Engineering Commons^™

Comparison Of New Metrics For Assessment Of Risks Of Occupational Noise, Wisam Al-Dayyeni, Jun Qin

ASA Multidisciplinary Research Symposium

The acoustic environment nowadays is filled with excessive noise sources. Here, we will compare the conventional noise metrics(A-weighting and C-weighting) with our two developed advanced models (the adaptive weighting (F-weight) and the complex velocity level (CVL) auditory fatigue model).

Integrative Computational Modeling For Developing Means To Manipulate Biological Cells And For Solving Complex Engineering Problems, Yu Zhao, Guigen Zhang

Commonwealth Computational Summit

A brief discussion on reductive vs integrative investigation

A case study: how integrative computational modeling helps advance the understanding and application of dielectrophoresis (DEP) in various situations

Other applications in advancing the design and development of nanopore, medical devices, novel materials, actuation devices, and coupled spectroscopic techniques, etc.

Parallelization Of A Three-Dimensional Full Multigrid Algorithm To Simulate Tumor Growth, Dylan Goodin, Chin F. Ng, Hermann B. Frieboes

Commonwealth Computational Summit

We present the performance gains of an openMP implementation of a fully adaptive nonlinear full multigrid (FMG) algorithm to simulate three-dimensional multispecies desmoplastic tumor growth on computer systems of varying processing capabilities. The FMG algorithm is applied to solve a recently published thermodynamic mixture model that uses a diffuse interface approach with fourth-order reaction-advection-diffusion PDEs (Cahn-Hilliard-type equations) that are coupled, nonlinear, and numerically stiff. The model includes multiple cell species and extracellular matrix (ECM), with adhesive and elastic energy contributions in chemical potential terms, as well as including blood and lymphatic vessels represented as continuous vasculatures. Advection-reaction-diffusion PDEs are employed …

Integrative Computational Modeling For Developing Means To Manipulate Biological Cells And For Solving Complex Engineering Problems, Yu Zhao, Guigen Zhang

Commonwealth Computational Summit

Computational modeling has become more widely used to guide the design of microfluidic devices for manipulating cells using Dielectrophoresis (DEP), and devise novel means for advancing the study of cellular science and engineering. Conventionally, cells are treated as volumeless points in the system, which allows study of the movement of groups of particles under the effect of field. However, this approach often neglects the distortion effect of particle on external field, as well as interactions among particles. Moreover, it ignores the complex inner structures of cell, which are the causes of distinctive cell behavior. To more accurately model the behavior …

Co-Existence Of Microbial Ecology In A Chemostat Using A Robust Feedback, Hector Puebla, Mariana Rodriguez-Jara, Margarita M. Gonzalez-Brambila, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez, Ennio Piceno-Diaz

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Open Source Artificial Intelligence In A Biological/Ecological Context, Trevor Grant

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Food Web Control And Synchronization Using A Robust Feedback, Hector Puebla, Mariana Rodriguez-Jara, Cesar S. Lopez-Monsalvo, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Chronically Implanted, Continuous Ph Monitoring System For Rats, Ryan B. Budde, Pedro P. Irazoqui

The Summer Undergraduate Research Fellowship (SURF) Symposium

Many body systems operate within a strict pH range, and any deviation can cause harm. pH measurement systems are used in many biomedical research fields. Measurement systems have been able to continuously record pH for a short period of time wirelessly, or over a long period of time with wires, but no system is currently capable of long term, wireless, continuous pH recording. This paper proposes a new pH measurement system that is capable of such measurement. The system is composed of inexpensive, micro-scale, and easy to manufacture pH sensitive and reference electrodes and a data acquisition and transmission module …

A Novel High-Throughput, High-Content Three-Dimensional Assay For Determination Of Tumor Invasion And Dormancy, Mahera M. Husain, Theodore J. Puls, Sherry Voytik-Harbin

The Summer Undergraduate Research Fellowship (SURF) Symposium

Metastasis accounts for most cancer deaths, while dormancy of tumor cells leads to unexpected cancer recurrence. These two aspects of cancer remain relatively untreatable in part because current two-dimensional (2D) methods of high-throughput drug screening cannot quantify outcomes related to these phenotypes. Three-dimensional (3D) in-vitro tumor models are a promising alternative because they better recreate the tumor microenvironment and relevant phenotypes. However, outcome measures for high-throughput screening of these systems are often limited to single measures such as metabolic activity using assays that are not standardized or optimized for 3D models. To address this gap, the objective of this work …

Localized Immunosuppression Therapy For Islet Cell Encapsulation, Madeline Mclaughlin, Clarissa Stephens, Sherry Voytik-Harbin

The Summer Undergraduate Research Fellowship (SURF) Symposium

Type 1 diabetes, an autoimmune disease in which the body’s immune system destroys the insulin-producing beta cells necessary for managing a person’s blood glucose levels, affects 1.25 million Americans. A potential treatment for this disease is islet cell transplantation where Islets of Langerhans, containing the beta cells, are transplanted from a normal donor to a diabetic recipient to regulate blood glucose levels and provide insulin independence. Similar to whole organ transplantation, immune modulation through immunosuppression therapy is necessary for successful transplantation of islets without rejection. However, long-term systemic immunosuppression therapy can be toxic to the patient and the islets. Because …

Development Of Portable Hyperspectral Imaging Device, Chenxi Li, Youngkee Jung, Iyll-Joon Doh, Euiwon Bae

The Summer Undergraduate Research Fellowship (SURF) Symposium

Most of the conventional hyperspectral imaging devices require sophisticated optical components, occupy a large footprint, and requires an initial capital investment for laboratories which mostly suits for laboratories benchtop system. The requirement of shipping the sample and waiting an extended period of time to get the results are the main downsides of this traditional approach. Capitalize in many specific field applications and diagnosis, portable devices provide both convenience and on-site results which are desirable for government agencies and food safety inspectors. This project was aimed to develop a low-cost, portable hyperspectral device for food safety applications. A smartphone was used …

Comparative Analysis Of Nanoscale Ultrasound Contrast Agents, Elly Y. Lambert, Luis Solorio

The Summer Undergraduate Research Fellowship (SURF) Symposium

Current ultrasound contrast agents utilize microbubbles as a blood pooling agent, but the size inhibits access to small capillaries. The development of nanoscale ultrasound contrast agents can enter small capillaries of tissues and aid in the detection of diseased states. However, current nano-formulations are flushed from the body over a short period of time. We developed a nanoscale ultrasound contrast agent with increased circulation time to allow for better detection of diseased states in the microvasculature of the body. Characterization (zeta potential, size, echogenicity and stability) and pharmacokinetic analysis were conducted on three nanoscale formulations: 1) Liquid based Bovine Serum …

Temporal Resolution Of Cell Death Signaling Events Induced By Cold Atmospheric Plasma And Electroporation In Human Cancer Cells, Danielle M. Krug, Prasoon K. Diwakar, Ahmed Hassanein

The Summer Undergraduate Research Fellowship (SURF) Symposium

Cancer treatment resistance and their invasive and expensive nature is propelling research towards developing alternate approaches to eradicate cancer in patients. Non-thermal, i.e., cold atmospheric plasma (CAP) and electroporation (EP) applied to the surface of cancerous tissue are new methods that are minimally invasive, safe, and selective. These approaches, both independently and synergistically, have been shown to deplete cancer cell populations, but the signaling mechanisms of death and their timelines of action are still widely unknown. To better understand the timeframe of signaling events occurring upon treatment, human cancer cell lines were treated with CAP, EP, and combined CAP with …

The Response Of Schwann Cells To Weak Dc Electric Fields, Alexander T. Lai, Jianming Li

The Summer Undergraduate Research Fellowship (SURF) Symposium

Schwann cells are glial cells that serve the vital role of supporting neurons in the peripheral nervous system. While their primary function is to provide insulation (myelin) for axons, they also help regenerate injured axons by digesting severed axons and providing scaffolding to guide the regeneration process. This specific role of Schwann cells makes them highly important cellular targets following nerve injury. Although some efforts have been made to encourage Schwann cell migration after nerve damage, the use of electric fields to control cell responses remain unexplored; therefore, this experiment serves to characterize the behavior of Schwann cells to weak …

Fundamental Characterization Of Oxygen Nanobubbles, John Hamlin, Yi Wen, Joseph Irudayaraj

The Summer Undergraduate Research Fellowship (SURF) Symposium

A hypoxic environment is created by tumors’ incredible growth rate. Hypoxia provides radioresistance to the tumors, thus making radiation treatment less effective. The issue is that increasing the radiation leads to increased side effects in patients. Our goal for the oxygen-filled nanobubble is to deliver oxygen to the tumor to lessen radioresistance and make radiation treatment more efficient. However, we need preliminary research to understand and improve the nanobubbles before further research and implementation. To do this, we synthesized different batches of nanobubbles to optimize the production method and find the best container and temperature to store nanobubbles. We measured …

Localized Blood Occlusion Generation In An In-Vitro Circulatory Catheter System, Ryan D. Harris, Qi Yang, Hyowon Lee

The Summer Undergraduate Research Fellowship (SURF) Symposium

Hydrocephalus is a debilitating neurological disorder that involves the accumulation of cerebrospinal fluid in a ventricle of the brain. The implantation of a catheter commonly treats hydrocephalus with drainage. These catheters have a short lifespan due to obstruction from biological materials. Shunt systems have an extremely high failure rate of more than 40% failed within 1 year and up to 85% failed within 10 years. Previously, polymer-based flexible implantable magnetic micro-actuators were developed to clean up the catheter by mechanical vibration. We have demonstrated clearing of bacteria attachment and are proceeding to examine clearing effects on larger clotting materials, such …

Fret Biosensors: Engineering Fluorescent Proteins As Biological Tools For Studying Parkinson’S Disease, Nathan J. Leroy, Jacob R. Norley, Saranya Radhakrishnan, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s Disease (PD) is a common neurodegenerative disease with over 200,000 new cases each year. In general, the cause of the disease is unknown, but oxidative stress inside of neurons has been associated with the disease’s pathology for some time. Currently, techniques to study the onset of PD inside of neurons are limited. This makes treatments and causes difficult to discover. One solution to this has been fluorescent protein biosensors. In short, these proteins can be engineered to glow when a certain state is achieved inside a cell. The present research discusses the engineering of a genetically-encoded fluorescent protein (FP) …

Dual-Tuned Removable Common-Mode Current Trap For Mri, Angel G. Enriquez, Joseph V. Rispoli

The Summer Undergraduate Research Fellowship (SURF) Symposium

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) are preferred methods of gathering information from the body due to their non-invasive approach of obtaining a diagnosis. MRI can obtain spatial mappings from a region of interest, while MRS can obtain metabolic information from different elements. Dual-tuned radiofrequency (RF) coils are able to capture signals produced by both hydrogen atoms and a second atom of interest. Unwanted shield currents occur in these scans, which can cause image distortion, while the high energy dissipated can create harmful heat, which can injure the patient. These shield currents, also known as common-mode currents, …

Acoustic Analysis Of Vocalizations For Detecting Separation Anxiety In Dogs, Karina Sequera, Nan Kong, Niwako Ogata

The Summer Undergraduate Research Fellowship (SURF) Symposium

Separation anxiety in dogs is a clinical condition in which a dog develops an intense dependence on their caretaker. It manifests itself in maladaptive physical and psychological behaviors that are similar to that of panic attacks in humans when the dog is isolated from its owner. These include excessive vocalizations, destructive behaviors, and in more extreme cases, self-mutilation. Currently, there are no direct ways to diagnose separation anxiety without the aid an owner’s report. To ease this diagnostic process, it would be useful to utilize a tool that can distinguish between certain vocalization patterns in dogs. Literature suggests that some …

Low Power, Low Noise Circuit For Biological Signal Recording, Rachael A. Swenson, Daniel J. Pederson, Pedro Irazoqui

The Summer Undergraduate Research Fellowship (SURF) Symposium

Implantable devices are ideal for recording biological signals in animal models as they have minimal effect on the animal’s normal behavior during observation. The creation of the circuitry for an implantable device has several restrictions including size, power consumption, and noise reduction. These factors compete against each other, making it necessary to carefully optimize circuit components for a given application. This study evaluates the design of a four-channel analog front end circuit board to record cardiac, neural, and respiratory biological signals. Through a critical analysis of component specifications for the circuit’s components and an evaluation of the circuits’ power and …

Multi-Color Ultra-High Resolution Imaging, David A. Miller, Michael Mlodzianoski, Sheng Liu, Fang Huang

The Summer Undergraduate Research Fellowship (SURF) Symposium

Fluorescence microscopy, which allows multiple-color imaging, plays an important role in observing structures inside cells with high specificity. The advent of super-resolution fluorescence microscopy, or nanoscopy techniques such as single-molecule switching nanoscopy (SMSN), has extended the application range of fluorescence microscopy beyond the diffraction limit, achieving up to 10-fold improvement in spatial resolution. At the same time, the recent development of expansion microscopy (ExM) allows samples to be physically expanded by 4-fold in the lateral dimensions providing another independent method to resolve structures beyond the diffraction limit. When combined, ExM-SMSN makes it possible to achieve another significant leap in resolution …

Single Cell Epigenetics, Li F. Lin, Chongli Yuan, Oscar F. Sanchez-Medina

The Summer Undergraduate Research Fellowship (SURF) Symposium

Epigenetics refers to the chromatin modifications that can change the expression of phenotypes but does not alter the underlining DNA. These modifications include but are not limited to histone methylation, histone acetylation, and chromatin folding. Studies suggested that methylation can activate or silence the expression of genes; and that histone acetylation can alter the chromatin structure. The changes in chromatin structure can expose hidden transcriptional factor binding sides and thus affect the differentiation potential. Moreover, these histone modifications are affected by the introduction of different metabolites and cellular microenvironment. To achieve a better understanding of how metabolites and environmental chemical …

Co-Modulation Masking Release Begins In The Auditory Periphery, Kareem R. Hussein, Agudemu Borjigan, Mark Sayles

The Summer Undergraduate Research Fellowship (SURF) Symposium

Understanding speech in noisy environments can be difficult, especially for people with hearing loss. The background noise can cover up the sounds of interest. Normally, the auditory system works to alleviate this problem by tagging and then cancelling the noise. Our experiments are aimed at understanding the mechanism of this noise cancellation process. We hypothesize that non-linear signal processing in the mammalian cochlea (the most peripheral part of the auditory system) is the basis of noise cancellation. To test this hypothesis, we measured the responses of auditory-nerve fibers (ANFs) to sounds embedded in background noise with different statistical properties. ANFs …

How Strongly Do Oysters Stick?, Nicolás M. Morato, Andrés M. Tibabuzo, Jonathan J. Wilker

The Summer Undergraduate Research Fellowship (SURF) Symposium

Biological adhesives are a type of interfacial material that has incredible potential to generate new biomimetic compounds that can replace current strong, but toxic, adhesives. Therefore, a study of the chemical composition and mechanical properties of those bio-adhesives is necessary. However, in the case of oysters, despite known chemical characterization of the adult’s adhesive, there are almost no studies on its mechanical properties. Furthermore, there is no available information on the adhesive properties of spat (oysters in their larvae state). Herein, we present the first mechanical characterization of the spat adhesive, measuring its adhesion strength by hydrodynamic determination using a …

A Spatial Stochastic Model Of Ampar Trafficking And Subunit Dynamics, Tyler Vandyk, Matthew C. Pharris, Tamara L. Kinzer-Ursem

The Summer Undergraduate Research Fellowship (SURF) Symposium

In excitatory neurons, the ability of a synaptic connection to strengthen or weaken is known as synaptic plasticity and is thought to be the cellular basis for learning and memory. Understanding the mechanism of synaptic plasticity is an important step towards understanding and developing treatment methods for learning and memory disorders. A key molecular process in synaptic plasticity for mammalian glutamatergic neurons is the exocytosis (delivery to the synapse) of AMPA-type glutamate receptors (AMPARs). While the protein signaling pathways responsible for exocytosis have long been investigated with experimental methods, it remains unreasonable to study the system in its full complexity …

Bacterial Motility And Its Role In Biofilm Formation, Clayton J. Culp, Arezoo M. Ardekani, Adib Ahmadzadegan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bacterial biofilms are known to cause millions of dollars in damage in the medical industry per year via infection of central venous catheters, urinary catheters, and mechanical heart valves. Unfortunately, there are some characteristics of biofilm formation that are yet to be fully understood. Recently much work has been done to investigate the motility characteristics of bacteria with hopes of better understanding the phenomena of biofilm formation. Still, one of the least understood stages is bacterial attachment or adhesion, a process designed to anchor bacteria in an advantageous environment. Providing a better understanding of bacterial motility near solid interfaces will …

Pathogenic Dna Detection Using Dna Hairpins: A Non-Linear Hybridization Chain Reaction Platform, Lance Novak, Tamara L. Kinzer-Ursem

The Summer Undergraduate Research Fellowship (SURF) Symposium

Currently, 3.2 billion people are at risk of being infected with malaria, with 1.2 billion of those being at high risk (>1 in 1000 chance of getting malaria in a year). Thus, there is a need for a biosensor that is highly sensitive, cost effective, and simple to use for point-of-care diagnosis. The biosensing platform, PathVis, has achieved this by measuring changes in fluid properties after a loop-mediated isothermal amplification (LAMP). LAMP is a DNA amplification system that requires enzymes and a temperature of 65degrees C. LAMP currently limits PathVis by being costly, requiring refrigeration, and difficult to design. …

Intrinsic Regulators Of Actomyosin Contractility Engendering Pulsatile Behaviors, Qilin Yu, Jing Li, Taeyoon Kim

The Summer Undergraduate Research Fellowship (SURF) Symposium

Actomyosin contractility regulates various biological processes including cell migration, muscle contraction, and tissue morphogenesis. Cell cortex underlying a membrane, which is a representative actomyosin network in eukaryote cells, exhibits dynamic contractile behaviors. Interestingly, the cell cortex shows reversible aggregation of actin and myosin called pulsatile contraction in diverse cellular phenomena, such as embryogenesis and tissue morphogenesis. While contractile behaviors have been studied in several in vitro experiments and computational studies, none of them demonstrated the pulsatile contraction of actomyosin networks observed in vivo. Here, we used an agent-based computational model based on Brownian dynamics to identify factors facilitating the pulsatile …

Smartphone-Based Microscope For Pathogen Detection, Meghan E. Henderson, Katherine N. Clayton, Ryan M. Preston, Jacqueline Linnes, Tamara L. Kinzer-Ursem

The Summer Undergraduate Research Fellowship (SURF) Symposium

Vibrio cholerae is a water and food borne bacteria that causes cholera, a severe acute diarrheal disease, when ingested and when left untreated, can cause patient death within hours. Currently there is a lack of both sensitive and rapid portable detection technologies of V. cholerae for testing water and food samples. Combining nucleic acid amplification and particle diffusometry present an alternative detection method for V. cholerae in under 30 minutes, but the process requires an expensive laboratory microscope. In this work, we develop a smartphone-based microscope to detect V. cholerae DNA in environmental water samples using particle diffusometry. A modular …

Effects Of Stroma On Er+ Breast Cancer Cell Metastasis, Shipeng Xu, Luis Solorio, Sarah Calve

The Summer Undergraduate Research Fellowship (SURF) Symposium

Breast cancer is one of the most wide-spread diseases among women in America. If the cancer is local, it is easily controlled by surgical resection. However, if the cancer cells metastasize, patient survival is significantly reduced. 70% of breast cancers can be targeted through estrogen receptors (ER) on the membrane, with compounds such as tamoxifen. However, tamoxifen shows unreliable outcomes on different patients and it is believed that the ineffectiveness of tamoxifen is related to the epithetical-mesenchymal transition (EMT) of cancer cells. To address this problem, we are designing a system that stimulates metastasis activation with the aim of incorporating …