Genetic sequences are being collected at an ever increasing rate due to rapid cost reductions; however, experimental approaches to determine the structure and function of the protein(s) each gene codes are not keeping pace. Therefore, computational methods to augment experimental structures with comparative (i.e. homology) models using physics-based methods for building residues, loops and domains are needed to thread new sequences onto homologous structures. In addition, even experimental structure determination relies on analogous first principles structure refinement and prediction algorithms to place structural elements that are not defined by the data alone. Computational methods developed to find the global free energy minimum of an amino acid sequence (i.e. the protein folding problem) are increasingly successful, but limitations in accuracy and efficiency remain. Optimization efforts have focused on subsets of systems and environments by utilizing potential energy functions ranging from fixed charged force fields (Fiser, Do, & Sali, 2000; Jacobson et al., 2004), statistical or knowledge based potentials (Das & Baker, 2008) and/or potentials incorporating experimental data (Brunger, 2007; Trabuco, Villa, Mitra, Frank, & Schulten, 2008). Although these methods are widely used, limitations include 1) a target function global minimum that does not correspond to the actual free energy minimum and/or 2) search protocols that are inefficient or not deterministic due to rough energy landscapes characterized by large energy barriers between multiple minima. Our Global Optimization Using Metadynamics and a Polarizable Force Field (GONDOLA) approach tackles the first limitation by incorporating experimental data (i.e. from X-ray crystallography, CryoEM or NMR experiments) into a hybrid target function that also includes information from a polarizable molecular mechanics force field (Lopes, Roux, & MacKerell, 2009; Ponder & Case, 2003). The second limitation is overcome by driving the sampling of conformational space by adding a time-dependent bias to the objective function, which pushes the search toward unexplored regions (Alessandro Barducci, Bonomi, & Parrinello, 2011; Zheng, Chen, & Yang, 2008). The GONDOLA approach incorporates additional efficiency constructs for search space exploration that include Monte Carlo moves and fine grained minimization. Furthermore, the dimensionality of the search is reduced by fixing atomic coordinates of known structural regions while atoms of interest explore new coordinate positions. The overall approach can be used for optimization of side-chains (i.e. set side-chain atoms active while constraining backbone atoms), residues (i.e. side-chain atoms and backbone atoms active), ligand binding pose (i.e. set atoms along binding interface active), protein loops (i.e. set atoms connecting two terminating residues active) or even entire protein domains or complexes. Here we focus on using the GONDOLA general free energy driven optimization strategy to elucidate the structural details of missing protein loops, which are often missing from experimental structures due to conformational heterogeneity and/or limitations in the resolution of the data. We first show that the correlation between experimental data and AMOEBA (i.e. a polarizable force field) structural minima is stronger than that for OPLS-AA (i.e. a fixed charge force field). This suggests that the higher order multipoles and polarization of the AMOEBA force field more accurately represented the true crystalline environment than the simpler OPLS-AA model. Thus, scoring and optimization of loops with AMOEBA is more accurate than with OPLS-AA, albeit at a slightly increased computational cost. Next, missing PDZ domain protein loops and protein loops from a loop decoy data set were optimized for 5 ns using the GONDOLA approach (i.e. under the AMOEBA polarizable force field) as well as a commonly used global optimization procedure (i.e. simulated annealing under the OPLS-AA fixed charge force field). The GONDOLA procedure was shown to provide more accurate structures in terms of both experimental metrics (i.e. lower Rfree values) and structural metrics (i.e. using the MolProbity structure validation tool). In terms of Rfree, only one out of seven simulated annealing results was better than the Gondola global optimization. Similarly, one simulated anneal loop had a better MolProbity score, but none of the simulated annealing loops were better in both categories. On average, GONDOLA achieved an Rfree value 19.48 and simulated annealing saw an average Rfree value of 19.63, and the average MolProbity scores were 1.56 for GONDOLA and 1.75 for simulated annealing. In addition to providing more accurate predictions, GONDOLA was shown to converge much faster than the simulated annealing protocol. Ten separate 5 ns optimizations of the 4 residue loop missing from one of the PDZ domains were conducted. Five were done using GONDOLA and five with the simulated annealing protocol. The fastest four converging results belonged to the GONDOLA approach. Thus, this work demonstrates that GONDOLA is well-suited to refine or predict the coordinates of missing residues and loops because it is both more accurate and converges more rapidly.

It is well established that cathodal transcranial direct current stimulation (tDCS) can decrease the excitability of the primary motor cortex (M1) in humans. Despite the cortical inhibition caused by cathodal tDCS, it remains unknown how this intervention alters unrestrained dynamic reaching movements qualitatively. Accordingly, we designed this study to examine how cathodal tDCS impacts unrestrained dynamic reaching as measured by qualitative kinematic features and electromyography (EMG). Ten young, healthy adult subjects were recruited to participate in a two day protocol involving repetitively reaching to two different targets (large and small) both before and following cathodal tDCS applied over the contralateral M1 during one session and before and following sham tDCS over the same brain region during another session. We discovered that cathodal tDCS was not able to alter the kinematic features of reaching in these subjects but did degrade the EMG performance, specifically by increasing the amount of co-contraction between muscle pairs. Because co-contraction is an indicator of relatively unskilled performance, these results seem to indicate that cathodal tDCS of M1 preferentially disrupts the learning or execution of highly coordinated muscle firing patterns during dynamic reaching. This work adds to the growing body of knowledge about how tDCS applied over M1 affects our movements. Moreover, it leads us to believe that tDCS can be utilized to assist in rehabilitation of patient populations who suffer from neurological dysfunctions but EMG assessments may need to be included in order to more effectively assess the patient performance.

The cause and best treatment option for mechanical low back pain due to disc degeneration remains unsolved, despite `spinal fusion' being the gold standard of surgical treatment, post conservative care, for a very long time. However, the potential drawbacks of spinal fusion and the ongoing evolution in the understanding of normal and symptomatic spine biomechanics, biology and mechanobiology in conjunction with the advancements in material sciences, and tissue engineering has led to a change in the clinical perspective towards treatment methodologies for spinal disorders. Clinically, a gradual shift in philosophy is being observed from a `one size fits all', i.e. spinal fusion for all patients with symptomatic low back pain to a `customized approach', i.e. patient and indication specific treatment modalities for spine care. This philosophy has laid the ground for concepts of `motion preservation' and `dynamic stabilization', the former being an established treatment modality in orthopedics for a long time. The aim of the current study is to perform a comprehensive scientific investigation to understand, evaluate and establish the in vitro biomechanical characteristics and performance of indication specific treatment modalities incorporating the concept of Posterolateral Disc Arthroplasty and Posterior Dynamic Stabilization for the treatment of symptomatic mechanical back pain. The results of this comprehensive study may help the clinicians to make an informed decision while selecting and designing a treating modality for their patients. To this end, the current thesis was undertaken to study the biomechanics of indication specific treatment modalities like motion preservation and dynamic stabilization with a goal to guide clinical and product development decision making. Through the comprehensive biomechanical investigation conducted in the current thesis we were able to theoretically prove the importance of a customized approach towards the treatment of spine care. Also, the most important conclusion of the biomechanical investigation was the fact that Range of Motion results alone are not sufficient to draw significant conclusions. It is imperative that in depth analysis of the quality of motion through the determination of instantaneous center of rotation is extremely important. Previous studies have shown only a single center of rotation between the extremes of motion which is also insufficient as the end points do not determine the path taken to reach the endpoints. This in depth analysis is also important for biomedical engineers to design and develop physiologically viable implants that will mimic the performance of the physiologic spine. Clinical studies are extremely important as a next step towards validating this customized approach towards spine care.

The delivery of nutrients to the surface of marine algae can be controlled by the local hydrodynamic regime: in higher flow velocities, the Diffusive Boundary Layer (DBL) at the uptake surface is thinner, which can increase the flux of dissolved chemicals to the algal surface. If the primary productivity of an alga is controlled by the availability of a dissolved chemical, increased water flow should result in greater primary productivity due to increased chemical flux. To test the hypothesis that increased water flow will increase Photosystem II kinematics (PSII) in the green alga Caulerpa we used a Diving Pam Fluorometer to measure the maximum relative electron transport rate (Pmax), Saturation Irradiance (Ik), Non-photochemical quenching (NPQ), the light limited slope of photosynthesis vs. irradiance curve (α) and photo-chemical quenching (qP) and compared these measured values among treatments of varying flow speeds in a portable laboratory flume. We also measured the influence of water flow on values of Pmax, Ik, α , qP and NPQ in the field. Results showed that in C. racemosa collected from Tampa bay, and tested in a laboratory flume, values of Pmax and Ik were positively correlated to increase water flow, possibly indicating mass-transfer limitation. C. mexicana, collected from the Florida Keys, showed a decrease in values of Pmax, and Ik with increasing water velocity in flume experiments, indicating that the increased flow was resulting in physiological stress. This result was supported with field measurements for C. sertularioides, which showed a negative correlation between Pmax and flow velocity and Ik and flow velocity.

The ability of an organism to modulate its feeding behavior is an important focus of feeding ecology studies. Modulation is the ability to distinctly and consistently alter a behavior to accommodate different stimuli. The goal of this study was to examine the ability of the nurse shark Ginglymostoma cirratum to modulate its food capture behavior with different sizes and types of food items. This was carried out through kinematic and electromyographic analysis. Eight sub-adult specimens of G. cirratum were filmed feeding on two different food types (squid and fish) and sizes (gape size and larger than gape size). Filming consisted of high-speed videography utilizing a low-light digital video system. Kinematic variables related to lower jaw movement, mouth width, and head angle were measured from video footage. Up to twelve muscles in each of six specimens were implanted with bipolar electrodes to measure the onset and duration of motor activity. There were no significant differences between food sizes and any of the kinematic variables. Only two muscles showed significant differences in onset time based on food size. In regards to food types, squid bites were significantly faster than fish bites, but when examined proportionately to bite duration only the time to jaw closure remained significantly different. The motor pattern of G. cirratum demonstrates an anterior to posterior sequence, which corresponds to the anterior to posterior kinematic sequence. Little cranial elevation is present during feeding sequences and is not thought to contribute significantly to feeding. Ginglymostoma cirratum is a stereotyped, inertial suction feeder. There is little evidence that there is modulation in feeding behavior based on food size or food type. If modulation does exist in the feeding behavior, it is more likely to occur after prey capture while the prey is being processed and manipulated prior to transport. Initial observations suggested that a novel behavior termed 'spit-suck manipulation' is utilized for larger prey items.

Current clinical practice regarding upper body prosthesis prescription and training is lacking a standarized, quantitative method to evaluate the impact of the prosthetic device. The amputee care team typically uses prior experiences to provide prescription and training customized for each individual. As a result, it is quite challenging to determine the right type and fit of a prosthesis and provide appropriate training to properly utilize it early in the process. It is also very difficult to anticipate expected and undesired compensatory motions due to reduced degrees of freedom of a prosthesis user. In an effort to address this, a tool was developed to predict and visualize the expected upper limb movements from a prescribed prosthesis and its suitability to the needs of the amputee. It is expected to help clinicians make decisions such as choosing between a body-powered or a myoelectric prosthesis, and whether to include a wrist joint. To generate the motions, a robotics-based model of the upper limbs and torso was created and a weighted least-norm (WLN) inverse kinematics algorithm was used. The WLN assigns a penalty (i.e. the weight) on each joint to create a priority between redundant joints. As a result, certain joints will contribute more to the total motion. Two main criteria were hypothesized to dictate the human motion. The first one was a joint prioritization criterion using a static weighting matrix. Since different joints can be used to move the hand in the same direction, joint priority will select between equivalent joints. The second criterion was to select a range of motion (ROM) for each joint specifically for a task. The assumption was that if the joints' ROM is limited, then all the unnatural postures that still satisfy the task will be excluded from the available solutions solutions. Three sets of static joint prioritization weights were investigated: a set of optimized weights specifically for each task, a general set of static weights optimized for all tasks, and a set of joint absolute average velocity-based weights. Additionally, task joint limits were applied both independently and in conjunction with the static weights to assess the simulated motions they can produce. Using a generalized weighted inverse control scheme to resolve for redundancy, a human-like posture for each specific individual was created. Motion capture (MoCap) data were utilized to generate the weighting matrices required to resolve the kinematic redundancy of the upper limbs. Fourteen able-bodied individuals and eight prosthesis users with a transradial amputation on the left side participated in MoCap sessions. They performed ROM and activities of daily living (ADL) tasks. The methods proposed here incorporate patient's anthropometrics, such as height, limb lengths, and degree of amputation, to create an upper body kinematic model. The model has 23 degrees-of-freedom (DoFs) to reflect a human upper body and it can be adjusted to reflect levels of amputation. The weighting factors resulted from this process showed how joints are prioritized during each task. The physical meaning of the weighting factors is to demonstrate which joints contribute more to the task. Since the motion is distributed differently between able-bodied individuals and prosthesis users, the weighting factors will shift accordingly. This shift highlights the compensatory motion that exist on prosthesis users. The results show that using a set of optimized joint prioritization weights for each specific task gave the least RMS error compared to common optimized weights. The velocity-based weights had a slightly higher RMS error than the task optimized weights but it was not statistically significant. The biggest benefit of that weight set is their simplicity to implement compared to the optimized weights. Another benefit of the velocity based weights is that they can explicitly show how mobile each joint is during a task and they can be used alongside the ROM to identify compensatory motion. The inclusion of task joint limits gave lower RMS error when the joint movements were similar across subjects and therefore the ROM of each joint for the task could be established more accurately. When the joint movements were too different among participants, the inclusion of task limits was detrimental to the simulation. Therefore, the static set of task specific optimized weights was found to be the most accurate and robust method. However, the velocity-based weights method was simpler with similar accuracy. The methods presented here were integrated in a previously developed graphical user interface (GUI) to allow the clinician to input the data of the prospective prosthesis users. The simulated motions can be presented as an animation that performs the requested task. Ultimately, the final animation can be used as a proposed kinematic strategy that a prosthesis user and a clinician can refer to, during the rehabilitation process as a guideline. This work has the potential to impact current prosthesis prescription and training by providing personalized proposed motions for a task.

The objective of the dissertation is to develop and describe kinematic models (Pseudo-Rigid-Body Models) for approximating large-deflection of spatial (3D) cantilever beams that undergo multiple bending motions thru end-moment loading. Those models enable efficient design of compliant mechanisms, because they simply and accurately represent the bending and stiffness of compliant beams. To accomplish this goal, the approach can be divided into three stages: development of the governing equations of a flexible cantilever beam, development of a PRBM for axisymmetric cantilever beams and the development of spatial PRBMs for rectangular cross-section beam with multiple end moments. The governing equations of a cantilever beam that undergoes large deflection due to force and moment loading, contains the curvature, location and rotation of the beam. The results where validated with Ansys, which showed to have a Pearson's correlation factor higher than 0.91. The resulting deflections, curvatures and angles were used to develop a spatial pseudo-rigid-body model for the cantilever beam. The spatial pseudo-rigid-body model consists of two links connected thru a spherical joint. For an axisymmetric beam, the PRB parameters are comparable with existing planar PRBMs. For the rectangular PRBM, the parameters depend on the aspect ratio of the beam (the ratio of the beam width over the height of the cross-section). Tables with the parameters as a function of the aspect ratio are included in this work.

Oil spills in the marine environment can threaten vulnerable ecosystems that support ecologically and economically significant organisms, such as the eastern oyster (Crassostrea virginica), in coastal habitats. The use of chemical dispersant (Corexit 9500) was applied as a cleanup effort in response to the Deepwater Horizon blowout to minimize crude oil slicks, but also resulted in increased concentrations of polycyclic aromatic hydrocarbons in the water column. The effects of increased soluble fractions of crude oil and dispersant components may be harmful to marine organisms. This study aimed to investigate possible sublethal impacts to the eastern oyster at multiple life history stages in order to understand potential implications on performance at an organismal, population, and ecosystem levels. Specifically, this study addressed 1) veliger swimming, 2) pediveliger settlement rates, 3) pollutant induced larval inactivity and 4) adult clearance rates after acute exposures to relevant concentrations (10 – 100 µL L-1) of water accommodated fractions of crude oil (WAF) and with a combination of chemical dispersant (CEWAF). No significant differences were observed in any tested swimming kinematics between controls and WAF or CEWAF treatments after 24 hour exposures for early staged veligers at concentrations up to 100 µL L-1 WAF and CEWAF. However, settlements rates of competent pediveligers were significant decreased compared to control (52.1 % s.d. 1.66) rates at concentrations of 50 µL L-1 WAF (30.9% s.d. 6.16) and 10 (41.2 % s.d. 0.857) and 50 (22.0% s.d. 1.23) µL L-1 CEWAF. Later staged larvae also showed increased vulnerability to oil pollution given that a higher percentage of organisms were inactive (48.3% s.d. 4.80) compared to early staged larvae (12.7% s.d. 7.68 ) after initial exposure at 50 µL L-1 CEWAF. Based on this result, we assumed effects of oil pollution were not manifested until the later larval life history stage evident by metamorphosis failure during the complex settlement transformation that results in reduced spat and eventually reduced adult oysters. Adult oysters were also exposed to increasing concentrations of WAF and CEWAF for 24 hours and feeding experiments were conducted in both clean seawater and the same oiled seawater conditions as their initial exposure. Oysters fed in oiled seawater had decreased clearance rates, but oysters fed in clean water had increased clearance rates, suggesting feeding efficiency can be returned to control rates when moved to the presence of clean water. However, our long term study conducted in clean seawater suggested of the oysters exposed to crude oil only (9.31 L h-1 g-1 s.d. 2.04) are able to return to clearance rates comparable to controls (7.69 L h-1 g-1 s.d. 1.89) after the 33 day time period but oysters exposed to crude oil with a combination of chemical dispersant (2.12 L h-1 g-1 s.d. 1.08) were not. Decreased feeding efficiency can have negative impacts on water quality in estuarine ecosystems that support productive habitats. Understanding the impacts of crude oil, and crude oil with a combination of chemical dispersant on ecologically significant organisms can aid in future oil spill response decisions in order to minimize environmental impacts.

Improvement of prostheses requires knowledge of how the body adapts. A transradial prosthesis without a dynamic wrist component may cause awkward compensatory motion leading to fatigue, injury or rejection of the prosthesis. This work analyzed the movements of shoulder, elbow and torso during four tasks: drinking from a cup, opening a door, lifting a box and turning a steering wheel. The main purpose of this study was to determine if using a basic transradial prosthesis that lacks motion of the forearm and wrist would cause significant compensatory motion of the shoulder, elbow and torso during the tasks. The second purpose of the study was to determine if the location of added mass would affect compensatory movements during these tasks. A group of able-bodied participants were asked to complete the tasks, without and with a brace, simulating a basic transradial prosthesis to determine if bracing is an appropriate way to study prosthetic use. Transradial prosthesis wearers also completed the tasks without and with added mass at the elbow or at the wrist to determine if distribution of mass has an effect on the motions. Using a motion capture system movements of the shoulder, elbow and torso were analyzed. For the bilateral tasks, the degree of asymmetry (DoA) was calculated for each subject. Statistical analysis was completed within subject comparing the mass interventions and between subjects comparing the control, braced and prosthesis wearing groups. While opening a door and lifting a box, prosthesis users compensated predominantly by bending the torso sideways toward affected side. During the steering wheel task, amputees used more elbow flexion to accommodate for the lack of forearm rotation. While drinking from a cup, compensation occurred by bending the cervical spine, although this was not measured. Adding mass increased the joint forces and moments during the box lift. This research can be used for transradial prosthesis design improvements as well as improving methods of prosthesis fitting and therapeutic training by providing quantitative data of compensatory motion. The data from this study is being used to develop a model for an upper limb prosthesis.

Lower back injury remains the most important injury problem in professional cricket with lumbar stress fractures in fast bowlers accounting for the most lost playing time. Previous research has associated workload, paraspinal muscle asymmetry and technique factors with lower back injury in fast bowlers, however, preventative strategies such as workload directives and coaching guidelines have not reduced the incidence and prevalence of these injuries. Recent developments in medical imaging technology have improved diagnosis of pathologies such as lumbar posterior bony element (partes interarticulares and pedicles) stress fractures and intervertebral disc degeneration in athletes whilst also allowing quantification of other, potentially associated factors such as paraspinal muscle asymmetry. However, there is very little published research regarding the use of modalities such as magnetic resonance imaging (MRI) in the identification and prognosis of these types of injuries in fast bowlers. Similarly, advances in three-dimensional (3D) motion analysis has aided technique evaluation in a variety of sports, however, little remains known about the pathomechanics of lower back injury in fast bowling. Therefore, the aim of this doctoral research was to investigate relationships between lower back injury and; the MRI appearance of the lumbar posterior bony elements and intervertebral discs, MRI-derived lumbar muscle morphology and the three-dimensional (3D) trunk kinematics of professional fast bowlers in cricket. This was examined in a series of five studies. The first study undertaken was an investigation of the MRI appearance of the lumbar spines of 36 asymptomatic professional fast bowlers and 17 active controls. / It was identified that the fast bowlers had a high prevalence of multi-level, predominantly non-dominant side, acute and chronic stress changes in the posterior bony elements of the lumbar spine. Multiple level disc degeneration was also more advanced in the fast bowlers compared with the control - iv - participants. However, disc degeneration appeared not to be associated with lumbar stress injury. The second study investigated the reliability and accuracy of using MRI to determine the FCSA of the lumbar paraspinal muscles (psoas, quadratus lumborum, erector spinae and multifidus). The novel methodology developed in this study was determined to be both valid and highly reliable. In the third study, this technique was then used to describe the functional crosssectional area (FCSA) morphology of the paraspinal muscles in a group of 46 professional fast bowlers and the 17 control participants scanned in the first study. It reinforced that there was a higher prevalence of lumbar muscle asymmetry in the fast bowler group. Paraspinal muscle asymmetry, consistent with hypertrophy of the dominant side muscle, was most prevalent in the quadratus lumborum of fast bowlers, and was also evident in the lumbar multifidus in both groups of subjects. The aims of the fourth study of the thesis were to quantify the proportion of lower trunk motion utilised during the delivery stride of fast bowling and to investigate the relationship between the most accepted fast bowling action classification system and potentially injurious kinematics of the lower trunk. 3D kinematic data were collected from 50 male professional fast bowlers during fast bowling trials and these were normalised to each bowler’s standing lower trunk range of motion. A high percentage of the fast bowlers used a mixed bowling action attributable to having shoulder counter-rotation greater than 30°. / The greatest proportion of lower trunk extension (26%), contralateral side-flexion (129%) and ipsilateral rotation (79%) was utilised during the front foot contact phase of the fast bowling delivery stride. There was no significant difference between mixed and non-mixed bowlers in the range of motion used during fast bowling. It was concluded that fast bowling action characteristics currently used to identify potentially dangerous action types may not be directly related to the likely pathomechanics of contralateral side lumbar stress injuries. It is proposed that coupled lower trunk extension, ipsilateral rotation in addition to extreme contralateral side-flexion, during the early part of the front foot contact phase of the bowling action may be an important mechanical factor in the aetiology of this type of injury. In the final study, a combination of the factors described in earlier studies i.e. the lumbar MRI appearance of the partes interarticulares and intervertebral discs, paraspinal muscle asymmetry and selected bowling action and delivery stride trunk kinematic variables, were examined. Therefore, the aim of this study was to examine the relationship between fast bowler lower back injury occurrence (one season either side of testing) and the aforementioned factors that were measured when participants were asymptomatic and bowling competitively. The results of this study indicated that a high percentage of professional fast bowlers in the United Kingdom continue to sustain a high number of acute lumbar stress injuries and these result a significant amount of lost playing and training time. Fast bowling action classification and lower trunk kinematic variables were not conclusively linked to acute lumbar stress injury occurrence. However, further investigation of the effect of coupled lower trunk motion on nondominant side lumbar bone stress is indicated. / The presence of acute MRI stress changes (particularly acute stress changes such as bone marrow oedema, periostitis and acute fracture lines) in the non-dominant side lumbar posterior elements seem to have a relationship with acute stress injury occurrence. Regular lumbar MRI scanning may assist in identifying early acute stress changes prior to the onset of symptoms. Intervertebral disc degeneration was less prevalent amongst professional fast bowlers who suffered acute stress injuries than those who had no significant lower back injury. Finally, although fast bowlers have a high prevalence of quadratus lumborum and lumbar multifidus asymmetry (larger on the dominant side), there was no observed relationship between acute lumbar stress injury and these findings.