Coherent Modulation of Quasiparticle Scattering Rates in a Photoexcited Charge-Density-Wave System
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75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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Results for “Greens function”
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Resonantly Enhanced Electromigration Forces for Adsorbates on Graphene
We investigate the electromigration forces for weakly bonded adsorbates on graphene by using density-functional based calculations. We find that the nature of electromigration forces on an adsorbate critically depends on the energy level alignment between the adsorbate state and the Fermi level of the graphene. For a resonant adsorbate, whose frontier orbitals lie close to the Fermi level, the electromigration force is dominated by the electron wind force that is strongly enhanced along the electron flow direction, irrespective of the sign of the adsorbate charge. For a nonresonant adsorbate, the electromigration force is essentially the direct force that depends on the adsorbate charge. We also show that the magnitude of electromigration forces can be continuously tunable through electrostatic gating for resonant adsorbates. Our results provide new insight for understanding and controlling how nanoscale objects behave in or on host materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
A complex guided spectral transform Lanczos method for studying quantum resonance states
A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths, and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the original Hamiltonian in the spectral range of interest. Therefore, the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO{sub 2}, and compared to previous calculations.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Visualization of defect induced in-gap states in monolayer MoS 2
Atomic-scale intrinsic defects play a key role in controlling functional electronic properties of two-dimensional (2D) materials. Here, we present a low-temperature scanning–tunneling microscopy and spectroscopy investigation of a common point-defect in monolayer molybdenum disulfide (MoS 2 ). We employ a sample preparation method in which the film surface is never exposed to air so that the native dangling bonds surrounding the defects in the film are preserved. Molybdenum vacancies are identified by their three characteristic in-gap resonances by combining scanning–tunneling measurements with parallel Green’s function-based theoretical modeling. The relative energy shifts between the various in-gap states allow us to identify a relative charge difference between two of the observed vacancies. The role of the substrate on the band structure of the defective MoS 2 monolayer is unveiled. Our study highlights the effects of the substrate on the in-gap states of common defects found in MoS 2 providing a pathway in designing and optimizing 2D materials for electronic applications.
36 MATERIALS SCIENCE↗
Optimization of Energy Flow through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe
Photosynthetic organisms have recently gained considerable attention for a role in development of renewable energy sources. Genome-enabled systems biology methods, coupled with functional and synthetic genomics, present opportunities to develop sustainable and economical applications such as fuel production within the next 10 to 15 years. However, optimization of light-driven metabolism for biomass or biofuel production will require a detailed systems biology understanding of photosynthetic processes and cellular metabolism. Genome-scale metabolic models (GEMs) are at the core of systems analysis of cellular processes and form a common organizational framework for analyses of data resulting from functional genomics experimental work and computational studies. Therefore, there is a clear demand for high quality photosynthetic model organisms and the appropriate computational tools that enable systems analysis of light-driven metabolism. Through research conducted we expanded the currently available repertoire of photosynthetic GEMs to include the commercially valuable model diatom Phaeoctylum tricornutum. Diatoms have a peculiar and distinct evolutionary footprint and represent a major eukaryotic lineage that is taxonomically and functionally distinct from green and red algae and vascular plants. Therefore, the true potential for light-driven metabolism aimed at biofuel production remains poorly understood at a systems level for a large subset of the global diversity of photosynthetic organisms. The metabolic capabilities of P. tricornutum were comparatively modeled with those from other photosynthetic groups in order to elucidate the occurrence of metabolic traits within and between phototrophs. Additionally, this research resulted in significant extension of the COnstraints Based Reconstruction and Analysis (COBRA) Toolbox to accommodate the crucial need for infrastructure required for ‘omics data integration and analysis in the context of genome-scale models. Therefore, the proposed research achieved two important goals. First, within the broad scope of photosynthetic organisms, we functionally compared and, as a result, identified cellular processes that require optimization in order to enable deployment as biofuel feedstock. Second, the proposed research resulted in development of key computational infrastructure, which can be further extended to other biological systems, that is currently lacking but necessary for multiple ‘omics data integration.
59 BASIC BIOLOGICAL SCIENCES↗
Summability of Connected Correlation Functions of Coupled Lattice Fields
We consider two nonindependent random fields ψ and ϕ defined on a countable set Z. For instance, Z=ℤ{sup d} or Z=ℤ{sup d}×I, where I denotes a finite set of possible “internal degrees of freedom” such as spin. We prove that, if the cumulants of ψ and ϕ enjoy a certain decay property, then all joint cumulants between ψ and ϕ are ℓ{sub 2}-summable in the precise sense described in the text. The decay assumption for the cumulants of ψ and ϕ is a restricted ℓ{sub 1} summability condition called ℓ{sub 1}-clustering property. One immediate application of the results is given by a stochastic process ψ{sub t}(x) whose state is ℓ{sub 1}-clustering at any time t: then the above estimates can be applied with ψ=ψ{sub t} and ϕ=ψ{sub 0} and we obtain uniform in t estimates for the summability of time-correlations of the field. The above clustering assumption is obviously satisfied by any ℓ{sub 1}-clustering stationary state of the process, and our original motivation for the control of the summability of time-correlations comes from a quest for a rigorous control of the Green–Kubo correlation function in such a system. A key role in the proof is played by the properties of non-Gaussian Wick polynomials and their connection to cumulants.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Importance of charge self-consistency in first-principles description of strongly correlated systems
First-principles approaches have been successful in solving many-body Hamiltonians for real materials to an extent when correlations are weak or moderate. As the electronic correlations become stronger often embedding methods based on first-principles approaches are used to better treat the correlations by solving a suitably chosen many-body Hamiltonian with a higher level theory. The success of such embedding theories, often referred to as second-principles, is commonly measured by the quality of self-energy Σ which is either a function of energy or momentum or both. However, Σ should, in principle, also modify the electronic eigenfunctions and thus change the real space charge distribution. While such practices are not prevalent, some works that use embedding techniques do take into account these effects. In such cases, choice of partitioning, of the parameters defining the correlated Hamiltonian, of double-counting corrections, and the adequacy of low-level Hamiltonian hosting the correlated subspace hinder a systematic and unambiguous understanding of such effects. Further, for a large variety of correlated systems, strong correlations are largely confined to the charge sector. Then an adequate nonlocal low-order theory is important, and the high-order local correlations embedding contributes become redundant. Here we study the impact of charge self-consistency within two example cases, TiSe 2 and CrBr 3 , and show how real space charge re-distribution due to correlation effects taken into account within a first-principles Green’s function-based many-body perturbative approach is key in driving qualitative changes to the final electronic structure of these materials.
36 MATERIALS SCIENCE↗
Large-scale GW calculations on pre-exascale HPC systems
The ab initio GW approach is a rigorous Green’s-function-based framework that can be employed to compute electronic excitation properties of a wide variety of materials such as extended systems, molecules, as well as confined and nanostructured materials with a very satisfactory accuracy. However, GW calculations on complex systems are often hindered by the high computational cost associated with the method. Here, in this study, we demonstrate how to significantly speedup GW calculations with a novel algorithm for the computationally intense kernel based on a non-blocking chunked cyclic communication scheme that minimizes latency in MPI messages, allows for overlapping of communication and computation, and improves cache usage in matrix multiplication operations. The optimized version of the code, implemented in the BerkeleyGW software package, is capable of scaling well to the full Cori computer at NERSC (Cray XC40) and achieves over 11 Peta FLOP/s of sustained performance. We showcase our work by performing large-scale GW calculations of defect structures on silicon, which require simulation cells containing over 1700 atoms, and which can now be efficiently executed in just a few minutes on large pre-exascale high-performance computing systems.
97 MATHEMATICS AND COMPUTING↗
Electrochemically Mediated Au–C(sp 2 ) Anchors for Molecular Electronics
Terminal anchor groups play a key role in the stability and electronic properties of molecular junctions. Single molecule junctions typically consist of two preinstalled terminal anchors linking organic molecules to metal electrodes. Here, in this work, we show that p -terphenyl derivatives containing only a single terminal anchor show conductance features similar to junctions with two preinstalled terminal anchors. A set of p -terphenyl derivatives with one terminal anchor was prepared using automated chemical synthesis and characterized using single molecule electronics experiments, molecular dynamics (MD) simulations, bulk electrochemistry and spectroscopy, and nonequilibrium Green’s function-density functional theory (NEGF-DFT) calculations. Our results show that 4-amino- p -terphenyl (PPP) and related analogs exhibit a well-defined high conductance state that is diminished or absent in other p-terphenyl derivatives lacking a preinstalled amine terminal anchor or fluorine or methyl substitutions at the terminal para position. However, a low conductance state is observed in all amino- p -terphenyl derivatives with one preinstalled anchor due to molecular junctions formed by noncovalent dimeric π–π stacking interactions. The observed high conductance state diminishes upon the addition of reducing agents and is restored upon the addition of an oxidizing agent. Our results suggest that the high conductance state arises due to Au–C(sp 2 ) bond formation facilitated by a single electron oxidation event at the electrode surface. A series of control experiments with different anchor groups shows that primary amines play a key role in forming Au–C bonds for molecular junctions. Overall, these results suggest that Au–C bond formation gives rise to high conductance pathways in organic molecules containing only one preinstalled terminal anchor. Insights from this work can be leveraged in the design of molecular electronic devices, particularly in understanding the mechanisms of molecular binding and junction formation.
charge transport↗
Competing incommensurate spin fluctuations and magnetic excitations in infinite-layer nickelate superconductors
The recently discovered infinite-layer nickelates show great promise in helping to disentangle the various cooperative mechanisms responsible for high-temperature superconductivity. However, lack of antiferromagnetic order in the pristine nickelates presents a challenge for connecting the physics of the cuprates and nickelates. Here, by using a quantum many-body Green’s function-based approach to treat the electronic and magnetic structures, we unveil the presence of many two- and three-dimensional magnetic stripe instabilities that are shown to persist across the phase diagram of LaNiO 2 . Our analysis indicates that the magnetic properties of the infinite-layer nickelates are closer to those of the doped cuprates, which host a stripe ground state, rather than the undoped cuprates. The computed longitudinal-spin, transverse-spin, and charge spectra of LaNiO 2 are found to contain an admixture of contributions from localized and itinerant carriers. Theoretically obtained dispersion of magnetic excitations (spin-flip) is found to be in good accord with the results of recent resonant inelastic X-ray scattering experiments. Our study gives insight into the origin of strong magnetic competition in the infinite-layer nickelates and their relationship with the cuprates.
36 MATERIALS SCIENCE↗
The role of cytosine methylation on charge transport through a DNA strand
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sparsified time-dependent Fourier neural operators for fusion simulations
This paper presents a sparsified Fourier neural operator for coupled time-dependent partial differential equations (ST-FNO) as an efficient machine learning surrogate for fluid and particle-based fusion codes such as NIMROD (Non-Ideal Magnetohydrodynamics with Rotation - Open Discussion) and GTC (Gyrokinetic Toroidal Code). ST-FNO leverages the structures in the governing equations and utilizes neural operators to represent Green's function-like numerical operators in the corresponding numerical solvers. Once trained, ST-FNO can rapidly and accurately predict dynamics in fusion devices compared with first-principle numerical algorithms. In general, ST-FNO represents an efficient and accurate machine learning surrogate for numerical simulators for multi-variable nonlinear time-dependent partial differential equations, with the proposed architectures and loss functions. The efficacy of ST-FNO has been demonstrated using quiescent H-mode simulation data from NIMROD and kink-mode simulation data from GTC. The ST-FNO H-mode results show orders of magnitude reduction in memory and central processing unit usage in comparison with the numerical solvers in NIMROD when computing fields over a selected poloidal plane. The ST-FNO kink-mode results achieve a factor of 2 reduction in the number of parameters compared to baseline FNO models without accuracy loss.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Scattering solution of an interacting Hamiltonian for the electronic control of molecular spin qubits
We theoretically study how a scattered electron can entangle molecular spin qubits (MSQs). This requires solving the inelastic transport of a single electron through a scattering region described by a tight-binding interacting Hamiltonian. We accomplish this using a Green's-function solution. We can model realistic physical implementations of MSQs by parametrizing the tight-binding Hamiltonian with first-principles descriptions of magnetic anisotropy and exchange interactions. As a result, we find that, for two-MSQ systems with inversion symmetry, projective measurement of the spin degree of freedom of the scattered electron offers probabilistic control of the degree of entanglement between the MSQs.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Techniques for improved statistical convergence in quantification of eddy diffusivity moments
While recent approaches, such as the macroscopic forcing method (MFM) or Green's function-based approaches, can be used to compute Reynolds-averaged Navier-Stokes closure operators using forced direct numerical simulations, MFM can also be used to directly compute moments of the effective nonlocal and anisotropic eddy diffusivities. The low-order spatial and temporal moments contain limited information about the eddy diffusivity but are often sufficient for quantification and modeling of nonlocal and anisotropic effects. However, when using MFM to compute eddy diffusivity moments, the statistical convergence can be slow for higher-order moments. In this work, we demonstrate that using the same direct numerical simulation (DNS) for all forced MFM simulations improves statistical convergence of the eddy diffusivity moments. We present its implementation in conjunction with a decomposition method that handles the MFM forcing semianalytically and allows for consistent boundary condition treatment, which we develop for both scalar and momentum transport. We demonstrate that for a two-dimensional Rayleigh-Taylor instability case study, using the same DNS for all forced MFM simulations results in convergence with 𝒪(100) simulations rather than 𝒪(1000) simulations. In conclusion, we then demonstrate the impacts of improved convergence on the quantification of the eddy diffusivity.
general physics↗
Theoretical investigation of surface chemical reactivity of compositionally disordered multi-metallic alloys
Alloys are widely used in both academic and industrial research as heterogeneous catalysts for accelerating technologically important reactions ranging from hydrocarbon reforming, selective hydrogenation, to electrochemical reactions involving hydrogen and oxygen that are fundamental and indispensable to a sustainable future energy infrastructure. Most basic catalysis research has been limited to combinations of two elements that are usually ordered in some manner at the nanoscale because doing so allows observable results to be easily rationalized. It however leaves a huge material space consisting of multi metallic, compositionally disordered alloys unexplored. This research demonstrates a viable theoretical approach combining different types of first principles calculations (including Green’s function-based Korringa–Kohn–Rostoker coherent potential approximation (KKR–CPA) and planewave-based density functional theory) to enable the surface chemical reactivity of compositionally complex alloy surfaces to be investigated. We demonstrate the approach by investigating hydrogen adsorption and evolution on two types of compositionally disordered alloys: a quaternary CoCrFeNi high-entropy alloy, and binary Pt-3d base metal alloys.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Geodesic synchrotron radiation
This paper presents the results and methods of computing the high-frequency radiation emitted by freely falling particles moving in circular geodesic orbits in a spherically symmetric gravitational field. The high-frequency radiation, to which the methods of this paper apply, is the principal part of radiated energy only in the case of a particle moving in a highly relativistic, and therefore unstable, circular geodesic. The geodesic synchrotron radiation emitted in this case shows excitation of high-frequency harmonics and a narrow angular distribution. A Green's-function solution of the scalar wave equation is obtained using WKB methods. For application to relativistic circular orbits, a parabolic WKB approximation is required and yields solutions in terms of parabolic cylinder functions.
Breuer, R. A.↗
Acoustic propagation in rigid sharp bends and branches
The linear acoustic propagation in rigid planar sharp bends and bifurcation ducts is analyzed using a Green's-function integral technique often known as the surface element method. The acoustic characteristics of the sharp bend differ substantially from those of a circular bend with identical turning angle, width, and centerline length. The acoustic loading resulting from a duct bifurcation is highly two dimensional beyond the first cutoff frequency.
El-Raheb, M.↗
Semiconductor surface sublimation energies and atom-atom interactions
The energy required to remove an atom from semiconductor surfaces is calculated using a Green's-function approach. Contrary to intuition, it is found that, in some cases, less energy is needed to remove an atom from the nearly full surface than from a nearly empty surface. The results are explained in terms of the relative energies of anion and cation dangling bonds, and the charge transfers between them. The deducted effective pair-interaction energies and their effects on surface morphology and growth perfection are discussed.
Krishnamurthy, Srinivasan↗