Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17
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Burnaman, Shelley H.↗
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En route Spacing Tool: Efficient Conflict-free Spacing to Flow-Restricted Airspace
This paper describes the Air Traffic Management (ATM) problem within the U.S. of flow-restricted en route airspace, an assessment of its impact on airspace users, and a set of near-term tools and procedures to resolve the problem. The FAA is committed, over the next few years, to deploy the first generation of modem ATM decision support tool (DST) technology under the Free-Flight Phase-1 (FFp1) program. The associated en route tools include the User Request Evaluation Tool (URET) and the Traffic Management Advisor (TMA). URET is an initial conflict probe (ICP) capability that assists controllers with the detection and resolution of conflicts in en route airspace. TMA orchestrates arrivals transitioning into high-density terminal airspace by providing controllers with scheduled times of arrival (STA) and delay feedback advisories to assist with STA conformance. However, these FFPl capabilities do not mitigate the en route Miles-In-Trail (MIT) restrictions that are dynamically applied to mitigate airspace congestion. National statistics indicate that en route facilities (Centers) apply Miles-In-Trail (MIT) restrictions for approximately 5000 hours per month. Based on results from this study, an estimated 45,000 flights are impacted by these restrictions each month. Current-day practices for implementing these restrictions result in additional controller workload and an economic impact of which the fuel penalty alone may approach several hundred dollars per flight. To mitigate much of the impact of these restrictions on users and controller workload, a DST and procedures are presented. The DST is based on a simple derivative of FFP1 technology that is designed to introduce a set of simple tools for flow-rate (spacing) conformance and integrate them with conflict-probe capabilities. The tool and associated algorithms are described based on a concept prototype implemented within the CTAS baseline in 1995. A traffic scenario is used to illustrate the controller's use of the tool, and potential display options are presented for future controller evaluation.
Green, S.↗
Moving-Base Simulation Evaluation of Control/Display Integration Issues for ASTOVL Aircraft
A moving-base simulation has been conducted on the Vertical Motion Simulator at Ames Research Center using a model of an advanced, short takeoff and vertical landing (STOVL) lift fan fighter aircraft. This experiment expanded on investigations during previous simulations with this STOVL configuration with the objective of evaluating (1) control law modifications over the low speed flight envelope, (2) integration of the throttle inceptor with flight control laws that provide direct thrust command for conventional flight, vertical and short takeoff, and flightpath or vertical velocity command for transition, hover, and vertical landing, (3) control mode blending for pitch, roll, yaw, and flightpath control during transition from wing-borne to jet-borne flight, and (4) effects of conformal versus nonconformal presentation of flightpath and pursuit guidance symbology on the out-the-window display for low speed STOVL operations. Assessments were made for takeoff, transition, hover, and landing, including precision hover and landing aboard an LPH-type amphibious assault ship in the presence of winds and rough seas. Results yielded Level 1 pilot ratings for the flightpath and vertical velocity command modes for a range of land-based and shipboard operation and were consistent with previous experience with earlier control laws and displays for this STOVL concept. Control mode blending was performed over speed ranges in accord with the pilot's tasks and with the change of the basic aircraft's characteristics between wing-borne and hover flight. Blending of yaw control from heading command in hover to sideslip command in wing-borne flight performed over a broad speed range helped reduce yaw transients during acceleration through the low speed regime. Although the pilots appreciated conformality of flightpath and guidance symbols with the external scene during the approach, increased sensitivity of the symbols for lateral path tracking elevated the pilots' control activity in the presence of turbulence. The pilots preferred the choice of scaling that was originally established during the display development and in-flight evaluations.
Franklin, James A.↗
B-DNA to Z-DNA structural transitions in the SV40 enhancer: stabilization of Z-DNA in negatively supercoiled DNA minicircles
During replication and transcription, the SV40 control region is subjected to significant levels of DNA unwinding. There are three, alternating purine-pyrimidine tracts within this region that can adopt the Z-DNA conformation in response to negative superhelix density: a single copy of ACACACAT and two copies of ATGCATGC. Since the control region is essential for both efficient transcription and replication, B-DNA to Z-DNA transitions in these vital sequence tracts may have significant biological consequences. We have synthesized DNA minicircles to detect B-DNA to Z-DNA transitions in the SV40 enhancer, and to determine the negative superhelix density required to stabilize the Z-DNA. A variety of DNA sequences, including the entire SV40 enhancer and the two segments of the enhancer with alternating purine-pyrimidine tracts, were incorporated into topologically relaxed minicircles. Negative supercoils were generated, and the resulting topoisomers were resolved by electrophoresis. Using an anti-Z-DNA Fab and an electrophoretic mobility shift assay, Z-DNA was detected in the enhancer-containing minicircles at a superhelix density of -0.05. Fab saturation binding experiments demonstrated that three, independent Z-DNA tracts were stabilized in the supercoiled minicircles. Two other minicircles, each with one of the two alternating purine-pyrimidine tracts, also contained single Z-DNA sites. These results confirm the identities of the Z-DNA-forming sequences within the control region. Moreover, the B-DNA to Z-DNA transitions were detected at superhelix densities observed during normal replication and transcription processes in the SV40 life cycle.
Non-NASA Center↗
A tunable autonomous RNA-fueled micro-engine
Autonomous molecular machines capable of converting chemical energy into mechanical motion are foundational components for synthetic nanoscale systems. Inspired by biological motors, we report the construction of a tunable, RNA-fueled DNA origami engine that drives the cyclic movement of a 500 nm-diameter particle at the microscale. The engine operates via sequential RNA–DNA hybridization and enzymatic cleavage by RNase H, enabling reversible switching between folded and unfolded conformations without external intervention. By modulating RNA and enzyme concentrations and controlling temperature, we achieve tunable switching kinetics, with transition periods as short as ~10 s. Kinetic modeling reveals that the folding pathway is governed by both productive RNA binding and the enzymatic clearance of misfolded intermediates, while unfolding is primarily controlled by RNase H activity. Since the RNA fuel binds specifically to the DNA strands, each engine is addressable simply by changing the sequences. This work demonstrates a programmable, self-resetting molecular actuator and offers a blueprint for building more complex nanomechanical systems with forces and energies comparable to molecular motors.
DNA nanomachines↗
Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids
Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigating Local Carrier Dynamics in PERC Patterned CdTe Solar Cells
Remarkable progress has been achieved in CdTe photovoltaics (PVs) to further improve cell performance while reducing manufacturing costs. Researchers optimized the front contact that leads the short-circuit current density (J sc ) over 31mA/cm 2 (e.g., (Zn, Mg)O buffer layer and/or alloying CdTe with Se). Reese et al. reported an open-circuit voltage (V oc ) over 1 V with group-V doped single crystal, showing the feasibility of increasing V oc in CdTe PV that is fixed to less than 900 mV in most cases. Recent studies suggested that the V oc improvement in polycrystalline CdTe PVs requires well-passivated back contact. One possible strategy is to use CdMgTe alloy (E g > 1.8 eV), where the band-gap offset (ΔE CB ≈ 0.2 eV) reflects minority carrier electrons, thereby decreasing surface recombination. Another strategy is to utilize a stable Al 2 O 3 layer as an electron reflector; experimental works confirmed the improved performance with a conformal Al 2 O 3 layer. In this configuration, the precise control of Al 2 O 3 (≈1 nm) over the entire CdTe layer is essential because the J sc greatly depends on the tunneling current. While promising, both CdMgTe and Al 2 O 3 passivation on CdTe introduce unfavorable valence band offset that blocks the hole transport. Kephart et al. proposed a patterned passixc vation layer (≈ 20 nm Al 2 O 3 ) with point contacts (≈ 3 μm in diameter) that extract hole carriers. This configuration is similar to the passive emitter and rear contact (PERC) design that has been extensively studied in Si PVs. While remarkably high carrier lifetime and photoluminescence (> 10 X) were measured, consistent improvement in V oc and efficiency in this CdTe PERC were not yet observed. At this time, it is unclear how the surface potential is distributed in the presence of patterned Al 2 O 3 reflectors and how this additional field impacts the PV performance for Cu-doped and group-V doped CdTe PERC devices. To tackle this challenge, we develop robust nanofabrication and characterization platform to study CdTe PERC devices consisting of a patterned Al 2 O 3 layer on CdSe( 1-x )Te x (Cu-doped, GrV-doped; x = 0 to 1; CST). First Solar supplies high-quality CST materials. The dark and light I-Vs under 1-sun illumination are extracted for a series of each set of devices. We perform quantitative and qualitative PV analysis for a series of Cu-doped and Gr-V doped PERC devices, showing notably different V oc changes for GrV-doped compared to Cu-doped PERC devices. This project attempts to produce individual contacts on single grains and grain boundaries to measure lateral transport. As a model system, we use a CdSe( 1-x )Te x film on glass prepared by a colossal grain growth (CGG) technique at National Renewable Research Laboratories (NREL). Our preliminary results confirm that intergranular transport is hindered by the electrical barrier formed near grain boundaries. The PERC fabrication and the lateral transport measurement platform developed in this project can easily be applied to other types of advanced CdSe( 1-x )Te x architectures to better understand local photocarrier transport, in turn, providing the fundamental knowledge to improve the performance of CdTe PVs.
14 SOLAR ENERGY↗
Lifting MGARD: Construction of (pre)wavelets on the interval using polynomial predictors of arbitrary order
MGARD (MultiGrid Adaptive Reduction of Data) is an algorithm for compressing and refactoring scientific data, based on the theory of multigrid methods. The core algorithm is built around stable multilevel decompositions of conforming piecewise linear $C^0$ finite element spaces, enabling accurate error control in various norms and derived quantities of interest. In this work, we extend this construction to arbitrary order Lagrange finite elements $\mathbb{Q}_p$, $p \geq 0$, and propose a reformulation of the algorithm as a lifting scheme with polynomial predictors of arbitrary order. Additionally, a new formulation using a compactly supported wavelet basis is discussed, and an explicit construction of the proposed wavelet transform for uniform dyadic grids is described.
Reshniak, Viktor [Oak Ridge National Laboratory (O↗
A conformal block structured grid for turbomachinery cascades in two dimensions
A block structured conformal transformation is presented for application to turbomachinery cascades. In comparison with the traditional single block cases that are, at best, supplemented with branch cuts, there is a richer variety of choices for the grid topology. The choice presented leads to a substantial improvement in the grid quality. This is reflected in a relatively uniform covering of the cascade region. While grid clustering is not intended or supplied with the block conformal structure, it can be injected afterwards. When viewed as a controlled experiment, the present study provides a significant example of the effect of grid topology upon the grid quality. In a larger sense, this puts some focus upon the effects of grid topology in more general situations.
Wang, Zhu↗
Fail-Safe Pressure Plug
Protective plug resists slowly built-up pressure or automatically releases itself if pressure rises suddenly. Seals out moisture at pressures ranging from 50 micrometers of mercury to 200 pounds per square inch. Designed to seal throat of 38 Reaction Control Thrusters on Space Shuttle protecting internal components from corrosion. Plug conforms to contour of nozzle throat, where O-ring forms pressure seal. After plug inserted, cover attached by use of cover-fitting assembly. Modified versions useful in protecting engines, pumps, reaction vessels, and other industrial equipment during shipment and maintenance.
Svejkovsky, Paul A.↗
Megafans of the Northern Kalahari Basin
We identify eleven megafans (partial cones of fluvial sediment, >80 km radius) in the northern Kalahari Basin, using several criteria based on VIS and IR remotely sensed data and SRTM-based surface morphology reconstructions. Two other features meet fewer criteria of the form which we class as possible megafans. The northern Kalahari megafans are located in a 1700 km arc around the southern and eastern flanks of the Angola's Bié Plateau, from northern Namibia through northwest Botswana to western Zambia. Three lie in the Owambo subbasin centered on the Etosha Pan, three in the relatively small Okavango rift depression, and five in the Upper Zambezi basin. The population includes the well-known Okavango megafan (150 km), Namibia's Cubango megafan, the largest megafan in the region (350 km long), and the largest nested group (the five major contiguous megafans on the west slopes of the upper Zambezi Valley). We use new, SRTM-based topographic roughness data to discriminate various depositional surfaces within the flat N. Kalahari landscapes. We introduce the concepts of divide megafans, derived megafans, and fan-margin rivers. Conclusions. (i) Eleven megafan cones total an area of ~190,000 sq km. (ii) Different controls on megafan size operate in the three component basins: in the Okavango rift structural controls become the prime constraint on megafan length by controlling basin dimensions. Megafans in the other les constricted basins appear to conform to classic relationships fan area, slope, and feeder-basin area. (iii) Active fans occupy the Okavango rift depression with one in the Owambo basin. The rest of the population are relict but recently active fans (surfaces are relict with respect to activity by the feeder river). (iv) Avulsive behavior of the formative river-axiomatic for the evolution of megafans-has resulted in repeated rearrangements of regional drainage, with likely effects in the study area well back into the Neogene. Divide megafans comprise the majority of the identified features, some of which have delivered water and sediment alternately to neighboring basins in the course of normal avulsion activity, likely resulting in significant changes in the hydrologies of two of the study-area subbasins. (v) Paleoclimatic inferences extracted from fluvial and lacustrine sediments therefore need to take account of avulsion-driven drainage configurations, especially where these are autogenically controlled.
Wilkinson, M. J.↗
Synthetic Vision for Lunar and Planetary Landing Vehicles
The Crew Vehicle Interface (CVI) group of the Integrated Intelligent Flight Deck Technologies (IIFDT) has done extensive research in the area of Synthetic Vision (SV), and has shown that SV technology can substantially enhance flight crew situation awareness, reduce pilot workload, promote flight path control precision and improve aviation safety. SV technology is being extended to evaluate its utility for lunar and planetary exploration vehicles. SV may hold significant potential for many lunar and planetary missions since the SV presentation provides a computer-generated view of the terrain and other significant environment characteristics independent of the outside visibility conditions, window locations, or vehicle attributes. SV allows unconstrained control of the computer-generated scene lighting, terrain coloring, and virtual camera angles which may provide invaluable visual cues to pilots/astronauts and in addition, important vehicle state information may be conformally displayed on the view such as forward and down velocities, altitude, and fuel remaining to enhance trajectory control and vehicle system status. This paper discusses preliminary SV concepts for tactical and strategic displays for a lunar landing vehicle. The technical challenges and potential solutions to SV applications for the lunar landing mission are explored, including the requirements for high resolution terrain lunar maps and an accurate position and orientation of the vehicle that is essential in providing lunar Synthetic Vision System (SVS) cockpit displays. The paper also discusses the technical challenge of creating an accurate synthetic terrain portrayal using an ellipsoid lunar digital elevation model which eliminates projection errors and can be efficiently rendered in real-time.
Williams, Steven P.↗
Simulation of Controller Pilot Data Link Communications over VHF Digital Link Mode 3
The Federal Aviation Administration (FAA) has established an operational plan for the future Air Traffic Management (ATM) system, in which the Controller Pilot Data Link Communications (CPDLC) is envisioned to evolve into digital messaging that will take on an ever increasing role in controller to pilot communications, significantly changing the way the National Airspace System (NAS) is operating. According to FAA, CPDLC represents the first phase of the transition from the current analog voice system to an International Civil Aviation Organization (ICAO) compliant system in which digital communication becomes the alternate and perhaps primary method of routine communication. The CPDLC application is an Air Traffic Service (ATS) application in which pilots and controllers exchange messages via an addressed data link. CPDLC includes a set of clearance, information, and request message elements that correspond to existing phraseology employed by current Air Traffic Control (ATC) procedures. These message elements encompass altitude assignments, crossing constraints, lateral deviations, route changes and clearances, speed assignments, radio frequency assignments, and various requests for information. The pilot is provided with the capability to respond to messages, to request clearances and information, to report information, and to declare/rescind an emergency. A 'free text' capability is also provided to exchange information not conforming to defined formats. This paper presents simulated results of the aeronautical telecommunication application Controller Pilot Data Link Communications over VHF Digital Link Mode 3 (VDL Mode 3). The objective of this simulation study was to determine the impact of CPDLC traffic loads, in terms of timely message delivery and capacity of the VDL Mode 3 subnetwork. The traffic model is based on and is used for generating air/ground messages with different priorities. Communication is modeled for the en route domain of the Cleveland Center air traffic (ZOB ARTCC).
Bretmersky, Steven C.↗
Application of statistical process control and process capability analysis procedures in orbiter processing activities at the Kennedy Space Center
Successful ground processing at KSC requires that flight hardware and ground support equipment conform to specifications at tens of thousands of checkpoints. Knowledge of conformance is an essential requirement for launch. That knowledge of conformance at every requisite point does not, however, enable identification of past problems with equipment, or potential problem areas. This paper describes how the introduction of Statistical Process Control and Process Capability Analysis identification procedures into existing shuttle processing procedures can enable identification of potential problem areas and candidates for improvements to increase processing performance measures. Results of a case study describing application of the analysis procedures to Thermal Protection System processing are used to illustrate the benefits of the approaches described in the paper.
Safford, Robert R.↗
Guideline 36 Conformance Test v2.0
ASHRAE Guideline 36 provides guidance for how typical commercial building HVAC systems should be controlled to reduce energy costs and improve the indoor environmental quality for occupants. An industry-led effort is developing test scripts for how control manufacturers can test that the control logic in their control products follows Guideline 36. This software intends to support that effort in two ways. First, by providing a testbed for control manufacturers to run the test scripts against their own control products and compare their generated results to the expected results provided by the test scripts. Second, by providing a testbed that can be used during the development of test scripts to rapidly and repeatably verify they exercise Guideline 36 logic as desired and generate accurate expected results that control products can be compared to. An initial version of the software has already been developed and released open-source by a previous CEC-funded project that implemented the first use case (https://github.com/LBNL-ETA/guideline36_conformance_test/blob/master/LICENSE.txt), while this software disclosure will add the functionality of the second use case, as well as update the software where needed, all open-source. We intend to extend and contribute to the existing open-source software repository.
Blum, David [Lawrence Berkeley National Laboratory↗
Quality-Control Mechanism for Telomerase RNA Folding in the Cell
Long non-coding RNAs can often fold into different conformations. Telomerase RNA, an essential component of the telomerase ribonucleoprotein (RNP) enzyme, must fold into a defined structure to fulfill its function with the protein catalytic subunit (TERT) and other accessory factors. However, the mechanism by which the correct folding of telomerase RNA is warranted in a cell is still unknown. Here we show that La-related protein Pof8 specifically recognizes the conserved pseudoknot region of telomerase RNA and instructs the binding of the Lsm2-8 complex to its mature 3' end, thus selectively protecting the correctly folded RNA from exonucleolytic degradation. In the absence of Pof8, TERT assembles with misfolded RNA and produces little telomerase activity. Therefore, Pof8 plays a key role in telomerase RNA folding quality control, ensuring that TERT only assembles with functional telomerase RNA to form active telomerase. Our finding reveals a mechanism for non-coding RNA folding quality control.
59 BASIC BIOLOGICAL SCIENCES↗
Gating choreography and mechanism of the human proton-activated chloride channel $\mathrm{ASOR}$
The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. The molecular mechanisms of pH-dependent control are not understood, in part because structural information for an activated conformation of ASOR is lacking. Here, we reconstitute function from purified protein and present a 3.1-Å-resolution cryo–electron microscopy structure of human ASOR at acidic pH in an activated conformation. The work contextualizes a previous acidic pH structure as a desensitized conformation. Combined with electrophysiological studies and high-resolution structures of resting and desensitized states, the work reveals mechanisms of proton sensing and ion pore gating. Clusters of extracellular acidic residues function as pH sensors and coalesce when protonated. Ensuing conformational changes induce metamorphosis of transmembrane helices to fashion an ion conduction pathway unique to the activated conformation. The studies identify a new paradigm of channel gating in this ubiquitous ion channel.
59 BASIC BIOLOGICAL SCIENCES↗
Synthetic Vision Displays for Planetary and Lunar Lander Vehicles
Aviation research has demonstrated that Synthetic Vision (SV) technology can substantially enhance situation awareness, reduce pilot workload, improve aviation safety, and promote flight path control precision. SV, and related flight deck technologies are currently being extended for application in planetary exploration vehicles. SV, in particular, holds significant potential for many planetary missions since the SV presentation provides a computer-generated view for the flight crew of the terrain and other significant environmental characteristics independent of the outside visibility conditions, window locations, or vehicle attributes. SV allows unconstrained control of the computer-generated scene lighting, terrain coloring, and virtual camera angles which may provide invaluable visual cues to pilots/astronauts, not available from other vision technologies. In addition, important vehicle state information may be conformally displayed on the view such as forward and down velocities, altitude, and fuel remaining to enhance trajectory control and vehicle system status. The paper accompanies a conference demonstration that introduced a prototype NASA Synthetic Vision system for lunar lander spacecraft. The paper will describe technical challenges and potential solutions to SV applications for the lunar landing mission, including the requirements for high-resolution lunar terrain maps, accurate positioning and orientation, and lunar cockpit display concepts to support projected mission challenges.
Arthur, Jarvis J., III↗