Browsing by Subject "Biomedical engineering"

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All-optical ultrasound transducers for high resolution imaging
(2014-12) Sheaff, Clay
High frequency ultrasound (HFUS) has increasingly been used within the past few decades to provide high resolution (< 200 µm) imaging in medical applications such as endoluminal imaging, intravascular imaging, ophthalmology, and dermatology. The optical detection and generation of HFUS using thin films offers numerous advantages over traditional piezoelectric technology. Circumvention of an electronic interface with the device head is one of the most significant given the RF noise, crosstalk, and reduced capacitance that encumbers small-scale electronic transducers. Thin film Fabry-Perot interferometers - also known as etalons - are well suited for HFUS receivers on account of their high sensitivity, wide bandwidth, and ease of fabrication. In addition, thin films can be used to generate HFUS when irradiated with optical pulses - a method referred to as Thermoelastic Ultrasound Generation (TUG). By integrating a polyimide (PI) film for TUG into an etalon receiver, we have created for the first time an all-optical ultrasound transducer that is both thermally stable and capable of forming fully sampled 2-D imaging arrays of arbitrary configuration. Here we report (1) the design and fabrication of PI-etalon transducers; (2) an evaluation of their optical and acoustic performance parameters; (3) the ability to conduct high-resolution imaging with synthetic 2-D arrays of PI-etalon elements; and (4) work towards a fiber optic PI-etalon for in vivo use. Successful development of a fiber optic imager would provide a unique field-of-view thereby exposing an abundance of prospects for minimally-invasive analysis, diagnosis, and treatment of disease.
Brightness analysis in finite geometries: probing protein interactions in cellular, cell-free and aqueous environments
(2012-12) Macdonald, Patrick
Fluorescence fluctuation spectroscopy (FFS) is a powerful technique for quantitatively analyzing protein interactions. Using brightness analysis methods, we are uniquely able to measure the stoichiometry of protein complexes. FFS is particularly valuable because it allows measurements within living cells. This thesis demonstrates that measuring in very small volumes, such as E. coli cells, introduces a bias into the measured brightness. We show that this bias is a result of accumulative sample loss, or photodepletion, and that we can account for this effect and recover correct brightness values. Similarly, very thin samples, such as cell cytoplasm, introduce a bias due to the sample being shorter along the vertical axis than the volume of the excitation light. We introduce z-scan FFS and theory to identify and model thin samples and to recover unbiased data. Although measuring in cells is a primary strength of the FFS technique, some studies require the greater degree of experimental control afforded by solution measurements. Thus, we characterize cell-free expression solution for FFS measurements, an environment that offers increased control but permits genetic fluorescent labeling. We take advantage of this system to perform chromophore maturation experiments as a function of temperature on three common fluorescent proteins: EGFP, EYFP and mCherry. Our results prove that EGFP has fast maturation and is a good reporter for fluorescence experiments. Finally, we apply FFS and brightness analysis to the enzyme, APOBEC3G. We reveal that APOBEC3G interactions with RNA and single-stranded DNA are sequence dependent, which has important implications for the mechanism by which APOBEC3G packages itself into HIV-1 viral particles and restricts the virus to prevent infection.
The Comparative assessment of clinical ablative therapies: effects on physiological and biomechanical properties of contractile tissues in response to therapeutic doses
(2014-09) Singal, Ashish
Tissue ablation is a common medical procedure that involves manipulation of the target tissue with an aim to restore normal structure and function. Ablations are performed throughout the human body for treating various carcinomas and disease conditions. Although a routine clinical procedure, in a small percentage of patients it may cause collateral damage to surrounding structures which can have severe clinical implications. The collateral damage results in altered tissue properties those are dependent on the level of ablative energy and extent of tissue injury. Therefore, assessment of tissue properties is fundamental to advancing the understanding of underlying basic and clinical science of ablations, especially to maximize therapy efficacy and minimize procedural complications. Thus, a thorough understanding of tissue properties is essential to the successful outcome of all ablation procedures.Unique laboratory methodologies were developed that were used to assess the physiological and biomechanical properties of respiratory diaphragm, esophagus, cardiac trabeculae, and vastus lateralis tissues following exposure to five different therapeutic ablative modalities: radiofrequency ablation, cryoablation, high-intensity focused ultrasound, microwave ablation, and chemical ablation (with acetic acid, ethanol, hypertonic sodium chloride, and urea). The changes in physiological properties were quantified by measuring changes in peak force (strength of contractions) and baseline force (resting muscle tension) in response to ablations. The changes in biomechanical properties were quantified by measuring the stress-strain characteristics, avulsion forces, and elastic moduli in response to ablations. Dose effect responses of each ablative modality were quantified. To our knowledge these are the first reports of such methodological comparative assessment of tissue properties following treatment with therapeutic ablative modalities at clinically relevant doses. The understanding of tissue properties has wide applications ranging from applied research to the development of novel tools, ablation techniques, and innovative clinical treatment options. These findings may provide novel insights into the effects of ablations which may allow further improvements in ablative techniques to increase the overall safety and efficacy of ablative procedures. It is clear that the understanding of collateral damage at the cellular level, isolated tissue level, and whole organ level will be important to the future of this evolving era of ablations.
Degradation Properties of Bioresorbable Material Candidates for Congenital Heart Defect Repair
(2013-08) Holst, Jessica Mae
The goal of this project is to investigate the use of bioresorbable materials for congenital heart defect repair. This investigation focused on the in vitro degradation over eight weeks of several biodegradable polymers including: Poly (L-lactide) or PLLA, 70:30 Poly (L-lactide)-Polycaprolactone or PLLA/PCL and Polyglycolide or PGA. Since surface area can affect degradation rates several morphologies of these polymers were included in the study such as knits, films, felts, electrospun materials and sponges. The degradation was characterized by: tensile testing, scanning electron microscope (SEM) visualization, differential scanning calorimetry (DSC) and gel permeation chromatography (GPC). Results of these tests do not directly provide recommendation for specific materials for use as implantable, bioresorbable materials but they do confirm that the combination of chemical composition and material morphology significantly affect the degradation rate as measured by changes in molecular weight with time. This finding supports the possibility of fine tuning manufacturing processes of these materials to obtain a specific degradation profile. PLLA film material 3 was the only material tested that maintained its peak stress and peak strain behavior over the 8 week degradation time period. This does not necessarily rule out the other materials as long as they maintain mechanical integrity over the required time period. In addition, the changes in molecular weight (but not stress and strain behavior) over time were significantly affected by the type of degradation environment the material was placed in, static vs. agitated or dynamic. The importance of the degradation rate and mechanism for this application is extremely important so the inclusion of some form of agitation in future degradation experiments is recommended. Finally, the degradation environment in this experiment was relatively inert and testing with digestive enzymes or other blood components is also recommended.
Implications of percutaneous delivery of cardiac devices on interatrial septal anatomy and biomechanics
(2014-03) Howard, Stephen Andrew
The anatomy and physiology of the interatrial septum in the heart is fairly well understood. However, the biomechanical properties, as they relate to percutaneous medical device therapy, have not been fully studied. The aim of this dissertation is to better understand how the anatomy and physiology of the cardiac interatrial septum interplays with medical devices such as percutaneous transseptal equipment and atrial septal occluders. To do this, we employed 2D functional imaging of human hearts as well as 3D computational modeling of the anatomy to determine the size, shape and physiology of the atrial septum. Further, the models were utilized to understand anomalous human anatomy and how atrial septal occluder devices may distort the anatomy if placed into a defect like a patent foramen ovale. The wide variability found in the anomalous anatomy will likely cause difficulty in placement of such occluder devices in a patent foramen ovale anatomy since the overlap of the two septa can range anywhere from 2-20mm in length. This knowledge of the anatomy can also feed into design considerations for occluder devices aimed specifically at this anatomy. The second portion of the thesis looks specifically at transseptal punctures and the defects that are a result of this procedure. Following an extensive literature review of reports analyzing the prevalence of iatrogenic atrial septal defects following such procedures, the data suggested that the size of the catheter, time post procedure and the procedure time all impacted its prevalence following a procedure. To further investigate the way in which the catheters interact with the septum, the biomechanical properties of the septum, tensile testing, ripping, tenting and puncturing forces were determined and related to the orientation of the septum. Ultimately it was found that the fossa ovalis will preferentially rip in the superior to inferior direction as opposed to the anterior posterior direction. This suggests that extensive manipulations in the former direction could cause a larger defect following procedures. These data should be considered and understood while performing such procedures and for designing next generation transseptal devices or computer simulations.
Intrapericardial delivery of Omega-3 Polyunsaturated fatty acids
(2012-08) Rolfes, Christopher David
The intrapericardial delivery of antiarrhythmic drugs is very promising, with positive results seen in several animal models to date. The primary purpose of this thesis is to evaluate the efficacies of antiarrhythmic therapies delivered to the pericardial space so as to reduce susceptibility to arrhythmias during cardiothoracic procedures. To accomplish this, a swine model of localized therapy delivery was used to treat intraoperative atrial fibrillation, using metoprolol and omega-3 polyunsaturated fatty acids. Metoprolol administered to the pericardial space had minimal effect on atrial fibrillation or atrial contractility, but significantly reduced heart rate. Certain formulations of fatty acids reduced atrial fibrillation and improved cardiac function upon reanimation in the Visible Heart
Investigations into the effects of transcatheter valve implantations on the cardiac conduction system and cardiac anatomy
(2012-08) Bateman, Michael G.
Investigations into the Effects of Transcatheter Valve Implantations on the Cardiac Conduction System and Cardiac Anatomy Michael G. Bateman MEng.As of 2006, approximately 3 million people in the US alone had been diagnosed with either mitral regurgitation or aortic stenosis. Today, with the increasing prevalence of cardiac diseases, including chronic cardiomyopathies, these values of valvular disease may be gross underestimations of the current patient populations. The work presented here describes the development of a strong foundation of anatomical knowledge to develop a better understanding of the potential complications that transcatheter devices may impose on a patients' cardiac anatomy. Using real-time clinical imaging and Visible Heart® methodologies models of three such disease states were created: 1) aortic stenosis, 2) mitral prolapse and 3) pulmonary valve insufficiency. These simulated disease states are used test the next generation of transcatheter valve replacements. Furthermore to better understand the effect of these therapies on cardiac electrophysiology, several collaborations have been initiated to investigate the anatomical position and the associated activation sequences of the cardiac conduction system in relation to the hearts' four valves. It is considered here that a better understanding of the interactions of novel transcatheter devices and their delivery systems with both the human functional/structural cardiac anatomy and conduction system is critical for the development/advancement of these medical devices.
Magnetoacoustic tomography with magnetic induction for electrical conductivity based tissue imaging
(2014-08) Mariappan, Leo
Electrical conductivity imaging of biological tissue has attracted considerable interest in recent years owing to research indicating that electrical properties, especially electrical conductivity and permittivity, are indicators of underlying physiological and pathological conditions in biological tissue. Also, the knowledge of electrical conductivity of biological tissue is of interest to researchers conducting electromagnetic source imaging and in design of devices that apply electromagnetic energy to the body such as MRI. So, the need for a non-invasive, high resolution impedance imaging method is highly desired. To address this need we have studied the magnetoacoustic tomography with magnetic induction (MAT-MI) method. In MAT-MI, the object is placed in a static and a dynamic magnetic field giving rise to ultrasound waves. The dynamic field induces eddy currents in the object, and the static field leads to generation of acoustic vibrations from Lorentz force on the induced currents. The acoustic vibrations are at the same frequency as the dynamic magnetic field, which is chosen to match the ultrasound frequency range. These ultrasound signals can be measured by ultrasound probes and are used to reconstruct MAT-MI acoustic source images using possible ultrasound imaging approaches .The reconstructed high spatial resolution image is indicative of the object's electrical conductivity contrast. We have investigated ultrasound imaging methods to reliably reconstruct the MAT-MI image under the practical conditions of limited bandwidth and transducer geometry. The corresponding imaging algorithm, computer simulation and experiments are developed to test the feasibility of these different methods. Also, in experiments, we have developed a system with the strong static field of an MRI magnet and a strong pulsed magnetic field to evaluate MAT-MI in biological tissue imaging. It can be seen from these simulations and experiments that conductivity boundary images with millimeter resolution can be reliably reconstructed with MAT-MI. Further, to estimate the conductivity distribution throughout the object, we reconstruct a vector source image corresponding to the induced eddy currents. As the current source is uniformly present throughout the object, we are able to reliably estimate the internal conductivity distribution for a more complete imaging. From the computer simulations and experiments it can be seen that MAT-MI method has the potential to be a clinically applicable, high resolution, non-invasive method for electrical conductivity imaging.
Mechanistic insight into cationic polymer mediated gene delivery
(2014-12) Zhong, Xiao
Gene therapy holds great potential to enhance human medicine since it could provide treatment to a vast variety of diseases. Viral gene delivery vectors have high transfection efficiency, but often they are associated with high risk of immunogenicity as well. Non-viral vectors, especially polycationic polymer based gene carriers provide the advantages of low immunogenicity and ease of synthesis, but they face two major challenges for a broader application in clinical trials: high toxicity and low transfection efficiency. In this study, we performed experiments to gain a better understanding of the mechanisms and pathways underlying the high toxicity and low transfection efficiency associated with polyplex-mediated gene delivery. In the first part of the thesis, we studied the toxicity resulted from polyplex-mediated gene delivery and found that polyplexes made from PEI/DNA plasmids were able to induce autophagy in fibroblasts, a third type of cytotoxicity besides apoptosis and necrosis. With the proper choice of treatment time and drug concentrations, we decoupled cell cytotoxicity due to apoptosis and necrosis from autophagy, and found that transfection efficiency is positively correlated with the regulation of autophagy. In the second part of the thesis, we performed in vitro physical characterization of polyplexes formed from six different polymers in order to understand their local in vivo performance. Homopolymer with a larger molecular weight (and polymer chain) was able to transfect cells in vitro, but not in vivo. On the other hand, a shorter polymer chain favored local in vivo transfection. PEGylation helped the polyplexes to be stable against serum protein, but PEGylation of long chain homopolymer did not improve its in vivo performance. Taken together, these findings could help us to improve transfection efficiency through modulation of cytotoxicity (autophagy) and gain a better understanding of polyplex in vivo performance based on its in vitro behavior and therefore providing insight into the design of gene delivery vehicle.
A molecular dynamics investigation of side-chain influence on the formation of A8-35 amphipol particles.
(2012-01) Drasler, William Joseph
We present all-atom molecular dynamics simulations of A8-35 amphipol, a polymer designed to stabilize the native conformation of membrane proteins in aqueous solution. These simulations were designed to reproduce the experimentally observed self-assembly of four A8-35 chains into a particle with an approximate molar mass of 40 kD as previously reported by Gohon et al. Comparison between the simulations and small angle neutron scattering confirms the nanometer scale structure of the particle. Using atomistic resolution, we have studied the polymers ability to form microdomains of like moieties, a feature with implications in the stabilization of membrane proteins. Using five distinct side-chain sequences, we observe different extents of side-chain self-association. An additional simulation describes the affect of a higher ionic concentration, which causes a dramatic reorganization of the particle, leading to increased side-chain self-association. Collectively, these simulations describe with atomistic detail the range of structures observed in a statistical polymerization, suggesting which features may be exploited for the improvement of membrane protein stabilization.
Multi-contrast optical coherence tomography for brain imaging and mapping
(2014-08) Wang, Hui
Although our knowledge of neuronal function and regional activity has been tremendously enriched in the past decades, coordination of these neurons to form the complex behaviors has yet to be understood. The neuronal pathways (also named connectome) form the structural foundation of the dynamic circuits in the brain. The recent interests in connectome and brainwide database have imposed a pressing need for high-resolution imaging techniques that allows large coverage. This dissertation develops a novel multi-contrast optical coherence tomography (MC-OCT) technique for the application of brainwide imaging and architectural mapping in 3D at high spatiotemporal resolution, with an emphasis on the connective tracts. The image contrasts originate from intrinsic optical properties of the brain tissues in which light propagates, back-scatters, attenuates, and changes its polarization state. Due to a birefringence property of the myelin sheath, MC-OCT specially targets the white matter, with qualitative architecture and quantitative orientation maps produced. The fiber tracts with diameters of a few tens of micrometers are visualized and tracked in 3D. As a further advance, a serial optical coherence scanner (SOCS) integrating the MC-OCT and a Vibratome slicer is realized for large-scale brain imaging and mapping at high resolution. The 3D fiber architecture and fiber orientation in rat brain are reconstructed at a resolution of 15 x 15 x 5.5 µm3. SOCS enables systematic validations of diffusion magnetic resonance imaging (dMRI) at microscopic resolution. A cross-validation in a postmortem human medulla sample shows remarkably good agreement on fiber structures and orientations between the two techniques. In addition, SOCS resolves intricate fiber patterns that are not captured by the dMRI. Taken together, the serial MC-OCT technique has the potential to bridge cross-scale investigations for a hierarchical view of neuroanatomical connections, thus opening intriguing applications in brain mapping and neural disorders.
Multi-joint rigidity-testing device for titrating medication and deep brain stimulation therapies
(2014-08) Mohsenian, Kevin J.
Disabling motor signs of Parkinson's Disease including akinesia, bradykinesia, tremor, and muscle rigidity are typically quantified by clinicians using the Unified Parkinson's Disease Rating Scale (UPDRS). These subjective assessments, while useful, often vary among clinicians, making it challenging to evaluate medication and deep brain stimulation (DBS) therapies in multi-center trials. In this study, two designs for a multi-joint rigidity-testing device were developed to enable objective, quantitative measures of rigidity. The investigator passively manipulated the subject's joints while stabilizing the appendage distal to the joint with two opposing force transducers, providing a measurement of differential force during the movement. These forces were synchronized to the joint angle, measured by a motion capture camera system. Here, we show feasibility data for detecting changes in muscle rigidity in a parkinsonian non-human primate treated with Sinemet, Globus Pallidus internal (GPi) DBS and/or subthalamic nucleus (STN) DBS. For design 1, the device was tested on six joints: elbow, wrist, shoulder, hip, knee and ankle, and in three states: MPTP, DBS stimulation, and drug therapy. Device 1 was effectively able to quantify rigidity and determine changes in rigidity states among all joints except elbow (p<0.05). For design 2, the device was tested on only the shoulder abduction/adduction and was tested in three states: MPTP, DBS stimulation, and post-DBS stimulation. Design 2 was effectively able to quantify changes in rigidity as well (p<0.05). Ergonomics and durability were considered in the evaluation of the devices. While each device showed promising results, future iterations will also need to address several limitations of the current devices. The eventual goal of this rigidity testing device would be to use it in the clinic to assist neurologists in titrating medication levels and DBS parameters.
Multiscale modeling and analysis of microtubule self-assembly dynamics
(2014-08) Castle, Brian Thomas
Microtubules are dynamic biopolymers that self-assemble from individual subunits of αβ-tubulin. Self-assembly dynamics are characterized by stochastic switching between extended phases of growth and shortening, termed dynamic instability. Cellular processes, including the chromosome segregation during mitosis and the proper partitioning of intracellular proteins, are dependent on the dynamic nature of microtubule assembly, which facilitates rapid reorganization and efficient exploration of cellular volume. Microtubule-targeting chemotherapeutic agents, used to treat a wide range of cancer types, bind directly to tubulin subunits and suppress dynamic instability, ultimately impeding the capacity to complete cellular processes. Microscale length changes observed during dynamic instability are the net-effect of the addition and loss of individual subunits, dictated by the interdimer molecular interactions. Therefore, a multiscale approach is necessary to extrapolate submolecular level effects of microtubule-targeting agents to dynamic instability. The work presented in this dissertation integrates multiscale computational modeling and experimental observations with the goal of better understanding the functional mechanisms of microtubule-targeting agents. First, we develop a computational model for the association and dissociation of tubulin subunits, in which the interdimer interaction potentials are specifically simulated. Simulation results indicate that the local polymer end structure sterically inhibits subunit association as much as an order of magnitude. Additionally, the model informs how microtubule-targeting agents could alter assembly dynamics through the properties of the interdimer interactions. Second, the mechanisms of kinetic stabilization by microtubule-targeting agents are tested and constrained by combining predictions from a computational model for microtubule self-assembly and experimental observations in mammalian cells. We find that assembly- and disassembly-promoting agents induce kinetic stabilization via separate mechanisms. One is a true kinetic stabilization, in which the kinetic rates of subunit addition and loss are reduced 10- to 100-fold, while the other is a pseudo-kinetic stabilization, dependent upon mass action of tubulin subunits between polymer and solution. Overall, this work advances our knowledge of the basic physical principles underlying multistranded polymer self-assembly and can inform the future design and development of more effective and tolerable microtubule-targeting drugs.
Noninvasive Imaging of Cardiac Electrophysiology in Pathological Hearts
(2016-10) Zhou, Zhaoye
Noninvasive imaging of cardiac electrical activity is important to both basic cardiovascular research and clinical treatment. It offers the capability to translate body surface electrical signals into cardiac electrical activities and provide direct information on the electrical status of the heart. This dissertation research is aimed to investigate a novel physical-model-based cardiac electrical imaging technique (CEI) under different pathological conditions, for the purpose of further developing it into a clinical useful tool. The CEI technique is adapted to image myocardial infarction and atrial arrhythmias. For the imaging of myocardial infarction, the computer simulation was performed by using a cellular automaton heart model with simulated myocardial infarctions. The simulation results demonstrate that CEI can quantify myocardial infarction and offer the potential to distinguish between epicardial and endocardial infarctions. Furthermore, the CEI approach was adapted to image atrial electrical activities. A frequency-based CEI technique has been proposed to incorporated spectral analysis with the electrical source imaging technique to localize high-frequency drivers during atrial fibrillation (AF). The imaging results were compared with clinical electrophysiological mappings and shown good consistency. The CEI technique was also applied to image atrial excitations in subjects with normal atrial activation and atrial flutter. The results from patients with atrial flutter demonstrated that CEI is also capable of imaging reentrant pattern. The performance of CEI was also experimentally evaluated in in situ swine heart with induced ventricular tachycardia. The consistency between the non-invasively imaged electrical activities and computer simulation or the directly measured counterparts from clinical/animal study implies that CEI is capable of localizing electrically-abnormal substrate, extracting the spectral features during AF, reconstructing the global patterns of atrial and ventricular activation sequences, localizing the arrhythmogenic foci, and imaging dynamically changing arrhythmia on a beat-to-beat basis. The promising results presented in this dissertation study suggest that the cardiac electrical imaging technique has the potential to assist in the diagnosis and treatment of cardiovascular diseases. The present dissertation research takes an important step towards further translating this technique into clinical assistive tool by extending the application to hearts with electrophysiological abnormal substrates, adapting it to image atrial electrical activities, and further evaluating the performance in a clinical setting on human subjects.
Noninvasive imaging of three-dimensional ventricular electrical activity
(2012-08) Han, Chengzong
Noninvasive imaging of cardiac electrical activity is of great importance and can facilitate basic cardiovascular research and clinical diagnosis and management of various malignant cardiac arrhythmias. This dissertation research is aimed to investigate a novel physical-model-based 3-dimensional cardiac electrical imaging (3DCEI) approach. The 3DCEI approach is developed by mathematically combining high-density body surface electrocardiograms (ECGs) with the anatomical information. Computer simulation study and animal experiments were conducted to rigorously evaluate the performance of 3DCEI. The simulation results demonstrate that 3DCEI can localize the origin of activation and image the activation sequence throughout the three-dimensional ventricular myocardium. The performance of 3DCEI was also experimentally and rigorously evaluated through well-controlled animal validation studies in both the small animal model (rabbit) and large animal model (canine), with the aid of simultaneous intramural recordings from intra-cardiac mapping using plunge-needle electrodes inserted in the ventricular myocardium. The clinical relevance of 3DCEI was further demonstrated by investigating 3DCEI in cardiac arrhythmias from animal models with experimentally-induced cardiovascular diseases. The consistent agreement between the non-invasively imaged activation sequences and its directly measured counterparts in both the rabbit heart and canine heart implies that 3DCEI is feasible in reconstructing the spatial patterns of ventricular activation sequences, localizing the arrhythmogenic foci, and imaging dynamically changing arrhythmia on a beat-to-beat basis. The promising results presented in this dissertation study suggest that this cardiac electrical imaging approach may provide an important alternative for non-invasively imaging cardiac electrical activity throughout ventricular myocardium and may potentially become an important tool to facilitate clinical diagnosis and treatments of malignant ventricular arrhythmias.
Optical micromachined ultrasound transducers (OMUT) : a new approach for high frequency ultrasound imaging
(2014-11) Tadayon, Mohammad Amin
Piezoelectric technology is the backbone of most medical ultrasound imaging arrays, however, in scaling the technology to sizes required for high frequency operation (> 20 MHz), it encounters substantial difficulties in fabrication and signal transduction efficiency. These limitations particularly affect the design of intravascular ultrasound (IVUS) imaging probes whose operating frequency can approach 60 MHz. Optical technology has been proposed and investigated for several decades as an alternative approach for high frequency ultrasound transducers. However, to apply this promising technology in guiding clinical operations such as in interventional cardiology, brain surgery, and laparoscopic surgery further raise in the sensitivity is required. Here, in order to achieve the required sensitivity for an intravascular ultrasound imaging probe, we introduce design changes making use of alternative receiver mechanisms. First, we present an air cavity detector that makes use of a polymer membrane for increased mechanical deflection. We have also significantly raised the thin film detector sensitivity by improving its optical characteristics. This can be achieved by inducing a refractive index feature inside the Fabry-Perot resonator that simply creates a waveguide between the two mirrors. This approach eliminates the loss in energy due to diffraction in the cavity, and therefore the Q-factor is only limited by mirror loss and absorption. To demonstrate this optical improvements, a waveguide Fabry-Perot resonator has been fabricated consisting of two dielectric Bragg reflectors with a layer of photosensitive polymer between them. The measured finesse of the fabricated resonator was 692, and the Q-factor was 55000. The fabrication process of this device has been modified to fabricate an ultrasonically testable waveguide Fabry-Perot resonator. By applying this method, we have achieved a noise equivalent pressure of 178 Pa over a bandwidth of 28 MHz or 0.03 Pa/Hz1/2 which is approximately 20-fold better than a similar device without a waveguide. The finesse of the tested Fabry-Perot resonator was around 200. This result is 5 times higher than the finesse measured in the same device outside the waveguide region. In future, our developed technology can be integrated on the tip of an optical fiber bundle and applied for intravascular ultrasound imaging.
The predicted role of stereospecificity in crowding-mediated effects on reversible association: a Brownian Dynamics investigation
(2013-08) Powers, Joseph Daniel
Macromolecular crowding refers to the presence of inert molecules in close proximity to other reacting molecules, and is often discussed in the context of biochemical reactions in the cytoplasm. This phenomenon has been proposed to cause alterations in the intrinsic kinetics and thermodynamics of chemical reactions, which has led to certain undefined caveats when relating biochemical characteristics observed in vitro to those seen in vivo. In this work, the effects of macromolecular crowding were studied by means of a computational, Monte Carlo simulation using Brownian Dynamics, where generalized chemical association and dissociation reaction kinetics of varying degrees of stereospecificity were modeled both in the absence and presence of crowding molecules of different sizes. It was found that crowded environments impose energetic contributions to reactant pairs through depletion forces, which bias their translational and rotational diffusion in such a way that overall net assembly is favored, with stronger effects on reactants with higher degrees of stereospecificity than for those with low stereospecificity. These favorable forces are insufficient to overcome the slowing of translational diffusion by crowders for low stereospecificity reactions, but more than compensate for the translational slowing for high stereospecificity reactions. In general, the effects observed in the simulation are relatively modest, with k_on decreasing by 2-fold for low stereospecificity reactions, and increasing by 3-fold for high stereospecificity reactions. In addition, k_off decreases by ~30-60% in the presence of crowders (depending on the strength of the bond between the reactant pair), so that the equilibrium constant is increased by at most ~3.5-fold (ΔΔGo = -1.3k_BT). The moderate effects of crowding predicted in this work through strictly geometric constraints suggest that any effects observed in vitro larger than those found here are due to other energetic effects, such as solvent reordering. More generally, the results suggest that reactions in the cytoplasm are fundamentally insensitive to the physical presence of crowders over a large range of volume fractions (0-0.3).
Self-assembly of ssDNA-amphiphiles into micelles, nanotapes and nanotubes
(2014-12) Pearce, Timothy R.
The field of DNA nanotechnology utilizes DNA as a construction material to create functional supramolecular and multi-dimensional structures like two-dimensional periodic lattices and three-dimensional polyhedrons with order on the nanometer scale for many nanotechnology applications including molecular templating, nanosensors, and drug delivery. Single-stranded DNA (ssDNA) is often used to create these nanostructures as the DNA bases provide an intrinsic molecular code that can be exploited to allow for the programmed assembly of structures based upon Watson-Crick base-pairing. However, engineering these complex structures from biopolymers alone requires careful design to ensure that the intrinsic forces responsible for organizing the materials can produce the desired structures. Additional control over supramolecular assembly can be achieved by chemically modifying the ssDNA with hydrophobic moieties to create amphiphilic molecules, which adds the hydrophobic interaction to the list of contributing forces that drive the self-assembly process. We first explored the self-assembly behavior of a set of ssDNA aptamer-amphiphiles composed of the same hydrophobic tail and hydrophilic ssDNA aptamer headgroup but with different spacer molecules linking these groups together. Through the use of cryo-transmission electron microscopy (cryo-TEM), small angle x-ray scattering (SAXS), and circular dichroism (CD) we show that the aptamer-amphiphiles can assemble into a variety of structures depending on the spacer used. We demonstrated, for the first time, the creation of self-assembled aptamer-amphiphile nanotape structures and show that the choice of the spacer used in the design of aptamer-amphiphiles can influence their supramolecular self-assembly as well as the secondary structure of the aptamer headgroup. We next explored the role of the ssDNA headgroup on the amphiphile self-assembly behavior by designing amphiphiles with headgroups of multiple lengths and nucleotides sequences. Amphiphiles of each headgroup length that contained hydrophobic spacers were found to assemble into twisted nanotapes, helical nanotapes and nanotubes as the nanotapes grew in width. In few instances, guanine-rich headgroups were capable of forming nanotape and nanotube structures in the absence of the hydrophobic spacer. Together, these studies demonstrate the ability of ssDNA-amphiphiles to form complex nanostructures that may be useful in a variety of DNA nanotechnology applications.
Swelling properties of phenylboronic acid containing hydrogels.
(2012-01) Kim, Arum
Glucose-sensitive hydrogels have been of interest for developing a glucose sensor for management of diabetes. In this thesis, swelling behavior and mechanical properties of glucose-sensitive hydrogels containing phenylboronic acid (PBA) were investigated. Swelling studies were conducted at different pH values and at different sugar concentrations. At pH values lower than the pKa of PBA, the hydrogel swells with increased glucose concentration due to progressive charging of the polymer chains. At pH values higher than the pKa of PBA, extra reversible crosslinks form in the hydrogel due to complexation of PBA sidechains on separate polymer chains with glucose molecules, which causes hydrogel shrinking to occur. By incorporating a tertiary amine, reversible crosslinking by glucose occursat physiological pH,7.4. Modeling of pH and fructose effects on the swelling of MPBA-co-AAm hydrogels was also researched. Extended Flory-Rehner-Donnan-Langmuir (FRDL) models were applied to our data, and good fits were obtained. Auxiliary experiments to validate the models were carried out. Compression tests provided a value for crosslink density that was not consistent with that determined by the model fits to swelling data.. Osmotic deswelling experiments using poly(N-vinyl-pyrrolidone) (PVP) were also carried out to challenge the FRDL models. This work provides both experimental and theoretical input to the development of novel glucose sensors based on PBA-based hydrogel swelling.
Understanding the membrane biophysics of alpha-Synuclein and its role in membrane curvature induction and structural remodeling
(2014-07) Braun, Anthony Robert
Alpha-Synuclein (aSyn) is a 140 amino acid, intrinsically disordered protein that adopts an extended amphipathic alpha-helical structure upon binding the membrane. aSyn is the major proteinaceous component of insoluble fibrillar Lewy bodies, a hallmark of Parkinson's disease (PD). The precise roles of both native and pathological forms of aSyn remain unclear. However, the interaction of aSyn with cellular membranes is now thought to be critical to its native function, and potentially to its role in PD. In vivo studies with overexpressed aSyn shows a stalling of vesicle fusion at the plasma membrane, whereas in vitro studies of small lipid vesicles and aSyn demonstrate an inhibition of vesicle fusion. In addition, numerous biophysical studies have identified potential curvature sensing and curvature inducing characteristics for aSyn, however the mechanism behind these processes is not well understood. The work in this thesis explores the membrane remodeling capacity of aSyn using a combination of computational (molecular dynamics simulation, MD) and experimental (x-ray scattering) methods to try to understand how aSyn interacts with lipid bilayers and potentially gain insight into the native function of the protein. Using a novel set of analysis algorithms we show that binding of aSyn to lipid bilayers thins the membrane and induces a stabilized intrinsic curvature field--whose magnitude matches the curvature of vesicles that aSyn has the highest binding affinity for. We also show that with equal surface density of protein, aSyn vesiculates giant unilamellar vesicles in a lipid-headgroup charge dependent manner. Using an extensive series of MD simulations we demonstrate that aSyn induced membrane remodeling is driven by the protein's binding affinity, partition depth, and induced inter-leaflet order asymmetry. In order to study the more physiologically relevant vesicle bound state, we have also simulated a series of lipid vesicles (with and without bound aSyn). Analysis of these systems required a new algorithm that employed spherical harmonics analysis to extract both structural and mechanical properties from the vesicles. We observe a reduction in bending rigidity and surface tension due to binding of aSyn. This result supports our hypothesis that aSyn stabilized highly curve vesicles--inhibiting vesicle fusion--through a relief of curvature stress (surface tension) inherent to the highly curved membrane.

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