Engineering Commons^™

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Multichannel Modulation Of Depolarizing And Repolarizing Ion Currents Increases The Positive Rate-Dependent Action Potential Prolongation, Candido Cabo

Publications and Research

Prolongation of the action potential duration (APD) could prevent reentrant arrhythmias if prolongation occurs at the fast excitation rates of tachycardia with minimal prolongation at slow excitation rates (i.e., if prolongation is positive rate-dependent). APD prolongation by current anti-arrhythmic agents is either reverse (larger APD prolongation at slow rates than at fast rates) or neutral (similar APD prolongation at slow and fast rates), which may not result in an effective anti-arrhythmic action. In this report we show that, in computer models of the human ventricular action potential, the combined modulation of both depolarizing and repolarizing ion currents results in a …

Electromagnetic Theory And Applications, Nicholas Madamopoulos, George Kliros

Open Educational Resources

This book intends to provide both the fundamentals of Electromagnetics but also some practical applications of the concepts covered. Having taught electromagnetics for several years, the authors feel that many times the field of electromagnetics comes as “old” and often times students do not appreciate the concepts and their importance in everyday applications. The authors intend to accompany the EM concepts with life applications. Hence, students may see the direct impact of the knowledge they acquire through the study of the field of electromagnetics and better appreciate the field.

Soft X-Ray And Susceptibility Based Magnetic Resonance Imaging To Map Iron Distribution In Apples: Initial Results To Model Iron Storage In Water-Deficient Or Dehydrated Biological Tissue, Subhendra Sarkar, Eric Lobel, Evans Lespinasse, Zoya Vinokur, Analia Basilicata, Sonia Orellana, Maria Orellana, Aaliyah Salmon, Joanna Syska, Aravis Mcbroom, Jian Wang, Anam Riaz, Jody-Ann Douglas

Publications and Research

Radiology departments have contributed significantly to greenhouse gases including release of toxic imaging contrast media to environment. We feel Radiology also has several spectroscopy and imaging tools that may apply to monitor and support cleaner environmental goals. The current manuscript is one of the firsts to prompt Radiology to move in that direction by non-invasive imaging of bio metals that are less abundant in biological tissues but play key roles as co-factors in tissue structure and function. Conventional analytical tools are mostly invasive and cannot characterize the native oxidation states of bio metals. We chose carbohydrate matrix of metal-rich fruits …

Ultra-High Field Mri Methods For Precise Anatomical And Spectroscopic Measurements In The Brain And Application To Neurological And Neuropsychiatric Diseases, Judy Alper

Dissertations and Theses

Neurological and neuropsychiatric diseases and disorders are a major burden on society, impairing the health and functioning of millions of people every year. There is a need to define the biological bases of these diseases and identify potential biomarkers to improve diagnosis, monitoring, and treatment efficacy across multiple diseases.

Magnetic resonance imaging (MRI) is a noninvasive imaging technique which facilitates detection of brain lesions and visualization of the brain overall. However, limitations in contrast and resolution at clinical field strengths may hinder investigation of the underlying biological mechanisms of these diseases. Ultra-high field MRI scanners, such as those at 7-Tesla, …

Measurement Of Fluid Movement Throughout The Brain Via Multiple Magnetic Resonance Imaging Techniques During High-Definition Transcranial Direct Current Stimulation, Jack W. Beaty Mr

Dissertations and Theses

Transcranial Direct Current Stimulation (tDCS) is a non-invasive method of neuromodulation with applications in neuroscience, clinical care, and biomedical engineering. tDCS has been well established as a safe method of applying low amplitude current between two or more electrodes to alter excitation thresholds and neuroplasticity. Recently, in-vitro and clinical studies have suggested that DC stimulation can induce a transient, polarity-specific, effect of increased water exchange across the blood-brain barrier (BBB). The electroosmotic effect, the proposed phenomenon driving water exchange, is a biophysical response of charged ions moving across an oppositely-charged surface, i.e., the tight junction, when subjected to an electric …

Positive Rate-Dependent Action Potential Prolongation By Modulating Potassium Ion Channels, Candido Cabo

Publications and Research

Pharmacological agents that prolong action potential duration (APD) to a larger extent at slow rates than at the fast excitation rates typical of ventricular tachycardia exhibit reverse rate dependence. Reverse rate dependence has been linked to the lack of efficacy of class III agents at preventing arrhythmias because the doses required to have an anti-arrhythmic effect at fast rates may have pro-arrhythmic effects at slow rates due to an excessive APD prolongation. In this report we show that, in computer models of the ventricular action potential, APD prolongation by accelerating phase 2 repolarization (by increasing I_Ks) and decelerating …

Recent Advances In Bone Research 2022 Edition, Jean-Philippe Berteau, Laurent Pujo-Menjouet

Publications and Research

More and more scientific and engineering applications in bone research make pivotal advances in treating patients with orthopedics issues. Hence, bone research in the 21st century combines, inter alia, biology, chemistry, mathematics, and mechanics with complementary characteristics that help a holistic approach to bone-related pathologies. Nowadays, it is hard to connect new evidence when jargoning and money remain two significant obstacles to sharing knowledge. “Recent Advances In Bone Research” is a free book – no money involved at any stage - that combines the most recent efforts in bone research from several experts with different backgrounds, every expert seeks to …

Representation Learning For Chemical Activity Predictions, Mohamed S. Ayed

Dissertations, Theses, and Capstone Projects

Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery and many other applications. Chemical fingerprints derived from chemical structures are a widely used feature to build machine learning models. However, the fingerprints ignore the biological context, thus, they suffer from several problems such as the activity cliff and curse of dimensionality. Fundamentally, the chemical modulation of biological activities is a multi-scale process. It is the genome-wide chemical-target interactions that modulate chemical phenotypic responses. Thus, the genome-scale chemical-target interaction profile will more directly correlate with in vitro and in …

Transcranial Direct Current Stimulation On Parkinson’S Disease: Systematic Review And Meta-Analysis, Paloma Cristina Alves De Oliveira, Thiago Anderson Brito De Araújo, Daniel Gomes Da Silva Machado, Abner Cardoso Rodrigues, Marom Bikson, Suellen Marinho Andrade, Alexandre Hideki Okano, Hougelle Simplicio, Rodrigo Pegado, Edgard Morya

Publications and Research

Background: Clinical impact of transcranial direct current stimulation (tDCS) alone for Parkinson’s disease (PD) is still a challenge. Thus, there is a need to synthesize available results, analyze methodologically and statistically, and provide evidence to guide tDCS in PD.

Objective: Investigate isolated tDCS effect in different brain areas and number of stimulated targets on PD motor symptoms.

Methods: A systematic review was carried out up to February 2021, in databases: Cochrane Library, EMBASE, PubMed/MEDLINE, Scopus, and Web of science. Full text articles evaluating effect of active tDCS (anodic or cathodic) vs. sham or control on motor symptoms of PD were …

Glycocalyx Mechanotransduction Mechanisms Are Involved In Renal Cancer Metastasis, Heriberto Moran, Limary M. Cancel, Peigen Huang, Sylvie Roberge, Tuoye Xu, John M. Tarbell, Lance L. Munn

Publications and Research

Mammalian cells, including cancer cells, are covered by a surface layer containing cell bound proteoglycans, glycoproteins, associated glycosaminoglycans and bound proteins that is commonly referred to as the glycocalyx. Solid tumors also have a dynamic fluid microenvironment with elevated interstitial flow. In the present work we further investigate the hypothesis that interstitial flow is sensed by the tumor glycocalyx leading to activation of cell motility and metastasis. Using a highly metastatic renal carcinoma cell line (SN12L1) and its low metastatic counterpart (SN12C) we demonstrate in vitro that the small molecule Suberoylanilide Hydroxamic Acid (SAHA) inhibits the heparan sulfate synthesis enzyme …

Toward A Multimodal Computer-Aided Diagnostic Tool For Alzheimer’S Disease Conversion, Danilo Pena, Jessika Suescun, Mya Schiess, Timothy M. Ellmore, Luca Giancardo, Alzheimer’S Disease Neuroimaging Initiative

Publications and Research

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder. It is one of the leading sources of morbidity and mortality in the aging population AD cardinal symptoms include memory and executive function impairment that profoundly alters a patient’s ability to perform activities of daily living. People with mild cognitive impairment (MCI) exhibit many of the early clinical symptoms of patients with AD and have a high chance of converting to AD in their lifetime. Diagnostic criteria rely on clinical assessment and brain magnetic resonance imaging (MRI). Many groups are working to help automate this process to improve the clinical workflow. Current …

Modulation Of Brain Tissue Transport And Endothelial Glycocalyx And Tight Junctions Of The Blood-Brain Barrier By Transcranial Direct Current Stimulation, Yifan Xia

Dissertations and Theses

Transcranial direct current stimulation (tDCS) is a non-invasive approach to treat a broad range of brain disorders and to enhance memory and cognition in healthy individuals. In addition to directly acting on neurons by modulating the membrane potential, inducing neuronal polarization and changing cortical excitability in the brain to achieve its therapeutic effects, prior studies found that tDCS can transiently enhance the permeability (P) of the blood-brain barrier (BBB), the interface between blood circulation and brain tissue. Brain extracellular space (ECS) is a narrow microenvironment which surrounds every cell in the central nervous system (CNS). ECS occupies ~20% of brain …

Analysis Of Eye Movements To Cartoon Faces In Videos, Kaustubh Sapru

Dissertations and Theses

Saccades are rapid eye movements that move our gaze between successive points of fixation. They are indicative of how we direct our attention and therefore play a role in memory and cognition. For static images, it is established that saccades move faster to faces compared to other objects. We hypothesize that the same is true for videos. To test this hypothesis, saccades to faces in motion pictures have been analyzed. The analysis here entails the recording of saccades to two videos followed by a statistical study of saccades going towards faces or going away from faces. What makes this study …

Biomedical Applications Of Lanthanide Nanomaterials, For Imaging, Sensing And Therapy, Qize Zhang, Stephen O'Brien, Jan Grimm

Publications and Research

The application of nanomaterials made of rare earth elements within biomedical sciences continues to make significant progress. The rare earth elements, also called the lanthanides, play an essential role in modern life through materials and electronics. As we learn more about their utility, function, and underlying physics, we can contemplate extending their applications to biomedicine. This particularly applies to diagnosis and radiation therapy due to their relatively unique features, such as an ultra-wide Stokes shift in the luminescence, variable magnetism and potentially tunable properties, due to the library of lanthanides available and their multivalent oxidation state chemistry. The ability to …

Novel Mechanisms Of Dc And Kilohertz Electrical Stimulation, Zeinab Esmaeilpour

Dissertations and Theses

Transcranial electrical stimulation is a promising technique where a weak electrical current is applied to the scalp with the goal of modulating brain activity. Understanding the cellular mechanism of direct current (DC) and kilohertz (kHz) electrical stimulation is of broad interest in neuromodulation. More specifically, there is a large mismatch between enthusiasm for clinical applications of the method and understanding of DC and kHz novel mechanisms of action. This dissertation is centered around two main fundamental aims: 1) systematic study of the acute and long-term effects of kilohertz electrical stimulation and amplitude-modulated waveform with kHz carrier frequency using a well-established …

Impact Of Percutaneous Transluminal Intervention On Vascular Hypoxia And The Role Of Micro-Calcifications On Atherosclerotic Plaque Rupture, Andrea Corti

Dissertations and Theses

Atherosclerotic disease is initiated by cholesterol build-up beneath the endothelium, which evolves into a fibroatheroma, a lipid-rich plaque covered by a fibrous cap. Many of these plaques are considered as vulnerable, as they grow to occlude the luminal section of the artery (chronically stenotic) or become mechanically unstable with a higher chance of rupturing (rupture-prone). On one hand, chronically stenotic vulnerable plaques are symptomatic lesions that are often treated with Percutaneous Transluminal Intervention (PTI). Unfortunately, approximately 10% of PTI procedures are followed by severe Neointima Hyperplasia (NH), which causes a new occlusion and failure of the implant. A significant precursor …

Neural Processing Of Semantic Content In Movies, Maximilian Nentwich

Dissertations and Theses

Naturalistic stimuli, such as movies, contain interacting, multimodal and semantic features and allow for free exploration through eye movements. The full extent of neural responses to features such as motion, film cuts and eye movement behavior has not been established. The main hypothesis of this thesis is that complex multimodal and semantic stimuli in naturalistic movies engage a widespread ensemble of locations across the entire brain. To address this question I analyzed simultaneous intracranial and eyetracking data from over 6,000 electrodes across 23 patients with intractable epilepsy. Responses to fast eye movements – saccades – and film cuts are widespread …

Exosome- And Microrna-Based Therapeutic Approach For Tendinopathy, Angela Wang Ilaltdinov

Dissertations and Theses

Tendinopathy, characterized by degeneration and chronic inflammation, is a significant clinical burden. Current treatments focus on symptom management but do not sufficiently address its underlying pathology; however, stem cell-based approaches aimed at repairing diseased tissues may overcome this limitation. Therapeutic effects of stem cells may be due in part to paracrine actions, including some mediated by exosomes – extracellular vesicles secreted by cells that play a role in cell communication. MicroRNA (miRNA), small non-coding RNA carried by exosomes, are likely responsible for many exosome effects. Exosomes and miRNA therapies show promise in treating diseases such as cancer and arthritis, but …

Osseointegration Of A Cementless Total Knee Arthroplasty In A Murine Model Of Glucocorticoid Induced Osteoporosis, Elexis C. Baral

Dissertations and Theses

Glucocorticoid-Induced Osteoporosis (GIOP) is the second largest cause of osteoporosis worldwide. Glucocorticoid-Induced osteoporosis is rapidly, driven principally by deficient osteoblast activity (i.e., decreased bone formation) rather than increased osteoclastic activity. Glucocorticoid-type steroids (GC) are used long-term typically for inflammatory diseases such as rheumatoid arthritis, lupus, multiple sclerosis, and other autoimmune disorders. Inflammatory arthritis often leads to joint replacement at relatively young ages. However, patients who are on GC treatment appear to have poorer outcomes for total joint arthroplasty compared to healthy patients. This is thought to be due to the anti-anabolic effects of GCs and impaired bone healing and osseous …

Computational Model Of Electroconvulsive Therapy Considering Electric Field Dependent Skin Conductivity, Gozde Unal

Dissertations and Theses

Improvements in electroconvulsive therapy (ECT) outcomes have followed refinement in device electrical output and electrode montage. The physical properties of the ECT stimulus, together with those of the patient’s head, determine the impedances measured by the device and govern current delivery to the brain and ECT outcomes. However, the precise relations among physical properties of the stimulus, patient head anatomy, and patient-specific impedance to the passage of current are long-standing questions in ECT research and practice. In this thesis, we develop a computational framework based on diverse clinical data sets. We developed anatomical MRI-derived models of transcranial electrical stimulation (tES) …

Development Of Cellulose-Based, Semi-Interpenetrating Network Hydrogels As Tissue-Adhesive, Thermoresponsive, Injectable Implants, Jesse Martin

Dissertations and Theses

Abstract Development of Cellulose-Based, Semi-Interpenetrating Network Hydrogels as Tissue-Adhesive, Thermoresponsive, Injectable Implants

Hydrogels are three-dimensional polymer networks with high water content and tunable mechanical properties, which have been widely investigated as replacements for soft tissues, such as the intervertebral disc (IVD). Various derivatives of the plant polysaccharide, cellulose, have been explored for use as injectable hydrogel implants. Methylcellulose (MC), which exhibits thermogelation at temperatures above 32°C, and relatively hydrophilic carboxymethyl-cellulose (CMC), are versatile cellulosic polymers that have shown promise as base materials for such applications. In prior work, functionalization with methacrylate groups allowed for the formation of stable, covalently crosslinked …

Low-Intensity Ultrasonic Neuromodulation Of The Rat Hippocampus, Duc Nguyen

Dissertations and Theses

Techniques to non-invasively modulate brain activity are important for mapping human brain circuits, and also for the treatment of a host of neurological and psychiatric disorders marked by aberrant brain activity. Though a wide range of techniques for non-invasive neuromodulation have been proposed, the conventional approaches suffer from significant limitations. Most notably, focal stimulation of deep brain regions is presently only possible with invasive optogenetic and chemogenetic approaches that require craniotomies and genetic access to the brain.

Transcranial focused ultrasound stimulation (tFUS) possesses many of the characteristics desirable from a neuromodulation approach: non-invasiveness, a spatial resolution in the order of …

Inter-Subject Correlation While Listening To Minimalist Music: A Study Of Electrophysiological And Behavioral Responses To Steve Reich’S Piano Phase, Tysen Dauer, Duc T. Nguyen, Nick Gang, Jacek P. Dmochowski, Jonathan Berger, Blair Kaneshiro

Publications and Research

Musical minimalism utilizes the temporal manipulation of restricted collections of rhythmic, melodic, and/or harmonic materials. One example, Steve Reich’s Piano Phase, offers listeners readily audible formal structure with unpredictable events at the local level. For example, pattern recurrences may generate strong expectations which are violated by small temporal and pitch deviations. A hyper-detailed listening strategy prompted by these minute deviations stands in contrast to the type of listening engagement typically cultivated around functional tonal Western music. Recent research has suggested that the inter-subject correlation (ISC) of electroencephalographic (EEG) responses to natural audio-visual stimuli objectively indexes a state of “engagement,” demonstrating …

Dataset Of Concurrent Eeg, Ecg, And Behavior With Multiple Doses Of Transcranial Electrical Stimulation, Nigel Gebodh, Zeinab Esmaeilpour, Abhishek Datta, Marom Bikson

Publications and Research

We present a dataset combining human-participant high-density electroencephalography (EEG) with physiological and continuous behavioral metrics during transcranial electrical stimulation (tES). Data include within participant application of nine High-Definition tES (HD-tES) types, targeting three cortical regions (frontal, motor, parietal) with three stimulation waveforms (DC, 5 Hz, 30 Hz); more than 783 total stimulation trials over 62 sessions with EEG, physiological (ECG, EOG), and continuous behavioral vigilance/alertness metrics. Experiment 1 and 2 consisted of participants performing a continuous vigilance/alertness task over three 70-minute and two 70.5-minute sessions, respectively. Demographic data were collected, as well as self-reported wellness questionnaires before and after each …

Physiological Processes, Chirag B. Raval

Open Educational Resources

Physiological Processes is designed to introduce fundamental concepts of physiology to biomedical engineering learners. Areas covered include: neural, muscular, cardiovascular, respiratory and renal system function; bioelectrical signals, capillary-level transport, organ-level exchange. Whenever possible, analysis will be quantitative in order to fulfill the course goals and to build the foundation for the subsequent biomedical engineering curriculum. This course is for Biomedical Engineering majors only.

During Natural Viewing, Neural Processing Of Visual Targets Continues Throughout Saccades, Atanas D. Stankov, Jonathan Touryan, Stephen Gordon, Anthony J. Ries, Jason Ki, Lucas C. Parra

Publications and Research

Relatively little is known about visual processing during free-viewing visual search in realistic dynamic environments. Free-viewing is characterized by frequent saccades. During saccades, visual processing is thought to be suppressed, yet we know that the presaccadic visual content can modulate postsaccadic processing. To better understand these processes in a realistic setting, we study here saccades and neural responses elicited by the appearance of visual targets in a realistic virtual environment. While subjects were being driven through a 3D virtual town, they were asked to discriminate between targets that appear on the road. Using a system identification approach, we separated overlapping …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …