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Pages
- Title
- Multichix, a computer model that projects receipts and expenses for egg production enterprises
- Creator
- Jacobs, Roger Dean
- Date
- 1978
- Collection
- Electronic Theses & Dissertations
- Title
- IFLMAPS : an interactive farm level marketing and production simulator intended for research, teaching and extension applications
- Creator
- Rister, M. Edward (Milton Edward)
- Date
- 1981
- Collection
- Electronic Theses & Dissertations
- Title
- Empirical analysis of the effects of decision type and control over data access and model access on user preference for modeling environments
- Creator
- Dawson, Margaret (Margaret Leigh)
- Date
- 1988
- Collection
- Electronic Theses & Dissertations
- Title
- Parallel computation models : representation, analysis and applications
- Creator
- Sun, Xian-He
- Date
- 1990
- Collection
- Electronic Theses & Dissertations
- Title
- Logic simulation on massively parallel SIMD machines
- Creator
- Chung, Yunmo
- Date
- 1991
- Collection
- Electronic Theses & Dissertations
- Title
- A multiport approach to modeling and solving large-scale dynamic systems
- Creator
- Wang, Yanying
- Date
- 1992
- Collection
- Electronic Theses & Dissertations
- Title
- Evaluation of the impacts of a simulated irrigation withdrawal on the habitat and populations of brook trout and benthic macroinvertebrates in Hunt Creek, Michigan
- Creator
- Baker, Edward Allen
- Date
- 1995
- Collection
- Electronic Theses & Dissertations
- Title
- Computer simulations of high-energy heavy ion collisions
- Creator
- Kortemeyer, Gerd
- Date
- 1997
- Collection
- Electronic Theses & Dissertations
- Title
- Energy utilization modeling of animal draft power (EUMDAP) for Kenyan small-holder semi-arid agriculture
- Creator
- Mungai, George S. N.
- Date
- 1998
- Collection
- Electronic Theses & Dissertations
- Title
- Using computer simulations to study relativistic heavy ion collisions
- Creator
- Murray, Joelle
- Date
- 1998
- Collection
- Electronic Theses & Dissertations
- Title
- Ring pack behavior and oil consumption modeling in ic engines
- Creator
- Ejakov, Mikhail Aleksandrovich
- Date
- 1998
- Collection
- Electronic Theses & Dissertations
- Title
- Modular modeling of engineering systems using fixed input-output structure
- Creator
- Byam, Brooks Philip
- Date
- 1999
- Collection
- Electronic Theses & Dissertations
- Title
- Parallel discrete event simulation and its application on logic simulation
- Creator
- Xu, Jinsheng
- Date
- 2002
- Collection
- Electronic Theses & Dissertations
- Title
- Designing a package for pharmaceutical tablets in relation to moisture and dissolution
- Creator
- Yoon, Seungyil
- Date
- 2003
- Collection
- Electronic Theses & Dissertations
- Title
- Calibration of optical see through head mounted displays for augmented reality
- Creator
- Zhou, Ji
- Date
- 2007
- Collection
- Electronic Theses & Dissertations
- Title
- On the beneficial effects of deleterious mutations
- Creator
- Covert, Arthur W.
- Date
- 2010
- Collection
- Electronic Theses & Dissertations
- Title
- Surface matching and chemical scoring to detect unrelated proteins binding similar small molecules
- Creator
- Van Voorst, Jeffrey Ryan
- Date
- 2011
- Collection
- Electronic Theses & Dissertations
- Description
-
SURFACE MATCHING AND CHEMICAL SCORING TO DETECT UNRELATED PROTEINS BINDING SIMILAR SMALL MOLECULESByJeffrey Ryan Van VoorstHow can one deduce if two clefts or pockets in different protein structures bind the same small molecule if there is no significant sequence or structural similarity between the proteins? Human pattern recognition, based on extensive structural biology or ligand design experience, is the best choice when the number of sites is small. However, to be able to scale to the...
Show moreSURFACE MATCHING AND CHEMICAL SCORING TO DETECT UNRELATED PROTEINS BINDING SIMILAR SMALL MOLECULESByJeffrey Ryan Van VoorstHow can one deduce if two clefts or pockets in different protein structures bind the same small molecule if there is no significant sequence or structural similarity between the proteins? Human pattern recognition, based on extensive structural biology or ligand design experience, is the best choice when the number of sites is small. However, to be able to scale to the thousands of structures in structural databases requires implementing that experience as computational method. The primary advantage of such a computational tool is to be able to focus human expertise on a much smaller set of enriched binding sites.Although a number of tools have been developed for this purpose by many groups [61, 51, 86, 88, 91], to our knowledge, a basic hypothesis remains untested: two proteins that bind the same small molecule have binding sites with similar chemical and shape features, even when the proteins do not share significant sequence or structural similarity. A computational method to compare protein small molecule binding sites based on surface and chemical complementarity is proposed and implemented as a software package named SimSite3D. This method is protein structure based, does not rely on explicit protein sequence or main chain similarities, and does not require the alignment of atomic centers. It has been engineered to provide a detailed search of one fragment site versus a dataset of about 13,000 full ligand sites in 2&ndash4 hours (on one processor core).Several contributions are presented in this dissertation. First, several examples are presented where SimSite3D is able to find significant matches between binding sites that have similar ligand fragments bound but are unrelated in sequence or structure. Second, including the complementarity of binding site molecular surfaces helps to distinguish between sites that share a similar chemical motif, but do not necessarily bind the same molecule. Third, a number of clear examples are provided to illustrate the challenges in comparing binding sites which should be addressed in order for a binding site comparison method to gain widespread acceptance similar to that enjoyed by BLAST[3, 4]. Finally, an optimization method for addressing protein (and small molecule) flexibility in the context of binding site comparisons is presented, prototyped, and tested.Throughout the work, computational models were chosen to strike a delicate balance between achieving sufficient accuracy of alignments, discriminating between accurate and poor alignments, and discriminating between similar and dissimilar sites. Each of these criteria is important. Due to the nature of the binding site comparison problem, each criterion presents a separate challenge and may require compromises to balance performance to achieve acceptable performance in all three categories.At the present, the problem of addressing flexibility when comparing binding site surfaces has not been presented or published by any other research group. In fact, the problem of modeling flexibility to determine correspondences between binding sites is an untouched problem of great importance. Therefore, the final goal of this dissertation is to prototype and evaluate a method that uses inverse kinematics and gradient based optimization to optimize a given objective function subject to allowed protein motions encoded as stereochemical constraints. In particular, we seek to simultaneously maximize the surface and chemical complementarity of two closely aligned sites subject to directed changes in side chain dihedral angles.
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- Title
- On the evolution of mutation bias in digital organisms
- Creator
- Rupp, Matthew
- Date
- 2011
- Collection
- Electronic Theses & Dissertations
- Description
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Mutation is one of the primary drivers of genetic change. In this work I study mutation biases, which are sets of different genetic-state inflow probabilities. Mutation biases have the potential to change the composition of genomes over time, leading to divergent short- and long-term evolutionary outcomes. I use digital organisms, self-replicating computer programs, to explore whether or not mutation biases are capable of altering the long-term adaptive behavior of populations; whether...
Show moreMutation is one of the primary drivers of genetic change. In this work I study mutation biases, which are sets of different genetic-state inflow probabilities. Mutation biases have the potential to change the composition of genomes over time, leading to divergent short- and long-term evolutionary outcomes. I use digital organisms, self-replicating computer programs, to explore whether or not mutation biases are capable of altering the long-term adaptive behavior of populations; whether mutation biases can be competitive traits; and whether mutation biases can evolve. I find that mutation biases can alter the long-term adaptive behavior of mutation bias-obligate populations in terms of both mean fitness and complex trait evolution. I also find that mutation biases can compete against one another under a variety of conditions, meaning mutation bias can selectable over relatively-short periods of time. The competitive success of a mutation bias does not always depend upon the presence of beneficial mutations, implicating an increase in the probability of neutral mutations as a sufficient mechanism for bias selection. Finally, I demonstrate that by giving organisms a mutable mutation bias allele, populations preferentially evolve to possess specific biases over others. Overall, this work shows that mutation bias can act as a selectable trait, influencing the evolution of populations with regard to both their internal-genetic and external environments.
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- Title
- The evolution of division of labor in digital organisms
- Creator
- Goldsby, Heather J.
- Date
- 2011
- Collection
- Electronic Theses & Dissertations
- Description
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Division of labor is a hallmark strategy employed by a wide variety of groups ranging in complexity from bacteria to human economies. Within these groups, some individuals, such as worker ants, sacrifice their ability to reproduce and instead dedicate their lives to the maintenance of the colony and success of their kin. A worker ant may spend its entire life performing a single task, such as defending the colony or tending to the brood. The complexity of the strategies employed by these...
Show moreDivision of labor is a hallmark strategy employed by a wide variety of groups ranging in complexity from bacteria to human economies. Within these groups, some individuals, such as worker ants, sacrifice their ability to reproduce and instead dedicate their lives to the maintenance of the colony and success of their kin. A worker ant may spend its entire life performing a single task, such as defending the colony or tending to the brood. The complexity of the strategies employed by these groups, combined with their rampant success, gives rise to questions regarding why division of labor exists. While extensive research has been done to better understand the patterns and mechanisms of division of labor, exploring this topic in an evolutionary context remains challenging to study due to the slow pace of evolution and imperfect historical data. Understanding how and why division of labor arises is pertinent not just for understanding biological phenomena, but also as a means to enable evolutionary computation techniques to address complex problems using problem decomposition. The objective of problem-decomposition approaches is to have a group of individuals cooperatively solve a complex task by breaking it into pieces, having specialist individuals solve the pieces, and reassembling the solution. Essentially, problem-decomposition approaches use division of labor to enable groups to solve more challenging problems than any individual could alone. Unfortunately, human engineers have struggled with creating effective, automated problem-decomposition approaches.In this dissertation, I use digital evolution (i.e., populations of self-replicating computer programs that undergo open-ended evolution) to investigate questions related to the evolution of division of labor and to apply these insights to problem decomposition techniques. This dissertation has three primary components: First, we provide experimental evidence that evolutionary computation techniques can evolve groups of individuals that exhibit division of labor. Second, we explore two hypotheses for the evolution of division of labor. Specifically, we find support for the hypothesis that temporal polyethism (i.e., where a worker's age is related to the task it performs within the colony) may result from the evolutionary pressures of aging and risks associated with tasks. Additionally, we find support for a hypothesis initially proposed by Adam Smith, the premier economist, that the presence of task-switching costs results in an increase in the amount of division of labor exhibited by groups. Third, we describe how our analyses revealed that groups of organisms evolved as part of our task-switching work exhibit complex problem decomposition strategies that can potentially be applied to other evolutionary computation challenges. This work both informs biological studies of division of labor and also provides insights that can enable the development of new mechanisms for using evolutionary computation to solve increasingly complex engineering problems.
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- Title
- The evolutionary potential of populations on complex fitness landscapes
- Creator
- Bryson, David Michael
- Date
- 2012
- Collection
- Electronic Theses & Dissertations
- Description
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Evolution is a highly contingent process, where the quality of the solutions produced is affected by many factors. I explore and describe the contributions of three such aspects that influence overall evolutionary potential: the prior history of a population, the type and frequency of mutations that the organisms are subject to, and the composition of the underlying genetic hardware. I have systematically tested changes to a digital evolution system, Avida, measuring evolutionary potential in...
Show moreEvolution is a highly contingent process, where the quality of the solutions produced is affected by many factors. I explore and describe the contributions of three such aspects that influence overall evolutionary potential: the prior history of a population, the type and frequency of mutations that the organisms are subject to, and the composition of the underlying genetic hardware. I have systematically tested changes to a digital evolution system, Avida, measuring evolutionary potential in seven different computational environments ranging in complexity of the underlying fitness landscapes. I have examined trends and general principles that these measurements demonstrate and used my results to optimize the evolutionary potential of the system, broadly enhancing performance. The results of this work show that history and mutation rate play significant roles in evolutionary potential, but the final fitness levels of populations are remarkably stable to substantial changes in the genetic hardware and a broad range of mutation types.
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