Artificial and natural nucleic acid self assembling systems

Nucleic acids are good candidates for nanomachine construction. They participate in all the processes of life, and so can function as structural building blocks and dynamic catalysts. However, to use nucleic acids as nanomachines, a better understanding of their material properties, how to design structures using them, and their dynamics is needed. We have tried to address these issues, in a small way, with nucleic acid force field development, an attempt at nanostructural design and synthesis using DNA, and a study of the RNA/protein regulatory dynamics of the tryptophan regulatory attenuation protein

Bayesian Inference in Estimation of Distribution Algorithms

Metaheuristics such as Estimation of Distribution Algorithms and the Cross-Entropy method use probabilistic modelling and inference to generate candidate solutions in optimization problems. The model fitting task in this class of algorithms has largely been carried out to date based on maximum likelihood. An alternative approach that is prevalent in statistics and machine learning is to use Bayesian inference. In this paper, we provide a framework for the application of Bayesian inference techniques in probabilistic model-based optimization. Based on this framework, a simple continuous Bayesian Estimation of Distribution Algorithm is described. We evaluate and compare this algorithm experimentally with its maximum likelihood equivalent, UMDAG c

Structured Prediction of Sequences and Trees using Infinite Contexts

Linguistic structures exhibit a rich array of global phenomena, however commonly used Markov models are unable to adequately describe these phenomena due to their strong locality assumptions. We propose a novel hierarchical model for structured prediction over sequences and trees which exploits global context by conditioning each generation decision on an unbounded context of prior decisions. This builds on the success of Markov models but without imposing a fixed bound in order to better represent global phenomena. To facilitate learning of this large and unbounded model, we use a hierarchical Pitman-Yor process prior which provides a recursive form of smoothing. We propose prediction algorithms based on A* and Markov Chain Monte Carlo sampling. Empirical results demonstrate the potential of our model compared to baseline finite-context Markov models on part-of-speech tagging and syntactic parsing

History and prophecy in the Qumran Pesharim: an examination of the key figures and groups in the Dead Sea Scrolls by way of their prophetic designations.

The thesis examines the Qumran pesharim and seeks to test the claim that these texts are solely 'historically' based. Instead, it finds that the interpretations are driven by prophetic concerns, founded on and guided by the biblical concept of 'pesher' as dream-interpretation. The study concentrates on the various sobriquets in the pesharim, and is loosely divided into two main parts. Part one examines those designations of groups, including the Kittim, Ephraim and Manasseh, and the Seekers of Smooth Things. Part two, meanwhile, focuses on the interrelationship between the Teacher of Righteousness, the Wicked Priest, and the Man of Falsehood. One of the dominating themes of the thesis is the stress laid on the relationship between the Teacher and the Man of Falsehood, while the thesis also proposes that 'Ephraim' and 'Seekers of Smooth Things' are an offshoot of the Man of Falsehood's original followers. This allows the opposition to this group in 4QpNahum to be properly understood, and suggests a lurk between the Qumran group and the proto-Pharisaic movement. In concluding, the study condemns the suggestion that the 'masking' by sobriquets intentionally conceals these subjects' identity. Rather, such masking links the intended target with prophetic expectations. In short, the thesis finds that although the two are often distinguished in modem scholarship, the correct interpretation of any aspect of the 'historical' pesharim inevitably relies on the understanding of the prophetic term 'pesher' - and vice versa. The thesis does not tackle the issue of the dating of these texts. Rather, it assumes the consensus view that the pesharim were composed during the first century BCE. Occasionally, it will be evident that a text requires a composition before or after a particular date or event, or even that it must postdate another Qumran text, but in general the question has not been an overriding concern

MacWilliams' Extension Theorem for Bi-Invariant Weights over Finite Principal Ideal Rings

A finite ring R and a weight w on R satisfy the Extension Property if every R-linear w-isometry between two R-linear codes in R^n extends to a monomial transformation of R^n that preserves w. MacWilliams proved that finite fields with the Hamming weight satisfy the Extension Property. It is known that finite Frobenius rings with either the Hamming weight or the homogeneous weight satisfy the Extension Property. Conversely, if a finite ring with the Hamming or homogeneous weight satisfies the Extension Property, then the ring is Frobenius. This paper addresses the question of a characterization of all bi-invariant weights on a finite ring that satisfy the Extension Property. Having solved this question in previous papers for all direct products of finite chain rings and for matrix rings, we have now arrived at a characterization of these weights for finite principal ideal rings, which form a large subclass of the finite Frobenius rings. We do not assume commutativity of the rings in question.Comment: 12 page

(Non-)Equivalence of Universal Priors

Ray Solomonoff invented the notion of universal induction featuring an aptly termed "universal" prior probability function over all possible computable environments. The essential property of this prior was its ability to dominate all other such priors. Later, Levin introduced another construction --- a mixture of all possible priors or `universal mixture'. These priors are well known to be equivalent up to multiplicative constants. Here, we seek to clarify further the relationships between these three characterisations of a universal prior (Solomonoff's, universal mixtures, and universally dominant priors). We see that the the constructions of Solomonoff and Levin define an identical class of priors, while the class of universally dominant priors is strictly larger. We provide some characterisation of the discrepancy.Comment: 10 LaTeX pages, 1 figur

Baraminological Analysis of Jurassic and Cretaceous Avialae

The baraminic status of Jurassic and Cretaceous Avialae was evaluated using statistical baraminology. Baraminic distance correlation (BDC) and three dimensional multidimensional scaling (MDS) was applied to six previously published character matrices. The results reveal discontinuities between most Avialae and the Deinonychosauria (Troodontidae + Dromaeosauridae) and little evidence of continuity between modern birds and dinosaurs, suggesting that recent claims that statistical baraminology supports the evolution of birds from dinosaurs are misplaced. Nevertheless, we did find positive BDC and MDS clustering of some Avialae and deinonychosaurs in four of our analyses, suggesting that at least some Jurassic and Cretaceous Avialae may be clustered with dinosaurs. This observation raises the interesting philosophical question: what is a bird

Future Needs for Tribo-Corrosion Research and Testing

Tribo-corrosion is an emerging interdisciplinary subject that spans from basic research on the behavior of surfaces in mechanical contact in chemically active surroundings to the test methods needed to quantify its effects, and from the selection of materials for bio-implants to the minimization of surface degradation and wastage in advanced energy conversion systems. Such a diverse field brings with it many challenges in understanding, testing, standardization, and application to engineering practice. This paper summarizes a panel discussion and participant survey held at the Third International Symposium on Tribo-Corrosion in Atlanta, Georgia, USA, in April 2012. It reflects a sense of agreement on many of the key scientific challenges in the field and the fact that tribo-corrosion is still in its infancy in terms of broad industry recognition, education, and the ability of those who conduct tribo-corrosion research to connect their laboratory results and theories to applications. Some sub-fields, notably the bio-tribo-corrosion of medical implants, have witnessed active international research efforts, but the engineering community in many other important areas of technology may not yet be aware of the field despite numerous tribo-corrosion problems that may exist within their purview