SEARCH · Engineering Papers

Results for “EXCLUSIVE INTERACTIONS”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5

All sources NASA NTRS DOE OSTI

DOE OSTI2017

Role of Interactions and Correlations on Collective Dynamics of Molecular Motors Along Parallel Filaments

Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest molecules of their filament while performing any mechanical work. These interactions modify the microscopic level properties of motor proteins. In this work, a new version of two-channel totally asymmetric simple exclusion process, that incorporates the intra-channel interactions in a thermodynamically consistent way, is proposed. As the existing approaches for multi-channel systems deviate from analyzing the combined effect of inter and intra-channel interactions, a new approach known as modified vertical cluster mean field is developed. The approach along with Monte Carlo simulations successfully encounters some correlations and computes the complex dynamic properties of the system. Role of symmetry of interactions and inter-channel coupling is observed on the phase diagrams, maximal particle current and its corresponding optimal interaction strength. Surprisingly, for all values of coupling rate and most of the interaction splittings, the optimal interaction strength corresponding to maximal current belongs to the case of weak repulsive interactions. Moreover, for weak interaction splittings and with an increase in the coupling rate, the optimal interaction strength tends towards the known experimental results. The effect of coupling as well as interaction energy is also measured for correlations. They are found to be short-range and weaker for repulsive and weak attractive interactions while they are long-range and stronger for large attractions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography

Antibody 10E8 is capable of effectively neutralizing HIV through its recognition of the membrane-proximal external region (MPER), and a suitably optimized version of 10E8 might have utility in HIV therapy and prophylaxis. However, 10E8 displays a three-peak profile on size-exclusion chromatography (SEC), complicating its manufacture. Here we show cis-trans conformational isomerization of the Tyr-Pro-Pro (YPP) motif in the heavy chain 3rd complementarity-determining region (CDR H3) of antibody 10E8 to be the mechanistic basis of its multipeak behavior. We observed 10E8 to undergo slow conformational isomerization and delineate a mechanistic explanation for effective comodifiers that were able to resolve its SEC heterogeneity and to allow an evaluation of the critical quality attribute of aggregation. We determined crystal structures of single and double alanine mutants of a key di-proline motif and of a light chain variant, revealing alternative conformations of the CDR H3. We also replicated both multi-peak and delayed SEC behavior with MPER-antibodies 4E10 and VRC42, by introducing a Tyr-Pro (YP) motif into their CDR H3s. Our results show how a conformationally dynamic CDR H3 can provide the requisite structural plasticity needed for a highly hydrophobic paratope to recognize its membrane-proximal epitope.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Hints on nuclear effects from ArgoNeuT data

Initial results from a topological analysis of CC “0 pion” muon neutrino events in LAr collected by the ArgoNeuT experiment on the NuMI LE beam at Fermilab (in the few GeV energy region) are presented and compared with predictions from MC simulations. A new analysis method, based on the reconstruction of exclusive topologies, fully exploiting the LArTPC technique capabilities, is used to analyze the events and study nuclear effects in neutrino interactions on Argon nuclei. Multiple protons accompanying the leading muon and the presence of vertex activity are clearly visible (and measured) in the events. Ratios among rates of different exclusive topologies provide indications of the size of nuclear effects in neutrino-nucleus interactions in LAr.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme–substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. Here, these results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Molecular Dynamics Simulations of Anion Exclusion in Clay Interlayer Nanopores

© 2016, Clays and Clay Minerals. All rights reserved. The aqueous chemistry of water films confined between clay mineral surfaces remains an important unknown in predictions of radioelement migration from radioactive waste repositories. This issue is particularly important in the case of long-lived anionic radioisotopes ( 129 I - , 99 TcO - 4 , 36 Cl - ) which interact with clay minerals primarily by anion exclusion. For example, models of ion migration in clayey media do not agree as to whether anions are completely or partially excluded from clay interlayer nanopores. In the present study, this key issue was addressed for Cl - using MD simulations for a range of nanopore widths (6 to 15 Å) overlapping the range of average pore widths that exists in engineered clay barriers. The MD simulation results were compared with the predictions of a thermodynamic model (Donnan Equilibrium model) and two pore-scale models based on the Poisson-Boltzmann equation under the assumption that interlayer water behaves as bulk liquid water. The simulations confirmed that anion exclusion from clay interlayers is greater than predicted by the pore-scale models, particularly at the smallest pore size examined. This greater anion exclusion stems from Cl - being more weakly solvated in nano-confined water than it is in bulk liquid water. Anion exclusion predictions based on the Poisson-Boltzmann equation were consistent with the MD simulation results, however, if the predictions included an ion closest approach distance to the clay mineral surface on the order of 2.0 ± 0.8 Å. These findings suggest that clay interlayers approach a state of complete anion exclusion (hence, ideal semi-permeable membrane properties) at a pore width of 4.2 ± 1.5 Å.

Tournassat, Christophe↗

DOE OSTI2024

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Functional relaxant effect of 6,7-dipropoxy-2H-chromen-2-one is mainly by calcium channel blockade in ex vivo assay of tracheal rings

Asthma is a prevalent disease characterized by airway chronic inflammation, airway hyperresponsiveness, edema and excess of mucus production. Molecules with coumarin scaffold have shown multiple biological effects, including anti-asthmatic. This study describes relaxant effect and mechanism of action of novel semisynthetic 6,7-dipropoxy-2H-chromen-2-one (6,7-DPC) on smooth muscle airways and in silico approaches. 6,7-DPC induced significant relaxant effect on tracheal rings pre-contracted with carbachol (E{sub max} = 100%; EC{sub 50} = 89 µM). Concentration-response curve of 6,7-DPC showed a significant shift to the left with respect to theophylline (positive control). Moreover, pre-treatment with 6,7-DPC inhibited the carbachol-induced contraction in a concentration-dependent manner with suppression of the maximum response. Also, KCl [80 mM]-induced contraction was partially abolished by 6,7-DPC compared with nifedipine; however, CaCl{sub 2} contraction curve only reached 30% of maximal response in the tissues pre-incubated with the test sample. 6,7-DPC was docked on an outer cavity located on the intracellular side of the human L-type calcium channel model and interacts in the following chains and residues: IIIS5.M26, IIIP.T45, IIIP.F49, IIIP.G51, IIIP.P53, IVP.C46, IVP.G49, IVP.E50, IVP.A51, IVP.W52, IVP.Q53, IVP.D54, IVS6.I4, IVS6.F7, IVS6.I8, IVS6.F10, and IVS6.F11. Also, nifedipine made unique interactions with IIIP.E50, IIIP.W52, IIIP.L55. Meanwhile, 6,7-DPC interacted with IIIS5.A22, IIIS2.Q27, and IVS6.C14, exclusively. In conclusion, 6,7-DPC showed a relaxant effect due to combined mechanism of action on rat tracheal rings, through non-competitive muscarinic receptor functional antagonism and preventing the calcium influx. This provides pharmacological basis for the use of 6,7-DPC in airways disorders, such as asthma or chronic obstructive pulmonary disease (COPD).

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Recognition of microbial glycans by human intelectin-1

The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. In this paper, we used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol–modified glycans, heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO). The 1.6-Å-resolution crystal structure of hIntL-1 complexed with β-Galf revealed that hIntL-1 uses a bound calcium ion to coordinate terminal exocyclic 1,2-diols. N-acetylneuraminic acid (Neu5Ac), a sialic acid widespread in human glycans, has an exocyclic 1,2-diol but does not bind hIntL-1, probably owing to unfavorable steric and electronic effects. hIntL-1 marks only Streptococcus pneumoniae serotypes that display surface glycans with terminal 1,2-diol groups. Finally, this ligand selectivity suggests that hIntL-1 functions in microbial surveillance.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

A systematic comparison of different approaches of density functional theory for the study of electrical double layers

Based on the best available knowledge of density functional theory (DFT), the reference-fluid perturbation method is here extended to yield different approaches that well account for the cross correlations between the Columbic interaction and the hard-sphere exclusion in an inhomogeneous ionic hard-sphere fluid. In order to quantitatively evaluate the advantage and disadvantage of different approaches in describing the interfacial properties of electrical double layers, this study makes a systematic comparison against Monte Carlo simulations over a wide range of conditions. The results suggest that the accuracy of the DFT approaches is well correlated to a coupling parameter that describes the coupling strength of electrical double layers by accounting for the steric effect and that can be used to classify the systems into two regimes. In the weak-coupling regime, the approaches based on the bulk-fluid perturbation method are shown to be more accurate than the counterparts based on the reference-fluid perturbation method, whereas they exhibit the opposite behavior in the strong-coupling regime. More importantly, the analysis indicates that, with a suitable choice of the reference fluid, the weighted correlation approximation (WCA) to DFT gives the best account of the coupling effect of the electrostatic-excluded volume correlations. As a result, a piecewise WCA approach can be developed that is robust enough to describe the structural and thermodynamic properties of electrical double layers over both weak- and strong-coupling regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

From hard spheres to hard-core spins

A system of hard spheres exhibits physics that is controlled only by their density. This comes about because the interaction energy is either infinite or zero, so all allowed configurations have exactly the same energy. The low-density phase is liquid, while the high-density phase is crystalline, an example of “order by disorder” as it is driven purely by entropic considerations. Here we study a family of hard spin models, which we call hard-core spin models, where we replace the translational degrees of freedom of hard spheres with the orientational degrees of freedom of lattice spins. Their hard-core interaction serves analogously to divide configurations of the many spin system into allowed and disallowed sectors. We present detailed results on the square lattice in d = 2 for a set of models with $\mathbb{Z}_n$ symmetry, which generalize Potts models, and their U(1) limits, for ferromagnetic and antiferromagnetic senses of the interaction, which we refer to as exclusion and inclusion models. As the exclusion and inclusion angles are varied, we find a Kosterlitz-Thouless phase transition between a disordered phase and an ordered phase with quasi-long-ranged order, which is the form order by disorder takes in these systems. These results follow from a set of height representations, an ergodic cluster algorithm, and transfer matrix calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Technical Note: Relation between dual-energy subtraction of CT images for electron density calibration and virtual monochromatic imaging

Purpose: For accurate tissue inhomogeneity correction in radiotherapy treatment planning, the author previously proposed a simple conversion of the energy-subtracted computed tomography (CT) number to an electron density (ΔHU–ρ{sub e} conversion), which provides a single linear relationship between ΔHU and ρ{sub e} over a wide ρ{sub e} range. The purpose of the present study was to reveal the relation between the ΔHU image for ρ{sub e} calibration and a virtually monochromatic CT image by performing numerical analyses based on the basis material decomposition in dual-energy CT. Methods: The author determined the weighting factor, α{sub 0}, of the ΔHU–ρ{sub e} conversion through numerical analyses of the International Commission on Radiation Units and Measurements Report-46 human body tissues using their attenuation coefficients and given ρ{sub e} values. Another weighting factor, α(E), for synthesizing a virtual monochromatic CT image from high- and low-kV CT images, was also calculated in the energy range of 0.03 < E < 5 MeV, assuming that cortical bone and water were the basis materials. The mass attenuation coefficients for these materials were obtained using the XCOM photon cross sections database. The effective x-ray energies used to calculate the attenuation were chosen to imitate a dual-source CT scanner operated at 80–140 and 100–140 kV/Sn. Results: The determined α{sub 0} values were 0.455 for 80–140 kV/Sn and 0.743 for 100–140 kV/Sn. These values coincided almost perfectly with the respective maximal points of the calculated α(E) curves located at approximately 1 MeV, in which the photon-matter interaction in human body tissues is exclusively the incoherent (Compton) scattering. Conclusions: The ΔHU image could be regarded substantially as a CT image acquired with monoenergetic 1-MeV photons, which provides a linear relationship between CT numbers and electron densities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence

The high-resolution structure of glucan binding protein C (GbpC) at 1.14 Å, a sucrose-dependent virulence factor of the dental caries pathogen Streptococcus mutans , has been determined. GbpC shares not only structural similarities with the V regions of AgI/II and SspB but also functional adherence to salivary agglutinin (SAG) and its scavenger receptor cysteine-rich domains (SRCRs). This is not only a newly identified function for GbpC but also an additional fail-safe binding mechanism for S. mutans . Despite the structural similarities with S. mutans antigen I/II (AgI/II) and SspB of Streptococcus gordonii , GbpC remains unique among these surface proteins in its propensity to adhere to dextran/glucans. The complex crystal structure of GbpC with dextrose (β- d -glucose; Protein Data Bank ligand BGC) highlights exclusive structural features that facilitate this interaction with dextran. Targeted deletion mutant studies on GbpC's divergent loop region in the vicinity of a highly conserved calcium binding site confirm its role in biofilm formation. Finally, we present a model for adherence to dextran. The structure of GbpC highlights how artfully microbes have engineered the lectin-like folds to broaden their functional adherence repertoire.

Mieher, Joshua L.↗

DOE OSTI2026

Seeing through the nucleus: A review of color transparency phenomena

In this work, we review the current status of the phenomenon of color transparency (CT), a fundamental consequence of the description of hadrons from quantum chromodynamics. CT refers to the vanishing of final (and/or initial) state interactions with the nuclear medium for exclusive process at sufficiently high enough momentum transfers. We discuss the current experimental observations relating to CT and their theoretical implications for other high energy processes. Future CT experiments and facilities are also described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Sensitivity to Cabibbo-Suppressed $\Lambda$ Production in MicroBooNE

We present a procedure to measure a flux averaged, restricted phase space cross section for direct (Cabibbo suppressed) Λ production using the MicroBooNE detector. This is a rare process, exclusively occurring in anti-neutrino interactions and to maximise the sensitivity of this analysis we combine predictions using the NuMI flux from two data taking periods, one in which this beam was run in neutrino mode and one in anti-neutrino mode. The event selection for this analysis was previously described in MicroBooNE public note 1097. The calculation of systematic uncertainties is shown and a method to propagate them through to the final cross section calculation is described, with final sensitivities shown in the form of Bayesian posterior distributions on the extracted cross section.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2013

Rotary seal with improved film distribution

The present invention is a generally circular rotary seal that establishes sealing between relatively rotatable machine components for lubricant retention and environmental exclusion, and incorporates seal geometry that interacts with the lubricant during relative rotation to distribute a lubricant film within the dynamic sealing interface. The features of a variable inlet size, a variable dynamic lip flank slope, and a reduction in the magnitude and circumferentially oriented portion of the lubricant side interfacial contact pressure zone at the narrowest part of the lip, individually or in combination thereof, serve to maximize interfacial lubrication in severe operating conditions, and also serve to minimize lubricant shear area, seal torque, seal volume, and wear, while ensuring retrofitability into the seal grooves of existing equipment.

42 ENGINEERING↗

DOE OSTI2015

Rotary seal with improved film distribution

42 ENGINEERING↗

DOE OSTI2025

Expanding the physics reach of DUNE in the near and far detectors

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino oscillation experiment. Its primary goal is the determination of the neutrino mass hierarchy and the CP-violating phase. The DUNE physics programme also includes the detection of astrophysical neutrinos and the search for beyond the Standard Model (BSM) phenomena. DUNE will consist of a near detector (ND) complex placed at Fermilab, and a modular Liquid Argon Time Projection Chamber (LArTPC) far detector (FD) to be built in the Sanford Underground Research Facility (SURF), approximately 1300 km away from the neutrino production point. This thesis describes three different projects within DUNE. First, a novel strategy to improve the triggering capabilities of the DUNE FD is proposed. It uses matched filters to enhance the production of online hits across all charge collection planes. Next, the possibility of detecting neutrinos coming from dark matter (DM) annihilations in the Sun with the FD is explored. The complementarity of DUNE to this kind of DM searches is shown. Finally, the simulation and reconstruction framework of ND-GAr, the gas argon ND proposed for Phase II of DUNE, is presented. A number of additions to this are described, particularly focused on the development of the particle identification (PID) capabilities of the detector. These are then used to perform the first event selection studies with an end-to-end simulation in ND-GAr, in particular the selection of pion exclusive samples in $\nu_{\mu}$ CC interactions. All three of these projects share the common goal of enhancing the physics programme of DUNE.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

LHC forward physics

The goal of this report is to give a comprehensive overview of the rich field of forward physics, with a special attention to the topics that can be studied at the LHC. The report starts presenting a selection of the Monte Carlo simulation tools currently available, chapter 2, then enters the rich phenomenology of QCD at low, chapter 3, and high, chapter 4, momentum transfer, while the unique scattering conditions of central exclusive production are analyzed in chapter 5. The last two experimental topics, Cosmic Ray and Heavy Ion physics are presented in the chapter 6 and 7 respectively. Chapter 8 is dedicated to the BFKL dynamics, multiparton interactions, and saturation. The report ends with an overview of the forward detectors at LHC. Each chapter is correlated with a comprehensive bibliography, attempting to provide to the interested reader with a wide opportunity for further studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗