`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms

We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation

Decentralized Constraint Satisfaction

We show that several important resource allocation problems in wireless networks fit within the common framework of Constraint Satisfaction Problems (CSPs). Inspired by the requirements of these applications, where variables are located at distinct network devices that may not be able to communicate but may interfere, we define natural criteria that a CSP solver must possess in order to be practical. We term these algorithms decentralized CSP solvers. The best known CSP solvers were designed for centralized problems and do not meet these criteria. We introduce a stochastic decentralized CSP solver and prove that it will find a solution in almost surely finite time, should one exist, also showing it has many practically desirable properties. We benchmark the algorithm's performance on a well-studied class of CSPs, random k-SAT, illustrating that the time the algorithm takes to find a satisfying assignment is competitive with stochastic centralized solvers on problems with order a thousand variables despite its decentralized nature. We demonstrate the solver's practical utility for the problems that motivated its introduction by using it to find a non-interfering channel allocation for a network formed from data from downtown Manhattan

Complete Configuration Space Analysis for Structure Determination of Symmetric Homo-oligomers by NMR

Symmetric homo-oligomers (protein complexes with similar subunits arranged symmetrically) play pivotal roles in complex biological processes such as ion transport and cellular regulation. Structure determination of these complexes is necessary in order to gain valuable insights into their mechanisms. Nuclear Magnetic Resonance (NMR) spectroscopy is an experimental technique used for structural studies of such complexes. The data available for structure determination of symmetric homo-oligomers by NMR is often sparse and ambiguous in nature, raising concerns about existing heuristic approaches for structure determination. We have developed an approach that is complete in that it identifies all consistent conformations, data-driven in that it separately evaluates the consistency of structures to data and biophysical constraints and efficient in that it avoids explicit consideration of each of the possible structures separately. By being complete, we ensure that native conformations are not missed. By being data-driven, we are able to separately quantify the information content in the data alone versus data and biophysical modeling. We take a configuration space (degree-of-freedom) approach that provides a compact representation of the conformation space and enables us to efficiently explore the space of possible conformations. This thesis demonstrates that the configuration space-based method is robust to sparsity and ambiguity in the data and enables complete, data-driven and efficient structure determination of symmetric homo-oligomers

Revisiting the Evolution and Application of Assignment Problem: A Brief Overview

The assignment problem (AP) is incredibly challenging that can model many real-life problems. This paper provides a limited review of the recent developments that have appeared in the literature, meaning of assignment problem as well as solving techniques and will provide a review on   a lot of research studies on different types of assignment problem taking place in present day real life situation in order to capture the variations in different types of assignment techniques. Keywords: Assignment problem, Quadratic Assignment, Vehicle Routing, Exact Algorithm, Bound, Heuristic etc

Uncoded space-time labelling diversity : data rate & reliability enhancements and application to real-world satellite broadcasting.

Doctoral Degree. University of KwaZulu-Natal, Durban.Abstract available in PDF

Cryogenic Ion Vibrational Spectroscopy of Gas-Phase Clusters: Structure, Anharmonicity and Fluxionality

Gas-phase clusters are aggregates of a countable number of particles, which exhibit size-dependent physical and chemical properties that typically lie in the non-scalable size regime. These properties can be systematically characterized at a molecular level with respect to composition, size and charge state. This allows studying how macroscopic properties of condensed matter, e.g. phase transitions or metallic behavior, emerge from the atomic or molecular properties as a function of cluster size. Furthermore, smaller clusters are also amenable to high-level quantum chemical calculations, making them ideal model systems for understanding phenomena in more complex heterogeneous matter. The main advantage here is that clusters can be studied with a very high degree of selectivity and sensitivity, under well-defined conditions and in the absence of perturbing interaction with an environment. The studies presented in this theses focus on the structure characterization of ionic clusters using cryogenic ion vibrational spectroscopy. This technique combines cryogenic ion trapping with mass spectrometric schemes and infrared photodissociation (IRPD) spectroscopy. It makes use of an ion-trap triple mass spectrometer in combination with various light sources that grant access to a wide range of the infrared spectrum (210-4000 cm-1). Structures are typically assigned by comparing experimental IRPD spectra with computed vibrational spectra. The structures of aluminum oxide clusters and their interaction with water are studied in the framework of the collaborative research center CRC1109 "Understanding of Metal Oxide / Water Systems at the Molecular Scale: Structural Evolution, Interfaces, and Dissolution". This project aims at gaining a molecular level understanding of the mechanisms involved in oxide formation and dissolution. Section 4.1 and 4.2 present results of IRPD spectroscopy experiments on small mono and dialuminum oxide anions and on the anionic cluster series (Al2O3)nAlO2- with n = 0 to 6. These studies discuss the effects of the distribution of the excess charge on the cluster structure, analyze how structural properties evolve with size and how these relate to those of nanoparticles and crystal surfaces. The dissociative adsorption of water by Al-oxide clusters is investigated in Section 4.3.2. Boron exhibits a rich variety of polymorphs with the B12 icosahedron as a common building block. This three dimensional (3D) structure is retained in the halogenated closo-dodecaborate dianions (B12X122-). On the other hand, small pure boron clusters are essentially planar. The study presented in Section 5.2 investigates the 3D to 2D structural transition by probing the vibrational spectra of partially deiodinated B12In2- clusters as a function of decreasing n. The results presented in Section 5.1 show that B13+ has a planar structure consisting of two concentric rings. As a result of delocalized aromatic bonding, this structure is particularly stable without being rigid as it permits an almost free rotation of the inner ring. Protonated water clusters are model systems for understanding protons in aqueous solutions. The interpretation of their vibrational spectra is a challenge for state-of-the-art electronic structure calculations and therefore often prone to controversies. The results presented in Chapter 6 clear existing doubts over the assignment of the protonated water pentamer structure and the vibrational fingerprints of the embedded distorted H3O+. This study laid the foundation for a subsequent series of measurements which provided crucial new insights into the proton transfer mechanism in water