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Results for “Signaling molecules”

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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Detecting Atmospheric Molecules of Nontransiting Temperate Terrestrial Exoplanets Using High-resolution Spectroscopy in the Mid-infrared Domain

Motivated by the development of high-dispersion spectrographs in the mid-infrared (MIR) range, we study their application to the atmospheric characterization of nearby nontransiting temperate terrestrial planets around M-type stars. We examine the detectability of CO{sub 2}, H{sub 2}O, N{sub 2}O, and O{sub 3 }features in high-resolution planetary thermal emission spectra at 12–18 μm assuming an Earth-like profile and a simplified thermal structure. The molecular line width of such planets can be comparable to or broader than the Doppler shift due to the planetary orbital motion. Given the likely difficulty in knowing the high-resolution MIR spectrum of the host star with sufficient accuracy, we propose observing the target system at two quadrature phases and extracting the differential spectra as the planetary signal. In this case, the signals can be substantially suppressed compared with the case where the host star spectrum is perfectly known, as some parts of the spectral features do not remain in the differential spectra. Despite this self-subtraction, the CO{sub 2} and H{sub 2}O features of nearby (≲5 pc) systems with mid-/late-M host stars would be feasible with a 6.5 m class cryogenic space telescope, and orbital inclination could also be constrained for some of them. For CO{sub 2} and N{sub 2}O in a 1 bar Earth-like atmosphere, this method would be sensitive when the mixing ratio is 1–10{sup 3} ppm. The detectability of molecules except O{sub 3} is not significantly improved when the spectral resolution is higher than R≳10,000, although the constraint on the orbital inclination is improved. This study provides some benchmark cases useful for assessing the value of MIR high-resolution spectroscopy in terms of characterization of potentially habitable planets.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces

Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current interest as antifoulant strategies. Furthermore, despite significant proofs-of-concept, we still lack a fundamental understanding of how the nanoscopic structure of this hydration layer translates to reduced fouling, how surface chemistry can be tuned to achieve antifouling through hydration water, and why, in particular, zwitterionic surfaces seem so promising. Here, we use molecular dynamics simulations and free energy calculations to investigate the molecular relationships among surface chemistry, hydration water structure, and surface–solute affinity across a variety of surface-decorated chemistries. Specifically, we consider polypeptoid-decorated surfaces that display well-known experimental antifouling capabilities and that can be synthesized sequence specifically, with precise backbone positioning of, e.g., charged groups. Through simulations, we calculate the affinities of a range of small solutes to polypeptoid brush surfaces of varied side-chain chemistries. We then demonstrate that measures of the structure of surface hydration water in response to a particular surface chemistry signal solute–surface affinity; specifically, we find that zwitterionic chemistries produce solute–surface repulsion through highly coordinated hydration water while suppressing tetrahedral structuring around the solute, in contrast to uncharged surfaces that show solute–surface affinity. Based on the relationship of this structural perturbation to the affinity of small-molecule solutes, we propose a molecular mechanism by which zwitterionic surface chemistries enhance solute repulsion, with broader implications for the design of antifouling surfaces.

36 MATERIALS SCIENCE↗
NASA NTRS1978

Detectability limit and uncertainty considerations for laser induced fluorescence spectroscopy in flames

Laser induced fluorescence spectroscopy of flames is discussed, and derived uncertainty relations are used to calculate detectability limits due to statistical errors. Interferences due to Rayleigh scattering from molecules as well as Mie scattering and incandescence from particles have been examined for their effect on detectability limits. Fluorescence trapping is studied, and some methods for reducing the effect are considered. Fluorescence trapping places an upper limit on the number density of the fluorescing species that can be measured without signal loss.

Daily, J. W.↗
DOE OSTI2021

Plasminogen activator Inhibitor-2 inhibits pulmonary arterial smooth muscle cell proliferation in pulmonary arterial hypertension via PI3K/Akt and ERK signaling

Highlights: • Serum PAI-2 is decreased in patients with pulmonary arterial hypertension. • Serum PAI-2 is associated with disease severity in pulmonary arterial hypertension. • Exogenous PAI-2 attenuates monocrotaline induced pulmonary hypertension in rats. • PAI-2 inhibits pulmonary arterial smooth muscle proliferation via PI3K/Akt and ERK. The proliferation of pulmonary arterial smooth muscle cells (PASMCs) and subsequent pulmonary vascular remodeling leads to pulmonary arterial hypertension (PAH). Understanding the underlying mechanisms and identifying molecules that can suppress PASMCs proliferation is critical for developing effective pharmacological treatment. We previously showed that plasminogen activator inhibitor-2 (PAI-2) inhibited human PASMC (hPASMCs) proliferation in vitro. However, its inhibitory effect on PAH remains to be determined, and the mechanism remains to be illustrated.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Ultra-high SERS detection of consumable coloring agents using plasmonic gold nanostars with high aspect-ratio spikes

Solution-based SERS detection by using a portable Raman instrument has emerged as an important tool due to its simplicity, and flexibility for rapid and on-site screening of analyte molecules. However, this method has several shortcomings, including poor sensitivity especially for weak-affinity analyte molecules, where there is no close contact between the plasmonic metal surface and analyte molecule. Examples of weak-affinity molecules include pigment molecules that are commonly used as a consumable coloring agent, such as allura red (AR), and sunset yellow (SY). As high consumption of colorant agents has been shown to cause adverse effects on human health, there is a strong need to develop a simple and practical sensing system with high sensitivity for these agents. Here we present a novel, highly sensitive solution-based SERS detection method for AR, and SY by using CTAC capped gold nanostars (GNS) having different aspect ratios (GNS-2, GNS-4, and GNS-5) without utilizing any aggregating agents which can enhance SERS signal however it reduces batch to batch reproducibility. The influence of the aspect ratio of GNS on SERS properties was investigated. We have achieved a limit of detection (LOD) of AR and SY as low as 0.5 and 1 ppb, respectively by using GNS-5 with the advantages of minimal sample preparation by just mixing the analyte solution into a well plate containing GNS solution. In addition, excellent colloidal stability and reproducibility have further enhanced the applicability in real-world samples. Altogether, our results evidence that the solution-based SERS detection platform using high aspect-ratio GNS can be applied for practical application to detect pigment molecules in real samples with satisfactory results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Improved joint X-ray and neutron refinement procedure in Phenix

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Investigating the ultraviolet photodissociation of bromocyclopropane with ultrafast electron diffraction

We have studied the photodissociation of gas-phase bromocyclopropane by 200 nm wavelength ultraviolet radiation using ultrafast electron diffraction. Bromocyclopropane is a prototypical molecule in the study of organobromides, a class of molecules that have a significant impact on atmospheric ozone depletion through their photochemistry. Here, previous studies have revealed two possible reaction pathways for the photodissociation of bromine from bromocyclopropane; either the C–Br bond dissociates, leaving behind a cyclopropyl ring, or there is a concerted opening of the cyclopropyl ring along with the C–Br bond dissociation. In this work, both our experimental and simulation results indicate that the majority of the UV-photoexcited BCP molecules (88% ± 11% in the experiment) follow the first reaction pathway, in which the cyclopropyl ring remains closed after homolytic C–Br bond cleavage. This direct bond dissociation occurs within the experimental time resolution of 270 fs. In order to differentiate between the possible reaction end-products, both of which have diffraction signals dominated by the bromine atom, a new analysis method has been employed, which is more sensitive to the structure of the end-products.

Atmospheric chemistry↗
DOE OSTI2024

Mechanisms Underlying a Quantum Superposition Microscope Based on THz-Driven Coherent Oscillations in a Two-Level Molecular Sensor

Here we report pump-probe measurements of a hydrogen molecule (H 2 ) in the tunnel junction of a scanning tunneling microscope (STM) coupled to ultrashort terahertz (THz) pulses. The coherent oscillation of the THz induced DC tunneling current at a frequency of ~0.5 THz fingerprints the absorption by H 2 as a two-level system (TLS). Two components of the oscillatory signal are observed and point to both photon and field aspects of the THz pulses. A few loosely bound states with similar energies for the upper state of the TLS are evidenced by the coherent revival of oscillatory signal. Furthermore, the comparison of spectroscopic features of H 2 with different tips provides an understanding of the TLS for H 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2021

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Membrane-Based Functions in the Origin of Cellular Life

If peptides consist of nonpolar residues only, they become inserted into the nonpolar phase. As demonstrated by the example of the leucine undecamer, such peptides fold into an a-helix as they partition into the nonpolar medium. The folding proceeds through an intermediate, called the 310-helix, which remains in equilibrium with the a-helix. This process represents a simple, protobiologically relevant example of environmentally-mediated self-organization of biological molecules. Once in the nonpolar environment, the peptides can readily change their orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with changing external conditions may have provided a simple mechanism of transmitting signals from the environment to the interior of a protocell.

Wilson, Michael↗
NASA NTRS2026

CH3OH and HCN in Interstellar Comet 3I/ATLAS Mapped with the ALMA Atacama Compact Array: Distinct Outgassing Behaviors and a Remarkably High CH3OH/HCN Production Rate Ratio

We report the detection of methanol (CH3OH) toward interstellar comet 3I/ATLAS using the At-acama Compact Array of the Atacama Large Millimeter/Submillimeter Array (ALMA) on UT 2025 August 28, September 18 and 22, and October 1, and of hydrogen cyanide (HCN) on September 12 and 15. These observations spanned pre-perihelion heliocentric distances (r H ) of 2.6 – 1.7 au. The molecules showed outgassing patterns distinct from one another, with HCN production being depleted in the sunward hemisphere of the coma, whereas CH3OH was enhanced in that direction. Statistical analysis of molecular scale lengths in 3I/ATLAS indicated that CH3OH included production from coma sources at Lp > 258 km at 99% confidence. However low signal-to-noise on long baselines, which sample emission on small spatial scales closest to the nucleus, prevented definitively ruling out CH3OH as purely a parent species. In contrast, HCN production was indistinguishable from direct nucleus sublimation. The CH3OH production rate increased sharply from August through October, including an uptick near the inner edge of the H2O sublimation zone at rH = 2 au. Compared to comets measured to date at radio wavelengths, the derived CH3OH/HCN ratios in 3I/ATLAS of 124+30−34 and 79+11−14on September 12 and 15, respectively, are among the most enriched values measured in any comet, surpassed only by anomalous solar system comet C/2016 R2 (PanSTARRS)

Comae↗
DOE OSTI2024

Ultrafast Formation of Charge Transfer Trions at Molecular‐Functionalized 2D MoS 2 Interfaces

Abstract In this work, we investigate trion dynamics occurring at the heterojunction between organometallic molecules and a monolayer transition metal dichalcogenide (TMD) with transient electronic sum frequency generation (tr‐ESFG) spectroscopy. By pumping at 2.4 eV with laser pulses, we have observed an ultrafast hole transfer, succeeded by the emergence of charge‐transfer trions. This observation is facilitated by the cancellation of ground state bleach and stimulated emission signals due to their opposite phases, making tr‐ESFG especially sensitive to the trion formation dynamics. The presence of charge‐transfer trion at molecular functionalized TMD monolayers suggests the potential for engineering the local electronic structures and dynamics of specific locations on TMDs and offers a potential for transferring unique electronic attributes of TMD to the molecular layers.

Jing, Yuancheng↗
DOE OSTI2023

Emulating Quantum Entangled Biphoton Spectroscopy Using Classical Light Pulses

We show that for a class of quantum light spectroscopy (QLS) experiments using n = 0, 1, 2, ··· classical light pulses and an entangled photon pair (a biphoton state) where one photon acts as a reference without interacting with the matter sample, identical signals can be obtained by replacing the biphotons with classical-like coherent states of light, where these are defined explicitly in terms of the parameters of the biphoton states. An input-output formulation of quantum nonlinear spectroscopy is used to prove this equivalence. We demonstrate the equivalence numerically by comparing a classical pump–quantum probe experiment with the corresponding classical pump–classical probe experiment. This analysis shows that understanding the equivalence between entangled biphoton probes and carefully designed classical-like coherent state probes leads to quantum-inspired classical experiments that yield equivalent signals and provides insights for the future design of QLS experiments that could provide a true quantum advantage.

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

Analysis of vibronic coupling in a 4f molecular magnet with FIRMS

Vibronic coupling, the interaction between molecular vibrations and electronic states, is a fundamental effect that profoundly affects chemical processes. In the case of molecular magnetic materials, vibronic, or spin-phonon, coupling leads to magnetic relaxation, which equates to loss of magnetic memory and loss of phase coherence in molecular magnets and qubits, respectively. The study of vibronic coupling is challenging, and most experimental evidence is indirect. Here we employ far-infrared magnetospectroscopy to directly probe vibronic transitions in [Yb(trensal)] (where H 3 trensal = 2,2,2-tris(salicylideneimino)trimethylamine). We find intense signals near electronic states, which we show arise due to an “envelope effect” in the vibronic coupling Hamiltonian, which we calculate fully ab initio to simulate the spectra. We subsequently show that vibronic coupling is strongest for vibrational modes that simultaneously distort the first coordination sphere and break the C 3 symmetry of the molecule. With this knowledge, vibrational modes could be identified and engineered to shift their energy towards or away from particular electronic states to alter their impact. Hence, these findings provide new insights towards developing general guidelines for the control of vibronic coupling in molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Catalytic C 2 H 2 synthesis via low temperature CO hydrogenation on defect-rich 2D-MoS 2 and 2D-MoS 2 decorated with Mo clusters

Rational design of novel catalytic materials used to synthesize storable fuels via the CO hydrogenation reaction has recently received considerable attention. In this work, defect poor and defect rich 2D-MoS 2 as well as 2D-MoS 2 decorated with Mo clusters are employed as catalysts for the generation of acetylene (C 2 H 2 ) via the CO hydrogenation reaction. Temperature programmed desorption is used to study the interaction of CO and H2 molecules with the MoS 2 surface as well as the formation of reaction products. The experiments indicate the presence of four CO adsorption sites below room temperature and a competitive adsorption between the CO and H 2 molecules. The investigations show that CO hydrogenation is not possible on defect poor MoS 2 at low temperatures. However, on defect rich 2D-MoS 2 , small amounts of C 2 H 2 are produced, which desorb from the surface at temperatures between 170 K and 250 K. A similar C 2 H 2 signal is detected from defect poor 2D-MoS 2 decorated with Mo clusters, which indicates that low coordinated Mo atoms on 2D-MoS 2 are responsible for the formation of C 2 H 2 . Density functional theory investigations are performed to explore possible adsorption sites of CO and understand the formation mechanism of C 2 H 2 on MoS 2 and Mo 7 /MoS 2 . The theoretical investigation indicates a strong binding of C 2 H 2 on the Mo sites of MoS 2 preventing the direct desorption of C 2 H 2 at low temperatures as observed experimentally. Instead, the theoretical results suggest that the experimental data are consistent with a mechanism in which CHO radical dimers lead to the formation of C 2 H 2 that presents an exothermic desorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Optimization of microscopic and macroscopic second order optical nonlinearities

Nonlinear optical materials (NLO) can be used to extend the useful frequency range of lasers. Frequency generation is important for laser-based remote sensing and optical data storage. Another NLO effect, the electro-optic effect, can be used to modulate the amplitude, phase, or polarization state of an optical beam. Applications of this effect in telecommunications and in integrated optics include the impression of information on an optical carrier signal or routing of optical signals between fiber optic channels. In order to utilize these effects most effectively, it is necessary to synthesize materials which respond to applied fields very efficiently. In this talk, it will be shown how the development of a fundamental understanding of the science of nonlinear optics can lead to a rational approach to organic molecules and materials with optimized properties. In some cases, figures of merit for newly developed materials are more than an order of magnitude higher than those of currently employed materials. Some of these materials are being examined for phased-array radar and other electro-optic switching applications.

Marder, Seth R.↗