On erasure coding for distributed storage and streaming communications

The work presented in this thesis revolves around erasure correction coding, as applied to distributed data storage and real-time streaming communications.

First, we examine the problem of allocating a given storage budget over a set of nodes for maximum reliability. The objective is to find an allocation of the budget that maximizes the probability of successful recovery by a data collector accessing a random subset of the nodes. This optimization problem is challenging in general because of its combinatorial nature, despite its simple formulation. We study several variations of the problem, assuming different allocation models and access models, and determine the optimal allocation and the optimal symmetric allocation (in which all nonempty nodes store the same amount of data) for a variety of cases. Although the optimal allocation can have nonintuitive structure and can be difficult to find in general, our results suggest that, as a simple heuristic, reliable storage can be achieved by spreading the budget maximally over all nodes when the budget is large, and spreading it minimally over a few nodes when it is small. Coding would therefore be beneficial in the former case, while uncoded replication would suffice in the latter case.

Second, we study how distributed storage allocations affect the recovery delay in a mobile setting. Specifically, two recovery delay optimization problems are considered for a network of mobile storage nodes: the maximization of the probability of successful recovery by a given deadline, and the minimization of the expected recovery delay. We show that the first problem is closely related to the earlier allocation problem, and solve the second problem completely for the case of symmetric allocations. It turns out that the optimal allocations for the two problems can be quite different. In a simulation study, we evaluated the performance of a simple data dissemination and storage protocol for mobile delay-tolerant networks, and observed that the choice of allocation can have a significant impact on the recovery delay under a variety of scenarios.

Third, we consider a real-time streaming system where messages created at regular time intervals at a source are encoded for transmission to a receiver over a packet erasure link; the receiver must subsequently decode each message within a given delay from its creation time. For erasure models containing a limited number of erasures per coding window, per sliding window, and containing erasure bursts whose maximum length is sufficiently short or long, we show that a time-invariant intrasession code asymptotically achieves the maximum message size among all codes that allow decoding under all admissible erasure patterns. For the bursty erasure model, we also show that diagonally interleaved codes derived from specific systematic block codes are asymptotically optimal over all codes in certain cases. We also study an i.i.d. erasure model in which each transmitted packet is erased independently with the same probability; the objective is to maximize the decoding probability for a given message size. We derive an upper bound on the decoding probability for any time-invariant code, and show that the gap between this bound and the performance of a family of time-invariant intrasession codes is small when the message size and packet erasure probability are small. In a simulation study, these codes performed well against a family of random time-invariant convolutional codes under a number of scenarios.

Finally, we consider the joint problems of routing and caching for named data networking. We propose a backpressure-based policy that employs virtual interest packets to make routing and caching decisions. In a packet-level simulation, the proposed policy outperformed a basic protocol that combines shortest-path routing with least-recently-used (LRU) cache replacement.

The head-body weight and head-body length relationship of Synodontis schall (Bloch and Schneider 1801) in Asa Lake, Ilorin, Nigeria

A total of 710 specimens of Synodontis schall were analyzed for the head body weight and head body length relationship. The head constituted 40% of the total body weight and 30% of the total body length. The mean head weight for male and female computed was 23.90g and 29.13g respectively. Head weight in both male and female was significantly different (P<0.01) while the head length for the combined sexes showed no significant difference (P>0.05). Fat accumulation in the body tissue was prominent in the females than males usually before the breeding season. The significance of the cephalo-nuchal shield in the bony head of Synodontis species compared with some other catfishes in the lake was also discussed

Fishery resource surveys: beyond length-weight relationship models

Fisheries resource surveys are regular management tools for rational exploitation of commercial fisheries. In a growing number of cases, the use of these resource surveys has been largely restricted to assessment of the relative well being of fish stocks and the potential yields of such fisheries. This paper seeks to demonstrate that the data from such surveys can also be easily used to evaluate species diversity of such fisheries, both in terms of species richness and equitability of distribution. Using published data on two freshwater and two marine fisheries as case studies, Shannon-Wiener Diversity Function and Simpson's Index were computed for each of these fisheries. These biodiversity indices gave a deeper insight into the environmental status of each of these fisheries, beyond what the length-weight relationship models can reveal. Generally, while the marine fisheries showed more species richness, the freshwater fisheries apparently had more stable and equilibrated fish communities

Influence of Coulomb potential for photoionization of H atoms in an elliptically polarized laser field: Velocity gauge versus length gauge

We theoretically study the influence of Coulomb potential for photoionization of hydrogen atoms in an intense laser field with elliptical polarization. The total ionization rates, photoelectron energy spectra, and photoelectron angular distributions are calculated with the Coulomb-Volkov wave functions in the velocity gauge and compared with those calculated in the length gauge as well as those calculated with the Volkov wave functions. By comparing the results obtained by the Coulomb-Volkov and Volkov wave functions, we find that for linear polarization the influence of Coulomb potential is obvious for low-energy photoelectrons, and as the photoelectron energy and/or the laser intensity increase, its influence becomes smaller. This trend, however, is not so clear for the case of elliptical polarization. We also find that the twofold symmetry in the photoelectron angular distributions for elliptical polarization is caused by the cooperation of Coulomb potential and interference of multiple transition channels. About the gauge issue, we show that the difference in the photoelectron angular distributions obtained by the velocity and length gauges becomes rather obvious for elliptical polarization, while the difference is generally smaller for linear polarization.

Proteolytic processing of the nonstructural proteins of dengue 2 virus

The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

Determination of optimum stocking density of Macrobrachium rosenbergii larvae using multiple feed in a commercial hatchery at Cox’s Bazar, Bangladesh

Experimental stocking density of Macrobrachium rosenbergii in larval rearing was conducted in A.G. Aqua Hatchery, Chakaria, Bangladesh to study the effect of different stocking densities on growth, survival rate and diseases stress under hatchery condition. The research work was conducted using six cemented rectangular tanks having 3m3 capacity (1.5mX2mX1m) each. Stocking density were maintained in three experimental setup as 200, 150 and 100ind/L of the T1, T2 and T3 respectively with one replicate each. The larvae were fed with Artemia nauplii, Custard, Maxima and brine shrimp flakes. Water quality was maintained by exchanging 20-30% (12ppt saline water) daily. During the study period, temperature, pH, DO, salinity, nitrite-nitrogen, ammonia and alkalinity were maintained from 28.5-31.5ºC, 7.5-7.8, 5.8-5.9mg/L, 12-13ppt, 0.14-0.2 mg/L, 0.22-0.3mg/L, and 140-160mg/L respectively. The growth rates of larvae at 11th stage were recorded in terms of body length 0.115, 0.136, and 0.169 mm/day whereas body weight were observed 0.000115, 0.000180, and 0.000240g/day. The survival rate of larvae were found 21.8%, 30.4% and 51.3% in treatments T1, T2 and T3 respectively. PL was obtained as 43, 45, and 51PL/L and days required of 41, 38 and 34 days in stocking density of 200, 150, and 100ind/L respectively. It was found that the minimum of 34 days was required to attain the PL (12th stage) using the stocking density of 100 individuals/L. Cannibalism, Zoothamnium, Exuvia Entrapment Disease (EED), and Bacterial Necrosis (BN) were found to be the threat to the commercial hatchery operation that might responsible for potential larval damages which can be reduced by lowering the stocking densities in larval rearing tank that also increased the survival and growth rate.

Effects of self energy of the ions on the double layer structure and properties at the dielectric interface

Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.

In this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.

Next, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.

Next, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.

Then, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.

Finally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.

The theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.

Spatial longitudinal coherence length of a thermal source and its influence on lensless ghost imaging

The spatial longitudinal coherence length (SLCL), which is determined by the size of and the distance from the source, is introduced to investigate the longitudinal resolution of lensless ghost imaging. Its influence is discussed quantitatively by simulation. The discrepancy of position sensitivity between Scareelli et al. [Appl. Phys. Lett. 88, 061106 (2006)] and Basano and Ottonello [Appl. Phys. Lett. 88, 091109 (2006)] is clarified. (C) 2008 Optical Society of America.

On the methods of determining size/weight characteristics of food organisms of fish. (Determination of the length of Copepoda in larval stages by egg-laying females of the free living freshwater Copepoda). [Translation from: Voprosy Ikhtiologii 14, 182-194, 1960. ]

As is known, copepods play an important role in the nutrition of fish. Therefore with a view to facilitating research on the study of the quantitative side of feeding, there have recently appeared a considerable number of papers devoted to the development of methods for determining the wet. weight of these crustaceans. For the further facilitating of research in the nutrition of fish it would be of great interest to clarify the problem, is there not some kind of rule in the growth of the crustaceans during metamorphosis, and if there is such a rule is it not possible, to determine the length of the larvae at each stage, not by measuring them, but by using the formulae derived on the basis of these rules. This article examines the growth curves of different species of freshwater Copepoda, obtained on the basis of experimental observations in cultures or by way of measurement of mass material at all stages of development in samples from water-bodies. The authors study in particular the ratio of the mean diameter of the eggs to the mean length of the egg-bearing females.

参变过程中的群速延迟对晶体匹配长度的影响

基于能量守恒和三波耦合波方程, 建立了超短脉冲在参变过程中二次谐波产生时的I类和II类相位匹配条件、基波与谐波之间的群速延迟时间、以及群速失配对晶体长度限制的理论基础。以负单轴非线性光学晶体CsLiB6O10为例, 分析和数值计算了超短脉冲宽度为100 fs时, 谐波的群速匹配长度随基波波长变化的规律。研究结果表明在I类相位匹配条件下, 基波波长为642 nm时, 群速延迟最小, 相应的群速匹配晶体长度最长为19.1 mm;在II类相位匹配条件下, 基波波长为767 nm, 群速延迟最小, 群速匹配长度最

Algebraic Techniques in Coding Theory: Entropy Vectors, Frames, and Constrained Coding

The study of codes, classically motivated by the need to communicate information reliably in the presence of error, has found new life in fields as diverse as network communication, distributed storage of data, and even has connections to the design of linear measurements used in compressive sensing. But in all contexts, a code typically involves exploiting the algebraic or geometric structure underlying an application. In this thesis, we examine several problems in coding theory, and try to gain some insight into the algebraic structure behind them.

The first is the study of the entropy region - the space of all possible vectors of joint entropies which can arise from a set of discrete random variables. Understanding this region is essentially the key to optimizing network codes for a given network. To this end, we employ a group-theoretic method of constructing random variables producing so-called "group-characterizable" entropy vectors, which are capable of approximating any point in the entropy region. We show how small groups can be used to produce entropy vectors which violate the Ingleton inequality, a fundamental bound on entropy vectors arising from the random variables involved in linear network codes. We discuss the suitability of these groups to design codes for networks which could potentially outperform linear coding.

The second topic we discuss is the design of frames with low coherence, closely related to finding spherical codes in which the codewords are unit vectors spaced out around the unit sphere so as to minimize the magnitudes of their mutual inner products. We show how to build frames by selecting a cleverly chosen set of representations of a finite group to produce a "group code" as described by Slepian decades ago. We go on to reinterpret our method as selecting a subset of rows of a group Fourier matrix, allowing us to study and bound our frames' coherences using character theory. We discuss the usefulness of our frames in sparse signal recovery using linear measurements.

The final problem we investigate is that of coding with constraints, most recently motivated by the demand for ways to encode large amounts of data using error-correcting codes so that any small loss can be recovered from a small set of surviving data. Most often, this involves using a systematic linear error-correcting code in which each parity symbol is constrained to be a function of some subset of the message symbols. We derive bounds on the minimum distance of such a code based on its constraints, and characterize when these bounds can be achieved using subcodes of Reed-Solomon codes.

偏振模色散和时延抖动对啁啾光纤光栅色散补偿特性的影响

对存在偏振模色散(PMD)和群时延(GD)抖动的非理想线性啁啾光纤光栅的色散补偿特性进行了研究。实验测量了啁啾光纤光栅的群时延谱和偏振模色散光谱，理论分析和实验测量表明，啁啾光纤光栅差分群时延(DGD)抖动与其时延抖动密切相关。通过数值模拟方法，计算了线性啁啾光纤光栅偏振模色散眼图代价与入射到啁啾光纤光栅色散补偿器的光信号的偏振方向的关系，计算结果表明在使用啁啾光纤光栅色散补偿器时应对光信号的偏振方向进行调整，以获得最佳补偿效果。另外结合实验数据，模拟计算并讨论了非理想线性啁啾光纤光栅群时延抖动和偏振模色

平面弯曲波导耦合器的特性分析

根据耦合模理论和弯曲波导耦合器的结构特点,对平面弯曲波导耦合器的特性进行了分析,结果表明弯曲波导耦合器的弯曲半径和最小间距两个可调变量,增加了波导器件设计的灵活性;同时由于等效耦合长度的调制作用使得弯曲波导耦合器在波分复用/解复用中比平行直波导耦合器具有更大的复用带宽;分析了弯曲半径和最小间距对弯曲波导耦合器复用带宽的影响,为实际波导器件的设计制作提供了一定的理论依据.

Force chains, friction, and flow: Behavior of granular media across length scales

We study the behavior of granular materials at three length scales. At the smallest length scale, the grain-scale, we study inter-particle forces and "force chains". Inter-particle forces are the natural building blocks of constitutive laws for granular materials. Force chains are a key signature of the heterogeneity of granular systems. Despite their fundamental importance for calibrating grain-scale numerical models and elucidating constitutive laws, inter-particle forces have not been fully quantified in natural granular materials. We present a numerical force inference technique for determining inter-particle forces from experimental data and apply the technique to two-dimensional and three-dimensional systems under quasi-static and dynamic load. These experiments validate the technique and provide insight into the quasi-static and dynamic behavior of granular materials.

At a larger length scale, the mesoscale, we study the emergent frictional behavior of a collection of grains. Properties of granular materials at this intermediate scale are crucial inputs for macro-scale continuum models. We derive friction laws for granular materials at the mesoscale by applying averaging techniques to grain-scale quantities. These laws portray the nature of steady-state frictional strength as a competition between steady-state dilation and grain-scale dissipation rates. The laws also directly link the rate of dilation to the non-steady-state frictional strength.

At the macro-scale, we investigate continuum modeling techniques capable of simulating the distinct solid-like, liquid-like, and gas-like behaviors exhibited by granular materials in a single computational domain. We propose a Smoothed Particle Hydrodynamics (SPH) approach for granular materials with a viscoplastic constitutive law. The constitutive law uses a rate-dependent and dilation-dependent friction law. We provide a theoretical basis for a dilation-dependent friction law using similar analysis to that performed at the mesoscale. We provide several qualitative and quantitative validations of the technique and discuss ongoing work aiming to couple the granular flow with gas and fluid flows.

The photorefractive sensitivity and the effective electron transport length in two-centre holographic recording

In this paper the photorefractive sensitivity defined for single-centre holographic recording is modified to adapt two-centre holographic recording. Based on the time analytic solution of Kukhtarev equations for doubly doped crystals, the analytical expression of photorefractive sensitivity is given. For comparison with single-centre holographic recording and summing the electron competition effects between the deeper and shallower traps, an effective electron transport length is proposed, which varies with the intensity ratios of recording light to sensitive light. According to analyses in this paper, the lower photorefractive sensitivity in two-centre holographic recording is mainly due to the lower concentration of unionized dopants in the shallower centre and the lower effective electron transport length.