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At least 1,171 records · Page 65

Quantifying the propagation of parametric uncertainty on flux balance analysis

Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g mmol –1 , and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.

59 BASIC BIOLOGICAL SCIENCES↗

Iodosylbenzene Coordination Chemistry Relevant to Metal–Organic Framework Catalysis

Hypervalent iodine compounds formally feature expanded valence shells at iodine. These reagents are broadly used in synthetic chemistry due to the ability to participate in well-defined oxidation-reduction processes and because the ligand-exchange chemistry intrinsic to the hypervalent center allows hypervalent iodine compounds to be applied to a broad array of oxidative substrate functionalization reactions. We have recently developed methods to generate these compounds from O 2 that are predicated on diverting reactive intermediates of aldehyde autoxidation towards the oxidation of aryl iodides. Coupling the aerobic oxidation of aryliodides with catalysts that effect C–H bond oxidation would provide a strategy to achieve aerobic C–H oxidation chemistry. In this Forum article we discuss the aspects of hypervalent iodine chemistry and bonding that render this class of reagents attractive lynchpins for aerobic oxidation chemistry. We then discuss the oxidation processes relevant to the aerobic preparation of 2-(tertbutylsulfonyl) iodosylbenzene, which is a popular hypervalent iodine reagent for use with porous metal-organic framework-based catalysts because it displays significantly enhanced solubility as compared with unsubstituted iodosylbenzene. We demonstrate that popular synthetic methods to this reagent often provide material that displays unpredictable disproportionation behavior due to the presence of trace impurities. We provide a revised synthetic route that avoids impurities common in the reported methods and provides access to material that displays predictable stability. Lastly, we describe the coordination chemistry of hypervalent iodine compounds with metal clusters relevant to MOF chemistry and discuss the potential implications of this coordination chemistry to catalysis in MOF scaffolds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics

This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number of benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A unified theory of quasibound states

We report a formalism for the study of quasibound states, defined here broadly as those states having a connectedness to true bound states through the variation of some physical parameter. The theory admits quasibound states with real energies (stationary quasibound states) and quantum resonances within the same framework, and makes a clean distinction between these states and those of the associated continuum. The approach taken here builds on our earlier work by clarifying several crucial points and extending the formalism to encompass a variety of continuous spectra, including those with degeneracies. The theory is illustrated by examining several cases pertinent to applications widely discussed in the literature. The related issue of observing stationary quasibound states also is addressed. We argue that the Adiabatic Theorem of quantum mechanics not only establishes the criteria necessary for their detection, but also engenders a method for assigning to them a level width that is sufficiently distinct from that of quantum resonances so as to allow the two to be differentiated experimentally.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

General framework for calculating spin–orbit couplings using spinless one-particle density matrices: Theory and application to the equation-of-motion coupled-cluster wave functions

Standard implementations of nonrelativistic excited-state calculations compute only one component of spin multiplets (i.e., Ms = 0 triplets); however, matrix elements for all components are necessary for deriving spin-dependent experimental observables. Wigner–Eckart’s theorem allows one to circumvent explicit calculations of all multiplet components. We generate all other spin–orbit matrix elements by applying Wigner–Eckart’s theorem to a reduced one-particle transition density matrix computed for a single multiplet component. In addition to computational efficiency, this approach also resolves the phase issue arising within Born–Oppenheimer’s separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculation of spin–orbit couplings using equation-of-motion coupled-cluster wave functions are presented. The two-electron contributions are included via the mean-field spin–orbit treatment. Intrinsic issues of constructing spin–orbit mean-field operators for open-shell references are discussed, and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the barrier for spin inversion in a high-spin tris(pyrrolylmethyl)amine Fe(II) complex.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Entropy-Maximization Approach to Automated Training Set Generation for Interatomic Potentials

Machine learning-based interatomic potentials are currently garnering a lot of attention as they strive to achieve the accuracy of electronic structure methods at the computational cost of empirical potentials. Given their generic functional forms, the transferability of these potentials is highly dependent on the quality of the training set, the generation of which can be highly labor-intensive. Good training sets should at once contain a very diverse set of configurations while avoiding redundancies that incur cost without providing benefits. We formalize these requirements in a local entropy-maximization framework and propose an automated sampling scheme to sample from this objective function. We show that this approach generates much more diverse training sets than unbiased sampling and is competitive with hand-crafted training sets.

74 ATOMIC AND MOLECULAR PHYSICS↗

Gaunt and Breit two-electron contributions to mean-field transformations and fine structure splitting

Materials utilized by novel energy systems are often studied using weakly correlated mean-field theories. However, if these systems incorporate heavy elements, relativistic effects must be included. Therefore, a Kramers unrestricted coupled cluster with singles and doubles excitation formalism within a molecular mean-field exact two-component framework (X2C mmf ) using a four-component Dirac–Hartree–Fock (DHF) reference state is presented. The exact X2C mmf transformed normal-order Hamiltonian incorporates all one-electron and two-electron (2e) contributions from the Coulomb, Gaunt, and Breit operators and is used with the equation of motion method to calculate the excitation energies of the alkali group of elements. Using this framework, the effects of 2e Gaunt and Breit integrals are studied. Results demonstrate growing contributions from these integrals to the generated X2C mmf mean-fields and electronic fine structure calculations with increasing atomic number. Overall, this paper outlines the method, its effect within the X2C mmf approach, and lays the foundation for future theoretical development of relativistic calculations within this framework.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fine structure of current noise spectra in nanoelectromechanical resonators

Here, we study the frequency-dependent noise of a suspended carbon nanotube quantum dot nanoelectromechanical resonator induced by electron-vibration coupling. Using a rigorous Keldysh diagrammatic technique, we establish a formal framework connecting the vibrational properties to electrical measurements. We find that the noise power spectrum exhibits a narrow resonant peak at the frequency of the vibrational modes. However, this fine structure tends to disappear due to a coherent cancellation effect when the tunneling barriers are tuned to a symmetric point. Notably, measuring the electrical current noise spectra provides a sensitive alternative method for detecting the damping and dephasing of quantum vibrational modes.

Electric measurements↗

Preliminary NoMAD Results of the MUSIC Experiment

The Measurement of Uranium Subcritical and Critical (MUSiC) experiment was carried out from December 2020 through April 2021 at the National Criticality Experiments Research Center (NCERC). This measurement campaign featured bare configurations of the Rocky Flats highly-enriched uranium (HEU) shells, with each configuration having different numbers of these shells. The goal of the experiment was to test multiple neutron multiplicity detectors and measurement methods for a large range of neutron multiplication values, to see when the combination of detectors and methods break down as the configurations reach the delayed supercritical window. Adding subcritical integral benchmarks gives additional validation to nuclear data. These benchmarks provide additional parameters against which to validate the data. While critical benchmarks have just a single value, $K_{eff}$ , subcritical benchmarks can be used to infer multiple parameters. As an example, recent subcritical benchmarks utilizing the Hage-Cifarelli formalism have three quantities of interest ($R_{1}$, $R_{2}$, and $M_{L}$). This gives nuclear data evaluators additional data to use when performing their evaluations, and allows for these benchmarks to be useful for additional types of nuclear data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Work Plan for the Site-wide SSHAC Level 3 Probabilistic Seismic Hazard Analysis at INL

This work plan provides the overall framework, key activities, key tasks, and schedule for the execution of a probabilistic seismic hazard analysis at Idaho National Laboratory (INL). The probabilistic seismic hazard analysis will follow processes and procedures appropriate for the Senior Seismic Hazard Analysis Committee (SSHAC) Level 3 study provided in U. S. Nuclear Regulatory Commission guidance, NUREG-2213. The SSHAC Level 3 probabilistic seismic hazard analysis (PSHA) is being conducted as an INL site-wide effort. The work plan was developed and revised by participants who will perform the SSHAC Level 3 PSHA. The work plan also includes the quality assurance requirements commensurate with American Society of Mechanical Engineers Nuclear Quality Assurance NQA 1 2008/2009 and 2011 Addendum for design nuclear facilities under the U.S. Department of Energy and U. S. Nuclear Regulatory Commission. The scope of the SSHAC Level 3 PSHA is designed to produce the mean-centered definition of the seismic hazard with the appropriate treatment of uncertainties supported by the associated technical justifications. The SSHAC Level 3 study will properly implement and completely document the activities of evaluation, integration, and documentation. The evaluation process will consider data, models, and methods proposed by the larger technical community that are relevant to the PSHA at INL. The integration process will build seismic-source and ground-motion characterization models that represent the center, body, and range of technically defensible interpretations, taking into consideration the outcomes of the evaluation process. Key tasks and activities—such as a project kickoff meeting, three workshops, four formal working meetings, and a briefing meeting with the Participatory Peer Review Panel—will occur for the seven-member technical integration teams to construct seismic-source and ground-motion-characterization models. Both preliminary and final hazard-input documents will be developed to perform sensitivity analyses and the final PSHA, respectively. The entire study will be thoroughly documented in draft and final reports. The Participatory Peer Review Panel will review the SSHAC Level 3 study from start to finish, including the draft and final INL Site-wide PSHA reports, so they can provide a closure letter documenting the study’s adherence to SSHAC processes and technical adequacy of the final products.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The 2.4 μ m Galaxy Luminosity Function as Measured Using WISE . III. Measurement Results

The Widefield Infrared Survey Explorer (WISE) satellite surveyed the entire sky multiple times in four infrared wavelengths (3.4, 4.6, 12, and 22 μm). The unprecedented combination of coverage area and depth gives us the opportunity to measure the luminosity function (LF) of galaxies, one of the fundamental quantities in the study of them, at 2.4 μm to an unparalleled level of formal statistical accuracy in the near-infrared. The big advantage of measuring LFs at wavelengths in the window of ≈2–3.5 μm is that it correlates more closely to the total stellar mass in galaxies than others. In this paper we report on the parameters of the 2.4 μm LF of galaxies obtained from applying the spectro-luminosity-functional-based methods to datasets from the previous papers in this series using the mean and covariance of 2.4 μm normalized spectral energy distributions (SEDs) from our previous work. In terms of the single Schechter function parameters evaluated at the present epoch, the combined result is: ${\phi }_{\star }=5.8\,\pm [{0.3}_{\mathrm{stat}},{0.4}_{\mathrm{sys}}]\times {10}^{-3}\,{\mathrm{Mpc}}^{-3}$, ${L}_{\star }=6.4\pm [{0.1}_{\mathrm{stat}},{0.3}_{\mathrm{sys}}]\times {10}^{10}\,{L}_{2.4\mu {\rm{m}}\odot }$ (M$_{\star}$ = -21.67 ± [0.02 stat , 0.05 sys ] AB mag), and $α$ = -1.050 ± [0.004 stat , 0.04 sys ]. The high statistical accuracy comes from combining public redshift surveys with the wide coverage from WISE, and the unevenness in statistical accuracy is a result of our efforts to work around biases of uncertain origin that affect resolved and marginally resolved galaxies. With further refinements, the techniques applied in this work promise to advance the study of the SED of the universe.

79 ASTRONOMY AND ASTROPHYSICS↗

Asymmetric Semiconductor Nanorod/Oxide Nanoparticle Hybrid Materials: Model Nanomaterials for Light-Activated Formation of Fuels from Sunlight. Formal Progress Report -- Award DE-FG02-05ER15753

Executive Summary on Project Accomplishments: We focused our efforts for this project on the synthesis and characterization of semiconductor nanomaterials composed of semiconductor nanorods (NRs - e.g., CdSe, CdSe@CdS, CdS) with metal (Au, Pt, Co) or metal oxide (CoxOy) nanoparticle (NP) “tips.” These systems are attractive model systems where control of spatial, energetic and compositional features of both NRs and NP tips potentially enhances the efficiency of photogeneration and directional transport of charges, and photoelectrochemical conversion of sunlight to fuels. Synthetic methods to control material dimensions (20-200 nm in length), topology (one vs. two NP tips) and NR/NP tip compositions have been developed in the current project period (Pyun). We also achieved, for the first time in heterostructured nanorod materials, estimates of both valence band energies (E VB ) and conduction band energies (E CB ), using unique combinations of in vacuuo ultraviolet photoelectron spectroscopy (UPS, Armstrong), and waveguide spectroelectrochemistry (Saavedra), respectively. The spectroelectrochemical measurements in particular provide a unique path to estimation of E CB , and the distribution in E CB brought about by modification of NR composition. The combination of both approaches promises to be universally applicable to the characterization of energetics in nanomaterials of interest both for photovoltaic and sunlight-to-fuel photoelectrochemical assemblies.

14 SOLAR ENERGY↗

Inertial dynamics of an interface with interfacial mass flux: Stability and flow fields’ structure, inertial stabilization mechanism, degeneracy of Landau’s solution, effect of energy fluctuations, and chemistry-induced instabilities

This work focuses on the long-standing problem of inertial dynamics of an interface with interfacial mass flux and reports new mechanisms for the interface stabilization and destabilization. The interface is a phase boundary separating fluids of different densities and having interfacial mass flux. To analyze the interface dynamics from a far field, we develop and apply the general matrix method to rigorously solve the boundary value problem involving the governing equations in the fluid bulk and the boundary conditions at the interface and at the outside boundaries of the domain. We find the fundamental solutions for the linearized system of equations and analyze the interplay of interface stability with flow fields’ structure by directly linking rigorous mathematical attributes to physical observables. We find that the interface is stable when the dynamics conserves the fluxes of mass, momentum, and energy; the stabilization is due to an inertial mechanism causing small oscillations of the interface velocity. In the classic Landau’s dynamics, the postulate of perfect constancy of the interface velocity leads to the development of Landau–Darrieus instability. This destabilization is also linked to the imbalance of the perturbed energy at the interface. The classic Landau’s solution is found to have degeneracy; lifting of the degeneracy may lead to singularity and self-similar dynamics. Our results compare well with traditional theories of combustion and propose new experiments to study the dynamics of the interface and the flow fields in combustible systems. We further conduct reactive molecular dynamics simulations to elucidate the complexity of chemical processes, to study the destabilizing effect of energy fluctuations on the interface stability, and to illustrate the chemistry-induced instabilities. In summary, we identify the extreme sensitivity of the interface dynamics to the interfacial boundary conditions, including the formal properties of fundamental solutions and the qualitative and quantitative properties of the flow fields. This provides new opportunities for studies, diagnostics, and control of multiphase flows in a broad range of processes in nature and technology.

42 ENGINEERING↗

S-type and P-type habitability in stellar binary systems: A comprehensive approach. I. Method and applications

A comprehensive approach is provided for the study of both S-type and P-type habitability in stellar binary systems, which in principle can also be expanded to systems of higher order. P-type orbits occur when the planet orbits both binary components, whereas in the case of S-type orbits, the planet orbits only one of the binary components with the second component considered a perturbator. The selected approach encapsulates a variety of different aspects, which include: (1) the consideration of a joint constraint, including orbital stability and a habitable region for a putative system planet through the stellar radiative energy fluxes ({sup r}adiative habitable zone{sup ;} RHZ), needs to be met; (2) the treatment of conservative, general, and extended zones of habitability for the various systems as defined for the solar system and beyond; (3) the provision of a combined formalism for the assessment of both S-type and P-type habitability; in particular, mathematical criteria are presented for the kind of system in which S-type and P-type habitability is realized; (4) applications of the attained theoretical approach to standard (theoretical) main-sequence stars. In principle, five different cases of habitability are identified, which are S-type and P-type habitability provided by the full extent of the RHZs; habitability, where the RHZs are truncated by the additional constraint of planetary orbital stability (referred to as ST- and PT-type, respectively); and cases of no habitability at all. Regarding the treatment of planetary orbital stability, we utilize the formulae of Holman and Wiegert as also used in previous studies. In this work, we focus on binary systems in circular orbits. Future applications will also consider binary systems in elliptical orbits and provide thorough comparisons to other methods and results given in the literature.

79 ASTRONOMY AND ASTROPHYSICS↗

Magnetism, half-metallicity and electrical transport properties of V- and Cr-doped semiconductor SnTe: A theoretical study

This work presents results for the electronic structure, magnetic properties, and electrical resistivity of the semiconductor SnTe doped with 3d transition metals V and Cr. From the standpoint of potential application in spintronics, we look for half-metallic states and analyze their properties in both rock salt and zinc blende structures using ab initio electronic structure methods. In both cases, it is the Sn-sublattice that is doped with the transition metals, as has been the case with experiments performed so far. We find four half-metallic compounds at their optimized cell volumes. Results of exchange interactions and the Curie temperature are presented and analyzed for all the relevant cases. Resistivity calculation based on Kubo-Greenwood formalism shows that the resistivities of these alloys due to transition metal doping of the Sn-sublattice may vary, in most cases, from typical liquid metal or metallic glass value to 2–3 times higher. 25% V-doping of the Sn-sublattice in the rock salt structure gives a very high resistivity, which can be traced to high values of the lattice parameter resulting in drastically reduced hopping or diffusivity of the states at the Fermi level.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Transform-limited-pulse representation of excitation with natural incoherent light

The excitation of molecular systems by natural incoherent light relevant, for example, to photosynthetic light-harvesting is examined. We show that the result of linear excitation with natural incoherent light can be obtained using incident light described in terms of transform limited pulses, as opposed to conventional classical representations with explicit random character. The derived expressions allow for computations to be done directly for any thermal light spectrum using a simple wave function formalism and provide a route to the experimental determination of natural incoherent excitation using pulsed laser techniques. Pulses associated with solar and cosmic microwave background radiation are provided as examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Orthogonality broadcasting and quantum position verification

The no-cloning theorem leads to information-theoretic security in various quantum cryptographic protocols. However, this security typically derives from a possibly weaker property that classical information encoded in certain quantum states cannot be broadcast. To formally capture this property, we introduce the study of ‘orthogonality broadcasting.’ When attempting to broadcast the orthogonality of two different qubit bases, we establish that the power of classical and quantum communication is equivalent. However, quantum communication is shown to be strictly more powerful for broadcasting orthogonality in higher dimensions. We then relate orthogonality broadcasting to quantum position verification and provide a new method for establishing error bounds in the no pre-shared entanglement model that can address protocols previous methods could not. Our key technical contribution is an uncertainty relation that uses the geometric relation of the states that undergo broadcasting rather than the non-commutative aspect of the final measurements.

quantum cryptography↗