Applied Mathematics 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.

Invariance Of Chsh Parameters When Projecting Weakly Signaling Distribution Into A No Signaling Subspace, Aaditya Paudel

LSU New Orleans Theses and Dissertations

The seminal 1935 paper by Einstein, Podolsky, and Rosen (EPR) sparked a fundamental debate in quantum mechanics about the completeness of physical reality through the EPR paradox. They questioned local realism by suggesting that particles could exhibit instantaneous correlations across any distance, challenging classical physics. Bell's theorem (1964) argued that no local hidden variable theory could replicate quantum predictions, introducing Bell's inequalities and their experimental tests. These tests, particularly through violations of Bell's inequalities, confirmed quantum predictions of non-local correlations that local realism could not account for. Quantum theory, while supporting such correlations, adheres to the no-signaling principle to prevent …

Tools For Biomolecular Modeling And Simulation, Xin Yang

Mathematics Theses and Dissertations

Electrostatic interactions play a pivotal role in understanding biomolecular systems, influencing their structural stability and functional dynamics. The Poisson-Boltzmann (PB) equation, a prevalent implicit solvent model that treats the solvent as a continuum while describes the mobile ions using the Boltzmann distribution, has become a standard tool for detailed investigations into biomolecular electrostatics. There are two primary methodologies: grid-based finite difference or finite element methods and body-fitted boundary element methods. This dissertation focuses on developing fast and accurate PB solvers, leveraging both methodologies, to meet diverse scientific needs and overcome various obstacles in the field.

Generation, Dynamics, And Interaction Of Quartic Solitary Waves In Nonlinear Laser Systems, Sabrina Hetzel

Mathematics Theses and Dissertations

Solitons are self-reinforcing localized wave packets that have remarkable stability features that arise from the balanced competition of nonlinear and dispersive effects in the medium. Traditionally, the dominant order of dispersion has been the lowest (second), however in recent years, experimental and theoretical research has shown that high, even order dispersion may lead to novel applications. Here, the focus is on investigating the interplay of dominant quartic (fourth-order) dispersion and the self-phase modulation due to the nonlinear Kerr effect in laser systems. One big factor to consider for experimentalists working in laser systems is the effect of noise on the …

Methods, Analyses, And Applications Of Multilayer Temporal Link Prediction In Networks, Xie He

Dartmouth College Ph.D Dissertations

Many applications stem from the possibility of accurately predicting links in various types of networks. In this thesis, we present methods, analyses, and applications for static, temporal, and multilayer networks. The first part of this thesis demonstrates how static network features serve as efficient and accurate predictors for link prediction in temporal networks. It includes an ensemble learning method we developed and presents experimental results on 90 synthetic stochastic block models and 19 real-world datasets. The second part closely follows, showcasing 20 different sampling methods and their effects on nine different link prediction algorithms for 250 real-world networks across 6 …

Scaled And Graduated Learning In Deep Relu Networks And Reconstructing Depp Inelastic Scattering Kinematics, Abdullah Ayar Farhat

Mathematics & Statistics Theses & Dissertations

To address computational challenges in learning deep neural networks, properties of deep RELU networks were studied to develop a multi-scale learning model. The multi-scale model was compared to the multi-grade learning models. Unlike the deep neural network learned from the standard single-scale, single-grade model, the multi-scale neural networks use low scale information from all hidden layers, and thusly provide a robust approximation method that requires fewer parameters, lower computational time, and is resistant to noise. It is shown that the multiscale method is not subject to issues arising from the vanishing gradient problem. This allows very deep multi-scale networks to …

Modeling And Numerical Analysis Of The Cholesteric Landau-De Gennes Model, Andrew L. Hicks

LSU Doctoral Dissertations

This thesis gives an analysis of modeling and numerical issues in the Landau-de Gennes (LdG) model of nematic liquid crystals (LCs) with cholesteric effects. We derive various time-step restrictions for a (weighted) $L^2$ gradient flow scheme to be energy decreasing. Furthermore, we prove a mesh size restriction, for finite element discretizations, that is critical to avoid spurious numerical artifacts in discrete minimizers that is not well-known in the LC literature, particularly when simulating cholesteric LCs that exhibit ``twist''. Furthermore, we perform a computational exploration of the model and present several numerical simulations in 3-D, on both slab geometries and spherical …

Analyzing The Influence Of Design And Operating Conditions On Combustion And Emissions In Premixed Turbulent Flames: A Comprehensive Review, Medhat Elkelawy Prof. Dr. Eng., E. A. El Shenawy Prof. Dr., Hagar Alm-Eldin Bastawissi, Ibrahim Ali Mousa Eng., Mohamed M. Abdel-Raouf Ibrahim Dr. Eng.

Journal of Engineering Research

Recently, premixed combustion has dominated the field of combustion research worldwide. The current work is a review that addresses the effects of design and operating regimes on the combustion and emission characteristics of premixed turbulent flames. The study accounts for recent developments aimed at overcoming combustor operability issues that influence emissions and flame stability. Various experimental setups have been utilized in investigations, with results pertaining to performance and emissions concerning premixed turbulent flames. Thus, the objective of this paper is to provide a comprehensive review of the effects of swirl vane angles and equivalence fuel-air ratios for tests conducted both …

Building For Safety: Design Considerations For Refuge Areas In Tall Buildings From Quality Management Perspective, Enass. A. Salama, Heba. M. Gaber, Ahmed. M. Selim

Journal of Engineering Research

New El Alamein City is one of the largest urban projects in Egypt, and the largest project on the north coast. Tall buildings (super high-rise buildings) are considered the prevailing trend by architectural designers to obtain the maximum view of the Mediterranean Sea. The provision of safety evacuation in emergencies for these buildings’ occupants is a crucial challenge from the Quality management point of view. In contrast, there are no sufficient architectural design guidelines for the tall buildings provided by the Egyptian code for protecting buildings from fire, especially the design of the refuge areas. This study aims to investigate …

Effect Of Organic Compounds Additives For Biodiesel Fuel Blends On Diesel Engine Vibrations And Noise Characteristics, Medhat Elkelawy Prof. Dr, Eng., Hagar Alm-Eldin Bastawissi Prof. Dr. Eng., E. A. El Shenawy Prof. Dr., Mahmoud Soliman Eng.

Journal of Engineering Research

The extensive consumption of petroleum fuel directly correlates with both hazardous exhaust emissions affecting human health and contributing to global warming. Initially, biodiesel fuels were proposed as a viable alternative to address these issues. This perspective finds support in numerous published studies that highlight how the significant catalytic effect of nanoparticles allows for their integration into biodiesel blends, resulting in improved combustion characteristics, reduced exhaust emissions, and enhanced performance. This study investigates the impact of additives on biodiesel fuel properties and its effects on engine performance metrics such as brake power, brake thermal efficiency, exhaust gas concentration, engine vibration, and …

Investigation Into The Impact Of Ammonia Hydroxide On Performance And Emissions In Compression Ignition Engines Utilizing Diesel/Biodiesel Blends, Medhat Elkelawy Prof. Dr, Eng., Hagar Alm-Eldin Bastawissi, Mohammed Osama Elsamadony Dr. Eng., Abdallah Salem Abdalhadi

Journal of Engineering Research

In recent times, there has been a surge in scientific endeavors aimed at combating global warming. Various methods have been employed to address this issue, including the substitution of fossil fuels with more environmentally sustainable alternatives and the combination of different fuel types. This can be achieved through the integration of innovative injection systems and the simultaneous combustion of alternative fuels alongside fossil fuels, or by modifying fuel injection systems such as in the PCCI, RCCI, or HCCI systems. In a particular research investigation, a blend of ammonia hydroxide and diesel, with volume percentages of 7.5% and 92.5% respectively, was …

Enhancing Diesel Engine Performance By Directly Injecting Blends Of Ammonium Hydroxide And Including Liquid Petroleum Gas As A Partially Premixed Charge, Medhat Elkelawy Prof. Dr, Eng., Hagar Alm-Eldin Bastawissi, Mohammed Osama Elsamadony Dr. Eng., Abdallah Salem Abdalhadi

Journal of Engineering Research

Recently, scientists have made significant strides in addressing or mitigating environmental issues. Researchers have adopted various approaches to tackle these issues, such as replacing fossil fuels with more environmentally friendly alternatives or blending multiple fuel types. This can be achieved by either integrating these two trends through the use of new injection systems and simultaneous combustion of alternative fuels with fossil fuels or by modifying fuel injection systems, exemplified by the PCCI, RCCI, or HCCI systems. Consequently, these methods have proven effective in reducing environmental pollutants, enhancing thermal efficiency, and decreasing specific fuel consumption. In this study, ammonia hydroxide and …

Experimental Investigation On Combustion And Emission Characteristics Of Co-Combustion Of Pulverized Biomass With Diesel Fuel In An Industrial Burner, Medhat Elkelawy Prof. Dr, Eng., Hagar Alm-Eldin Bastawissi, Ahmed Abou El-Yazied Prof. Dr., Saad El-Malla Dr. Eng.

Journal of Engineering Research

This study presents the combustion and emission results obtained from a laboratory furnace equipped with a 35 kW industrial burner that utilizes co-combustion of pulverized biomass and diesel fuel. The experiment compared the co-combustion of pulverized biomass and diesel fuel with diesel fuel alone. Three different loading ratios of pulverized biomass from residual beet samples were used. Temperatures were measured at various positions inside the furnace to analyze combustion performance. It was observed that increasing the biomass loading ratios led to higher flame temperatures and improved combustion compared to diesel fuel alone. The concentrations of pollutants such as Co, HC, …

Cfd Study On Two-Phase Flow Patterns In A Pipe With 90º Elbow In Different Operating Conditions, Hagar Alm-Eldin Bastawissi, Mohammed Ahmed Khafagy, E. A. El Shenawy Prof. Dr., Ahmed M. Salem Dr

Journal of Engineering Research

Recently, CFD has offered a technological solution for modelling multi-phase flow in which we can make endless simulations with reduced expenses and effort in high accuracy results; we shall also mention that experimental studies have limitations for safety considerations when experimenting with flow in high temperature or pressure values or medium nature as in nuclear or chemical flows.In this paper, we used the ANSYS FLUENT CFD program to simulate the two-phase flow in a pipe to study the effect of attaching a 90-degree elbow fitting to the piping system, seeking to find out the change in the pattern and resulting …

تقنيات الاضاءة الصناعية وتأثيرها فى الفراغ السكنى على السلوك الانسانى, Samah Kamal Elfeky, Walaa Ahmad Nour, Lobna Abdelfatah Agha

Journal of Engineering Research

* Lighting is considered of main items in daily life begining from natural Lighting to industrial lighting. with all of it's different shapes . it is considerdone of the most important data that point Blank spaces and works to show architectural spaces, aesthetic values through being sharp and weak, ensure borders show texture or hide Features, suggest wideness, narrowness of space as the most beautiful design don't see beautiful without good lighting which designed carefully.Due to diversity of human activities, architictums spaces and it is wideness. Increased dependence on industrial Lighting to strengthen Job of performance, beauty of internal, external …

Exploring Human Aging Proteins Based On Deep Autoencoders And K-Means Clustering, Sondos M. Hammad, Mohamed Talaat Saidahmed, Elsayed A. Sallam, Reda Elbasiony

Journal of Engineering Research

Aging significantly affects human health and the overall economy, yet understanding of the underlying molecular mechanisms remains limited. Among all human genes, almost three hundred and five have been linked to human aging. While certain subsets of these genes or specific aging-related genes have been extensively studied. There has been a lack of comprehensive examination encompassing the entire set of aging-related genes. Here, the main objective is to overcome understanding based on an innovative approach that combines the capabilities of deep learning. Particularly using One-Dimensional Deep AutoEncoder (1D-DAE). Followed by the K-means clustering technique as a means of unsupervised learning. …

Casar Public Lecture: "Women & Stem Education In Egypt & The Us: Stepping Into A Man's World Of Science & Technology", The Prince Alwaleed Center For American Studies And Research Casar, Yasmeen El Ghazaly, Mark W. Deets

Performances, Events, and Presentations

In celebration of International Women's Day this Month, we held a public lecture titled: "Women & STEM Education in Egypt & the US : Stepping into a Man's World of Science & Technology " on Thursday March 28th, 2024 from 12:15 pm to 1:15 pm (assembly hour) – Conference and Visitor Center, Mary Cross Hall AUC New Cairo Despite a plethora of advances made by women in the world we live in today, they are still woefully underrepresented in the realm of STEM education and the associated career paths. At this event, we uncovered the history, reasons & challenges women …

A Cohomological Perspective To Nonlocal Operators, Nicholas White

Honors Program: Senior Projects (Public)

Nonlocal models have experienced a large period of growth in recent years. In particular, nonlocal models centered around a finite horizon have been the subject of many novel results. In this work we consider three nonlocal operators defined via a finite horizon: a weighted averaging operator in one dimension, an averaging differential operator, and the truncated Riesz fractional gradient. We primarily explore the kernel of each of these operators when we restrict to open sets. We discuss how the topological structure of the domain can give insight into the behavior of these operators, and more specifically the structure of their …

Mathematically Modeling How Trapping Regimes That Target Specific Crayfish Life Stages Impact Removal Efficacy, Rini Pattison

Seaver College Research And Scholarly Achievement Symposium

The red swamp crayfish, Procambarus clarkii, is an invasive species introduced into several streams within the Santa Monica Mountains (SMM) in Southern California. Crayfish predation decimates native aquatic species. Thus, the Mountains Restoration Trust (MRT) and Environmental Restoration Group have worked to remove crayfish through regular trapping in Malibu Creek.

To aid conservation efforts, former SURB students William Milligan and Dev Patel developed mathematical models of crayfish removal efficacy. Milligan created a differential equation model of how crayfish removal affects local newt populations. Patel expanded Milligan’s crayfish model by creating a discrete model of the crayfish life cycle that newly …

Cell Motion And Multicellular Organization: A Mathematical Model For Pattern Formation In The Dictyostelium Discoideum Slug, Henry Tullis, Emily Evans, John Dallon

Library/Life Sciences Undergraduate Poster Competition 2024

Understanding multicellular behavior is key to biology and medicine

• Embryonic development requires coordinated cell motion, differentiation
• Wound healing also relies on emergent multicellular processes
• Dictyostelium discoideum (Dd) has been identified as a model organism for biomedical research, partly because it is a simple example of multicellularity
• Understanding Dd can improve, inform approaches to these tricky problems