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At least 685 records · Page 38

Extended q -Range X-Ray Scattering Reveals High-Resolution Structural Details of Biomacromolecules in Aqueous Solutions

Here, we communicate a feasibility study for high-resolution structural characterization of biomacromolecules in aqueous solution from X-ray scattering experiments measured over a range of scattering vectors (q) that is approximately two orders of magnitude wider than used previously for such systems. Scattering data with such an extended q-range enables the recovery of the underlying real-space atomic pair distribution function, which facilitates structure determination. We demonstrate the potential of this method for biomacromolecules using several types of cyclodextrins (CD) as model systems. We successfully identified deviations of the tilting angles for the glycosidic units in CDs in aqueous solutions relative to their values in the crystalline forms of these molecules. Such level of structural detail is inaccessible from standard small angle scattering measurements. Our results call for further exploration of ultra-wide-angle X-ray scattering measurements for biomacromolecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dark fluxes from electromagnetic cascades

We study dark sector production in electromagnetic (EM) cascades. This problem requires accurate simulations of Standard Model (SM) and dark sector processes, both of which impact angular and energy distributions of emitted particles that ultimately determine flux predictions in a downstream detector. We describe the minimal set of QED processes which must be included to faithfully reproduce a SM cascade, and identify a universal algorithm to generate a dark sector flux given a Monte-Carlo simulation of a SM shower. We provide a new tool, "Image missing", which simulates EM cascades with associated dark vector production, and compare it against existing literature and “off the shelf” tools. The signal predictions at downstream detectors can strongly depend on the nontrivial interplay (and modelling) of SM and dark sector processes, in particular multiple Coulomb scattering and positron annihilation. We comment on potential impacts of these effects for realistic experimental setups.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Discovery of tunable and soluble organic emitters for solid-state lasers with a self-driving laboratory

We have recently demonstrated the ability of using self-driving laboratories for AI-driven searches of organic emitters for solid-state lasing devices. Our past workflow featured solubility challenges for such large molecular moieties. In this next-generation study, we return to the drawing board to explore a family of com-pounds that are much solution processable and composed of a set of electronic cores that provide a broader color response. Out of 252 potential candidates,and with guidance from DFT calculations, we selectively perform a compre-hensive study exploring 51 fluorene-based A-B-A type organic laser oligomers, armed with our self-driving lab. The candidates range from simple hydrocarbon molecules to complex hetero atom-mixed molecules. As a result of this study, we highlight diketopyrrolopyrrole and benzodiazole derivatives for their largely red-shifted emissions. Furthermore, we investigate the effect of color change aris-ing from hetero atom permutation, fluorine addition, thiophene coupling, and a combination of fluorine addition and thiophene coupling. Amplified spontaneous emission (ASE) measurements in the solid state further corroborate the lasing potential of selected candidates, reinforcing their suitability for future device applications. The computational study with density functional theory confirms the experimental results.

fluorescence↗

Flowing plasma rearrangement in the presence of static perturbing fields

Charged particles interacting with electromagnetic waves have a portion of their energy tied up in wave-driven oscillations. When these waves are localized to the exhaust of linear magnetic confinement systems, this ponderomotive effect can be utilized to enhance particle confinement. The same effect can be derived for particles moving via an E×B drift into a region of a static perturbation to the electromagnetic fields which has a large wave vector component in the direction of the motion. In this work, we use a simplified slab model to self-consistently solve for the electromagnetic fields within the fluid flowing plasma of a static flute-like (k∥=0) perturbation and evaluate the resulting ponderomotive potential. We find that two types of perturbations can exist within the flowing plasma, which are an O wave and an X wave in the frame moving with the fluid. In the case of tenuous plasma, these perturbations are magnetostatic or electrostatic multipole-analog perpendicular to the guiding magnetic field in the lab frame, respectfully. For denser plasmas, the O wave-like perturbation is screened at the electron skin depth scale, and the X wave-like perturbation is a combination of a similar perpendicular electric perturbation and parallel magnetic perturbation. The ponderomotive potential generated in the X wave-like case is gyrofrequency-dependent and can be used as either potential barriers or potential wells, depending on the direction of the flow velocity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Responsive Assistant For Navigating And Guiding Engineering With Rigor (ranger)

The bot uses the GitHub API to fetch discussions from a MOOSE repository and store the data in a vector database. When a new discussion is initiated, the algorithm compares the discussion title with the content of all previous discussions (title + discussions) in the database and provides the most relevant posts to the user. The database is updated regularly to include all new posts, potentially on a monthly basis.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of lift force on ejecta transport

The possible effects of lift on individual ejecta trajectories after an impact event are examined, considering a dimensionless transport parameter (K), the initial velocity vector of the particles, and the ratio of the lift to drag coefficients. If this ratio is not equal to zero, the trajectory is greatly influenced by the lift coefficient, particularly for large values of K and high launch angles. It is suggested that lift potentially can affect small ejecta in the size range also affected by aerodynamic drag, thereby adding complexity to atmospheric effects discussed by Schultz and Gault (1978).

Pai, S. I.↗

Thermodynamic budget diagrams for the hurricane subcloud layer

The idealized hurricane boundary layer budget from Malkus and Riehl (1960) are reexamined using vector diagrams for the thermodynamic budgets in the light of recent observational studies. A large air-sea temperature difference can only be maintained with both large fluxes through cloud-base level and a large evaporative cooling of the subcloud layer. The high equivalent potential temperature values observed in hurricane eyewalls can be reached if these cloud-base and evaporative fluxes are reduced and the subcloud layer moves toward the sea surface virtual potential temperature.

Betts, Alan K.↗

Computer Modeling of Thermal Convection in Melts to Explain Glass Formation in Low Gravity and on Earth

Experiments conducted up to this time on glass forming melts in the low gravity environment of space show that glasses prepared in low-g are more chemically homogeneous and more resistant to crystallization than the comparable glasses prepared at 1-g on Earth. This result is somewhat surprising and opposite to the accepted concept on glass formation for a melt. A hypothesis based on "shear thinning" of a melt, a decrease in viscosity with increasing shear stress, is proposed as an explanation for the observed low-gravity results. This paper describes detailed simulation procedures to test the role of thermal convection in introducing shear stress in glass forming melts, using a lithium disilcate melt as a model. The simulation system in its idealized version consists of a cylinder that is heated at one end and cooled at the other with gravity acting in a transverse direction to the thermal gradient. The side wall of the cylinder is assumed to be insulating. The governing equations of motion and energy are solved using variable properties for viscosity (Arrehenius and non-Arrehenius behaviors) and density (constant and temperature dependent). Other parametric variables in the calculations include gravity level and gravity vector orientation. The shear stress in the system are then computed as a function of gravity from the calculated values of maximum melt velocity, and its effect on melt viscosity (shear thinning) is predicted. Also included and discussed are the modeling efforts related to other potential convective processes in glass forming melts and their possible effects on melt viscosity.

Ray, Chandra S.↗

CubeSat Constellation Cloud Winds(C3Winds) A New Wind Observing System to Study Mesoscale Cloud Dynamics and Processes

The CubeSat Constellation Cloud Winds (C3Winds) is a NASA Earth Venture Instrument (EV-I) concept with the primary objective to better understand mesoscale dynamics and their structures in severe weather systems. With potential catastrophic damage and loss of life, strong extratropical and tropical cyclones (ETCs and TCs) have profound three-dimensional impacts on the atmospheric dynamic and thermodynamic structures, producing complex cloud precipitation patterns, strong low-level winds, extensive tropopause folds, and intense stratosphere-troposphere exchange. Employing a compact, stereo IR-visible imaging technique from two formation-flying CubeSats, C3Winds seeks to measure and map high-resolution (2 km) cloud motion vectors (CMVs) and cloud geometric height (CGH) accurately by tracking cloud features within 5-15 min. Complementary to lidar wind observations from space, the high-resolution wind fields from C3Winds will allow detailed investigations on strong low-level wind formation in an occluded ETC development, structural variations of TC inner-core rotation, and impacts of tropopause folding events on tropospheric ozone and air quality. Together with scatterometer ocean surface winds, C3Winds will provide a more comprehensive depiction of atmosphere-boundary-layer dynamics and interactive processes. Built upon mature imaging technologies and long history of stereoscopic remote sensing, C3Winds provides an innovative, cost-effective solution to global wind observations with potential of increased diurnal sampling via CubeSat constellation.

mesoscale dynamics↗

Evaluation of two inoculation routes of an adenovirus-mediated viral protein inhibitor in a Crimean-Congo hemorrhagic fever mouse model

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne nairovirus with a wide geographic spread that can cause severe and lethal disease. No specific medical countermeasures are approved to combat this illness. The CCHFV L protein contains an ovarian tumor (OTU) domain with a cysteine protease thought to modulate cellular immune responses by removing ubiquitin and ISG15 post-translational modifications from host and viral proteins. Viral deubiquitinases like CCHFV OTU are attractive drug targets, as blocking their activity may enhance cellular immune responses to infection, and potentially inhibit viral replication itself. We previously demonstrated that the engineered ubiquitin variant CC4 is a potent inhibitor of CCHFV replication in vitro. A major challenge of the therapeutic use of small protein inhibitors such as CC4 is their requirement for intracellular delivery, e.g., by viral vectors. In this study, we examined the feasibility of in vivo CC4 delivery by a replication-deficient recombinant adenovirus (Ad-CC4) in a lethal CCHFV mouse model. Since the liver is a primary target of CCHFV infection, we aimed to optimize delivery to this organ by comparing intravenous (tail vein) and intraperitoneal injection of Ad-CC4. While tail vein injection is a traditional route for adenovirus delivery, in our hands intraperitoneal injection resulted in higher and more widespread levels of adenovirus genome in tissues, including, as intended, the liver. However, despite promising in vitro results, neither route of in vivo CC4 treatment resulted in protection from a lethal CCHFV infection.

59 BASIC BIOLOGICAL SCIENCES↗

Relativistic two-component projection-based quantum embedding for open-shell systems

In this work, we present a relativistic quantum embedding formalism capable of variationally treating relativistic effects, including scalar-relativity and spin–orbit coupling. We extend density functional theory (DFT)-in-DFT projection-based quantum embedding to a relativistic two-component formalism, where the full spin magnetization vector form is retained throughout the embedding treatment. To benchmark various relativistic embedding schemes, spin–orbit splitting of the nominally t 2g valence manifold of W(CO) 6 , exchange coupling of [(H 3 N) 4 Cr(OH) 2 Cr(NH 3 ) 4 ] 4+ , and the dissociation potential curve of WF 6 are investigated. The relativistic embedding formalism introduced in this work is well suited for efficient modeling of open-shell systems containing late transition metal, lanthanide, and actinide molecular complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.

59 BASIC BIOLOGICAL SCIENCES↗

The airborne laser ranging system, its capabilities and applications

The airborne laser ranging system is a multibeam short pulse laser ranging system on board an aircraft. It simultaneously measures the distances between the aircraft and six laser retroreflectors (targets) deployed on the Earth's surface. The system can interrogate over 100 targets distributed over an area of 25,000 sq, kilometers in a matter of hours. Potentially, a total of 1.3 million individual range measurements can be made in a six hour flight. The precision of these range measurements is approximately + or - 1 cm. These measurements are used in procedure which is basically an extension of trilateration techniques to derive the intersite vector between the laser ground targets. By repeating the estimation of the intersite vector, strain and strain rate errors can be estimated. These quantities are essential for crustal dynamic studies which include determination and monitoring of regional strain in the vicinity of active fault zones, land subsidence, and edifice building preceding volcanic eruptions.

Kahn, W. D.↗

Radar Investigations of Asteroids

Radar investigations of asteroids, including observations during 1984 to 1985 of at least 8 potential targets and continued analyses of radar data obtained during 1980 to 1984 for 30 other asteroids is proposed. The primary scientific objectives include estimation of echo strength, polarization, spectral shape, spectral bandwidth, and Doppler shift. These measurements yield estimates of target size, shape, and spin vector; place constraints on topography, morphology, density, and composition of the planetary surface; yield refined estimates of target orbital parameters; and reveals the presence of asteroidal satellites.

Ostro, S. J.↗

Calculations of rate constants for the three-body recombination of H2 in the presence of H2

A new global potential energy hypersurface for H2 + H2 is constructed and quasiclassical trajectory calculations performed using the resonance complex theory and energy transfer mechanism to estimate the rate of three body recombination over the temperature range 100 to 5000 K. The new potential is a faithful representation of ab initio electron structure calculations, is unchanged under the operation of exchanging H atoms, and reproduces the accurate H3 potential as one H atom is pulled away. Included in the fitting procedure are geometries expected to be important when one H2 is near or above the dissociation limit. The dynamics calculations explicitly include the motion of all four atoms and are performed efficiently using a vectorized variable-stepsize integrator. The predicted rate constants are approximately a factor of two smaller than experimental estimates over a broad temperature range.

Schwenke, David W.↗

Calculations of rate constants for the three-body recombination of H2 in the presence of H2

A new global potential energy hypersurface for H2 + H2 is constructed and quasiclassical trajectory calculations performed using the resonance complex theory and energy transfer mechanism to estimate the rate of three body recombination over the temperature range 100 to 5000 K. The new potential is a faithful representation of ab initio electron structure calculations, is unchanged under the operation of exchanging H atoms, and reproduces the accurate H3 potential as one H atom is pulled away. Included in the fitting procedure are geometries expected to be important when one H2 is near or above the dissociation limit. The dynamics calculations explicitly include the motion of all four atoms and are performed efficiently using a vectorized variable-stepsize integrator. The predicted rate constants are approximately a factor of two smaller than experimental estimates over a broad temperature range.

Schwenke, David W.↗

Onboard Classifiers for Science Event Detection on a Remote Sensing Spacecraft

Typically, data collected by a spacecraft is downlinked to Earth and pre-processed before any analysis is performed. We have developed classifiers that can be used onboard a spacecraft to identify high priority data for downlink to Earth, providing a method for maximizing the use of a potentially bandwidth limited downlink channel. Onboard analysis can also enable rapid reaction to dynamic events, such as flooding, volcanic eruptions or sea ice break-up. Four classifiers were developed to identify cryosphere events using hyperspectral images. These classifiers include a manually constructed classifier, a Support Vector Machine (SVM), a Decision Tree and a classifier derived by searching over combinations of thresholded band ratios. Each of the classifiers was designed to run in the computationally constrained operating environment of the spacecraft. A set of scenes was hand-labeled to provide training and testing data. Performance results on the test data indicate that the SVM and manual classifiers outperformed the Decision Tree and band-ratio classifiers with the SVM yielding slightly better classifications than the manual classifier.

classification↗