configuration of anode and cathode allows flexibility of operation and maintenance. Although the MDC has wastewater adjacent to seawater which are separated by a piece of anion exchange membrane, the microorganisms and viruses are effectively blocked by the membrane which has tiny pore size around 1 nm. Back diffusion of contaminants in wastewater into the desalinated water is minimal under bioelectricity generation condition. The MDC has proved to successfully remove various inorganic ions by itself as well as remove non-dissociable boron when coupled to other devices, such as Donnan Dialysis or Microbial Fuel Cell. The water product quality can meet irrigation guideline. Through mathematical modeling tools, we can better understand the MDC process, analyze it, and make informative predictions.