Analysis of game playing agents with fingerprints

Evolutionary computation (EC) can create a vast number of strategies for playing simple games in a short time. Analysis of these strategies is typically more time-consuming than their production. As a result, analysis of strategies produced by an EC system is often lacking or restricted to the extraction of superficial summary Statistics and Probability; This thesis presents a technique for extracting a functional signature from evolved agents that play games. This signature can be used as a visualization of agent behavior in games with two moves and also provides a numerical target for clustering and other forms of automatic analysis. The fingerprint can be used to induce a similarity measure on the space of game strategies. This thesis develops fingerprints in the context of the iterated prisoner\u27s dilemma; we note that they can be computed for any two player simultaneous game with a finite set of moves. When using a clustering algorithm, the results are strongly influenced by the choice of the measure used to find the distance between or to compare the similarity of the data being clustered. The Euclidean metric, for example, rates a convex polytope as the most compact type of object and builds clusters that are contained in compact polytopes. Presented here is a general method, called multi-clustering, that compensates for the intrinsic shape of a metric or similarity measure. The method is tested on synthetic data sets that are natural for the Euclidean metric and on data sets designed to defeat k-means clustering with the Euclidean metric. Multi-clustering successfully discovers the designed cluster structure of all the synthetic data sets used with a minimum of parameter tuning. We then use multi-clustering and filtration on fingerprint data. Cellular representation is the practice of evolving a set of instructions for constructing a desired structure. This thesis presents a cellular encoding for finite state machines and specializes it to play the iterated prisoner\u27s dilemma. The impact on the character and behavior of finite state agents of using the cellular representation is investigated. For the cellular representation resented a statistically significant drop in the level of cooperation is found. Other differences in the character of the automaton generated with a direct and cellular representation are reported

2023- The Twenty-seventh Annual Symposium of Student Scholars

The full program book from the Twenty-seventh Annual Symposium of Student Scholars, held on April 18-21, 2023. Includes abstracts from the presentations and posters.https://digitalcommons.kennesaw.edu/sssprograms/1027/thumbnail.jp

Crab and cockle shells as heterogeneous catalysts in the production of biodiesel

In the present study, the waste crab and cockle shells were utilized as source of calcium oxide to transesterify palm olein into methyl esters (biodiesel). Characterization results revealed that the main component of the shells are calcium carbonate which transformed into calcium oxide upon activated above 700 °C for 2 h. Parametric studies have been investigated and optimal conditions were found to be catalyst amount, 5 wt.% and methanol/oil mass ratio, 0.5:1. The waste catalysts perform equally well as laboratory CaO, thus creating another low-cost catalyst source for producing biodiesel. Reusability results confirmed that the prepared catalyst is able to be reemployed up to five times. Statistical analysis has been performed using a Central Composite Design to evaluate the contribution and performance of the parameters on biodiesel purity

Molecular phylogeny of horseshoe crab using mitochondrial Cox1 gene as a benchmark sequence

An effort to assess the utility of 650 bp Cytochrome C oxidase subunit I (DNA barcode) gene in delineating the members horseshoe crabs (Family: xiphosura) with closely related sister taxa was made. A total of 33 sequences were extracted from National Center for Biotechnological Information (NCBI) which include horseshoe crabs, beetles, common crabs and scorpion sequences. Constructed phylogram showed beetles are closely related with horseshoe crabs than common crabs. Scorpion spp were distantly related to xiphosurans. Phylogram and observed genetic distance (GD) date were also revealed that Limulus polyphemus was closely related with Tachypleus tridentatus than with T.gigas. Carcinoscorpius rotundicauda was distantly related with L.polyphemus. The observed mean Genetic Distance (GD) value was higher in 3rd codon position in all the selected group of organisms. Among the horseshoe crabs high GC content was observed in L.polyphemus (38.32%) and lowest was observed in T.tridentatus (32.35%). We conclude that COI sequencing (barcoding) could be used in identifying and delineating evolutionary relatedness with closely related specie

Investigation of Antimicrobial Peptides in Lipid Membranes by Solid-State NMR

Solid-state NMR spectroscopy is an important tool for studying the chemical and three-dimensional structures of organic and inorganic solids because of its intrinsic atomic-level structural information, nonperturbing nature, and the large range of dynamic time scales. It is especially powerful in studying insoluble and noncrystalline membrane proteins, which are difficult to analyze by traditional X-ray crystallography or solution NMR techniques. In this thesis, various NMR techniques are used to study the structure and dynamics of membrane proteins within lipid bilayers. The main protein we are focusing on is human neutrophil peptide 1 (HNP-1). It is a small cysteine-rich cationic antimicrobial protein found in human neutrophils. It forms the first line of defense by the innate immune system of humans against pathogens. The antimicrobial activity of HNP-1 is believed to be caused by disruption of the microbial cell membrane and various models of HNP-membrane interaction have been proposed. However, none of these mechanistic models are based on structure information from the lipid bilayer. Therefore, understanding the peptide structure in the presence of membrane and its interaction with the lipids will shed light on the antimicrobial mechanism of HNP-1. As a first step, we have calculated the minimum-energy structures of uniformly 13C, 15N-labeled microcrystalline HNP-1 based on all NMR torsion angle and distance restraints determined by various 2D and 3D correlation techniques. The solid-state NMR structure has close similarity to the crystal structures of the HNP family. Then we reconstituted HNP-1 into DMPC/DMPG lipid bilayers. We confirmed that the protein is predominantly dimerized at high protein/lipid molar ratios by 19F spin diffusion experiments. Various methods under magic-angle spinning (MAS) such as 13C-31P REDOR, 1H spin diffusion and 13C DIPSHIFT have been utilized to study the interaction of HNP-1 with lipid bilayers. The experimental results strongly support a dimer pore topology of HNP-1 in which the polar top of the dimer lines an aqueous pore while the hydrophobic bottom faces the lipid chains. The second focus of this thesis is the oriented bicelle alignment , we have studied the alignment of bicelles with different lipids combinations, long- to short-chain lipid ratios, hydration levels and a phase diagram was generated. We also show that the orientation of a protein called HNP-1, which has 3 β-strands and dimerizes, can be simulated by predicting the correlation of the 15N anisotropic chemical shift and the N-H dipolar coupling

Antimicrobial peptides from the Arctic ascidian Synoicum turgens

The rise in frequency of antibiotic resistant pathogenic bacteria makes the need for new treatment options for previously curable bacterial infections ever more important. In the process of discovering and developing antibacterial agents, one powerful approach has been borrowing wisdom from nature. Antimicrobial peptides (AMPs) are critical components of the innate immune systems found in almost all eukaryotic life forms. Their mode of action includes disruption of the bacterial membrane and to trigger supporting immune responses. Due to these properties, AMPs are considered promising lead structures that can be further developed into commercially available antibiotics to treat or prevent human diseases caused by bacteria. The work conducted in this thesis aims to discover and characterize novel antimicrobial peptides from the Arctic marine ascidian Synoicum turgens by using a marine bioprospecting approach. This includes collection, extraction and fractionation of biomass, antibacterial bioactivity testing and AMP isolation followed by chemical and biological characterization. For one isolated peptide class, truncated versions were prepared, aiming to produce shorter, linear variants with retained antimicrobial activity. In paper I, turgencin A and B and their oxidized derivatives were discovered through bioassay-guided purification. These peptides had an unusual disulfide connectivity, rarely seen in marine AMPs. Both turgencin A and B were potently active against all assayed bacterial strains. Membrane assays showed that the peptides cause bacterial membrane disruption within a few seconds. Turgencin A and B also displayed some cytotoxic activity against two human cell lines. Oxidation of the methionine present in both peptides decreased the bioactivities in all assays. Turgencin A, being the most potent AMP, was subject for sequence analysis and prediction of antimicrobial potential of different regions in paper II. Truncated and modified variants of turgencin A were synthetically produced to make smaller AMPs with the potential of being developed into antimicrobial drug leads. These 10-mer peptides, named StAMP-1–11, were made using an amino acid replacement strategy. Some of the Trp enriched peptides had similar bactericidal activity as the parent peptide turgencin A, and no cytotoxic activity against the mammalian cell lines. During turgencin isolation, a series of other smaller peptides were discovered in the same extracts presumably with antimicrobial activity. These isolated and characterized ~2 kDa, cysteine-rich peptides (CRPs) (described in paper III), were named St-CRP-1 and St-CRP-2 and contained 18-19 amino acids. The St-CRPs shared a disulfide connectivity pattern with alpha-defensins, had a neutral net charge, moderate antibacterial activity and showed no cytotoxicity. In addition, the introduction section provides background information on topics related to the thematic of the articles. This includes an introduction to bacteria, antibiotics and antibiotic resistance, AMPs, ascidians, and the marine environment