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At least 55 records · Page 3

On the nonadiabatic collisional quenching of OH(A) by H 2 : a four coupled quasi-diabatic state description

A four-state diabatic potential energy matrix (DPEM), H d , for the description of the nonadiabatic quenching of OH(A 2 Σ + ) by collisions with H 2 is reported. The DPEM is constructed as a fit to adiabatic energies, energy gradients, and derivative couplings obtained exclusively from multireference configuration interaction wave functions. A four-adiabatic-electronic-state representation is used in order to describe all energetically accessible regions of the nuclear coordinate space. Partial permutation-inversion symmetry is incorporated into the representation. Here, the fit is based on electronic structure data at 42 882 points, described by over 1.6 million least squares equations with a root mean square (mean unsigned) error of 178(83) cm –1 . Comparison of ab initio and H d determined minima, saddle points, and energy minimized points on C 2v , C s , C ∞v , and C 1 (noncoplanar) portions of two conical intersection seams are used to establish the accuracy of the H d .

74 ATOMIC AND MOLECULAR PHYSICS↗

Multistate, multichannel coupled diabatic state representations of adiabatic states coupled by conical intersections. CH 2 OH photodissociation

In this work, a coupled diabatic state representation, H d , of the 1, 2, 3 2 A states of CH 2 OH suitable for the description of the three channel, three state photodissociation process CH 2 OH(1 2 A) + hv → CH 2 OH(2, 3 2 A) → CH 2 O(X, A) + H, cis-CHOH + H, trans-CHOH + H, is reported. The representation is based on electronic structure data (energies, energy gradients, and derivative couplings) obtained exclusively from multireference configuration interaction single and double excitation wave functions. Diabat shifting is employed to improve the representation’s agreement with accurate experimental energetics. A careful analysis of the numerous minima, saddle points, and conical intersection seams is reported. The computed T 0 (3 2 A) ~ 35 220 cm -1 is in excellent agreement with the experimental estimate of 35 053 cm -1 , and the computed channel dissociation energies, D 0 , for CH 2 O 9453 (10 160), cis-HCOH 30 310.2 (29 923), and trans-HCOH 28 799 (28 391) cm -1 are in good accord with the measured values given parenthetically. Lastly, these accurate energetics over a wide range of nuclear configurations strongly support the ability of this H d to enable quality simulations of nonadiabatic dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single pion production and pion propagation in A chilles

We extend the applicability of A chilles (A CHIcagoLand Lepton Event Simulator) by incorporating the single pion production mechanism in a fully exclusive fashion. The electroweak interaction vertex is modeled by combining the state-of-the-art dynamical coupled-channels approach with realistic hole spectral functions, which account for correlations in both the initial target state and the residual spectator system. Final-state interactions are treated using a semiclassical intranuclear cascade that leverages nuclear configurations to determine the correlated spatial distribution of protons and neutrons. The meson-baryon scattering amplitudes used in the cascade are computed within the dynamical coupled-channels framework, consistent with the electroweak vertex. To model pion absorption, we employ the optical potential approach of Oset and Salcedo [Nucl. Phys. A484, 557 (1988).]. As an alternative approach, we explicitly model the production and propagation of resonances which mediate pion-nucleon scattering and pion absorption. We validate our approach against pion-nucleon and pion-nucleus scattering data, and present comparisons with electron- and neutrino-nucleus measurements from e⁢4⁢𝜈, T2K, MINER⁢𝜈⁢A, and MicroBooNE.

Isaacson, Joshua [Michigan State Univ., East Lansi↗

Quantum-Accurate Multiscale Modeling of Shock Hugoniots, Ramp Compression Paths, Structural and Magnetic Phase Transitions, and Transport Properties in Highly Compressed Metals

Fully characterizing high energy density (HED) phenomena using pulsed power facilities (Z machine) and coherent light sources is possible only with complementary numerical modeling for design, diagnostic development, and data interpretation. The exercise of creating numerical tests, that match experimental conditions, builds critical insight that is crucial for the development of a strong fundamental understanding of the physics behind HED phenomena and for the design of next generation pulsed power facilities. The persistence of electron correlation in HED materials arising from Coulomb interactions and the Pauli exclusion principle is one of the greatest challenges for accurate numerical modeling and has hitherto impeded our ability to model HED phenomena across multiple length and time scales at sufficient accuracy. An exemplar is a ferromagnetic material like iron, while familiar and widely used, we lack a simulation capability to characterize the interplay of structure and magnetic effects that govern material strength, kinetics of phase transitions and other transport properties. Herein we construct and demonstrate the Molecular-Spin Dynamics (MSD) simulation capability for iron from ambient to earth core conditions, all software advances are open source and presently available for broad usage. These methods are multi-scale in nature, direct comparisons between high fidelity density functional theory (DFT) and linear-scaling MSD simulations is done throughout this work, with advancements made to MSD allowing for electronic structure changes being reflected in classical dynamics. Main takeaways for the project include insight into the role of magnetic spins on mechanical properties and thermal conductivity, development of accurate interatomic potentials paired with spin Hamiltonians, and characterization of the high pressure melt boundary that is of critical importance to planetary modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

An experiment to search for dark-matter interactions using sodium iodide detectors

Observations of galaxies and primordial radiation suggest that the Universe is made mostly of non-luminous dark matter. Several new types of fundamental particle have been proposed as candidates for dark matter, such as weakly interacting massive particles (WIMPs). These particles would be expected to interact with nuclei in suitable detector materials on Earth, for example, causing them to recoil. However, no definitive signal from such dark-matter interactions has been detected despite concerted efforts by many collaborations. One exception is the much-debated claim by the DAMA collaboration of a statistically significant (more than nine standard deviations) annual modulation in the rate of nuclear interaction events. Annual modulation is expected because of the variation in Earth’s velocity relative to the Galaxy’s dark-matter halo that arises from Earth’s orbital motion around the Sun. DAMA observed a modulation in the rate of interaction events in their detector with a period and phase consistent with that expected for WIMPs. Several groups have been working to develop experiments with the aim of reproducing DAMA’s results using the same target medium (sodium iodide). To determine whether there is evidence for an excess of events above the expected background in sodium iodide and to look for evidence of an annual modulation, the COSINE-100 experiment uses sodium iodide as the target medium to carry out a model-independent test of DAMA’s claim. Here we report results from the initial operation of the COSINE-100 experiment related to the first task. We observe no excess of signal-like events above the expected background in the first 59.5 days of data from COSINE-100. Assuming the so-called standard dark-matter halo model, this result rules out spin-independent WIMP–nucleon interactions as the cause of the annual modulation observed by the DAMA collaboration. The exclusion limit on the WIMP–sodium interaction cross-section is 1.14 × 10 —40 cm 2 for 10-GeV c —2 WIMPs at a 90% confidence level. The COSINE-100 experiment will continue to collect data for two more years, enabling a model-independent test of the annual modulation observed by the DAMA collaboration.

79 ASTRONOMY AND ASTROPHYSICS↗

Peeling back the many layers of competitive exclusion

Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard ® ) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log 10 Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities’ response to Salmonella in chickens with low (≤5.85 Log 10 genomes/g) or high (≥6.00 Log 10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella’s SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community’s stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.

59 BASIC BIOLOGICAL SCIENCES↗

Dark tridents at off-axis liquid argon neutrino detectors

We present dark tridents, a new channel for exploring dark sectors in short-baseline neutrino experiments. Dark tridents are clean, distinct events where, like neutrino tridents, the scattering of a very weakly coupled particle leads to the production of a lepton-antilepton pair. Dark trident production occurs in models where long-lived dark-sector particles are produced along with the neutrinos in a beam-dump environment and interact with neutrino detectors downstream, producing an on-shell boson which decays into a pair of charged leptons. We focus on a simple model where the dark matter particle interacts with the standard model exclusively through a dark photon, and concentrate on the region of parameter space where the dark photon mass is smaller than twice that of the dark matter particle and hence decays exclusively into standard-model particles. We compute event rates and discuss search strategies for dark tridents from dark matter at the current and upcoming liquid argon detectors aligned with the Booster beam at Fermilab — MicroBooNE, SBND, and ICARUS — assuming the dark sector particles are produced off-axis in the higher energy NuMI beam. We find that MicroBooNE has already recorded enough data to be competitive with existing bounds on this dark sector model, and that new regions of parameter space will be probed with future data and experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Short Baseline Neutrino Program at Fermilab

The current status of the Short Baseline Neutrino (SBN) project at Fermilab is reviewed. While the installation of SBND is still in progress, ICARUS has taken its first neutrino data on beam:using both the Booster Neutrino Beam (BNB) and the Neutrino at the Main Injector (NuMI) beam.MicroBooNE has presently completed its data taking and is producing the world’s first high statistics results on neutrino Argon interactions, in both inclusive and exclusive channels. In parallel, the unexpected MiniBooNE “low energy excess” is under investigation, to search for sterile neutrinos.The physics potential for sterile neutrino searches at SBN will be outlined, with emphasis on the Neutrino-4 experiment and the possible ICARUS verification of this claim.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Swelling properties of montmorillonite and beidellite clay minerals from molecular simulation: Comparison of temperature interlayer cation, and charge location effects

In this study, the swelling properties of smectite clay minerals are relevant to many engineering applications including environmental remediation, repository design for nuclear waste disposal, borehole stability in drilling operations, and additives for numerous industrial processes and commercial products. We used molecular dynamics and grand canonical Monte Carlo simulations to study the effects of layer charge location, interlayer cation, and temperature on intracrystalline swelling of montmorillonite and beidellite clay minerals. For a beidellite model with layer charge exclusively in the tetrahedral sheet, strong ion–surface interactions shift the onset of the two-layer hydrate to higher water contents. In contrast, for a montmorillonite model with layer charge exclusively in the octahedral sheet, weaker ion–surface interactions result in the formation of fully hydrated ions (two-layer hydrate) at much lower water contents. Clay hydration enthalpies and interlayer atomic density profiles are consistent with the swelling results. Water adsorption isotherms from grand canonical Monte Carlo simulations are used to relate interlayer hydration states to relative humidity, in good agreement with experimental findings.

36 MATERIALS SCIENCE↗

Higgs boson production cross-section measurements and their EFT interpretation in the $4\ell $ decay channel at $\sqrt{s}=$13 TeV with the ATLAS detector

Higgs boson properties are studied in the four-lepton decay channel (where lepton = e, μ) using 139 fb -1 of proton–proton collision data recorded at $\sqrt{s}=$13 TeV by the ATLAS experiment at the Large Hadron Collider. The inclusive cross-section times branching ratio for H→ZZ* decay is measured to be 1.34±0.12 pb for a Higgs boson with absolute rapidity below 2.5, in good agreement with the Standard Model prediction of 1.33±0.08 pb. Cross-sections times branching ratio are measured for the main Higgs boson production modes in several exclusive phase-space regions. The measurements are interpreted in terms of coupling modifiers and of the tensor structure of Higgs boson interactions using an effective field theory approach. Exclusion limits are set on the CP-even and CP-odd ‘beyond the Standard Model’ couplings of the Higgs boson to vector bosons, gluons and top quarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Solution characterization of the dynamic conjugative entry exclusion protein TraG

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor–donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding–mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

59 BASIC BIOLOGICAL SCIENCES↗

Constraints on effective field theory couplings using 311.2 days of LUX data

We report here the results of an Effective Field Theory (EFT) WIMP search analysis using LUX data. We build upon previous LUX analyses by extending the search window to include nuclear recoil energies up to $\sim$180 keV$_{nr}$, requiring a reassessment of data quality cuts and background models. In order to use a binned Profile Likelihood statistical framework, the development of new analysis techniques to account for higher-energy backgrounds was required. With a 3.14$\times10^4$ kg$\cdot$day exposure using data collected between 2014 and 2016, we set 90\% C.L. exclusion limits on non-relativistic EFT WIMP couplings to neutrons and protons, providing the most stringent constraints on a significant fraction of the possible EFT WIMP interactions. Additionally, we report world-leading exclusion limits on inelastic EFT WIMP-nucleon recoils.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

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↗

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↗

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↗

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↗

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↗

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↗