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Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 32 for “"fitness landscape"”.
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Fitness Landscape Analysis for the Differential Evolution Algorithm
… parameter configurations and problem-specific landscape characteristics. This thesis undertakes a comprehensive investigation into three foundational aspects of DE design: the critical role and intricate interplay of its control parameters; the influence of fitness landscape characteristics …
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An Exploration of Fitness Landscapes: Theory and Experiments
Genotypes, phenotypes, and fitness are the ultimate determinants of evolution. The relationship between these three components is collectively referred to as the fitness landscape. Evolutionary biologists have been working to understand the mechanisms and processes governing the fitness landscape …
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Exploring protein fitness landscapes with new high-throughput technologies
The concept of a protein’s fitness landscape – an abstract space in which related sequences are close together and matched with their fitness – is a useful tool to visualize core principles of protein evolution. Acquiring a new function, for example the laboratory evolution of an enzyme to convert …
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Engineering and characterizing human T cell receptors for cancer immunotherapies
… binding to MART1/HLA-A2 to produce a sequence fitness landscape, which measured the effect that each individual substitution had on pepMHC binding. The sequence fitness landscape of RD1- MART1HIGH was compared to a sequence fitness landscape of its parent TCR A6 to identify the key residues …
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Problem dependent metaheuristic performance in Bayesian network structure learning.
… node ordering and the optimal BN structure; (c) Fitness landscape analysis for investigating the di erent performances of both chain score function and the CH score function; (d) A classifier method is constructed by utilizing receiver operating characteristic curve with the results on fitness …
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Adaptive challenge for algebraic and realistic dynamic optimisation benchmarks.
… establishes a theoretical framework for the fitness landscape rotation as a dynamic benchmark generator in order to demonstrate its preserving nature. Contributions here include using the fitness landscape rotation as a tilting strategy to redirect the search for algorithms that are stuck in …
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Characterizing the landscape of aminoacyl-tRNA synthetase protein production in Bacillus subtilis
… important native protein abundances are for cell fitness. Furthermore, linking changes in abundances with downstream effects on enzymatic output, pathway function, and ultimately cell fitness is unexplored in nearly all cases. Here I use a model enzyme family, the aminoacyl tRNA synthetases …
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Evolution and Engineering of RNA-based Macromolecular Machines
… activity, while also mapping the comprehensive fitness landscape of the ribozyme. In Chapter 3, I explore the potential of appending novel domains to the ribozyme in order to increase its contacts upstream of the triplet ligation junction. Using directed evolution, I identify new 5’ domains …
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Characterising fitness landscapes of protein evolution by next-generation sequencing
… is still incompletely understood. Protein fitness landscapes powerfully describe the sequence-function relationship by dividing sequence space into functional hills and valleys. This representation is often invoked yet lacks experimental evidence; the immense vastness of possible sequence …
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Evolvability of a viral protease: experimental evolution of catalysis, robustness and specificity
… as a model. I map key features of the local fitness landscape and characterise how they affect details of enzyme evolution. In order to investigate the evolution of core active site machinery, I mutated the nucleophile of TEV to serine. The differing chemical properties of oxygen and sulphur …
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Evolutionary Dynamics of Brown Treesnake (Boiga irregularis) Reproductive Ecology, with Implications for Invasive Species Control
… is that control measures subsequently alter the fitness landscape of an invasive over ecologically-relevant time, and lose their efficacy by so doing. However, adaptive management can be promoted by investigating the relationships between reproductive ecology, strength of selection, and …
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Modeling and Measuring Affordability as Fitness
… a broader concept of affordability – one of fitness to perform at the level of quality required by the consumer, to perform at that level whenever the product or service is used, and to do so with minimum consumption of resources. This concept of affordability is applied to technological …
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PRODUCTIVITY MANAGEMENT OF THE CACAO AGRO-FOOD SYSTEM IN TABASCO (MEXICO): A FITNESS APPROACH
… question that is addressed in this study. The fitness approach, an exploratory framework, is applied in order to study the Cacao Agro-food System (CAPS) in Tabasco. Mexico. The final sample consisted of 356 farmers, 37 curing plants, 6 wholesaling firms, and 7 chocolate firms. An anatomical …
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A test of the Snowball model
… are allowed to evolve in allopatry on a holey fitness landscape. I find that the number of DMIs involving pairs of loci (i.e., simple DMIs) does not snowball---rather, it increases approximately linearly with divergence. I show that the probability of emergence of a simple DMI is approximately …
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Evolutionary Consequences of Metabolic Competition and Cooperation in Microbial Communities
… for competition and cooperation to affect the fitness of individual species. Gaining a better understanding of the evolutionary process within such dense communities has important implications for both clarifying genomic variation observed in the present as well as predicting future changes in …
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Fitness Landscapes, Genetic Interactions, and the Fitness of Hybrids
… re-arranged into novel combinations. The fitness of these hybrids is central to the evolution of reproductive isolation, but also plays an important role in conservation policy, and in crop and animal breeding. Fitness landscapes are simple mathematical models that generate a rich variety …
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Intra and inter-specific communication in Heliconius
… existe en las señales miméticas a lo largo del fitness landscape (que puede comprender múltiples picos óptimos). En este estudio, haciendo uso de análisis de cuantificación del color, tamaño y forma de las alas, investigué el grado de semejanza fenotípica entre especies co-miméticas en múltiples …
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Computational Approaches to Understand Chemoresistance & Tumor Evolution Using Longitudinal Clinical Data and Lineage Tracing
… models. These models were used to identify the fitness landscape of individual tumor lineages under three different drugs. High-throughput isolation and profiling of resistant and sensitive lineages were used to establish, and profile them using RNASeq and whole-exome sequencing. The …
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Engineering developable miniprotein ligand scaffolds
… the vast, sparse, and rugged sequence-function fitness landscape. Protein scaffolds, characterized by a conserved framework to support an engineered variable active site, have proven effective in navigating this landscape. While monoclonal antibodies are established natural scaffolds, …
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In silico vaccine design for hepatitis C: A computational platform for fighting disease
… high-performance computing to define empirical fitness landscapes and conduct viral dynamics simulations to determine vulnerable viral targets and rationally design vaccine immunogens. This computational design protocol will guide and accelerate vaccine development efforts by massively reducing …
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