Physically constrained maximum likelihood (PCML) mode filtering and its application as a pre-processing method for underwater acoustic communication

Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2009Mode filtering is most commonly implemented using the sampled mode shape or pseudoinverse algorithms. Buck et al placed these techniques in the context of a broader maximum a posteriori (MAP) framework. However, the MAP algorithm requires that the signal and noise statistics be known a priori. Adaptive array processing algorithms are candidates for improving performance without the need for a priori signal and noise statistics. A variant of the physically constrained, maximum likelihood (PCML) algorithm is developed for mode filtering that achieves the same performance as the MAP mode filter yet does not need a priori knowledge of the signal and noise statistics. The central innovation of this adaptive mode filter is that the received signal's sample covariance matrix, as estimated by the algorithm, is constrained to be that which can be physically realized given a modal propagation model and an appropriate noise model. The first simulation presented in this thesis models the acoustic pressure field as a complex Gaussian random vector and compares the performance of the pseudoinverse, reduced rank pseudoinverse, sampled mode shape, PCML minimum power distortionless response (MPDR), PCML-MAP, and MAP mode filters. The PCML-MAP filter performs as well as the MAP filter without the need for a priori data statistics. The PCML-MPDR filter performs nearly as well as the MAP filter as well, and avoids a sawtooth pattern that occurs with the reduced rank pseudoinverse filter. The second simulation presented models the underwater environment and broadband communication setup of the Shallow Water 2006 (SW06) experiment. Data processing results are presented from the Shallow Water 2006 experiment, showing the reduced sensitivity of the PCML-MPDR filter to white noise compared with the reduced rank pseudoinverse filter. Lastly, a linear, decision-directed, RLS equalizer is used to combine the response of several modes and its performance is compared with an equalizer applied directly to the data received on each hydrophone

Modal processing for acoustic communications in shallow water experiment

Author Posting. © Acoustical Society of America, 2008. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 124 (2008): EL177-EL181, doi:10.1121/1.2960954.Acoustical array data from the Shallow Water Acoustics experiment was processed to show the feasibility of broadband mode decomposition as a preprocessing method to reduce the effective channel delay spread and concentrate received signal energy in a small number of independent channels. The data were collected by a vertical array designed at the Woods Hole Oceanographic Institution. Phase-shift Keying (PSK) m-sequence modulated signals with different carrier frequencies were transmitted at a distance 19.2 km from the array. Even during a strong internal waves activity a low bit error rate was achieved.The research was supported by ONR

Investigation of mode filtering as a preprocessing method for shallow-water acoustic communications

Author Posting. © IEEE, 2010. This article is posted here by permission of IEEE for personal use, not for redistribution. The definitive version was published in IEEE Journal of Oceanic Engineering 35 (2010): 744-755, doi:10.1109/JOE.2010.2045444.Acoustical array data from the 2006 Shallow Water Experiment (SW06) was analyzed to show the feasibility of broadband mode decomposition as a preprocessing method to reduce the effective channel delay spread and concentrate received signal energy in a small number of independent channels. The data were collected by a vertical array, which spans the water column from 12-m depth to the bottom in shallow water 80 m in depth. Binary-sequence data were used to phase-shift-keyed (PSK) modulate signals with different carrier frequencies. No error correction coding was used. The received signals were processed by a system that does not use training or pilot signals. Signals received both during periods of ordinary internal wave activity and during a period with unusually strong internal wave solitons were processed and analyzed. Different broadband mode-filtering methods were analyzed and tested. Broadband mode filtering decomposed the received signal into a number of independent signals with a reduced delay spread. The analysis of signals from the output of mode filters shows that even a simple demodulator can achieve a low bit error rate (BER) at a distance 19.2 km.This work was supported by the U.S. Office of Naval Research (ONR)

Design principles for high transition metal capacity in disordered rocksalt Li-ion cathodes

The discovery of facile Li transport in disordered, Li-excess rocksalt materials has opened a vast new chemical space for the development of high energy density, low cost Li-ion cathodes. We develop a strategy for obtaining optimized compositions within this class of materials, exhibiting high capacity and energy density as well as good reversibility, by using a combination of low-valence transition metal redox and a high-valence redox active charge compensator, as well as fluorine substitution for oxygen. Furthermore, we identify a new constraint on high-performance compositions by demonstrating the necessity of excess Li capacity as a means of counteracting high-voltage tetrahedral Li formation, Li-binding by fluorine and the associated irreversibility. Specifically, we demonstrate that 10–12% of Li capacity is lost due to tetrahedral Li formation, and 0.4–0.8 Li per F dopant is made inaccessible at moderate voltages due to Li–F binding. We demonstrate the success of this strategy by realizing a series of high-performance disordered oxyfluoride cathode materials based on Mn²+/⁴+ and V⁴+/⁵+ redox.Vehicle Technologies Program (U.S.) (Contract No. DE-AC02-05CH11231)United States. Department of Energy. Office of Energy Efficiency and Renewable Energy. Advanced Battery Materials Research Program (Subcontract No. 7056411)National Science Foundation (U.S.) (Reward No. OCI-1147503)National Science Foundation (U.S.) (grant number ACI- 105357)National Science Foundation (U.S.) (NSF DMR 172025)United States. Department of Energy (Contract No. DE-AC02-06C H11357)United States. Department of Energy. Office of Science (contract no. DE-AC02-05CH11231

Evolution of Mutational Robustness in the Yeast Genome: A Link to Essential Genes and Meiotic Recombination Hotspots

Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation

Nucleo-cytoplasmic transport of proteins and RNA in plants

Merkle T. Nucleo-cytoplasmic transport of proteins and RNA in plants. Plant Cell Reports. 2011;30(2):153-176.Transport of macromolecules between the nucleus and the cytoplasm is an essential necessity in eukaryotic cells, since the nuclear envelope separates transcription from translation. In the past few years, an increasing number of components of the plant nuclear transport machinery have been characterised. This progress, although far from being completed, confirmed that the general characteristics of nuclear transport are conserved between plants and other organisms. However, plant-specific components were also identified. Interestingly, several mutants in genes encoding components of the plant nuclear transport machinery were investigated, revealing differential sensitivity of plant-specific pathways to impaired nuclear transport. These findings attracted attention towards plant-specific cargoes that are transported over the nuclear envelope, unravelling connections between nuclear transport and components of signalling and developmental pathways. The current state of research in plants is summarised in comparison to yeast and vertebrate systems, and special emphasis is given to plant nuclear transport mutants

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Cotranslational protein folding can facilitate rapid formation of functional structures. However, it might also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched towards the C-termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur prior to assembly. Using high-throughput imaging of protein homomers in vivo in E. coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization

Evolution of a New Function by Degenerative Mutation in Cephalochordate Steroid Receptors

Gene duplication is the predominant mechanism for the evolution of new genes. Major existing models of this process assume that duplicate genes are redundant; degenerative mutations in one copy can therefore accumulate close to neutrally, usually leading to loss from the genome. When gene products dimerize or interact with other molecules for their functions, however, degenerative mutations in one copy may produce repressor alleles that inhibit the function of the other and are therefore exposed to selection. Here, we describe the evolution of a duplicate repressor by simple degenerative mutations in the steroid hormone receptors (SRs), a biologically crucial vertebrate gene family. We isolated and characterized the SRs of the cephalochordate Branchiostoma floridae, which diverged from other chordates just after duplication of the ancestral SR. The B. floridae genome contains two SRs: BfER, an ortholog of the vertebrate estrogen receptors, and BfSR, an ortholog of the vertebrate receptors for androgens, progestins, and corticosteroids. BfSR is specifically activated by estrogens and recognizes estrogen response elements (EREs) in DNA; BfER does not activate transcription in response to steroid hormones but binds EREs, where it competitively represses BfSR. The two genes are partially coexpressed, particularly in ovary and testis, suggesting an ancient role in germ cell development. These results corroborate previous findings that the ancestral steroid receptor was estrogen-sensitive and indicate that, after duplication, BfSR retained the ancestral function, while BfER evolved the capacity to negatively regulate BfSR. Either of two historical mutations that occurred during BfER evolution is sufficient to generate a competitive repressor. Our findings suggest that after duplication of genes whose functions depend on specific molecular interactions, high-probability degenerative mutations can yield novel functions, which are then exposed to positive or negative selection; in either case, the probability of neofunctionalization relative to gene loss is increased compared to existing models