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At least 289 records · Page 16

Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease

Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates in iron uptake from iron-withholding proteins of the host cell during infection.

60 APPLIED LIFE SCIENCES↗

Reaction Mechanism for the Conversion of γ-Valerolactone (GVL) over a Ru Catalyst: A First-Principles Study

Conversion of biomass-derived γ-valerolactone (GVL) to valuable chemicals has been studied extensively, and understanding the reaction mechanism is very valuable for improving turnover rates and selectivities. Here, we report first-principles density functional calculations, through which we show in detail the reaction pathways of GVL conversion on a Ru(0001) surface, in good agreement with recent experimental results performed on supported Ru catalysts. We find that (i) GVL undergoes a ring-opening reaction rather easily, and (ii) the rate-limiting step toward the formation of 1,4-pentanediol (1,4-PDO) and 2-pentanol (2-PeOH) is the hydrogenation step. The high energy barrier for this step is caused by a strong interaction between Ru and the unsaturated acyl intermediate that is formed after opening the ring. Among all the primary products, formation of 2-butanol (2-BuOH) has the smallest activation barrier, while the slowest step is C–C bond cleavage in the decarbonylation step. We further show that the same acyl intermediate after ring opening of GVL can also be formed by dehydrogenation of 1,4-PDO with a moderate activation barrier, which suggests that both 2-PeOH and 2-BuOH can also be produced in secondary steps.

Bababrik, Reda M.↗

Sulfur Diffusion within Nitrogen-Doped Ordered Mesoporous Carbons Determined by in Situ X-ray Scattering

The low intrinsic conductivity of sulfur necessitates conductive additives, such as mesoporous carbons, to the cathode to enable high-performance metal–sulfur batteries. Simultaneous efforts to address polysulfide shuttling have introduced nitrogen-doped carbons to provide both conductivity and suppressed shuttling because of their strong interaction with sulfur. The strength of this interaction will impact the ability to fill the mesopores with sulfur via melt infusion. Here in this study, we systematically investigate how nitrogen doping influences the rate that molten sulfur can infiltrate the mesopores and the overall extent of pore filling of highly ordered mesoporous doped carbons using in situ small angle X-ray scattering (SAXS). The similarity in electron density between molten sulfur and the soft carbon framework of the mesoporous material leads to a precipitous decrease in the scattered intensity associated with the ordered structure as voids are filled with sulfur. As the nitrogen doping increases from 1 to 20 at. %, the effective diffusivity of sulfur in the mesopores decreases by an order of magnitude (2.7 × 10 –8 to 2.3 × 10 –9 cm/s). The scattering becomes nearly invariant within 20 min of melt infiltration at 155 °C for all but the most doped carbon, which indicates that submicron-sized mesoporous carbon particles can be filled rapidly. Additionally, the nitrogen doping decreases the sulfur content that can be accommodated within the mesopores from 95% of the mesopores filled without doping to only 64% filled with 20 at. % N as determined by the residual scattering intensity. Sulfur does not crystallize within the mesopores of the nitrogen-doped carbons, which is further indicative of the strong interactions between the nitrogen species and sulfur that can inhibit polysulfide shuttling. Lastly, in situ SAXS provides insights into the diffusion of sulfur in mesopores and how the surface chemistry of nitrogen-doped carbon appears to significantly hinder the infiltration by sulfur.

36 MATERIALS SCIENCE↗

The spin structure of the nucleon

We review the present understanding of the spin structure of protons and neutrons, the fundamental building blocks of nuclei collectively known as nucleons. The field of nucleon spin provides a critical window for testing Quantum Chromodynamics (QCD), the gauge theory of the strong interactions since it involves fundamental aspects of hadron structure, and it can be probed in detail in experiments, particularly deep inelastic lepton scattering on polarized targets. QCD was initially probed in high energy deep inelastic lepton scattering with unpolarized beams and targets. With time, interest shifted from testing perturbative QCD to illuminating the nucleon structure itself. In fact, the spin degrees of freedom of hadrons provides an essential and detailed verification of both perturbative and nonperturbative QCD dynamics. Nucleon spin was initially thought of coming mostly from the spin of its quark constituents, based on intuition from the parton model. However, the first experiments showed that this expectation was incorrect. It is now clear that nucleon physics is much more complex, involving quark orbital angular momenta as well as gluonic and sea quark contributions. Thus, the nucleon spin structure remains a most active aspect of QCD research, involving important advances such as the developments of generalized parton distributions (GPD) and transverse momentum distributions (TMD). Elastic and inelastic lepton-proton scattering, as well as photoabsorption experiments provide various ways to investigate non-perturbative QCD. Fundamental sum rules --such as the Bjorken sum rule for polarized photoabsorption on polarized nucleons-- are also in the non-perturbative domain. This realization triggered a vigorous program to link the low energy effective hadronic description of the strong interactions to fundamental quarks and gluon degrees of freedom of QCD. This has also led to the development of holographic QCD ideas based on the AdS/CFT or gauge/gravity correspondence, a novel approach providing a well-founded semiclassical approximation to QCD. Any QCD-based model of the nucleon's spin and dynamics must also successfully account for the observed spectroscopy of hadrons. Analytic calculations of the hadron spectrum, a long sought goal of QCD research, has now being realized using light-front holography and superconformal quantum mechanics, a formalism consistent with the results from nucleon spin studies. We begin this review with a phenomenological description of nucleon structure in general and of its spin structure in particular, aimed to engage non-specialist readers. A fundamental tool is Dirac's front form and light-front quantization which provides a frame-independent, relativistic description of hadron structure and dynamics, the derivation of spin-sum rules, and a direct connection to the QCD Lagrangian. Next, we discuss the nucleon spin structure at high energy, including topics such as GPDs and TMDs, as well as nucleon spin observables sensitive to final-state interactions such as the Sivers effect. We then discuss experimental and theoretical advances in the nonperturbative domain --in particular the development of light-front holographic QCD and superconformal quantum mechanics, its predictions for the spin content of nucleons, the computation of PDFs and of hadron masses.

74 ATOMIC AND MOLECULAR PHYSICS↗

Electromagnetic and neutral-weak response functions of 4 He and 12 C

A major goal of nuclear theory is to understand the strong interaction in nuclei as it manifests itself in terms of two- and many-body forces among the nuclear constituents, the protons and neutrons, and the interactions of these constituents with external electroweak probes via one- and many-body currents. The objective of the present work is to calculate the quasielastic electroweak response functions in light nuclei within the realistic dynamical framework outlined above. These response functions determine the inclusive cross section as function of the lepton momentum and energy transfers. Their ab initio calculation is a very challenging quantum many-body problem, since it requires summation over the entire excitation spectrum of the nucleus and inclusion in the electroweak currents of one- and many-body terms. Green's functions Monte Carlo methods allow one to circumvent both difficulties by computing the response in imaginary time (the so-called Euclidean response) and hence summing implicitly over the bound and continuum states of the nucleus, and by implementing specific algorithms designed to deal with the complicated spin-isospin structure of nuclear many-body operators. Theoretical predictions for 4 He and 12 C, confirmed by experiment in the electromagnetic case, show that two-body currents generate excess transverse strength from threshold to the quasielastic to the dip region and beyond. In conclusion, these results challenge the conventional picture of quasielastic inclusive scattering as being largely dominated by single-nucleon knockout processes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Record High Hydrogen Storage Capacity in the Metal–Organic Framework Ni 2 ( m -dobdc) at Near-Ambient Temperatures

Hydrogen holds promise as a clean alternative automobile fuel, but its on-board storage presents significant challenges due to the low temperatures and/or high pressures required to achieve a sufficient energy density. The opportunity to significantly reduce the required pressure for high density H 2 storage persists for metal-organic frameworks due to their modular structures and large internal surface areas. The measurement of H 2 adsorption in such materials under conditions most relevant to on-board storage is crucial to understanding how these materials would perform in actual applications, although such data have to date been lacking. In the present work, the metal-organic frameworks M 2 (m-dobdc) (M = Co, Ni; m-dobdc 4- = 4,6-dioxido-1,3-benzenedicarboxylate) and the isomeric frameworks M 2 (dobdc) (M = Co, Ni; dobdc 4- = 1,4-dioxido-1,3-benzenedicarboxylate), which are known to have open metal cation sites that strongly interact with H 2 , were evaluated for their usable volumetric H 2 storage capacities over a range of near-ambient temperatures relevant to on-board storage. Based upon adsorption isotherm data, Ni 2 (m-dobdc) was found to be the top-performing physisorptive storage material with a usable volumetric capacity between 100 and 5 bar of 11.0 g/L at 25 °C and 23.0 g/L with a temperature swing between -75 and 25 °C. Additional neutron diffraction and infrared spectroscopy experiments performed with in situ dosing of D 2 or H 2 were used to probe the hydrogen storage properties of these materials under the relevant conditions. Finally, the results provide benchmark characteristics for comparison with future attempts to achieve improved adsorbents for mobile hydrogen storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Detector Design of the Jefferson Lab EIC

The Electron-Ion Collider (EIC) is envisioned as the next-generation U.S. facility to study quarks and gluons in strongly interacting matter. The broad physics program of the EIC aims to precisely image gluons in nucleons and nuclei and to reveal the origin of the nucleon spin by colliding polarized electrons with polarized protons, polarized light ions, and heavy nuclei at high luminosity. The Jefferson Lab EIC (JLEIC) design is based on a figure-8 shaped ring-ring collider. The luminosity, exceeding 1033cm -2 s -1 in a broad range of the center-of-mass energy and maximum luminosity above 1034cm -2 s -1 , is achieved by high-rate collisions of short small-emittance low-charge bunches made possible by high-energy electron cooling of the ion beam and synchrotron radiation damping of the electron beam. The polarization of light ion species (p, d, 3He) can be easily preserved and manipulated due to the unique figure-8 shape of the collider rings. The focus of this presentation is put on the JLEIC primary detector that has been designed to support the full physics program of the EIC and to provide essentially full acceptance to all fragments produced in collisions. The detector has been fully integrated with the accelerator and extended to the forward electron and hadron regions to achieve exceptional small-angle acceptance and resolution as well as high-precision electron polarimetry and low-Q 2 tagging. The Central Detector design allows for excellent tracking up to small angles and excellent hadron PID resulting and offers a great performance, in particular for semi-inclusive and exclusive measurements. The combination of high luminosity, highly polarized lepton and ion beams, and a full acceptance, multi-purpose detector fully integrated with the accelerator will allow JLEIC a unique opportunity to make breakthroughs in the investigation of the strong interaction.

43 PARTICLE ACCELERATORS↗

Novel phosphate halides BaMn{sup III}[PO{sub 4}]FCl and BaMn{sup III}[PO{sub 4}]F{sub 2}: Effects of mixed halides on crystal structures and magnetic properties

Two new phosphate halides BaMn{sup III}[PO{sub 4}]FCl (1) and BaMn{sup III}[PO{sub 4}]F{sub 2} (2), have been synthesized under hydrothermal conditions. Structural characterizations show that both new compounds adopt layered structures but with different polyhedral linkages. Introduction of Cl into Compound (1) results in isolated hemimorphic [MnO{sub 4}FCl] octahedra, different from the chain of [MnO{sub 4}F{sub 2}]/[MnO{sub 2}F{sub 4}] octahedra in Compound (2). These compounds have significantly different molecular vibration modes and thermal stabilities. Magnetic measurements reveal that Compound (2) has larger antiferromagnetic interactions than Compound (1), because the former has strong interactions between Mn{sup 3+}-Mn{sup 3+} ions within corner-shared Mn{sup 3+}-octahedral chains whereas the latter only possesses isolated Mn{sup 3+}-octahedra. Both compounds transform to a new orthorhombic compound BaMn{sup II}(PO{sub 4})F (3) after thermal decomposition. - Graphical abstract: The large radius of Cl{sup -} ions makesBaMn{sup III}[PO{sub 4}]FCl to adopt isolated [MnO{sub 4}FCl] rather than corner-sharing octahedra as observed in BaMn{sup III}[PO{sub 4}]F{sub 2}. - Highlights: • Two novel phosphate halides BaMn[PO{sub 4}]FCl and BaMn[PO{sub 4}]F{sub 2} have been prepared. • These new compounds adopt different types of layered structures. • They have different molecular vibration modes and thermal stabilities. • BaMn[PO{sub 4}]FCl has weaker antiferromagnetic interactions than BaMn[PO{sub 4}]F{sub 2}. • The former adopts isolated octahedra whereas the latter adopts octahedral chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modular Assembly of FTO|Chromophore-Catalyst Hierarchical Films Based on Strong Dipole Interactions

Here, we have designed and characterized modular self-assembled hierarchical films containing a molecular catalyst tethered to an anchoring molecule by means of dipole-induced dipole interactions. In order to do so, two new Co III -based molecular catalyst candidates were designed, namely, [Co III L 1 (pyrr) 2 ]ClO 4 (Co1) and [Co III L 2 (pyrr) 2 ]ClO 4 (Co2), where L 1 and L 2 are the respective deprotonated forms of N,N′-[4,5-bis(dodecyloxy)-1,2-phenylene]dipicolinamide and N,N′-[4,5-bis(methoxyethoxy)-1,2-phenylene]dipicolinamide and were characterized by electrochemical, electronic, and film formation properties. Species Co1 and Co2 were deposited onto an anchor molecule such as octylphosphonic acid (OPA) or the chromophoric [Ru II (bpy PO3H ) 2 (bpy C7 )]Cl 2 (Ru) previously attached onto conductive fluorine-doped tin oxide (FTO). Four hierarchical films of the form substrate|anchor-catalyst were obtained, namely, FTO|OPA-Co1, FTO|OPA-Co2, FTO|Ru-Co1, and FTO|Ru-Co2, and the role of dipole-dipole interactions between anchor and catalyst modules was assessed. These newly synthesized hierarchical films were characterized by a host of surface-specific methods that include X-ray photoelectron spectroscopy, ellipsometry, X-ray fluorescence, and water contact angle, thus enabling an unprecedented level of analysis. Compared to the weak C-H van der Waals interactions exhibited by Co1, the presence of alkoxy chains in Co2 ensures stronger dipole-dipole interactions with the alkyl chain of the anchors due to O···H formation. The persistence of their redox properties, which include metal oxidation, and directionality of electron transport were probed suggesting direct relevance to catalytic processes such as water oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Schrödinger operator with a strong varying interaction on a curve in R{sup 2}

In this paper, we study a two-dimensional quantum system governed by the Hamiltonian corresponding to the formal expression −Δ−(α+ω(·))δ(·−Γ), where α > 0, ω(·) is a continuous compactly supported function and Γ is a curve in R{sup 2}. We derive the asymptotics of eigenvalues for α→∞ and analyze consequences of introducing varying delta potential.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Switching between attractive and repulsive Coulomb-interaction-mediated drag in an ambipolar GaAs/AlGaAs bilayer device

We present measurements of Coulomb drag in an ambipolar GaAs/AlGaAs double quantum well structure that can be configured as both an electron-hole bilayer and a hole-hole bilayer, with an insulating barrier of only 10 nm between the two quantum wells. Coulomb drag resistivity is a direct measure of the strength of interlayer particle-particle interactions. We explore the strongly interacting regime of low carrier densities (2D interaction parameter r{sub s} up to 14). Our ambipolar device design allows a comparison between the effects of the attractive electron-hole and repulsive hole-hole interactions and also shows the effects of the different effective masses of electrons and holes in GaAs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Strong Kitaev Interaction in BaCo 2⁢ (AsO 4 ) 2

The inelastic neutron scattering results and their analysis unequivocally point to a dominant Kitaev interaction in the honeycomb-lattice cobaltate BaCo 2 ⁢(AsO 4 ) 2 . Our anisotropic-exchange model closely describes all available neutron scattering data in the material’s field-polarized phase. Furthermore, the density-matrix renormalization group results for our model are in close accord with the unusual double-zigzag magnetic order and the low in-plane saturation field of BaCo 2 ⁢(AsO 4 ) 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum thermodynamics from the nonequilibrium dynamics of open systems: Energy, heat capacity, and the third law

In a series of papers, we intend to take the perspective of open quantum systems and examine from their nonequilibrium dynamics the conditions when the physical quantities, their relations, and the laws of thermodynamics become well defined and viable for quantum many-body systems. We first describe how an open-system nonequilibrium dynamics (ONEq) approach is different from the closed combined system + environment in a global thermal state (CGTs) setup. Only after the open system equilibrates will it be amenable to conventional thermodynamics descriptions, thus quantum thermodynamics (QTD) comes at the end rather than assumed in the beginning. The linkage between the two comes from the reduced density matrix of ONEq in that stage having the same form as that of the system in the CGTs. We see the open-system approach having the advantage of dealing with nonequilibrium processes as many experiments in the near future will call for. Because it spells out the conditions of QTD's existence, it can also aid us in addressing the basic issues in quantum thermodynamics from first principles in a systematic way. We then study one broad class of open quantum systems where the full nonequilibrium dynamics can be solved exactly, that of the quantum Brownian motion of N strongly coupled harmonic oscillators, interacting strongly with a scalar-field environment. In this paper, we focus on the internal energy, heat capacity, and the third law. We show for this class of physical models, amongst other findings, the extensive property of the internal energy, the positivity of the heat capacity, and the validity of the third law from the perspective of the behavior of the heat capacity toward zero temperature. These conclusions obtained from exact solutions and quantitative analysis clearly disprove claims of negative specific heat in such systems and dispel allegations that in such systems the validity of the third law of thermodynamics relies on quantum entanglement. They are conceptually and factually unrelated issues. As a result, entropy and entanglement will be the main theme of our second paper on this subject matter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗