A statistical-mechanical analysis of coded CDMA with regular LDPC codes

We analyze, using the replica method of statistical mechanics, the theoretical performance of coded code-division multiple-access (CDMA) systems in which regular low-density parity-check (LDPC) codes are used for channel coding.

Generalized mean field approximation for parallel dynamics of the Ising model

The dynamics of the non-equilibrium Ising model with parallel updates is investigated using a generalized mean field approximation that incorporates multiple two-site correlations at any two time steps, which can be obtained recursively. The proposed method shows significant improvement in predicting local system properties compared to other mean field approximation techniques, particularly in systems with symmetric interactions. Results are also evaluated against those obtained from Monte Carlo simulations. The method is also employed to obtain parameter values for the kinetic inverse Ising modeling problem, where couplings and local field values of a fully connected spin system are inferred from data. © 2014 IOP Publishing Ltd and SISSA Medialab srl.

A meshless method for an inverse two-phase one-dimensional nonlinear Stefan problem

We extend a meshless method of fundamental solutions recently proposed by the authors for the one-dimensional two-phase inverse linear Stefan problem, to the nonlinear case. In this latter situation the free surface is also considered unknown which is more realistic from the practical point of view. Building on the earlier work, the solution is approximated in each phase by a linear combination of fundamental solutions to the heat equation. The implementation and analysis are more complicated in the present situation since one needs to deal with a nonlinear minimization problem to identify the free surface. Furthermore, the inverse problem is ill-posed since small errors in the input measured data can cause large deviations in the desired solution. Therefore, regularization needs to be incorporated in the objective function which is minimized in order to obtain a stable solution. Numerical results are presented and discussed. © 2014 IMACS.

Using cognitive load theory to interpret student difficulties with a problem-based learning approach to engineering education:a case study

This article reports on an investigationwith first year undergraduate ProductDesign and Management students within a School of Engineering and Applied Science. The students at the time of this investigation had studied fundamental engineering science and mathematics for one semester. The students were given an open ended, ill-formed problem which involved designing a simple bridge to cross a river.They were given a talk on problemsolving and given a rubric to follow, if they chose to do so.They were not given any formulae or procedures needed in order to resolve the problem. In theory, they possessed the knowledge to ask the right questions in order tomake assumptions but, in practice, it turned out they were unable to link their a priori knowledge to resolve this problem. They were able to solve simple beam problems when given closed questions. The results show they were unable to visualize a simple bridge as an augmented beam problem and ask pertinent questions and hence formulate appropriate assumptions in order to offer resolutions.

Matrix-Variate Statistical Distributions and Fractional Calculus

MSC 2010: 15A15, 15A52, 33C60, 33E12, 44A20, 62E15 Dedicated to Professor R. Gorenflo on the occasion of his 80th birthday

Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

Nonlinear quantum transport in low-dimensional electronic devices

The study of transport processes in low-dimensional semiconductors requires a rigorous quantum mechanical treatment. However, a full-fledged quantum transport theory of electrons (or holes) in semiconductors of small scale, applicable in the presence of external fields of arbitrary strength, is still not available. In the literature, different approaches have been proposed, including: (a) the semiclassical Boltzmann equation, (b) perturbation theory based on Keldysh's Green functions, and (c) the Quantum Boltzmann Equation (QBE), previously derived by Van Vliet and coworkers, applicable in the realm of Kubo's Linear Response Theory (LRT). ^ In the present work, we follow the method originally proposed by Van Wet in LRT. The Hamiltonian in this approach is of the form: H = H 0(E, B) + λV, where H0 contains the externally applied fields, and λV includes many-body interactions. This Hamiltonian differs from the LRT Hamiltonian, H = H0 - AF(t) + λV, which contains the external field in the field-response part, -AF(t). For the nonlinear problem, the eigenfunctions of the system Hamiltonian, H0(E, B), include the external fields without any limitation on strength. ^ In Part A of this dissertation, both the diagonal and nondiagonal Master equations are obtained after applying projection operators to the von Neumann equation for the density operator in the interaction picture, and taking the Van Hove limit, (λ → 0, t → ∞, so that (λ2 t)n remains finite). Similarly, the many-body current operator J is obtained from the Heisenberg equation of motion. ^ In Part B, the Quantum Boltzmann Equation is obtained in the occupation-number representation for an electron gas, interacting with phonons or impurities. On the one-body level, the current operator obtained in Part A leads to the Generalized Calecki current for electric and magnetic fields of arbitrary strength. Furthermore, in this part, the LRT results for the current and conductance are recovered in the limit of small electric fields. ^ In Part C, we apply the above results to the study of both linear and nonlinear longitudinal magneto-conductance in quasi one-dimensional quantum wires (1D QW). We have thus been able to quantitatively explain the experimental results, recently published by C. Brick, et al., on these novel frontier-type devices. ^

Nonlinear quantum transport in low-dimensional electronic devices

The study of transport processes in low-dimensional semiconductors requires a rigorous quantum mechanical treatment. However, a full-fledged quantum transport theory of electrons (or holes) in semiconductors of small scale, applicable in the presence of external fields of arbitrary strength, is still not available. In the literature, different approaches have been proposed, including: (a) the semiclassical Boltzmann equation, (b) perturbation theory based on Keldysh's Green functions, and (c) the Quantum Boltzmann Equation (QBE), previously derived by Van Vliet and coworkers, applicable in the realm of Kubo's Linear Response Theory (LRT). In the present work, we follow the method originally proposed by Van Vliet in LRT. The Hamiltonian in this approach is of the form: H = H°(E, B) + λV, where H0 contains the externally applied fields, and λV includes many-body interactions. This Hamiltonian differs from the LRT Hamiltonian, H = H° - AF(t) + λV, which contains the external field in the field-response part, -AF(t). For the nonlinear problem, the eigenfunctions of the system Hamiltonian, H°(E, B) , include the external fields without any limitation on strength. In Part A of this dissertation, both the diagonal and nondiagonal Master equations are obtained after applying projection operators to the von Neumann equation for the density operator in the interaction picture, and taking the Van Hove limit, (λ → 0 , t → ∞ , so that (λ2 t)n remains finite). Similarly, the many-body current operator J is obtained from the Heisenberg equation of motion. In Part B, the Quantum Boltzmann Equation is obtained in the occupation-number representation for an electron gas, interacting with phonons or impurities. On the one-body level, the current operator obtained in Part A leads to the Generalized Calecki current for electric and magnetic fields of arbitrary strength. Furthermore, in this part, the LRT results for the current and conductance are recovered in the limit of small electric fields. In Part C, we apply the above results to the study of both linear and nonlinear longitudinal magneto-conductance in quasi one-dimensional quantum wires (1D QW). We have thus been able to quantitatively explain the experimental results, recently published by C. Brick, et al., on these novel frontier-type devices.

How does problem based learning fit with cognitive load theory?

This paper reports on an investigation with first year undergraduate Product Design and Management students within a School of Engineering. The students at the time of this investigation had studied fundamental engineering science and mathematics for one semester. The students were given an open ended, ill formed problem which involved designing a simple bridge to cross a river. They were given a talk on problem solving and given a rubric to follow, if they chose to do so. They were not given any formulae or procedures needed in order to resolve the problem. In theory, they possessed the knowledge to ask the right questions in order to make assumptions but, in practice, it turned out they were unable to link their a priori knowledge to resolve this problem. They were able to solve simple beam problems when given closed questions. The results show they were unable to visualise a simple bridge as an augmented beam problem and ask pertinent questions and hence formulate appropriate assumptions in order to offer resolutions.

Some Inverse Problems in Analysis and Geometry

Thesis (Ph.D.)--University of Washington, 2016-08

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

THE PHYSICS OF IDEAS: INFERRING THE MECHANICS OF OPINION FORMATION FROM MACROSCOPIC STATISTICAL PATTERNS

In a microscopic setting, humans behave in rich and unexpected ways. In a macroscopic setting, however, distinctive patterns of group behavior emerge, leading statistical physicists to search for an underlying mechanism. The aim of this dissertation is to analyze the macroscopic patterns of competing ideas in order to discern the mechanics of how group opinions form at the microscopic level. First, we explore the competition of answers in online Q&A (question and answer) boards. We find that a simple individual-level model can capture important features of user behavior, especially as the number of answers to a question grows. Our model further suggests that the wisdom of crowds may be constrained by information overload, in which users are unable to thoroughly evaluate each answer and therefore tend to use heuristics to pick what they believe is the best answer. Next, we explore models of opinion spread among voters to explain observed universal statistical patterns such as rescaled vote distributions and logarithmic vote correlations. We introduce a simple model that can explain both properties, as well as why it takes so long for large groups to reach consensus. An important feature of the model that facilitates agreement with data is that individuals become more stubborn (unwilling to change their opinion) over time. Finally, we explore potential underlying mechanisms for opinion formation in juries, by comparing data to various types of models. We find that different null hypotheses in which jurors do not interact when reaching a decision are in strong disagreement with data compared to a simple interaction model. These findings provide conceptual and mechanistic support for previous work that has found mutual influence can play a large role in group decisions. In addition, by matching our models to data, we are able to infer the time scales over which individuals change their opinions for different jury contexts. We find that these values increase as a function of the trial time, suggesting that jurors and judicial panels exhibit a kind of stubbornness similar to what we include in our model of voting behavior.

Quantitative Derivation of Effective Evolution Equations for the Dynamics of Bose-Einstein Condensates

This thesis proves certain results concerning an important question in non-equilibrium quantum statistical mechanics which is the derivation of effective evolution equations approximating the dynamics of a system of large number of bosons initially at equilibrium (ground state at very low temperatures). The dynamics of such systems are governed by the time-dependent linear many-body Schroedinger equation from which it is typically difficult to extract useful information due to the number of particles being large. We will study quantitatively (i.e. with explicit bounds on the error) how a suitable one particle non-linear Schroedinger equation arises in the mean field limit as number of particles N → ∞ and how the appropriate corrections to the mean field will provide better approximations of the exact dynamics. In the first part of this thesis we consider the evolution of N bosons, where N is large, with two-body interactions of the form N³ᵝv(Nᵝ⋅), 0≤β≤1. The parameter β measures the strength and the range of interactions. We compare the exact evolution with an approximation which considers the evolution of a mean field coupled with an appropriate description of pair excitations, see [18,19] by Grillakis-Machedon-Margetis. We extend the results for 0 ≤ β < 1/3 in [19, 20] to the case of β < 1/2 and obtain an error bound of the form p(t)/Nᵅ, where α>0 and p(t) is a polynomial, which implies a specific rate of convergence as N → ∞. In the second part, utilizing estimates of the type discussed in the first part, we compare the exact evolution with the mean field approximation in the sense of marginals. We prove that the exact evolution is close to the approximate in trace norm for times of the order o(1)√N compared to log(o(1)N) as obtained in Chen-Lee-Schlein [6] for the Hartree evolution. Estimates of similar type are obtained for stronger interactions as well.

Which-path problem for one and two particles with two degrees of freedom and a relation between transverse spatial structure and group velocity of light

Quantum mechanics, optics and indeed any wave theory exhibits the phenomenon of interference. In this thesis we present two problems investigating interference due to indistinguishable alternatives and a mostly unrelated investigation into the free space propagation speed of light pulses in particular spatial modes. In chapter 1 we introduce the basic properties of the electromagnetic field needed for the subsequent chapters. In chapter 2 we review the properties of interference using the beam splitter and the Mach-Zehnder interferometer. In particular we review what happens when one of the paths of the interferometer is marked in some way so that the particle having traversed it contains information as to which path it went down (to be followed up in chapter 3) and we review Hong-Ou-Mandel interference at a beam splitter (to be followed up in chapter 5). In chapter 3 we present the first of the interference problems. This consists of a nested Mach-Zehnder interferometer in which each of the free space propagation segments are weakly marked by mirrors vibrating at different frequencies [1]. The original experiment drew the conclusions that the photons followed disconnected paths. We partition the description of the light in the interferometer according to the number of paths it contains which-way information about and reinterpret the results reported in [1] in terms of the interference of paths spatially connected from source to detector. In chapter 4 we briefly review optical angular momentum, entanglement and spontaneous parametric down conversion. These concepts feed into chapter 5 in which we present the second of the interference problems namely Hong-Ou-Mandel interference with particles possessing two degrees of freedom. We analyse the problem in terms of exchange symmetry for both boson and fermion pairs and show that the particle statistics at a beam splitter can be controlled for suitably chosen states. We propose an experimental test of these ideas using orbital angular momentum entangled photons. In chapter 6 we look at the effect that the transverse spatial structure of the mode that a pulse of light is excited in has on its group velocity. We show that the resulting group velocity is slower than the speed of light in vacuum for plane waves and that this reduction in the group velocity is related to the spread in the wave vectors required to create the transverse spatial structure. We present experimental results of the measurement of this slowing down using Hong-Ou-Mandel interference.

Geological realism in hydrogeological and geophysical inverse modeling: A review

Scientific curiosity, exploration of georesources and environmental concerns are pushing the geoscientific research community toward subsurface investigations of ever-increasing complexity. This review explores various approaches to formulate and solve inverse problems in ways that effectively integrate geological concepts with geophysical and hydrogeological data. Modern geostatistical simulation algorithms can produce multiple subsurface realizations that are in agreement with conceptual geological models and statistical rock physics can be used to map these realizations into physical properties that are sensed by the geophysical or hydrogeological data. The inverse problem consists of finding one or an ensemble of such subsurface realizations that are in agreement with the data. The most general inversion frameworks are presently often computationally intractable when applied to large-scale problems and it is necessary to better understand the implications of simplifying (1) the conceptual geological model (e.g., using model compression); (2) the physical forward problem (e.g., using proxy models); and (3) the algorithm used to solve the inverse problem (e.g., Markov chain Monte Carlo or local optimization methods) to reach practical and robust solutions given today's computer resources and knowledge. We also highlight the need to not only use geophysical and hydrogeological data for parameter estimation purposes, but also to use them to falsify or corroborate alternative geological scenarios.