Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

The wormlike chain (WLC) model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1-10 bp scale, which holds particular interest in biological contexts. Here we examine a class of microscopic models which allow for disruption of base pairing (i.e., a `melt' or `kink', generically an `excitation') and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain (MWLC) over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.Comment: 13 pages, 5 figure

Efficient control protocols for an active Ornstein-Uhlenbeck particle

Designing a protocol to efficiently drive a stochastic system is an active field of research. Here we extend such control theory to an active Ornstein-Uhlenbeck particle (AOUP) in a bistable potential, driven by a harmonic trap. We find that protocols designed to minimize the excess work (up to linear-response) perform better than naive protocols with constant velocity for a wide range of protocol durations.Comment: 10 pages, 8 figure

George C. Marshall Space Flight Center Research and Technology Report 2014

Many of NASA's missions would not be possible if it were not for the investments made in research advancements and technology development efforts. The technologies developed at Marshall Space Flight Center contribute to NASA's strategic array of missions through technology development and accomplishments. The scientists, researchers, and technologists of Marshall Space Flight Center who are working these enabling technology efforts are facilitating NASA's ability to fulfill the ambitious goals of innovation, exploration, and discovery

Patient specific ankle-foot orthoses using rapid prototyping

Background Prefabricated orthotic devices are currently designed to fit a range of patients and therefore they do not provide individualized comfort and function. Custom-fit orthoses are superior to prefabricated orthotic devices from both of the above-mentioned standpoints. However, creating a custom-fit orthosis is a laborious and time-intensive manual process performed by skilled orthotists. Besides, adjustments made to both prefabricated and custom-fit orthoses are carried out in a qualitative manner. So both comfort and function can potentially suffer considerably. A computerized technique for fabricating patient-specific orthotic devices has the potential to provide excellent comfort and allow for changes in the standard design to meet the specific needs of each patient. Methods In this paper, 3D laser scanning is combined with rapid prototyping to create patient-specific orthoses. A novel process was engineered to utilize patient-specific surface data of the patient anatomy as a digital input, manipulate the surface data to an optimal form using Computer Aided Design (CAD) software, and then download the digital output from the CAD software to a rapid prototyping machine for fabrication. Results Two AFOs were rapidly prototyped to demonstrate the proposed process. Gait analysis data of a subject wearing the AFOs indicated that the rapid prototyped AFOs performed comparably to the prefabricated polypropylene design. Conclusions The rapidly prototyped orthoses fabricated in this study provided good fit of the subject's anatomy compared to a prefabricated AFO while delivering comparable function (i.e. mechanical effect on the biomechanics of gait). The rapid fabrication capability is of interest because it has potential for decreasing fabrication time and cost especially when a replacement of the orthosis is required

Thermodynamic metrics and optimal paths

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.Comment: 5 page

Toward the development of a field methodology for evaluating discomfort glare from automobile headlamps

The aim of this research was to collect information and experimental data toward the development of a universally acceptable methodology for evaluating discomfort glare from vehicle headlamps. Three separate studies were performed: (a) an international survey of experts in headlighting and vision, soliciting opinions on desirable aspects of such a methodology; (b) a field evaluation of a proposed methodology at a speed of 50 km/hr (30 mph); and (c) a field evaluation at 100 km/hr (60 mph). The findings of this research suggest that the proposed methodology, which is easy to set up and implement, provides relatively reliable and valid measures of discomfort glare, and is time-efficient with respect to data collection.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27111/1/0000103.pd

Nighttime legibility of traffic signs: conditions eliminating the effects of driver age and disability glare

The effects of observer age and environmental glare on nighttime legibility of traffic signs were investigated in two field experiments with the subjects driving or riding in a car towards a sign. Experiment 1 showed that equating older and younger subjects in terms of their low luminance/high contrast visual acuity resulted in elimination of any age effects on legibility. Furthermore, the presence of a glare source with an illuminance of 0.17 or 0.017 lux offset 2[deg] from the sign legend improved legibility distance significantly. The results of Experiment 2 indicated that a glare source with an illuminance of 0.0098 lux had no effect on legibility when presented at an offset angle of 1.5[deg] or 0.6[deg], but it had a significant detrimental effect at an offset angle of 0.2[deg]. The present findings suggest that (1) the usually observed age-related performance decrement on nighttime legibility tasks is the result of visual-acuity deficits, and not shortcomings in information-processing ability; (2) legibility is relatively unaffected by glare, unless the glare angle is very small or glare level very high; and (3) glare sources positioned outside of the fovea might improve nighttime legibility performance under certain conditions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24010/1/0000259.pd

Marshall Space Flight Center Research and Technology Report 2015

The investments in technology development we made in 2015 not only support the Agency's current missions, but they will also enable new missions. Some of these projects will allow us to develop an in-space architecture for human space exploration; Marshall employees are developing and testing cutting-edge propulsion solutions that will propel humans in-space and land them on Mars. Others are working on technologies that could support a deep space habitat, which will be critical to enable humans to live and work in deep space and on other worlds. Still others are maturing technologies that will help new scientific instruments study the outer edge of the universe-instruments that will provide valuable information as we seek to explore the outer planets and search for life

Driver eye fixations and the optimal locations for automobile brake lights

This study evaluated the distributions of driver eye fixations when following other vehicles. The aim was to describe the areas of the forward field of view that are most frequently fixated. Such information is important for selecting optimal locations for automobile brake lights: Brake lights that are closer to eye fixations are likely to result in shorter driver reaction times than brake lights farther away from the fixations. A head-mounted, corneal-reflection device was used to monitor eye fixations. The data were collected during daylight hours in slow-moving urban traffic. A total of 3,600 eye fixations were analyzed for three different lead cars. The results indicate that, under the conditions of this study, the eye fixations tended to concentrate on the rear-window of the lead car and not in the neighborhood of the standard low-mounted brake lights. The results provide a possible behavioral explanation for the accident reductions found with high-mounted brake lights in previous field studies. Furthermore, high-mounted brake lights located at the edges of the vehicle might be even closer to eye fixations than a center-high-mounted brake light.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26203/1/0000283.pd