Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal motion of the DNA and other fluctuations of the cellular environment. We present single-molecule measurements of DNA loop formation and breakdown when an artificial fluctuating force, applied to mimic a fluctuating cellular environment, is imposed on the DNA. We show that loop formation is greatly enhanced in the presence of noise of only a fraction of $k_B T$, yet find that hypothetical regulatory schemes that employ mechanical tension in the DNA--as a sensitive switch to control transcription--can be surprisingly robust due to a fortuitous cancellation of noise effects

Nonequilibrium Ablation of Phenolic Impregnated Carbon Ablator

In previous work, an equilibrium ablation and thermal response model for Phenolic Impregnated Carbon Ablator was developed. In general, over a wide range of test conditions, model predictions compared well with arcjet data for surface recession, surface temperature, in-depth temperature at multiple thermocouples, and char depth. In this work, additional arcjet tests were conducted at stagnation conditions down to 40 W/sq cm and 1.6 kPa. The new data suggest that nonequilibrium effects become important for ablation predictions at heat flux or pressure below about 80 W/sq cm or 10 kPa, respectively. Modifications to the ablation model to account for nonequilibrium effects are investigated. Predictions of the equilibrium and nonequilibrium models are compared with the arcjet data

Arcjet Testing of Woven Carbon Cloth for Use on Adaptive Deployable Entry Placement Technology

This paper describes arcjet testing and analysis that has successfully demonstrated the viability of three dimensional woven carbon cloth for dual use in the Adaptive Deployable Entry Placement Technology (ADEPT). ADEPT is an umbrella-like entry system that is folded for stowage in the launch vehicle s shroud and deployed in space prior to reaching the atmospheric interface. A key feature of the ADEPT concept is its lower ballistic coefficient for delivery of a given payload than those for conventional, rigid body entry systems. The benefits that accrue from the lower ballistic coefficient include factor of ten reductions of deceleration forces and entry heating. The former enables consideration of new classes of scientific instruments for solar system exploration while the latter enables the design of a more efficient thermal protection system. The carbon cloth now base lined for ADEPT has a dual use in that it serves as ADEPT s thermal protection system and as the "skin" that transfers aerodynamic deceleration loads to its umbrella-like substructure. The arcjet testing described in this paper was conducted for some of the higher heating conditions for a future Venus mission using the ADEPT concept, thereby showing that the carbon cloth can perform in a relevant entry environment. The ADEPT project considered the carbon cloth to be mission enabling and was carrying it as a major risk during Fiscal Year 2012. The testing and analysis reported here played a major role in retiring that risk and is highly significant to the success and possible adoption of ADEPT for future NASA missions. Finally, this paper also describes a preliminary engineering level code, based on the arcjet data, that can be used to estimate cloth thickness for future missions using ADEPT and to predict carbon cloth performance in future arcjet tests

Domain-matched Pre-training Tasks for Dense Retrieval

Pre-training on larger datasets with ever increasing model size is now a proven recipe for increased performance across almost all NLP tasks. A notable exception is information retrieval, where additional pre-training has so far failed to produce convincing results. We show that, with the right pre-training setup, this barrier can be overcome. We demonstrate this by pre-training large bi-encoder models on 1) a recently released set of 65 million synthetically generated questions, and 2) 200 million post-comment pairs from a preexisting dataset of Reddit conversations. We evaluate on a set of information retrieval and dialogue retrieval benchmarks, showing substantial improvements over supervised baselines

Physics-Based Modeling of Meteor Entry and Breakup

A new research effort at NASA Ames Research Center has been initiated in Planetary Defense, which integrates the disciplines of planetary science, atmospheric entry physics, and physics-based risk assessment. This paper describes work within the new program and is focused on meteor entry and breakup. Over the last six decades significant effort was expended in the US and in Europe to understand meteor entry including ablation, fragmentation and airburst (if any) for various types of meteors ranging from stony to iron spectral types. These efforts have produced primarily empirical mathematical models based on observations. Weaknesses of these models, apart from their empiricism, are reliance on idealized shapes (spheres, cylinders, etc.) and simplified models for thermal response of meteoritic materials to aerodynamic and radiative heating. Furthermore, the fragmentation and energy release of meteors (airburst) is poorly understood. On the other hand, flight of human-made atmospheric entry capsules is well understood. The capsules and their requisite heatshields are designed and margined to survive entry. However, the highest speed Earth entry for capsules is less than 13 km/s (Stardust). Furthermore, Earth entry capsules have never exceeded diameters of 5 m, nor have their peak aerothermal environments exceeded 0.3 atm and 1 kW/cm2. The aims of the current work are: (i) to define the aerothermal environments for objects with entry velocities from 13 to greater than 20 km/s; (ii) to explore various hypotheses of fragmentation and airburst of stony meteors in the near term; (iii) to explore the possibility of performing relevant ground-based tests to verify candidate hypotheses; and (iv) to quantify the energy released in airbursts. The results of the new simulations will be used to anchor said risk assessment analyses. With these aims in mind, state-of-the-art entry capsule design tools are being extended for meteor entries. We describe: (i) applications of current simulation tools to spherical geometries of diameters ranging from 1 to 100 m for an entry velocity of 20 km/s and stagnation pressures ranging from 1 to 100 atm; (ii) the influence of shape and departure of heating environment predictions from those for a simple spherical geometry; (iii) assessment of thermal response models for silica subject to intense radiation; and (iv) results for porosity-driven gross fragmentation of meteors, idealized as a collection of smaller objects. Lessons learned from these simulations will be used to help understand the Chelyabinsk meteor entry up to its first point of fragmentation

Physics-Based Modeling of Meteor Entry and Breakup

A new research effort at NASA Ames Research Center has been initiated in Planetary Defense, which integrates the disciplines of planetary science, atmospheric entry physics, and physics-based risk assessment. This paper describes work within the new program and is focused on meteor entry and breakup.Over the last six decades significant effort was expended in the US and in Europe to understand meteor entry including ablation, fragmentation and airburst (if any) for various types of meteors ranging from stony to iron spectral types. These efforts have produced primarily empirical mathematical models based on observations. Weaknesses of these models, apart from their empiricism, are reliance on idealized shapes (spheres, cylinders, etc.) and simplified models for thermal response of meteoritic materials to aerodynamic and radiative heating. Furthermore, the fragmentation and energy release of meteors (airburst) is poorly understood.On the other hand, flight of human-made atmospheric entry capsules is well understood. The capsules and their requisite heatshields are designed and margined to survive entry. However, the highest speed Earth entry for capsules is 13 kms (Stardust). Furthermore, Earth entry capsules have never exceeded diameters of 5 m, nor have their peak aerothermal environments exceeded 0.3 atm and 1 kW/sq cm. The aims of the current work are: (i) to define the aerothermal environments for objects with entry velocities from 13 to 20 kms; (ii) to explore various hypotheses of fragmentation and airburst of stony meteors in the near term; (iii) to explore the possibility of performing relevant ground-based tests to verify candidate hypotheses; and (iv) to quantify the energy released in airbursts. The results of the new simulations will be used to anchor said risk assessment analyses. With these aims in mind, state-of-the-art entry capsule design tools are being extended for meteor entries. We describe: (i) applications of current simulation tools to spherical geometries of diameters ranging from 1 to 100 m for an entry velocity of 20 kms and stagnation pressures ranging from 1 to 100 atm; (ii) the influence of shape and departure of heating environment predictions from those for a simple spherical geometry; (iii) assessment of thermal response models for silica subject to intense radiation; and (iv) results for porosity-driven gross fragmentation of meteors, idealized as a collection of smaller objects. Lessons learned from these simulations will be used to help understand the Chelyabinsk meteor entry up to its first point of fragmentation

Ablation and Heating During Atmospheric Entry and Its Effect on Airburst Risk

Large meteoroids and asteroids entering the atmosphere endure tremendous heating from the shock heated air, and thereby lose a significant fraction of their mass during atmospheric entry a process known as ablation. The predicted evolution of the asteroids mass as it passes through the atmosphere can affect both the predicted energy deposition profile relevant to an airburst event, or the residual mass that strikes the ground in the case of an impact event. This presentation is divided roughly into two parts. In the first part, an overview of traditional models for heat transfer and ablation that are historically used in the meteor physics community is presented, and the validity in the asteroid entry regime discussed. Sensitivity analyses performed using the recently developed Fragment-Cloud Model (FCM) will be presented which show illustrate the range of sizes and entry parameters for which the predicted asteroid threat is most sensitive to the models for ablation and heat transfer. The second part of the presentation shall focus on recent work done under NASAs Asteroid Threat Assessment Project (ATAP) to develop new models for heat transfer and ablation using high-fidelity numerical simulation in concert with state-of-the-art experiments. Coupled computational fluid dynamics (CFD)radiation transport simulations preformed using the state-of-the-art entry modeling tools at NASA show that, for large meteoroids and asteroids, there can significant attenuation of the heat transfer to the surface (95 in some cases) by the products of ablation. In addition to the heat transfer, new models for the material response and ablation of asteroidal material have been developed [cite]. In the current work, we present finding from recent novel experiments performed in the arc jet facility at NASA Ames, which allows us to, in part, simulate the extreme environment experienced by the asteroid during entry. Briefly, the experimental set-up was comprised of a 1.5 conical article of machined H5 chondrite, which was exposed to a high-enthalpy flow resulting in approximately 4 kWcm2 of heating to the surface. A still frame capture from high-speed video taken during this experiment can be seen in Figure 1. In this figure, we can observe some of the major mechanisms for meteoroid ablation, such as melt flow, spallation (mechanical removal of material), and vaporization. Major findings from this, and other experiments will be discussed, as well progress on utilizing the data from the experiments to inform and develop improved models for ablation

A modified atmospheric non-hydrostatic model on low aspect ratio grids

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tellus A 64 (2012): 17516, doi:10.3402/tellusa.v64i0.17516.It is popular to use a horizontal explicit and a vertical implicit (HE-VI) scheme in the compressible nonhydrostatic (NH) model. However, when the aspect ratio becomes small, a small time-interval is required in HE-VI, because the Courant-Fredrich-Lewy (CFL) criterion is determined by the horizontal grid spacing. Furthermore, simulations from HE-VI can depart from the forward–backward (FB) scheme in NH even when the time interval is less than the CFL criterion allowed. Hence, a modified non-hydrostatic (MNH) model is proposed, in which the left-hand side of the continuity equation is multiplied by a parameter d (45d516, in this study). When the linearized MNH is solved by FB (can be other schemes), the eigenvalue shows that MNH can suppress the frequency of acoustic waves very effectively but does not have a significant impact on the gravity waves. Hence, MNH enables to use a longer time step than that allowed in the original NH. When the aspect ratio is small, MNH solved by FB can be more accurate and efficient than the NH solved by HE-VI. Therefore, MNH can be very useful to study cloud, Large Eddy Simulation (LES), turbulence, flow over complex terrains, etc., which require fine resolution in both horizontal and vertical directions

Neuromagnetic Index of Hemispheric Asymmetry Prognosticating the Outcome of Sudden Hearing Loss

The longitudinal relationship between central plastic changes and clinical presentations of peripheral hearing impairment remains unknown. Previously, we reported a unique plastic pattern of “healthy-side dominance” in acute unilateral idiopathic sudden sensorineural hearing loss (ISSNHL). This study aimed to explore whether such hemispheric asymmetry bears any prognostic relevance to ISSNHL along the disease course. Using magnetoencephalography (MEG), inter-hemispheric differences in peak dipole amplitude and latency of N100m to monaural tones were evaluated in 21 controls and 21 ISSNHL patients at two stages: initial and fixed stage (1 month later). Dynamics/Prognostication of hemispheric asymmetry were assessed by the interplay between hearing level/hearing gain and ipsilateral/contralateral ratio (I/C) of N100m latency and amplitude. Healthy-side dominance of N100m amplitude was observed in ISSNHL initially. The pattern changed with disease process. There is a strong correlation between the hearing level at the fixed stage and initial I/Camplitude on affected-ear stimulation in ISSNHL. The optimal cut-off value with the best prognostication effect for the hearing improvement at the fixed stage was an initial I/Clatency on affected-ear stimulation of 1.34 (between subgroups of complete and partial recovery) and an initial I/Clatency on healthy-ear stimulation of 0.76 (between subgroups of partial and no recovery), respectively. This study suggested that a dynamic process of central auditory plasticity can be induced by peripheral lesions. The hemispheric asymmetry at the initial stage bears an excellent prognostic potential for the treatment outcomes and hearing level at the fixed stage in ISSNHL. Our study demonstrated that such brain signature of central auditory plasticity in terms of both N100m latency and amplitude at defined time can serve as a prognostication predictor for ISSNHL. Further studies are needed to explore the long-term temporal scenario of auditory hemispheric asymmetry and to get better psychoacoustic correlates of pathological hemispheric asymmetry in ISSNHL