A Molecular-scale Programmable Stochastic Process Based On Resonance Energy Transfer Networks: Modeling And Applications

While molecular and cellular processes are often modeled as stochastic processes, such as Brownian motion, chemical reaction networks and gene regulatory networks, there are few attempts to program a molecular-scale process to physically implement stochastic processes. DNA has been used as a substrate for programming molecular interactions, but its applications are restricted to deterministic functions and unfavorable properties such as slow processing, thermal annealing, aqueous solvents and difficult readout limit them to proof-of-concept purposes. To date, whether there exists a molecular process that can be programmed to implement stochastic processes for practical applications remains unknown.

In this dissertation, a fully specified Resonance Energy Transfer (RET) network between chromophores is accurately fabricated via DNA self-assembly, and the exciton dynamics in the RET network physically implement a stochastic process, specifically a continuous-time Markov chain (CTMC), which has a direct mapping to the physical geometry of the chromophore network. Excited by a light source, a RET network generates random samples in the temporal domain in the form of fluorescence photons which can be detected by a photon detector. The intrinsic sampling distribution of a RET network is derived as a phase-type distribution configured by its CTMC model. The conclusion is that the exciton dynamics in a RET network implement a general and important class of stochastic processes that can be directly and accurately programmed and used for practical applications of photonics and optoelectronics. Different approaches to using RET networks exist with vast potential applications. As an entropy source that can directly generate samples from virtually arbitrary distributions, RET networks can benefit applications that rely on generating random samples such as 1) fluorescent taggants and 2) stochastic computing.

By using RET networks between chromophores to implement fluorescent taggants with temporally coded signatures, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the taggant detection process becomes highly efficient, and the Maximum Likelihood Estimation (MLE) based taggant identification guarantees high accuracy even with only a few hundred detected photons.

Meanwhile, RET-based sampling units (RSU) can be constructed to accelerate probabilistic algorithms for wide applications in machine learning and data analytics. Because probabilistic algorithms often rely on iteratively sampling from parameterized distributions, they can be inefficient in practice on the deterministic hardware traditional computers use, especially for high-dimensional and complex problems. As an efficient universal sampling unit, the proposed RSU can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator to bring substantial speedups and power savings.

Virtual reality rehabilitation as a treatment approach for older women with mixed urinary incontinence : a feasibility study

Background Motivated patients are more likely to adhere to treatment resulting in better outcomes. Virtual reality rehabilitation (VRR) is a treatment approach that includes video gaming to enhance motivation and functional training. Aims The study objectives were (1) to evaluate the feasibility of using a combination of pelvic floor muscles (PFM) exercises and VRR (PFM/VRR) to treat mixed urinary incontinence (MUI) in older women, (2) to evaluate the effectiveness of the PFM/VRR program on MUI symptoms, quality of life (QoL), and (3) gather quantitative information regarding patient satisfaction with this new combined training program. Methods Women 65 years and older with at least 2 weekly episodes of MUI were recruited. Participants were evaluated two times before and one time after a 12-week PFM/VRR training program. Feasibility was defined as the participants' rate of participation in and completion of both the PFM/VRR training program and the home exercise. Effectiveness was evaluated through a bladder diary, pad test, symptom and QoL questionnaire, and participant's satisfaction through a questionnaire. Results Twenty-four women (70.5 ± 3.6 years) participated. The participants complied with the study demands in terms of attendance at the weekly treatment sessions (91%), adherence to home exercise (92%) and completion of the three evaluations (96%). Post-intervention, the frequency and quantity of urine leakage decreased and patientreported symptoms and QoL improved significantly. Most participants were very satisfied with treatment (91%). Conclusion A combined PFM/VRR program is an acceptable, efficient, and satisfying functional treatment for older women with MUI and should be explore through further RCTs.

Virtual Reality as a tool to Assist Learning in Aerospace Assembly

This study examines whether virtual reality (VR) is more superior to paper-based instructions in increasing the speed at which individuals learn a new assembly task. Specifically, the work seeks to quantify any learning benefits when individuals have been given the opportunity and compares the performance of two groups using virtual and hardcopy media types to pre-learn the task. A build experiment based on multiple builds of an aircraft panel showed that a group of people who pre-learned the assembly task using a VR environment completed their builds faster (average build time 29.5% lower). The VR group also made fewer references to instructional materials (average number of references 38% lower) and made fewer errors than a group using more traditional, hard copy instructions. These outcomes were more pronounced during build one with differences in build time and number of references showing limited statistical differences.

Navigating 3d Scatter Plots in Immersive Virtual Reality

Thesis (Master's)--University of Washington, 2016-01

Competency Based Assessment Using Virtual Reality (VERT): Is It a Realistic Possibility ?

The education of the radiography profession is based within higher education establishments, yet a critical part of all radiography programmes is the clinical component where students learn the practical skills of the profession. Assessments therefore not only have to assess a student’s knowledge, but also their clinical competence and core skills in line with both Health and Care Professions Council and the Society and College of Radiographers requirements. This timely thesis examines the possibility of using the Virtual Environment for RadioTherapy (VERT) as an assessment tool to evaluate a student’s competence so giving the advantage of a standard assessment and relieving time pressures in the clinical department. A mixed methods approach was taken which can be described as a Quantitative Qualitative design with the emphasis being on the Quantitative element; a so called QUAN  qual design. The quantitative evaluation compared two simulations, one in the virtual reality environment and another in the department using a real treatment machine. Students were asked to perform two electron setups in each simulation; the order being randomly decided and so the study would be described as a randomised cross-over design. Following this, qualitative data was collected in student focus groups to explore student perspectives in more depth. Findings indicated that the performance between the two simulators was significantly different, p < 0∙001; the virtual simulation scoring significantly lower than the hospital based simulation overall and in virtually all parameters being assessed. Thematic analysis of the qualitative data supported this finding and identified 4 main themes; equipment use, a lack of reality, learning opportunities and assessment of competence. One other sub-theme identified for reality was that of the environment and senses.

Three dimensional modeling of contaminants transportation (oil spill) in Caspian Sea

Nowadays, Caspian Sea is in focus of more attentions than past because of its individualistic as the biggest lake in the world and the existing of very large oil and gas resources within it. Very large scale of oil pollution caused by development of oil exploration and excavation activities not only make problem for coastal facilities but also make severe damage on environment. In the first stage of this research, the location and quality of oil resources in offshore and onshore have been determined and then affected depletion factors on oil spill such as evaporation, emulsification, dissolution, sedimentation and so on have been studied. In second stage, sea hydrodynamics model is offered and tested by determination of governing hydrodynamic equations on sea currents and on pollution transportation in sea surface and by finding out main parameters in these equations such as Coriolis, bottom friction, wind and etc. this model has been calculated by using cell vertex finite volume method in an unstructured mesh domain. According to checked model; sea currents of Caspian Sea in different seasons of the year have been determined and in final stage different scenarios of oil spill movement in Caspian sea on various conditions have been investigated by modeling of three dimensional oil spill movement on surface (affected by sea currents) and on depth (affected by buoyancy, drag and gravity forces) by applying main above mentioned depletion factors.

Healthcare Network Modeling and Analysis

Part 20: Health and Care Networks

Modeling and analysis of thermoelectric energy conversion efficiency in nanostructures.

116 p.

3D Block Modeling and Reserve Estimation of a Garnet Deposit

The purpose of this project is to develop a three-dimensional block model for a garnet deposit in the Alder Gulch, Madison County, Montana. Garnets occur in pre-Cambrian metamorphic Red Wash gneiss and similar rocks in the vicinity. This project seeks to model the percentage of garnet in a deposit called the Section 25 deposit using the Surpac software. Data available for this work are drillhole, trench and grab sample data obtained from previous exploration of the deposit. The creation of the block model involves validating the data, creating composites of assayed garnet percentages and conducting basic statistics on composites using Surpac statistical tools. Variogram analysis will be conducted on composites to quantify the continuity of the garnet mineralization. A three-dimensional block model will be created and filled with estimates of garnet percentage using different methods of reserve estimation and the results compared.

One-dimensional Silicon And Germanium Nanostructures With No Carbon Analogues.

In this work we report new silicon and germanium tubular nanostructures with no corresponding stable carbon analogues. The electronic and mechanical properties of these new tubes were investigated through ab initio methods. Our results show that these structures have lower energy than their corresponding nanoribbon structures and are stable up to high temperatures (500 and 1000 K, for silicon and germanium tubes, respectively). Both tubes are semiconducting with small indirect band gaps, which can be significantly altered by both compressive and tensile strains. Large bandgap variations of almost 50% were observed for strain rates as small as 3%, suggesting their possible applications in sensor devices. They also present high Young's modulus values (0.25 and 0.15 TPa, respectively). TEM images were simulated to help in the identification of these new structures.

Two-dimensional Ultrasound And Ultrasound Elastography Imaging Of Trigger Points In Women With Myofascial Pain Syndrome Treated By Acupuncture And Electroacupuncture: A Double-blinded Randomized Controlled Pilot Study.

Chronic pain has been often associated with myofascial pain syndrome (MPS), which is determined by myofascial trigger points (MTrP). New features have been tested for MTrP diagnosis. The aim of this study was to evaluate two-dimensional ultrasonography (2D US) and ultrasound elastography (UE) images and elastograms of upper trapezius MTrP during electroacupuncture (EA) and acupuncture (AC) treatment. 24 women participated, aged between 20 and 40 years (M ± SD = 27.33 ± 5.05) with a body mass index ranging from 18.03 to 27.59 kg/m2 (22.59 ± 3.11), a regular menstrual cycle, at least one active MTrP at both right (RTPz) and left trapezius (LTPz) and local or referred pain for up to six months. Subjects were randomized into EA and AC treatment groups and the control sham AC (SHAM) group. Intensity of pain was assessed by visual analogue scale; MTrP mean area and strain ratio (SR) by 2D US and UE. A significant decrease of intensity in general, RTPz, and LTPz pain was observed in the EA group (p = 0.027; p < 0.001; p = 0.005, respectively) and in general pain in the AC group (p < 0.001). Decreased MTrP area in RTPz and LTPz were observed in AC (p < 0.001) and EA groups (RTPz, p = 0.003; LTPz, p = 0.005). Post-treatment SR in RTPz and LTPz was lower than pre-treatment in both treatment groups. 2D US and UE effectively characterized MTrP and surrounding tissue, pointing to the possibility of objective confirmation of subjective EA and AC treatment effects.

Structural and chemical basis for anticancer activity of a series of 'beta'-tubulin ligands: molecular modeling and 3D QSAR studies

An important approach to cancer therapy is the design of small molecule modulators that interfere with microtubule dynamics through their specific binding to the ²-subunit of tubulin. In the present work, comparative molecular field analysis (CoMFA) studies were conducted on a series of discodermolide analogs with antimitotic properties. Significant correlation coefficients were obtained (CoMFA(i), q² =0.68, r²=0.94; CoMFA(ii), q² = 0.63, r²= 0.91), indicating the good internal and external consistency of the models generated using two independent structural alignment strategies. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the 3D contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of discodermolide analogs, and should be useful for the design of new specific ²-tubulin modulators with potent anticancer activity.

Modeling and analysis of laminate composite plates with embedded active-passive piezoelectric networks

The objective of this work is to present the finite element modeling of laminate composite plates with embedded piezoelectric patches or layers that are then connected to active-passive resonant shunt circuits, composed of resistance, inductance and voltage source. Applications to passive vibration control and active control authority enhancement are also presented and discussed. The finite element model is based on an equivalent single layer theory combined with a third-order shear deformation theory. A stress-voltage electromechanical model is considered for the piezoelectric materials fully coupled to the electrical circuits. To this end, the electrical circuit equations are also included in the variational formulation. Hence, conservation of charge and full electromechanical coupling are guaranteed. The formulation results in a coupled finite element model with mechanical (displacements) and electrical (charges at electrodes) degrees of freedom. For a Graphite-Epoxy (Carbon-Fibre Reinforced) laminate composite plate, a parametric analysis is performed to evaluate optimal locations along the plate plane (xy) and thickness (z) that maximize the effective modal electromechanical coupling coefficient. Then, the passive vibration control performance is evaluated for a network of optimally located shunted piezoelectric patches embedded in the plate, through the design of resistance and inductance values of each circuit, to reduce the vibration amplitude of the first four vibration modes. A vibration amplitude reduction of at least 10 dB for all vibration modes was observed. Then, an analysis of the control authority enhancement due to the resonant shunt circuit, when the piezoelectric patches are used as actuators, is performed. It is shown that the control authority can indeed be improved near a selected resonance even with multiple pairs of piezoelectric patches and active-passive circuits acting simultaneously. (C) 2010 Elsevier Ltd. All rights reserved.

Modeling and Analysis of Piezoelectric Energy Harvesting From Aeroelastic Vibrations Using the Doublet-Lattice Method

Multifunctional structures are pointed out as an important technology for the design of aircraft with volume, mass, and energy source limitations such as unmanned air vehicles (UAVs) and micro air vehicles (MAVs). In addition to its primary function of bearing aerodynamic loads, the wing/spar structure of an UAV or a MAV with embedded piezoceramics can provide an extra electrical energy source based on the concept of vibration energy harvesting to power small and wireless electronic components. Aeroelastic vibrations of a lifting surface can be converted into electricity using piezoelectric transduction. In this paper, frequency-domain piezoaeroelastic modeling and analysis of a canti-levered platelike wing with embedded piezoceramics is presented for energy harvesting. The electromechanical finite-element plate model is based on the thin-plate (Kirchhoff) assumptions while the unsteady aerodynamic model uses the doublet-lattice method. The electromechanical and aerodynamic models are combined to obtain the piezoaeroelastic equations, which are solved using a p-k scheme that accounts for the electromechanical coupling. The evolution of the aerodynamic damping and the frequency of each mode are obtained with changing airflow speed for a given electrical circuit. Expressions for piezoaeroelastically coupled frequency response functions (voltage, current, and electrical power as well the vibratory motion) are also defined by combining flow excitation with harmonic base excitation. Hence, piezoaeroelastic evolution can be investigated in frequency domain for different airflow speeds and electrical boundary conditions. [DOI:10.1115/1.4002785]

Piezoaeroelastic Modeling and Analysis of a Generator Wing with Continuous and Segmented Electrodes

Unmanned air vehicles (UAVs) and micro air vehicles (MAVs) constitute unique application platforms for vibration-based energy harvesting. Generating usable electrical energy during their mission has the important practical value of providing an additional energy source to run small electronic components. Electrical energy can be harvested from aeroelastic vibrations of lifting surfaces of UAVs and MAVs as they tend to have relatively flexible wings compared to their larger counterparts. In this work, an electromechanically coupled finite element model is combined with an unsteady aerodynamic model to develop a piezoaeroelastic model for airflow excitation of cantilevered plates representing wing-like structures. The electrical power output and the displacement of the wing tip are investigated for several airflow speeds and two different electrode configurations (continuous and segmented). Cancelation of electrical output occurs for typical coupled bending-torsion aeroelastic modes of a cantilevered generator wing when continuous electrodes are used. Torsional motions of the coupled modes become relatively significant when segmented electrodes are used, improving the broadband performance and altering the flutter speed. Although the focus is placed on the electrical power that can be harvested for a given airflow speed, shunt damping effect of piezoelectric power generation is also investigated for both electrode configurations.