Physics Commons^™

Predicting Biomolecular Properties And Interactions Using Numerical, Statistical And Machine Learning Methods, Elyssa Sliheet

Mathematics Theses and Dissertations

We investigate machine learning and electrostatic methods to predict biophysical properties of proteins, such as solvation energy and protein ligand binding affinity, for the purpose of drug discovery/development. We focus on the Poisson-Boltzmann model and various high performance computing considerations such as parallelization schemes.

Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin

Research Symposium

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations to elucidate Pt(0)-mediated C–CP bond activation mechanisms in phosphaalkynes. Investigating the …

Accelerating Markov Chain Monte Carlo Sampling With Diffusion Models, N. T. Hunt-Smith, W. Melnitchouk, F. Ringer, N. Sato, A. W. Thomas, M. J. White

Physics Faculty Publications

Global fits of physics models require efficient methods for exploring high-dimensional and/or multimodal posterior functions. We introduce a novel method for accelerating Markov Chain Monte Carlo (MCMC) sampling by pairing a Metropolis-Hastings algorithm with a diffusion model that can draw global samples with the aim of approximating the posterior. We briefly review diffusion models in the context of image synthesis before providing a streamlined diffusion model tailored towards low-dimensional data arrays. We then present our adapted Metropolis-Hastings algorithm which combines local proposals with global proposals taken from a diffusion model that is regularly trained on the samples produced during the …

Applications Of Independent And Identically Distributed (Iid) Random Processes In Polarimetry And Climatology, Dan Kestner

Dissertations, Master's Theses and Master's Reports

The unifying theme of this thesis is the characterization of “perfect randomness,” i.e., independent and identically distributed (IID) stochastic processes as these are applied in physical science. Two specific and mathematically distinct applications are chosen: (i) Radar and optical polarimetry; (ii) Analysis of time series in meteorology. In (i), IID process of a special kind, namely, with a distribution defined by symmetry, is used to link its multivariate Gaussian density to uniformity on the Poincaré sphere. This “statistical ellipsometry” approach is then used to relate polarimetric mismatches or imbalances to ellipsometric variables and suitably chosen cross-correlation measures. In (ii), recently …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Human And Technical Factors In The Adoption Of Quantum Cryptographic Algorithms, Alyssa Pinkston

Mathematical Sciences Technical Reports (MSTR)

The purpose of this research is to understand what factors would cause users to choose quantum key distribution (QKD) over other methods of cryptography. An Advanced Encryption Standard (AES) key can be exchanged through communication using the Rivest, Shamir, Adleman (RSA) cryptographic algorithm, QKD, or post-quantum cryptography (PQC). QKD relies on quantum physics where RSA and PQC use complex mathematics to encrypt data. The BB84 quantum cryptographic protocol involves communication over a quantum channel and a public channel. The quantum channel can be technically attacked by beamsplitting or intercept/resend. QKD, like other forms of cryptography, is vulnerable to social attacks …

Machine Learning-Based Data And Model Driven Bayesian Uncertanity Quantification Of Inverse Problems For Suspended Non-Structural System, Zhiyuan Qin

All Dissertations

Inverse problems involve extracting the internal structure of a physical system from noisy measurement data. In many fields, the Bayesian inference is used to address the ill-conditioned nature of the inverse problem by incorporating prior information through an initial distribution. In the nonparametric Bayesian framework, surrogate models such as Gaussian Processes or Deep Neural Networks are used as flexible and effective probabilistic modeling tools to overcome the high-dimensional curse and reduce computational costs. In practical systems and computer models, uncertainties can be addressed through parameter calibration, sensitivity analysis, and uncertainty quantification, leading to improved reliability and robustness of decision and …

Applying Hallgren’S Algorithm For Solving Pell’S Equation To Finding The Irrational Slope Of The Launch Of A Billiard Ball, Sangheon Choi

Mathematical Sciences Technical Reports (MSTR)

This thesis is an exploration of Quantum Computing applied to Pell’s equation in an attempt to find solutions to the Billiard Ball Problem. Pell’s equation is a Diophantine equation in the form of x² − ny² = 1, where n is a given positive nonsquare integer, and integer solutions are sought for x and y. We will be applying Hallgren’s algorithm for finding irrational periods in functions, in the context of billiard balls and their movement on a friction-less unit square billiard table. Our central research question has been the following: Given the cutting sequence of the billiard …

Patch-Wise Training With Convolutional Neural Networks To Synthetically Upscale Cfd Simulations, John P. Romano, Alec C. Brodeur, Oktay Baysal

Mechanical & Aerospace Engineering Faculty Publications

This paper expands the authors’ prior work[1], which focuses on developing a convolutional neural network (CNN) model capable of mapping time-averaged, unsteady Reynold’s-averaged Navier-Stokes (URANS) simulations to higher resolution results informed by time-averaged detached eddy simulations (DES). The authors present improvements over the prior CNN autoencoder model that result from hyperparameter optimization, increased data set augmentation through the adoption of a patch-wise training approach, and the predictions of primitive variables rather than vorticity magnitude. The training of the CNN model developed in this study uses the same URANS and DES simulations of a transonic flow around several NACA 4-digit airfoils …

The Effect Of The Width Of The Incident Pulse To The Dielectric Transition Layer In The Scattering Of An Electromagnetic Pulse — A Qubit Lattice Algorithm Simulation, George Vahala, Linda Vahala, Abhay K. Ram, Min Soe

Electrical & Computer Engineering Faculty Publications

The effect of the thickness of the dielectric boundary layer that connects a material of refractive index n₁ to another of index n₂is considered for the propagation of an electromagnetic pulse. A qubit lattice algorithm (QLA), which consists of a specially chosen non-commuting sequence of collision and streaming operators acting on a basis set of qubits, is theoretically determined that recovers the Maxwell equations to second-order in a small parameter ϵ. For very thin boundary layer the scattering properties of the pulse mimics that found from the Fresnel jump conditions for a plane wave - except that …

Machine-Assisted Discovery Of Integrable Symplectic Mappings, T. Zolkin, Y. Kharkov, S. Nagaitsev

Physics Faculty Publications

We present a new automated method for finding integrable symplectic maps of the plane. These dynamical systems possess a hidden symmetry associated with an existence of conserved quantities, i.e., integrals of motion. The core idea of the algorithm is based on the knowledge that the evolution of an integrable system in the phase space is restricted to a lower-dimensional submanifold. Limiting ourselves to polygon invariants of motion, we analyze the shape of individual trajectories thus successfully distinguishing integrable motion from chaotic cases. For example, our method rediscovers some of the famous McMillan-Suris integrable mappings and ultradiscrete Painlevé equations. In total, …

Machine Learning-Based Jet And Event Classification At The Electron-Ion Collider With Applications To Hadron Structure And Spin Physics, Kyle Lee, James Mulligan, Mateusz Płoskoń, Felix Ringer, Feng Yuan

Physics Faculty Publications

We explore machine learning-based jet and event identification at the future Electron-Ion Collider (EIC). We study the effectiveness of machine learning-based classifiers at relatively low EIC energies, focusing on (i) identifying the flavor of the jet and (ii) identifying the underlying hard process of the event. We propose applications of our machine learning-based jet identification in the key research areas at the future EIC and current Relativistic Heavy Ion Collider program, including enhancing constraints on (transverse momentum dependent) parton distribution functions, improving experimental access to transverse spin asymmetries, studying photon structure, and quantifying the modification of hadrons and jets in …

Establishing The Legal Framework To Regulate Quantum Computing Technology, Kaya Derose

Catholic University Journal of Law and Technology

No abstract provided.

Hhl Algorithm On The Honeywell H1 Quantum Computer, Adrik B. Herbert, Eric A. F. Reinhardt

Discovery Undergraduate Interdisciplinary Research Internship

The quantum algorithm for linear systems of equations (HHL algorithm) provides an efficient tool for finding solutions to systems of functions with a large number of variables and low sensitivity to changes in inputs (i.e. low error rates). For complex problems, such as matrix inversion, HHL requires exponentially less computational time as compared with classical computation methods. HHL can be adapted to current quantum computing systems with limited numbers of qubits (quantum computation bits) but a high reusability rate such as the Honeywell H1 quantum computer. Some methods for improving HHL have been proposed through the combination of quantum and …

Quantum Federated Learning: Training Hybrid Neural Networks Collaboratively, Anneliese Brei

Undergraduate Honors Theses

This thesis explores basic concepts of machine learning, neural networks, federated learning, and quantum computing in an effort to better understand Quantum Machine Learning, an emerging field of research. We propose Quantum Federated Learning (QFL), a schema for collaborative distributed learning that maintains privacy and low communication costs. We demonstrate the QFL framework and local and global update algorithms with implementations that utilize TensorFlow Quantum libraries. Our experiments test the effectiveness of frameworks of different sizes. We also test the effect of changing the number of training cycles and changing distribution of training data. This thesis serves as a synoptic …

Unconventional Computation Including Quantum Computation, Bruce J. Maclennan

Faculty Publications and Other Works -- EECS

Unconventional computation (or non-standard computation) refers to the use of non-traditional technologies and computing paradigms. As we approach the limits of Moore’s Law, progress in computation will depend on going beyond binary electronics and on exploring new paradigms and technologies for information processing and control. This book surveys some topics relevant to unconventional computation, including the definition of unconventional computations, the physics of computation, quantum computation, DNA and molecular computation, and analog computation. This book is the content of a course taught at UTK.

A Super Fast Algorithm For Estimating Sample Entropy, Weifeng Liu, Ying Jiang, Yuesheng Xu

Mathematics & Statistics Faculty Publications

: Sample entropy, an approximation of the Kolmogorov entropy, was proposed to characterize complexity of a time series, which is essentially defined as − log(B/A), where B denotes the number of matched template pairs with length m and A denotes the number of matched template pairs with m + 1, for a predetermined positive integer m. It has been widely used to analyze physiological signals. As computing sample entropy is time consuming, the box-assisted, bucket-assisted, x-sort, assisted sliding box, and kd-tree-based algorithms were proposed to accelerate its computation. These algorithms require O(N²) or …

Numerical Treatment For Special Type Of Mixed Linear Delay Volterra Integro-Differential Equations, Atheer J. Kadhim

Emirates Journal for Engineering Research

The idea of research is a representation of the nonlinear pseudo-random generators using state-space equations that is not based on the usual description as shift register synthesis but in terms of matrices. Different types of nonlinear pseudo-random generators with their algorithms have been applied in order to investigate the output pseudo-random sequences. Moreover, two examples are given for conciliated the results of this representation.

Computer Program Simulation Of A Quantum Turing Machine With Circuit Model, Shixin Wu

Mathematical Sciences Technical Reports (MSTR)

Molina and Watrous present a variation of the method to simulate a quantum Turing machine employed in Yao’s 1995 publication “Quantum Circuit Complexity”. We use a computer program to implement their method with linear algebra and an additional unitary operator defined to complete the details. Their method is verified to be correct on a quantum Turing machine.

Computational Studies Of Carbon Nanocluster Solidification, Chathuri C. Silva

Dissertations

A subset of micron-size meteoritic carbon particles formed in red giant atmospheres show a core-rim structure, likely condensed from a vapor phase into super-cooled carbon droplets that nucleated graphene sheets (~40Å) on randomly oriented 5-atom loops during solidification, followed by coating with a graphite rim. Similar particles form during slow cooling of carbon vapor in the lab.

Here we investigate the nucleation and growth of carbon rings and graphene sheets using density functional theory (DFT). Our objectives: (1). explore different computational techniques in DFT-VASP for various carbon structures and compare the results with literature, (2). investigate the nucleation and growth …

Rotating Scatter Mask For Directional Radiation Detection And Imaging, Darren Holland, Robert Olesen, Larry Burggraf, Buckley O'Day, James E. Bevins

AFIT Patents

A radiation imaging system images a distributed source of radiation from an unknown direction by rotating a scatter mask around a central axis. The scatter mask has a pixelated outer surface of tangentially oriented, flat geometric surfaces that are spherically varying in radial dimension that corresponds to a discrete amount of attenuation. Rotation position of the scatter mask is tracked as a function of time. Radiation counts from gamma and/or neutron radiation are received from at least one radiation detector that is positioned at or near the central axis. A rotation-angle dependent detector response curve (DRC) is generated based on …

Solving Chromatic Number With Quantum Search And Quantum Counting, David Lutze

Master's Theses

This thesis presents a novel quantum algorithm that solves the Chromatic Number problem. Complexity analysis of this algorithm revealed a run time of O(2^n/2n²(log2n)²). This is an improvement over the best known algorithm, with a run time of 2ⁿn^O(1) [1]. This algorithm uses the Quantum Search algorithm (often called Grover's Algorithm), and the Quantum Counting algorithm. Chromatic Number is an example of an NP-Hard problem, which suggests that other NP-Hard problems can also benefit from a speed-up provided by quantum technology. This has wide implications as many real world problems can …

Data-Driven Approaches To Complex Materials: Applications To Amorphous Solids, Dil Kumar Limbu

Dissertations

While conventional approaches to materials modeling made significant contributions and advanced our understanding of materials properties in the past decades, these approaches often cannot be applied to disordered materials (e.g., glasses) for which accurate total-energy functionals or forces are either not available or it is infeasible to employ due to computational complexities associated with modeling disordered solids in the absence of translational symmetry. In this dissertation, a number of information-driven probabilistic methods were developed for the structural determination of a range of materials including disordered solids to transition metal clusters. The ground-state structures of transition-metal clusters of iron, nickel, and …

Implications Of The Quantum Dna Model For Information Sciences, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor, and this model has been supported by pilot research that experimentally demonstrated non-local communication between cells in separated cell cultures. This modeling and pilot research have important implications for information sciences, providing a potential architecture for quantum computing that operates at room temperature and is scalable to millions of qubits, and including the potential for an entanglement communication system based upon the quantum DNA architecture. Such a system could be used to provide non-local quantum key distribution that could not be blocked by any shielding or water depth, would …

Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore

Electronic Theses and Dissertations

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers …

Quantum Simulation Of Schrödinger's Equation, Mohamed Eltohfa

Capstone and Graduation Projects

Quantum computing is one of the promising active areas in physics research. This is because of the potential of quantum algorithms to outperform their classical counterparts. Grover’s search algorithm has a quadratic speed-up compared to the classical linear search. The quantum simulation of Schrödinger’s equation has an exponential memory save-up compared to the classical simulation. In this thesis, the ideas and tools of quantum computing are reviewed. Grover’s algorithm is studied and simulated as an example. Using the Qiskit quantum computing library, a code to simulate Schrödinger’s equation for a particle in one dimension is developed, simulated locally, and run …

Understanding The Research And Applications Of Quantum Computing, Joshua Foss

Williams Honors College, Honors Research Projects

In-Depth research of current quantum computing understanding and practices. Presentation of possible new and creative applications of quantum computing.

An Update On The Computational Theory Of Hamiltonian Period Functions, Bradley Joseph Klee

Graduate Theses and Dissertations

Lately, state-of-the-art calculation in both physics and mathematics has expanded to include the field of symbolic computing. The technical content of this dissertation centers on a few Creative Telescoping algorithms of our own design (Mathematica implementations are given as a supplement). These algorithms automate analysis of integral period functions at a level of difficulty and detail far beyond what is possible using only pencil and paper (unless, perhaps, you happen to have savant-level mental acuity). We can then optimize analysis in classical physics by using the algorithms to calculate Hamiltonian period functions as solutions to ordinary differential equations. The simple …

Benchmarks And Controls For Optimization With Quantum Annealing, Erica Kelley Grant

Doctoral Dissertations

Quantum annealing (QA) is a metaheuristic specialized for solving optimization problems which uses principles of adiabatic quantum computing, namely the adiabatic theorem. Some devices implement QA using quantum mechanical phenomena. These QA devices do not perfectly adhere to the adiabatic theorem because they are subject to thermal and magnetic noise. Thus, QA devices return statistical solutions with some probability of success where this probability is affected by the level of noise of the system. As these devices improve, it is believed that they will become less noisy and more accurate. However, some tuning strategies may further improve that probability of …

Machine Learning Corrected Quantum Dynamics Calculations, A. Jasinski, J. Montaner, R. C. Forrey, B. H. Yang, P. C. Stancil, Naduvalath Balakrishnan, J. Dai, A. Vargas-Hernandez, R. V. Krems

Chemistry and Biochemistry Faculty Research

Quantum scattering calculations for all but low-dimensional systems at low energies must rely on approximations. All approximations introduce errors. The impact of these errors is often difficult to assess because they depend on the Hamiltonian parameters and the particular observable under study. Here, we illustrate a general, system- and approximation-independent, approach to improve the accuracy of quantum dynamics approximations. The method is based on a Bayesian machine learning (BML) algorithm that is trained by a small number of exact results and a large number of approximate calculations, resulting in ML models that can generalize exact quantum results to different dynamical …