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Results for “molecular logic”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Structural basis of molecular logic OR in a dual-sensor histidine kinase

Signal detection and integration by sensory proteins constitute the critical molecular events as living organisms respond to changes in a complex environment. Many sensory proteins adopt a modular architecture that integrates the perception of distinct chemical or physical signals and the generation of a biological response in the same protein molecule. Currently, how signal perception and integration are achieved in such a modular, often dimeric, framework remains elusive. In this study, we report a dynamic crystallography study on the tandem sensor domains of a dual-sensor histidine kinase PPHK (phosphorylation-responsive photosensitive histidine kinase) that operates a molecular logic OR, by which the output kinase activity is modulated by a phosphorylation signal and a light signal. A joint analysis of ~170 crystallographic datasets probing different signaling states shows remarkable dimer asymmetry as PPHK responds to the input signals and transitions from one state to the other. Supported by mutational data and structural analysis, these direct observations reveal the working mechanics of the molecular logic OR in PPHK, where the light-induced bending of a long signaling helix at the dimer interface is counteracted by the ligand-induced structural changes from a different sensor domain. We propose that the logic OR of PPHK, together with an upstream photoreceptor, implements a “long-pass” red light response distinct from those accomplished by classical phytochromes.

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

A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex

During development, neural stem cells in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Sonic Hedgehog (Shh) signaling promotes the cortical RGC lineage switch to generate cortical oligodendrocytes and OB interneurons. During this process, cortical RGCs generate intermediate progenitor cells that express critical gliogenesis genes Ascl1, Egfr, and Olig2. The increased Ascl1 expression and appearance of Egfr + and Olig2 + cortical progenitors are concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Furthermore, the transcriptional regulation of Olig2 and Egfr has not been explored. Here, we show that in cortical progenitor cells, multiple regulatory programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between the mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Dipole-Phonon Quantum Logic with Trapped Polar Molecular Ions

The interaction between the electric dipole moment of a trapped molecular ion and the phonon modes of the confined Coulomb crystal couples the orientation of the molecule to its motion. We consider the practical feasibility of harnessing this interaction to initialize, process, and read out quantum information encoded in molecular ion qubits without ever optically illuminating the molecules. We present two schemes wherein a molecular ion can be entangled with a cotrapped atomic ion qubit, providing, among other things, a means for molecular state preparation and measurement. Here, we also show that virtual phonon exchange can significantly boost the range of the intermolecular dipole-dipole interaction, allowing strong coupling between widely separated molecular ion qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites

Mass spectrometry analyses have identified tens of thousands of unknown small molecule-associated peaks in different biological specimens. Notably, even the simplest and best studied organisms like Escherichia coli and Saccharomyces cerevisiae yield thousands of unknown peaks. A key question is how many of these reflect actual novel endogenous metabolites. To explore this, Mahieu and Patti used complete 13 C -labeling in E. coli to credential peaks as biological. This reduced the number of unknowns by more than 90%. Here, we carry out similar uniform 13 C-labeling in the Baker’s yeast S. cerevisiae and two less-studied bioenergy-relevant yeasts Rhodotorula toruloides (lipid producer) and Issatchenkia orientalis (organic acid producer). Identification of unknown metabolite peaks and their molecular formulas is facilitated through software tailored for 13 C labeling data and resulting knowledge of carbon atom count. A classification model evaluates the plausibility of each candidate formula, with peaks lacking plausible candidate formulas unlikely to reflect metabolite molecular ions. This approach prioritizes about one hundred candidate abundant unknown metabolites with logical molecular formulas. Most of these are species-specific rather than conserved across yeasts, and more are found in the nonmodel yeasts than S. cerevisiae. Thus, 13 C-labeling data on unknown metabolites highlights the potential for discovering new metabolites and pathways in nonmodel yeasts.

Carbon↗
DOE OSTI2019

Cell confinement reveals a branched-actin independent circuit for neutrophil polarity

Migratory cells use distinct motility modes to navigate different microenvironments, but it is unclear whether these modes rely on the same core set of polarity components. To investigate this, we disrupted actin-related protein 2/3 (Arp2/3) and the WASP-family verprolin homologous protein (WAVE) complex, which assemble branched actin networks that are essential for neutrophil polarity and motility in standard adherent conditions. Surprisingly, confinement rescues polarity and movement of neutrophils lacking these components, revealing a processive bleb-based protrusion program that is mechanistically distinct from the branched actin-based protrusion program but shares some of the same core components and underlying molecular logic. We further find that the restriction of protrusion growth to one site does not always respond to membrane tension directly, as previously thought, but may rely on closely linked properties such as local membrane curvature. Our work reveals a hidden circuit for neutrophil polarity and indicates that cells have distinct molecular mechanisms for polarization that dominate in different microenvironments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transfer

Biology and electronics are both expert at receiving, analyzing, and responding to information, yet they use entirely different information processing paradigms. Biology processes information using networks that are intrinsically molecular while electronics process information through circuits that control the flow of electrons. There is great interest in coupling the molecular logic of biology with the electronic logic of technology, and we suggest that redox (reduction-oxidation) is a uniquely-suited modality for interfacing biology with electronics. Specifically, redox is a native biological modality and is accessible to electronics through electrodes. Here, we summarize recent advances in mediated electrochemistry to direct information transfer into biological systems intentionally altering function, exposing it for more advanced interpretation, which can dramatically expand the biotechnological toolbox.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electrochemical Switching of a Fluorescent Molecular Rotor Embedded within a Bistable Rotaxane

We report how the nanoconfined environment, introduced by the mechanical bonds within an electrochemically switchable bistable [2]rotaxane, controls the rotation of a fluorescent molecular rotor, namely, an 8-phenyl-substituted boron dipyrromethene (BODIPY). The electrochemical switching of the bistable [2]rotaxane induces changes in the ground-state coconformation and in the corresponding excited-state properties of the BODIPY rotor. In the starting redox state, when no external potential is applied, the cyclobis(paraquat-p-phenylene) (CBPQT4+) ring component encircles the tetrathiafulvalene (TTF) unit on the dumbbell component, leaving the BODIPY rotor unhindered and exhibiting low fluorescence. Upon oxidation of the TTF unit to a TTF2+ dication, the CBPQT4+ ring is forced toward the molecular rotor, leading to an increased energy barrier for the excited state to rotate the rotor into the state with a high nonradiative rate constant, resulting in an overall 3.4-fold fluorescence enhancement. On the other hand, when the solvent polarity is high enough to stabilize the excited charge-transfer state between the BODIPY rotor and the CBPQT4+ ring, movement of the ring toward the BODIPY rotor produces an unexpectedly strong fluorescence signal decrease as the result of photoinduced electron transfer from the BODIPY rotor to the CBPQT4+ ring. The nanoconfinement effect introduced by mechanical bonding can effectively lead to modulation of the physicochemical properties as observed in this bistable [2]rotaxane. On account of the straightforward synthetic strategy and the facile modulation of switchable electrochromic behavior, our approach could pave the way for the development of new stimuli-responsive materials based on mechanically interlocked molecules for future electro-optical applications, such as sensors, molecular memories, and molecular logic gates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Dipolar quantum logic for freely rotating trapped molecular ions

We consider the practical feasibility of using the direct, electric dipole-dipole interaction between cotrapped molecular ions for robust quantum logic without the need for static polarizing fields. Here, the use of oscillating dipole moments, as opposed to static electric dipoles, dynamically decouples the dipoles from laboratory fields, including the electric fields of the trap itself. Further, this implementation does not require the quantum control of motion, potentially removing a major roadblock to ion trap quantum computing scalability. Since the polarizing field is electromagnetic radiation, even pairs of states with splittings in the THz regime can be fully polarized.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library

Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Recent advancements in chiral spintronics: from molecular-level insights to device applications. A prospect based on the interplay between physical and chemical properties of chiral systems

This review discusses recent advancements in chiral-based spin-electronic devices achieved using suitable combinations of organic, inorganic and hybrid materials. The focus is on how chirality can be effectively used to control spin in practical applications, particularly in spintronic sensors and consumer devices. Interestingly, the underlying mechanism for this control is the chiral-induced spin selectivity (CISS) effect, which links the structural chirality of a material to its spin-selective electronic transport properties. The CISS effect arises from the observation that charge transmission in chiral systems is spin selective. Experimental evidence suggests a relationship between electron spin and the structural handedness of the material. In conclusion, this unique structure-transport relationship can be exploited to design a wide range of spintronics devices, including memory, transistors, logic gates and molecular q-bits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Exploring Carbon Nanotubes for Nanoscale Devices

Carbon nanotubes (CNTs) are shown to promise great opportunities in nanoelectronic devices and nanoelectromechanical systems (NEMS) because of their inherent nanoscale sizes, intrinsic electric conductivities, and seamless hexagonal network architectures. I present our collaborative work with Stanford on exploring CNTs for nanodevices in this talk. The electrical property measurements suggest that metallic tubes are quantum wires. Furthermore, two and three terminal CNT junctions have been observed experimentally. We have proposed and studied CNT-based molecular switches and logic devices for future digital electronics. We also have studied CNTs based NEMS inclusing gears, cantilevers, and scanning probe microscopy tips. We investigate both chemistry and physics based aspects of the CNT NEMS. Our results suggest that CNT have ideal stiffness, vibrational frequencies, Q-factors, geometry-dependent electric conductivities, and the highest chemical and mechanical stabilities for the NEMS. The use of CNT SPM tips for nanolithography is presented for demonstration of the advantages of the CNT NEMS.

Han, Jie↗
DOE OSTI2022

A multi-stage single photochrome system for controlled photoswitching responses

The ability of molecular photoswitches to convert on/off responses into large macroscale property change is fundamental to light-responsive materials. However, moving beyond simple binary responses necessitates the introduction of new elements that control the chemistry of the photoswitching process at the molecular scale. To achieve this goal, we designed, synthesized and developed a single photochrome, based on a modified donor–acceptor Stenhouse adduct (DASA), capable of independently addressing multiple molecular states. The multi-stage photoswitch enables complex switching phenomena. To demonstrate this, we show spatial control of the transformation of a three-stage photoswitch by tuning the population of intermediates along the multi-step reaction pathway of the DASAs without interfering with either the first or final stage. This allows for a photonic three-stage logic gate where the secondary wavelength solely negates the input of the primary wavelength. Finally, these results provide a new strategy to move beyond traditional on/off binary photochromic systems and enable the design of future molecular logic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Magnetic force microscopy revealing long-range room temperature stable molecule bridge-induced magnetic ordering on magnetic tunnel junction (MTJ) pillars

Magnetic tunnel junctions (MTJs) can integrate novel single molecular device elements to overcome long-standing fabrication challenges, thus unlocking their novel potential. This study employs magnetic force microscopy (MFM) to demonstrate that organometallic molecules, when placed between two ferromagnetic electrodes along cross-junction shaped MTJ edges, dramatically altered the magnetic properties of the electrodes, affecting areas several hundred microns in size around the molecular junction vicinity at room temperature. These findings are supported by magnetic resonance and magnetometer studies on ∼7000 MTJ pillars. MFM on the pillar sample showed an almost complete disappearance of the magnetic contrast. The spatial magnetic image suggests that molecular channels significantly impacted the spin density of states in the ferromagnetic electrodes. This advancement in MTJ-based molecular devices paves the way for a new generation of commercially viable logic and memory devices controlled by molecular quantum states at near-room temperatures.

Tyagi, Pawan (ORCID:0000000275411344)↗
NASA NTRS2007

NASA Tech Briefs, September 2007

Topics covered include; Rapid Fabrication of Carbide Matrix/Carbon Fiber Composites; Coating Thermoelectric Devices To Suppress Sublimation; Ultrahigh-Temperature Ceramics; Improved C/SiC Ceramic Composites Made Using PIP; Coating Carbon Fibers With Platinum; Two-Band, Low-Loss Microwave Window; MCM Polarimetric Radiometers for Planar Arrays; Aperture-Coupled Thin-Membrane L-Band Antenna; WGM-Based Photonic Local Oscillators and Modulators; Focal-Plane Arrays of Quantum-Dot Infrared Photodetectors; Laser Range and Bearing Finder With No Moving Parts; Microrectenna: A Terahertz Antenna and Rectifier on a Chip; Miniature L-Band Radar Transceiver; Robotic Vision-Based Localization in an Urban Environment; Programs for Testing an SSME-Monitoring System; Cathodoluminescent Source of Intense White Light; Displaying and Analyzing Antenna Radiation Patterns; Payload Operations Support Team Tools; Space-Shuttle Emulator Software; Soft Real-Time PID Control on a VME Computer; Analyzing Radio-Frequency Coverage for the ISS; Nanorod-Based Fast-Response Pressure-Sensitive Paints; Capacitors Would Help Protect Against Hypervelocity Impacts; Diaphragm Pump With Resonant Piezoelectric Drive; Improved Quick-Release Pin Mechanism; Designing Rolling-Element Bearings; Reverse-Tangent Injection in a Centrifugal Compressor; Inertial Measurements for Aero-assisted Navigation (IMAN); Analysis of Complex Valve and Feed Systems; Improved Path Planning Onboard the Mars Exploration Rovers; Robust, Flexible Motion Control for the Mars Explorer Rovers; Solar Sail Spaceflight Simulation; Fluorine-Based DRIE of Fused Silica; Mechanical Alloying for Making Thermoelectric Compounds; Process for High-Rate Fabrication of Alumina Nanotemplates; Electroform/Plasma-Spray Laminates for X-Ray Optics; An Automated Flying-Insect Detection System; Calligraphic Poling of Ferroelectric Material; Blackbody Cavity for Calibrations at 200 to 273 K; KML Super Overlay to WMS Translator; High-Performance Tiled WMS and KML Web Server; Modeling of Radiative Transfer in Protostellar Disks; Composite Pulse Tube; Photometric Calibration of Consumer Video Cameras; Criterion for Identifying Vortices in High- Pressure Flows; Amplified Thermionic Cooling Using Arrays of Nanowires; Delamination-Indicating Thermal Barrier Coatings; Preventing Raman Lasing in High-Q WGM Resonators; Procedures for Tuning a Multiresonator Photonic Filter; Robust Mapping of Incoherent Fiber-Optic Bundles; Extended-Range Ultrarefractive 1D Photonic Crystal Prisms; Rapid Analysis of Mass Distribution of Radiation Shielding; Modeling Magnetic Properties in EZTB; Deep Space Network Antenna Logic Controller; Modeling Carbon and Hydrocarbon Molecular Structures in EZTB; BigView Image Viewing on Tiled Displays; and Imaging Sensor Flight and Test Equipment Software.

Source record↗
DOE OSTI2020

Error detection on quantum computers improving the accuracy of chemical calculations

The ultimate goal of quantum error correction is to achieve the fault-tolerance threshold beyond which quantum computers can be made arbitrarily accurate. This requires extraordinary resources and engineering efforts. We show that even without achieving full fault-tolerance, quantum error detection is already useful on the current generation of quantum hardware. We demonstrate this by executing an end-to-end chemical calculation for the hydrogen molecule encoded in the [[4, 2, 2]] quantum error-detecting code. The encoded calculation with logical qubits significantly improves the accuracy of the molecular ground-state energy.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2002

Transport of Space Environment Electrons: A Simplified Rapid-Analysis Computational Procedure

A computational procedure for describing transport of electrons in condensed media has been formulated for application to effects and exposures from spectral distributions typical of electrons trapped in planetary magnetic fields. The procedure is based on earlier parameterizations established from numerous electron beam experiments. New parameterizations have been derived that logically extend the domain of application to low molecular weight (high hydrogen content) materials and higher energies (approximately 50 MeV). The production and transport of high energy photons (bremsstrahlung) generated in the electron transport processes have also been modeled using tabulated values of photon production cross sections. A primary purpose for developing the procedure has been to provide a means for rapidly performing numerous repetitive calculations essential for electron radiation exposure assessments for complex space structures. Several favorable comparisons have been made with previous calculations for typical space environment spectra, which have indicated that accuracy has not been substantially compromised at the expense of computational speed.

Nealy, John E.↗
DOE OSTI2019

Low-Temperature Charging Dynamics of the Ionic Liquid and Its Gating Effect on FeSe 0.5 Te 0.5 Superconducting Films

Ionic liquids (ILs) have been investigated extensively because of their unique ability to form the electric double layer (EDL), which induces high electrical field. For certain materials, low-temperature IL charging is needed to limit the electrochemical etching. Here, we report our investigation of the low-temperature charging dynamics in two widely used ILs—DEME-TF 2 N and C4mim-TF 2 N. Results show that the formation of the EDL at ~220 K requires several hours relative to milliseconds at room temperature, and an equivalent voltage V e is introduced as a measure of the EDL formation during the biasing process. Here, the experimental observation is supported by molecular dynamics simulation, which shows that the dynamics are logically a function of gate voltage, time, and temperature. To demonstrate the importance of understanding the charging dynamics, a 140 nm thick FeSe 0.5 Te 0.5 film was biased using the DEME IL, showing a tunable T c between 18 and 35 K. Notably, this is the first observation of the tunability of the T c in thick film FeSe 0.5 Te 0.5 superconductors.

2D materials↗