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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

LANDO: Developing Autonomous Payload Offloading Capabilities for Lunar Surface Operations

Introduction: The Lightweight Surface Manipulation System (LSMS) AutoNomy capabilities Development for surface Operations and construction (LANDO) project is an Early Career Initiative selected for funding by NASA Space Technology Mission Directorate. LANDO is developing a general-purpose autonomy framework applicable to serial and tension-actuated manipulation agents, that will be validated using an existing prototype of the LSMS-L35 (35-kg wrist lift capacity on the lunar surface [Fig. 1], sized for a Commercial Lunar Pay-load Services (CLPS) mission). The autonomous LSMS-L35 will be used to demonstrate autonomous payload handling capabilities for Lunar and other planetary surfaces, directly addressing STMD capability gaps in autonomous excavation and construction operations, advanced robotics and spacecraft autonomy technologies, and technologies supporting emerging space industries including the In-Space Servicing, Assembly and Manufacturing national strategy. LSMS: The LSMS is a tension actuated robotic agent that is scalable (reach and lifting capacity in different gravity environments), versatile (types of surface operations), and reusable. Compared to serial arms, the LSMS provides significantly higher structural efficiency and mechanical advantage, enabling a greater payload lift capacity at a lower system mass. The LSMS is envisioned to be a crucial part of the excavation and construction portfolio, capable of supporting a variety of activities on the lunar surface. Autonomous payload handling is one of the first activities the LSMS can support that develops capabilities that are extensible to other surface operations. Payload handling is required to: remove payloads from a lander; place payloads on mobile agents for transport from a lander to construction site/assembly point; emplace payloads in their operational configuration, and aggregate components to create an asset. As an example of this critical gap, manifested CLPS missions do not currently have a ubiquitous payload offloading capability; payloads (excluding rovers) are designed to remain on the lander. Why Autonomy? Autonomous robotic systems capable of carrying out excavation and construction operations are a fundamental and critical capability required for realizing the NASA Artemis program vision to “emplace and build the infrastructure, systems, and robotic missions that can enable a sustained lunar surface presence.” While teleoperation is still feasible for lunar surface operations, increased latency at Mars will require validated supervised autonomous technologies capable of operating with minimal human involvement (human-on-the-loop) unless an unexpected event occurs requiring human intervention. Autonomy reduces operator burden, allows operations to continue during uncrewed periods, in-creases the safety of operations by automatically detecting and handling faults, and allows operating in high latency environments. Development Activities: LANDO is extending critical autonomous operations to the manipulation domain and creating an integrated system, based on reusable software modules, that is capable of planning and executing payload handling and autonomous surface operations without requiring hu-man intervention beyond a supervisory role. The priority features under development are 1) autonomously offload payloads from a tilted lander deck without buckling the LSMS; 2) sensing whether a payload is safe to lift and handle; and 3) integrate with Astrobotic’s CLPS lander. The poster presentation will highlight current development activities over the past year on LSMS-L35 prototype hard-ware design, and autonomy software.

in-space assembly↗
NASA NTRS2023

Solid-State Architecture Batteries for Enhanced Rechargeability and Safety (SABERS): Advanced Battery Technology for Sustainable Aviation

All-electric vertical take-off and landing vehicles (eVTOL) for urban air mobility (UAM) concepts face numerous challenging technical barriers before their introduction into the consumer marketplace. The primary barrier to overcome is developing an energy storage system capable of meeting the rigorous aerospace safety and performance criteria. The performance metrics for eVTOL vehicles are at least two times greater than those of electric ground vehicles. Furthermore, inherently non-flammable batteries are essential for safe operation of commercial electric aerovehicles. The SABERS concept proposes a battery that meets the key performance criteria through development of a solid-state architecture battery utilizing high-capacity sulfur-selenium cathode and lithium metal anode. The combination of sulfur and selenium offers a balanced energy-to-power density ratio, which can be tailored to the specific application by altering the stoichiometric ratios of sulfur to selenium. This hybrid cathode will be developed by implementing NASA patented holey graphene technology as a highly conductive, ultra-lightweight electrode scaffold. A solid-state electrolyte will be used as a safe, non-flammable replacement to the highly flammable liquid organic electrolytes currently used in SOA lithium-ion batteries. This solid-state lithium-sulfur/selenium cell will be designed into a serial stacking configuration to enable dense packaging of the battery cells. The serial stacking configuration is termed a bipolar stack, which has the advantages of reducing overall cell weight, simplifying the interfaced connections for the cell, and minimizing the cooling requirements. Lastly, optimization of battery components will occur through a robust and rigorous combination of various computational modeling techniques covering multiple length scales. The expected result will be a fully solid-state battery with operational temperatures up to 150 °C which provides the required energy density, discharge rates, and inherent safety to meet the strict aerospace mission performance criteria. This presentation will demonstrate a feasible path for solid-state cells that possess a specific energy of greater than 400 Wh/kg to enable electric aircraft. The presentation will also explore novel materials and computational models used to achieve all solid-state cells that operate safely at very high temperatures and specific energies. The cells can withstand damage while operating without an increase in temperature or spontaneous ignition.

Urban Air Mobility (UAM) Vehicles↗
NASA NTRSDate not supplied

Solid-state Architecture Batteries for Enhanced Rechargeability and Safety (SABERS) Beyond Li-Ion: Technology to Enable Sustainable Electric Aviation

All-electric and hybrid electric aerovehicle concepts face numerous technical barriers prior to their introduction into the consumer marketplace in order to meet sustainable aviation goals. One of the primary barriers to overcome is developing an energy dense storage system capable of meeting the rigorous aerospace safety and performance criteria. Additionally, the electric aviation market requires that the batteries be fabricated in a sustainable manner with materials that are readily available and abundant within the U.S. to ensure there are no supply chain issues during manufacturing. The performance metrics to enable electric aviation are at least two times greater than those of electric ground vehicles. Furthermore, inherently non-flammable batteries are essential for safe operation of commercial electric aerovehicles. The SABERS concept proposes a battery that meets the key performance criteria through development of a solid-state architecture battery utilizing high-capacity sulfur-selenium cathode and lithium metal anode. The combination of sulfur and selenium offers a balanced energy-to-power density ratio, which can be tailored to the specific application by altering the stoichiometric ratios of sulfur to selenium. The hybrid cathode has been developed by implementing NASA patented holey graphene technology as a highly conductive, ultra-lightweight electrode scaffold. A solid-state electrolyte has been used as a safe, non-flammable replacement to the highly flammable liquid organic electrolytes currently used in SOA lithium-ion batteries. This solid-state lithium-sulfur/selenium cell will be designed into a serial stacking configuration to enable dense packaging of the battery cells. The serial stacking configuration is termed a bipolar stack, which has the advantages of reducing overall cell weight, simplifying the interfaced connections for the cell, and minimizing the cooling requirements. Lastly, optimization of battery components will occur through a robust and rigorous combination of various computational modeling techniques covering multiple length scales. The expected result will be a fully solid-state battery with operational temperatures up to 150 °C which provides the required energy density, discharge rates, and inherent safety to meet the strict aerospace mission performance criteria. This poster summarizes recent results from battery component optimization to scale-up production of full SABERS pouch cells.

Urban Air Mobility (UAM) Vehicles↗
NASA NTRS2023

Multiyear Dry Periods in Southern Africa

Characteristics and physical features related to low precipitation across many years in Southern Africa that lead to societal disruptions are diagnosed using observed analyses and an ensemble of historical coupled climate model simulations during 1921 to 2014. Four regions are evaluated, as identified through a hierarchical clustering algorithm applied to the Standardized Precipitation Index (SPI) during the October–April precipitation season. Although dryness spanning many October–April occurs periodically in each region, they seldom occur simultaneously, consistent with largely insignificant SPI cross-correlations between them. However, characteristics relevant to low precipitation across many years are generalizable between the four regions, including the serial persistence of October–April precipitation, the likelihood of consecutive dry October–April, and the likelihood of dry October–April in temporal extents of up to 10 consecutive such 7-month seasons. Systematic precipitation persistence is not a feature in any of the four Southern Africa regions, as serial correlations of October–April SPI are not statistically significant at any time lags. It follows that there is an exponential-folding decay in the likelihood of consecutive October–April for various SPI thresholds and that there is a large spread in the likelihood of low October–April SPI across many years. In terms of physical features, low October–April SPI in each Southern Africa region is closely related to local atmospheric circulations; however, they are not as closely related to sea surface temperatures (SSTs). These results suggest that dryness spanning many years is determined primarily by persistent local circulations related to atmospheric variability and to a lesser extent variability related to SST anomalies, including the El Niño–Southern Oscillation.

subtropical Indian Ocean dipole↗
NASA NTRSDate not supplied

Formalization of the Bellman-Ford Algorithm for Airspace Applications

This paper describes the formal verification of one of the most well-known algorithms for finding the shortest path between all vertices in a directed graph, namely the Bellman-Ford algorithm. This formal verification, performed in the Prototype Verification System (PVS), is motivated by two applications in the aerospace domain which use the algorithm for path planning. The first is a pre-flight calculation that uses an adapted version of Bellman-Ford to find a route intended to maximize GNSS availability throughout the flight. The second is a more traditional application intended to find the shortest path between an autonomous aircraft's current position and a goal waypoint, while avoiding regions of space specified by geofences. A novel aspect of this formal verification effort is the inclusion of two distinct models of computation for the algorithm, one being a traditional serial computation, and the other being an explicitly parallel computation. The ability to use parallel computation in the Bellman-Ford algorithm is in fact why it was chosen over other traditionally more performant algorithms, especially for the GNSS application, where the size of the graph makes a purely serial computation infeasible.

formal verification↗
NASA NTRSDate not supplied

Rolling Horizon with K-Position Search Method for Strategic Deconfliction of Package Delivery UAS

This research focuses on the strategic deconfliction of unmanned aircraft systems (UAS) in an urban package delivery environment with two depots and multiple drop-off locations. Since the formulated mixed-integer nonlinear programming (MINLP) problem is non-deterministic polynomial-time (NP) hard, a heuristic algorithm called "rolling horizon with k-position search (KPS)" is used to compute the departure sequence and scheduled time of departure (STD) of each UAS at a depot, considering temporal constraints at en-route crossing waypoints and depots for strategic deconfliction. The simulation studies show that an increase in the value of k (local neighborhood search) in the KPS reduces the average ground delay at the cost of an increase in the computation time for a given number of UAS, size of the rolling horizon window, and number of depots involved in the local neighborhood search. The studies also show that for a given rolling horizon window, the computation time increases exponentially with an increase in the total number of UAS flights when serial processing the local neighborhood search of KPS (with k > 1) and drops by an order of magnitude upon performing the local neighborhood search of KPS using parallel processing instead of serial processing. The computation time drops with the reduction in air traffic complexity of a scenario for a given number of flights, k (local neighborhood search), and rolling horizon window.

UTM↗
NASA NTRSDate not supplied

Solid-State Architecture Batteries for Enhanced Rechargeability and Safety (SABERS) Beyond Li-Ion: Technology to Enable Next-Generation Sustainable Electric

All-electric vertical take-off and landing vehicles (eVTOL) for urban air mobility (UAM) concepts face numerous challenging technical barriers before their introduction into the consumer marketplace. The primary barrier to overcome is developing an energy storage system that meets rigorous aerospace safety and performance criteria. The performance metrics for eVTOL vehicles are at least two times greater than those of electric ground vehicles. Furthermore, inherently non-flammable batteries are essential for the safe operation of commercial electric aero vehicles. The SABERS concept proposes a battery that meets the critical performance criteria by developing a solid-state architecture battery utilizing a high-capacity sulfur-selenium cathode and lithium metal anode. The combination of sulfur and selenium offers a balanced energy-to-power density ratio, which can be tailored to the specific application by altering the stoichiometric ratios of sulfur to selenium. This hybrid cathode will be developed using NASA-patented holey graphene technology as a highly conductive, ultra-lightweight electrode scaffold. A solid-state electrolyte will be used as a safe, non-flammable replacement for the highly flammable liquid organic electrolytes currently in SOA lithium-ion batteries. This solid-state lithium-sulfur/selenium cell will be designed in a serial stacking configuration to enable the dense packaging of the battery cells. The serial stacking configuration is termed a bipolar stack, which has the advantages of reducing overall cell weight, simplifying the interfaced connections for the cell, and minimizing the cooling requirements. Lastly, the optimization of battery components will occur through a robust and rigorous combination of various computational modeling techniques covering multiple length scales. The expected result will be a fully solid-state battery with operational temperatures up to 150°C, providing the required energy density, discharge rates, and inherent safety to meet the strict aerospace mission performance criteria. The SABERS team employed novel materials development, computational modeling, and design-of-experiments (DOE) optimization studies in their research. This presentation will show the results of these studies and demonstrate a feasible path for solid-state cells with a specific energy greater than 400 Wh/kg to enable electric aircraft.

Computational Modeling↗
DOE OSTI2021

A Self-Synchronizing Underwater Acoustic Network for Mooring Load Monitoring of a Wave Energy Converter

This paper reports on the development of a self-synchronizing underwater acoustic network developed for remote monitoring of mooring loads in Wave Energy Converters (WECs). This network uses Time Division Multiple Access and operates self-contained with the ability for users to remotely transmit commands to the network as needed. Each node is a self-contained unit, consisting of a protocol adaptor board, an FAU-DPAM underwater acoustic modem and a battery pack. A node can be connected to a load cell, to a topside user or to the WEC. Every node is swapable. The protocol adaptor board, named Protocol Adaptor for Digital LOad Cell (PADLOC) supports a variety of digital load cell message formats (CAN, MODBUS, custom ASCII) and underwater acoustic modem serial formats. PADLOC enables topside users to connect to separate load cells through a user-specific command. This is especially important if the user is monitoring multiple load cells during deployment or maintenance, when the primary data system may be offline. Each PADLOC board handles formatting, buffering and has a one-on-one serial connection with each pair (node) of a digital load cell and acoustic modem. In addition, each PADLOC board handles the timekeeping and power saving features for each node. The only limitation is the data bit rate and delay limitations associated with the underwater acoustic modem. A four node self-synchronizing network has been developed to demonstrate the load cell monitoring capability using the PADLOC technology on the CalWave WEC.

acoustic↗
DOE OSTI2022

Dual-mode oscillator for stress compensated cut resonator

Both parallel-type and serial-type dual-mode oscillators employing stress compensated cut resonators having various configurations are disclosed. Both classes of dual-mode oscillators employ multiple tank circuits to pass one frequency of the resonator and block the other frequency. The tank circuits isolate the operation of the two oscillator sub-circuits that form the dual-mode oscillator from one another. The dual-mode oscillators may be implemented with either bipolar or CMOS transistors. The parallel-type dual-mode oscillators employ inverters to provide gain. The serial-type dual-mode oscillators employ a two (or three) stage design including a follower circuit first stage and an inverting amplifier/limiter circuit second stage, with an optional intervening transimpedance amplifier stage.

Wessendorf, Kurt O.↗
DOE OSTI2022

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structural Mechanism of an Efficacy Photoswitch Targeting the β 2 ‐adrenergic Receptor

The field of photopharmacology develops light-responsive drugs that can modulate protein activity, enabling precise and dynamic investigations of their roles in health and disease. Adrenergic receptors are prominent targets for this approach because they are prototypical G protein-coupled receptors with high clinical relevance in bronchial and cardiovascular diseases. Here, we employed the azobenzene-based compound photoazolol-1 in combination with time-resolved serial crystallography at X-ray free-electron lasers to resolve the molecular mechanisms by which photoswitchable β-blockers modulate activity of the β 2 -adrenoceptor (β 2 AR). Time-resolved structures of the receptor bound to trans-photoazolol-1 (pre-photoconversion), a strained intermediate in the nanosecond range, and the fully photoisomerized cis-photoazolol-1 reveal how isomerization of the azobenzene moiety induces distinct conformational changes within the orthosteric ligand binding pocket. Within seconds, light-excited photoazolol-1 adopts a new binding pose, altering interactions with extracellular loop 2 and shifting the positions of transmembrane helices 5, 6, and 7. Functional assays of β 2 AR in cellular membranes show that photoazolol-1 acts as an efficacy photoswitch, changing from an inverse agonist to a neutral antagonist upon isomerization without leaving the binding pocket. In combination, these findings suggest a molecular mechanism for activity modulation via efficacy photoswitches and provide a framework for designing ligands that exploit light-driven transitions within the binding pocket to achieve spatiotemporal control of receptor function.

G protein-coupled receptors↗
DOE OSTI2022

Rational Control of Off‐State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement**

Abstract Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non‐fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off ‐state conformations, trans1 and trans2 , located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off ‐state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high‐level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue‐ and red‐shifts of the absorption bands associated to trans1 and trans2 , respectively. Thus, due to elimination of trans2 , the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two‐fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2‐V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Recent Developments in Femtosecond Laser-Enabled TriBeam Systems

Streams of multimodal three-dimensional (3D) and four-dimensional (4D) data are revolutionizing our ability to design and predict the behavior of a broad array of advanced materials systems. Over the last 10 years, a new 3D imaging platform consisting of a femtosecond (fs) pulsed laser coupled with a focused ion beam scanning electron microscope (FIB SEM) has been developed by UC Santa Barbara in collaboration with Thermo Fisher Scientific (formerly FEI). The femtosecond-laser-enabled FIB SEM, called the TriBeam, has become one of the only 3D serial sectioning methods available that can gather millimeter-scaled multimodal datasets at sub-μm voxel resolutions; these length scales are critical for many materials problems. Multimodal chemical, crystallographic, and morphological information can be gathered rapidly on a layer-by-layer basis and reconstructed in 3D. Large (gigabyte to terabyte scale) 3D datasets have been generated for a broad array of materials systems, including metallic alloys, ceramics, biomaterials, polymer- and ceramic-matrix composites, and semiconductors. The research tasks conducted have resulted in a completely new design, operating with a dual-wavelength femtosecond-pulsed laser on a plasma focused ion beam (PFIB) platform.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Comparison of three measurement modalities for 3D characterization of manufactured features and process-induced porosity in titanium alloy additively manufactured parts

Nondestructive characterization of internal features and defects within complex components is vital for many industrial applications, particularly with the advent of additive manufacturing (AM) technologies. However, community understanding of the limitations of nondestructive methods such as X-ray Computed Tomography (CT) can be limited in certain industrial sectors as these may be emergent applications. In this paper, we investigate the limits of X-ray CT measurements and compare extracted data with mechanical polishing serial sectioning (MPSS) and confocal laser scanning microscopy (CLSM). The test object is an additively manufactured titanium alloy disk that contains both process-induced porosity and machined features, including focused ion beam milled features designed to probe the resolution limits of X-ray CT. Results show that each of these characterization techniques has advantages and disadvantages. We compare data acquisition times, spatial resolution, geometric measurement accuracy and defect visualization fidelity across these modalities to establish a practical framework.

Additive manufacturing↗
DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl – into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗