Engineering Commons^™

Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov

Doctoral Dissertations

Reactive chemistries for protein chemical modification play an instrumental role in chemical biology, proteomics, and therapeutics. Depending on the application, the selectivity of these modifications can range from precise modification of an amino acid sequence by genetic manipulation of protein expression machinery to a stochastic modification of lysine residues on the protein surface. Ligand-Directed (LD) chemistry is one of the few methods for targeted modification of endogenous proteins without genetic engineering. However, current LD strategies are limited by stringent amino acid selectivity. To bridge this gap, this thesis focuses on the development of highly reactive LD Triggerable Michael Acceptors (LD-TMAcs) …

Mining High Impact Combinations Of Conditions From The Medical Expenditure Panel Survey, Arjun Mohan

Masters Theses

The condition of multimorbidity — the presence of two or more medical conditions in an individual — is a growing phenomenon worldwide. In the United States, multimorbid patients represent more than a third of the population and the trend is steadily increasing in an already aging population. There is thus a pressing need to understand the patterns in which multimorbidity occurs, and to better understand the nature of the care that is required to be provided to such patients.

In this thesis, we use data from the Medical Expenditure Panel Survey (MEPS) from the years 2011 to 2015 to identify …

Unobtrusive Assessment Of Upper-Limb Motor Impairment Using Wearable Inertial Sensors, Brandon R. Oubre

Doctoral Dissertations

Many neurological diseases cause motor impairments that limit autonomy and reduce health-related quality of life. Upper-limb motor impairments, in particular, significantly hamper the performance of essential activities of daily living, such as eating, bathing, and changing clothing. Assessment of impairment is necessary for tracking disease progression, measuring the efficacy of interventions, and informing clinical decision making. Impairment is currently assessed by trained clinicians using semi-quantitative rating scales that are limited by their reliance on subjective, visual assessments. Furthermore, existing scales are often burdensome to administer and do not capture patients' motor performance in home and community settings, resulting in a …

Frontiers In The Self-Assembly Of Charged Macromolecules, Khatcher O. Margossian

Doctoral Dissertations

The self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context …

Decision-Analytic Models Using Reinforcement Learning To Inform Dynamic Sequential Decisions In Public Policy, Seyedeh Nazanin Khatami

Doctoral Dissertations

We developed decision-analytic models specifically suited for long-term sequential decision-making in the context of large-scale dynamic stochastic systems, focusing on public policy investment decisions. We found that while machine learning and artificial intelligence algorithms provide the most suitable frameworks for such analyses, multiple challenges arise in its successful adaptation. We address three specific challenges in two public sectors, public health and climate policy, through the following three essays. In Essay I, we developed a reinforcement learning (RL) model to identify optimal sequence of testing and retention-in-care interventions to inform the national strategic plan “Ending the HIV Epidemic in the US”. …

Visuomotor Adaptation During Asymmetric Walking, Charles Napoli

Masters Theses

Necessary for effective ambulation, head stability affords optimal conditions for the perception of visual information during dynamic tasks. This maintenance of head-in-space equilibrium is achieved, in part, by the attenuation of the high frequency impact shock resulting from ground contact. While a great deal of experimentation has been done on the matter during steady state locomotion, little is known about how head stability or dynamic visual acuity is maintained during asymmetric walking.

In this study, fifteen participants were instructed to walk on a split-belt treadmill for ten minutes while verbally reporting the orientation of a randomized Landolt-C optotype that was …

A Cloud Infrastructure For Large Scale Health Monitoring In Older Adult Care Facilities, Uchechukwu Gabriel David

Masters Theses

Technology development in the sub-field of older adult care has always been on the back-burner compared to other healthcare areas. But with increasing life expectancy, this is poised to change. With the increasing older adult population, the current older adult care facilities and personnel are struggling to keep up with demand. Research conducted in the Netherlands [1] found 33,000 older adults were awaiting admission into a home for the elderly showing that demand far exceeds availability. This huge demand for older adult care has resulted in a decrease in the quality of care being provided. A recent study involving older …

Raising Dielectric Permittivity Mitigates Dopant-Induced Disorder In Conjugated Polymers, Meenakshi Upadhyaya, Michael Lu-Díaz, Subhayan Samanta, Muhammad Abdullah, Keith Dusoe, Kevin R. Kittilstved, Dhandapani Venkataraman, Zlatan Akšamija

Electrical and Computer Engineering Faculty Publication Series

Conjugated polymers need to be doped to increase charge carrier density and reach the electrical conductivity necessary for electronic and energy applications. While doping increases carrier density, Coulomb interactions between the dopant molecules and the localized carriers are poorly screened, causing broadening and a heavy tail in the electronic density-of-states (DOS). The authors examine the effects of dopant-induced disorder on two complimentary charge transport properties of semiconducting polymers, the Seebeck coefficient and electrical conductivity, and demonstrate a way to mitigate them. Their simulations, based on a modified Gaussian disorder model with Miller-Abrahams hopping rates, show that dopant-induced broadening of the …

Engineered Nanoparticles For Site-Specific Bioorthogonal Catalysis: Imaging And Therapy, Riddha Das

Doctoral Dissertations

Bioorthogonal catalysis offers a strategy for chemical transformations complementary to bioprocesses and has proven to be a powerful tool in biochemistry and medical sciences. Transition metal catalysts (TMCs) have emerged as a powerful tool to execute selective chemical transformations, however, lack of biocompatibility and stability limits their use in biological applications. Incorporation of TMCs into nanoparticle monolayers provides a versatile strategy for the generation of bioorthogonal nanocatalysts known as “nanozymes”. We have fabricated a family of nanozymes using gold nanoparticles (AuNPs) as scaffolds featuring diverse chemical functional groups for controlled localization of nanozymes in biological environments, providing unique strategies for …

Engineering Nanomaterials For Imaging And Therapy Of Bacteria And Biofilm-Associated Infections, Akash Gupta

Doctoral Dissertations

Infections caused by multidrug-resistant (MDR) bacteria pose a serious global burden of mortality, causing thousands of deaths each year. The “superbug” risk is further exacerbated by chronic infections generated from antibiotic-resistant biofilms that are highly resistant to available treatments. Synthetic macromolecules such as polymers and nanoparticles have emerged as promising antimicrobials. Moreover, ability to modulate nanomaterial interaction with bacterial cellular systems plays a pivotal role in improving the efficacy of the strategy. In the initial studies on engineering nanoparticle surface chemistry, I investigated the role played by surface ligands in determining the antimicrobial activity of the nanoparticles. In further study, …

Three Essays On Data-Driven Optimization For Scheduling In Manufacturing And Healthcare, Ekin Koker

Doctoral Dissertations

This dissertation consists of three essays on data-driven optimization for scheduling in manufacturing and healthcare. In Chapter 1, we briefly introduce the optimization problems tackled in these essays. The first of these essays deals with machine scheduling problems. In Chapter 2, we compare the effectiveness of direct positional variables against relative positional variables computationally in a variety of machine scheduling problems and we present our results. The second essay deals with a scheduling problem in healthcare: the team primary care practice. In Chapter 3, we build upon the two-stage stochastic integer programming model introduced by Alvarez Oh (2015) to solve …

Combining Human Factors And Data Science Methods To Evaluate The Use Of Free Text Communication Orders In Electronic Health Records, Swaminathan Kandaswamy

Doctoral Dissertations

Medication errors are a leading cause of death in the United States. Electronic Health Records (EHR) along with Computerized Provider Order Entry (CPOE) are considered promising ways to reduce these errors. However, EHR systems have not eliminated medication errors. Moreover, in some cases they have facilitated errors due to issues such as poor usability and negative effects on clinical workflows. The use of unexpected free text within a CPOE system can serve as a marker that the system does not adequately support clinical workflow. Prior studies have looked at the use of free text within medication orders, but the inclusion …

Markov Decision Process Approach To Strategize National Breast Cancer Screening Policy In Data-Limited Settings, Vijeta Deshpande

Masters Theses

Early diagnosis is a promising strategy to reduce premature mortalities and for optimal use of resources. But the absence of mathematical models specific to the data settings in LMIC’s impedes the construction of economic analysis necessary for decision-makers in the development of cancer control programs. This thesis presents a new methodology for parameterizing the natural history model of breast cancer based on data availabilities in low and middle income countries, and formulation of a control optimization problem to find the optimal screening schedule for mammography screening, solved using dynamic programming. As harms and benefits are known to increase with the …

A Computational Simulation Model For Predicting Infectious Disease Spread Using The Evolving Contact Network Algorithm, Buyannemekh Munkhbat

Masters Theses

Commonly used simulation models for predicting outbreaks of re-emerging infectious diseases (EIDs) take an individual-level or a population-level approach to modeling contact dynamics. These approaches are a trade-off between the ability to incorporate individual-level dynamics and computational efficiency. Agent-based network models (ABNM) use an individual-level approach by simulating the entire population and its contact structure, which increases the ability of adding detailed individual-level characteristics. However, as this method is computationally expensive, ABNMs use scaled-down versions of the full population, which are unsuitable for low prevalence diseases as the number of infected cases would become negligible during scaling-down. Compartmental models use …

Direct Printing Of Conductive Inks For Organic Electronics And Wearable Microfluidics, Aditi Naik

Doctoral Dissertations

This dissertation examines the direct printing of conductive inks on polymeric substrates for applications in organic electronics, microfluidic valving systems, and wearable sweat sensors. The inexpensive production of solution-based electrodes with high electrical conductivity is necessary to enable the next-generation of printed, flexible, and organic electronics. Specifically, the optimization and printing of liquid-phase graphene ink and nanoparticle-based silver ink by soft nanoimprint lithography and inkjet-printing is discussed to achieve printed functional devices. Using scalable low-cost patterning systems, these flexible applications are compatible with roll-to-roll processing, enabling large-scale manufacturing. This research expands the knowledge of high-resolution printing optimization for the direct …

The Core Of Social Network Modeling: Industrial Engineering., Shannon C. Roberts, Chaitra Gopalappa, Nazanin Nazanin

Science and Engineering Saturday Seminars

Networks are abound in our everyday lives, from disaster response networks to cellular networks to social networks. In this workshop, we will introduce the different types of networks and how Industrial Engineering is used to model these networks. Next, we will describe current social network modeling research done at UMass. Finally, we will delve into hands-on activities that include social network analysis, such as the clustering of people into groups, and modeling of the spread of ideas in a social network, such as how tweets spread on Twitter.

Evaluating The Toxicity And Formation Of Halobenzoquinones In Point-Of-Use Chlorinated Drinking Water, Stephanie Hung

Masters Theses

Chlorine has effectively reduced the prevalence of waterborne diseases, however there are secondary consequences to this public health advancement. Disinfection byproducts (DBPs) are chemicals formed when chlorine reacts with natural organic matter (NOM) in water. A new class of DBPs, halobenzoquinones (HBQs), has recently been identified and data suggests it could be potentially carcinogenic and up to 1000 times more toxic than some regulated DBPs. So far, in vitro studies have assessed HBQ toxicity without taking into account its transformation in cell media into potentially less toxic compounds. This study evaluated the toxic effects of one HBQ, 2,6-DCBQ, and its …

Role Of Rigidity And Flexibility Of Functional Groups Within The Interior Of Supramolecular Assemblies And Their Implications, Oyuntuya Munkhbat

Doctoral Dissertations

Engineering of supramolecular assemblies at molecular level renders functional nanomaterials that present explicit response to certain environmental changes. Systematic structure-property correlation studies will unravel the fundamental design constraints of these functional nanomaterials that fulfill the emergent need. This dissertation will primarily focus on understanding the role of rigidity and flexibility of functional groups within amphiphilic assemblies and employing this basic concept in drug delivery and diagnostics applications. Supramolecular assemblies formed by amphiphilic dendrimers and polymers are preferred for this study as they exhibit high thermodynamic stability and structural flexibility. The role of aromatic interaction on the unimer-aggregate dynamic equilibrium was …

Syllabus: Drinking Water, Sanitation, And Global Development, Emily Kumpel

Sustainability Education Resources

Within the past three decades, more than 2.6 billion people have gained access to an improved water source and 2.1 billion have gained access to an improved sanitation facility. However, improved does not always mean people have safe, reliable, accessible, or equitable water and sanitation services. Waterborne diseases continue to cause and estimated 500,000 deaths each year. What causes waterborne diseases, and what is the role of engineered systems in their spread or prevention? How can we evaluate interventions to improve health and well-being? How can research address these challenges?

Brain Science = Biology + Engineering, Jennifer Welborn, Guangyu Xu, Morton Sternheim, Chris Emery

Science and Engineering Saturday Seminars

This interdisciplinary (physical and life sciences) seminar exposes participants to cutting edge research at UMASS, Amherst, on cell imaging using a chip which gathers a variety of data on the activities of single cells. Part of the seminar will be a presentation of current research in this area, followed by hands-on activities and a visit to the lab where this research is conducted. Application of this new technology to brain research will be discussed as well as the NGSS standards alignment and classroom applications at various levels and disciplines.

Effects Of Malformed Or Absent Valves To Lymphatic Fluid Transport And Lymphedema In Vivo In Mice, Akshay S. Pujari

Masters Theses

Lymph is primarily composed of fluid and proteins from the blood circulatory system that drain into the space surrounding cells, interstitial space. From the interstitial space, the fluid enters and circulates in the lymphatic system until it is delivered into the venous system. In contrast to the blood circulatory system, the lymphatic system lacks a central pumping organ dictating the predominant driving pressure and velocity of lymph. Transport of lymph via capillaries, pre-collecting and collecting lymphatic vessels relies on the synergy between pressure gradients, local tissue motion, valves and lymphatic vessel contractility. The direction of lymph transport is regulated by …

Total Organic Iodine Quantification And Occurrence In Drinking Water, And Toxicity Assessment Of Iodinated Disinfection By-Products, Rassil El Sayess

Doctoral Dissertations

The focus of this work has been placed is on iodinated DBPs (I-DBPs), measured using total organic iodine (TOI), a surrogate measure of iodinated organics. This is due to the growing toxicity literature that places I-DBPs among the most toxic of all DBPs. To measure TOI in water, a new method was developed. This method combines adsorption, combustion, and trapping of combustion products, with an offline inductively coupled plasma/mass spectrometer (ICP-MS) for iodide detection. Three factors were varied across two levels each in order to optimize the method. The chosen method used a sample pH of less than 1 prior …

Superhero Robotics, Frank Sup, Brian Umberger, Nick Sawyer

Science and Engineering Saturday Seminars

No abstract provided.

The Effect Of Interruptions On Primary Task Performance In Safety-Critical Environments, Cheryl Ann Nicholas

Doctoral Dissertations

Safety critical systems in medicine utilize alarms to signal potentially life threatening situations to professionals and patients. In particular, in the medical field multiple alarms from equipment are activated daily and often simultaneously. There are a number of alarms which require caregivers to take breaks in complex, primary tasks to attend to the interruption task which is signaled by the alarm. The motivation for this research is the knowledge that, in general, interrupting tasks can have a potentially negative impact on performance and outcomes of the primary task. The focus of this research is on the effect of an interrupting …

Multi-Classifier Fusion Strategy For Activity And Intent Recognition Of Torso Movements, Abhijit Kadrolkar

Doctoral Dissertations

As assistive, wearable robotic devices are being developed to physically assist their users, it has become crucial to develop safe, reliable methods to coordinate the device with the intentions and motions of the wearer. This dissertation investigates the recognition of user intent during flexion and extension of the human torso in the sagittal plane to be used for control of an assistive exoskeleton for the human torso. A multi-sensor intent recognition approach is developed that combines information from surface electromyogram (sEMG) signals from the user’s muscles and inertial sensors mounted on the user’s body. Intent recognition is implemented by following …

Design, Implementation, And Evaluation Of A User Training Program For Integrating Health Information Technology Into Clinical Processes, Ze He

Doctoral Dissertations

Health information technology (IT) implementation can be costly, and remains a challenging problem with mixed outcomes on patient safety and quality of care. Systems engineering and IT management experts have advocated the use of sociotechnical models to understand the impact of health IT on user and organizational factors. Sociotechnical models suggest the need for user-centered implementation approaches, such as user training and support, and focus on processes to mitigate the negative impact and facilitate optimal IT use during training. The training design and development should also follow systematic processes guided by instructional development models. It should take into account of …

Simulation Of 48-Hour Queue Dynamics For A Semi-Private Hospital Ward Considering Blocked Beds, Wei Chen

Masters Theses

This thesis study evaluates access to care at an internal medicine unit with solely semi-private rooms at Baystate Medical Center (BMC). Patients are divided into two types: Type I patient consumes one bed; Type II patient occupies two beds or an entire semi-private room as a private space for clinical reasons, resulting in one empty but unavailable (blocked) bed per Type II patient. Because little data is available on blocked beds and Type II patients, unit-level hospital bed planning studies that consider blocked beds have been lacking. This thesis study bridges that gap by building a single-stream and a two-stream …

Complex Coacervate-Based Materials For Biomedicine, Sarah L. Perry, Whitney C. Blocher

Chemical Engineering Faculty Publication Series

There has been increasing interest in complex coacervates for deriving and trans- porting biomaterials. Complex coacervates are a dense, polyelectrolyte-rich liq- uid that results from the electrostatic complexation of oppositely charged macroions. Coacervates have long been used as a strategy for encapsulation, par- ticularly in food and personal care products. More recent efforts have focused on the utility of this class of materials for the encapsulation of small molecules, pro- teins, RNA, DNA, and other biomaterials for applications ranging from sensing to biomedicine. Furthermore, coacervate-related materials have found utility in other areas of biomedicine, including cartilage mimics, tissue culture scaffolds, …

Generating Optimal Control Simulations Of Musculoskeletal Movement Using Opensim And Matlab, Leng-Feng Lee, Brian R. Umberger

Kinesiology Department Faculty Publication Series

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting …

Mimicking The Arterial Microenvironment With Peg-Pc To Investigate The Roles Of Physicochemical Stimuli In Smc Phenotype And Behavior, William G. Herrick

Doctoral Dissertations

The goal of this dissertation was to parse the roles of physical, mechanical and chemical cues in the phenotype plasticity of smooth muscle cells (SMCs) in atherosclerosis. We first developed and characterized a novel synthetic hydrogel with desirable traits for studying mechanotransduction in vitro. This hydrogel, PEG-PC, is a co-polymer of poly(ethylene glycol) and phosphorylcholine with an incredible range of Young’s moduli (~1 kPa - 9 MPa) that enables reproduction of nearly any tissue stiffness, exceptional optical and anti-fouling properties, and support for covalent attachment of extracellular matrix (ECM) proteins. To our knowledge, this combination of mechanical range, low …