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Accelerating the convergence of auxiliary-field quantum Monte Carlo in solids with optimized Gaussian basis sets
We investigate the use of optimized correlation-consistent Gaussian basis sets for the study of insulating solids with auxiliary-field quantum Monte Carlo (AFQMC). The exponents of the basis set are optimized through the minimization of the second-order Møller–Plesset perturbation theory (MP2) energy in a small unit cell of the solid. We compare against other alternative basis sets proposed in the literature, namely, calculations in the Kohn–Sham basis and in the natural orbitals of an MP2 calculation. We find that our optimized basis sets accelerate the convergence of the AFQMC correlation energy compared to a Kohn–Sham basis and offer similar convergence to MP2 natural orbitals at a fraction of the cost needed to generate them. We also suggest the use of an improved, method independent, MP2-based basis set correction that significantly reduces the required basis set sizes needed to converge the correlation energy. With these developments, we study the relative performance of these basis sets in LiH, Si, and MgO and determine that our optimized basis sets yield the most consistent results as a function of volume. Using these optimized basis sets, we systematically converge the AFQMC calculations to the complete basis set and thermodynamic limit and find excellent agreement with experiment for the systems studied. Although we focus on AFQMC, our basis set generation procedure is independent of the subsequent correlated wavefunction method used.
Bio-inspired nanocomposite assemblies as smart skin components.
There is national interest in the development of sophisticated materials that can automatically detect and respond to chemical and biological threats without the need for human intervention. In living systems, cell membranes perform such functions on a routine basis, detecting threats, communicating with the cell, and triggering automatic responses such as the opening and closing of ion channels. The purpose of this project was to learn how to replicate simple threat detection and response functions within artificial membrane systems. The original goals toward developing 'smart skin' assemblies included: (1) synthesizing functionalized nanoparticles to produce electrochemically responsive systems within a lipid bilayer host matrices, (2) calculating the energetics of nanoparticle-lipid interactions and pore formation, and (3) determining the mechanism of insertion of nanoparticles in lipid bilayers via imaging and electrochemistry. There are a few reports of the use of programmable materials to open and close pores in rigid hosts such as mesoporous materials using either heat or light activation. However, none of these materials can regulate themselves in response to the detection of threats. The strategies we investigated in this project involve learning how to use programmable nanomaterials to automatically eliminate open channels within a lipid bilayer host when 'threats' are detected. We generated and characterized functionalized nanoparticles that can be used to create synthetic pores through the membrane and investigated methods of eliminating the pores either through electrochemistry, change in pH, etc. We also focused on characterizing the behavior of functionalized gold NPs in different lipid membranes and lipid vesicles and coupled these results to modeling efforts designed to gain an understanding of the interaction of nanoparticles within lipid assemblies.
Permutation-adapted complete and independent basis for atomic cluster expansion descriptors
In many recent applications, particularly in the field of atom-centered descriptors for interatomic potentials, tensor products of spherical harmonics have been used to characterize complex atomic environments. When coupled with a radial basis, the atomic cluster expansion (ACE) basis is obtained. However, symmetrization with respect to both rotation and permutation results in an overcomplete set of ACE descriptors with linear dependencies occurring within blocks of functions corresponding to particular generalized Wigner symbols. All practical applications of ACE employ semi-numerical constructions to generate a complete, fully independent basis. While computationally tractable, the resultant basis cannot be expressed analytically, is susceptible to numerical instability, and thus has limited reproducibility. Here we present a procedure for generating explicit analytic expressions for a complete and independent set of ACE descriptors. The procedure uses a coupling scheme that is maximally symmetric w.r.t. permutation of the atoms, exposing the permutational symmetries of the generalized Wigner symbols, and yields a permutation-adapted rotationally and permutationally invariant basis (PA-RPI ACE). Theoretical support for the approach is presented, as well as numerical evidence of completeness and independence. A summary of explicit enumeration of PA-RPI functions up to rank 6 and polynomial degree 32 is provided. The PA-RPI blocks corresponding to particular generalized Wigner symbols may be either larger or smaller than the corresponding blocks in the simpler rotationally invariant basis. Finally, we demonstrate that basis functions of high polynomial degree persist under strong regularization, indicating the importance of not restricting the maximum degree of basis functions in ACE models a priori.
Radiative corrections to the non commutative photon propagator at one-loop order
We study the non-commutative gauge theory on the Moyal space. We add the harmonic potential introduced by Grosse and Wulkenhaar to the Maxwell Lagrange as well as the Gauge fixation. We determine the non-commutative U{sub *}(1) Gauge action which is invariant under the BRST transformations in the matrix basis. We determine in this basis the quadratic parts and the vertex of the Gauge field A{sub {mu}} and of the Faddeev-Popov ghost fields c(bar sign)andc. Finally, we study the perturbative correction to one loop order of the one point function in the matrix basis.
Electronic Structure of OR-AgInS{sub 2} and TiO{sub 2} Crystals and Its Differential Characteristics
The electronic structures of orthorhombic silver–indium sulfide and rutile titanium oxide were calculated within the framework of density functional theory using the basis of numerical pseudoatomic orbitals in the LDA and GGA approximations. The features of their electron energy spectra and the character of chemical bonds were considered. The comparative analysis of obtained bandgap widths and effective masses determined for heavy electrons and holes in the Brillouin zone center on the basis of analytical derivatives of one-electron energies was performed.
Stellar Mass Function of Active and Quiescent Galaxies via the Continuity Equation
The continuity equation is developed for the stellar mass content of galaxies and exploited to derive the stellar mass function of active and quiescent galaxies over the redshift range z∼0--8. The continuity equation requires two specific inputs gauged from observations: (i) the star formation rate functions determined on the basis of the latest UV+far-IR/submillimeter/radio measurements and (ii) average star formation histories for individual galaxies, with different prescriptions for disks and spheroids. The continuity equation also includes a source term taking into account (dry) mergers, based on recent numerical simulations and consistent with observations. The stellar mass function derived from the continuity equation is coupled with the halo mass function and with the SFR functions to derive the star formation efficiency and the main sequence of star-forming galaxies via the abundance-matching technique. A remarkable agreement of the resulting stellar mass functions for active and quiescent galaxies of the galaxy main sequence, and of the star formation efficiency with current observations is found; the comparison with data also allows the characteristic timescales for star formation and quiescence of massive galaxies, the star formation history of their progenitors, and the amount of stellar mass added by in situ star formation versus that contributed by external merger events to be robustly constrained. The continuity equation is shown to yield quantitative outcomes that detailed physical models must comply with, that can provide a basis for improving the (subgrid) physical recipes implemented in theoretical approaches and numerical simulations, and that can offer a benchmark for forecasts on future observations with multiband coverage, as will become routinely achievable in the era of JWST.
Binding and excitations in Si x H y molecular systems using quantum Monte Carlo
In this work, we present high-accuracy correlated calculations of small SixHy molecular systems in both the ground and excited states. We employ quantum Monte Carlo (QMC) together with a variety of many-body wave function approaches based on basis set expansions. The calculations are carried out in a valence-only framework using recently derived correlation consistent effective core potentials. Our primary goal is to understand the fixed-node diffusion QMC errors in both the ground and excited states with single-reference trial wave functions. Using a combination of methods, we demonstrate the very high accuracy of the QMC atomization energies being within ≈0.07 eV or better when compared with essentially exact results. By employing proper choices for trial wave functions, we have found that the fixed-node QMC biases for total energies are remarkably uniform ranging between 1% and 3.5% with absolute values at most ≈0.2 eV across the systems and several types of excitations such as singlets and triplets as well as low-lying and Rydberg-like states. Our results further corroborate that Si systems, and presumably also related main group IV and V elements of the periodic table (Ge, Sn, etc), exhibit some of the lowest fixed-node biases found in valence-only electronic structure QMC calculations.
Transverse structure of the pion beyond leading twist with basis light-front quantization
We investigate the twist-3transverse-momentum-dependent parton distribution functions (TMDs) of the pion with basis light-front quantization. The twist-3 TMDs are not independent and can be decomposed into twist-2and genuine twist-3 terms from the equations of motion (EOM). We compute the TMDs from the resulting light-front wave functions obtained by diagonalizing the light-front QCD Hamiltonian, determined for pion’s constituent quark-antiquark and quark-antiquark-gluon Fock sectors, with three-dimensional confinement. We also obtain the twist-3 parton distribution functions (PDFs) and show that they preserve the sum rule, which affirms the robustness of our approach. This is the first time that theoretical predictions are made for subleading twist structures of the pion containing interference terms between two light-front Fock sectors.
Transient work function gating: A new photoemission regime
We present the theoretical basis for a new photoemission regime, transient work function gating (TWFG), which temporally and energetically gates photoemission and produces near-threshold photoelectrons with thermally limited emittance, percent-level quantum efficiency, and control over temporal coherence. The technique consists of actively gating the work function of a generalized photocathode using a non-ionizing long-wavelength optical field to produce an adiabatic modulation of the carrier density at their surface. We examine TWFG as a means to circumvent the long-standing trade-off between low emittance and high quantum efficiency, untethered to particle source or photocathode specifics. TWFG promises new opportunities in photoemission physics for next generation electron and accelerator-based x-ray photon sources.
Stability of Solutions of Initial Boundary-Balue Problems of Aerohydroelasticity
In designing structures and devices interacting with the flow of gas or liquid, it is necessary to solve the problems associated with the investigation of the stability required for their functioning and operational reliability. The definition of stability of an elastic body taken in the article corresponds to Lyapunov’s concept of stability of a dynamical system. On the base of the proposed nonlinear mathematical model the dynamic stability of the elastic aileron of the wing taking into account the incident subsonic flow of gas or liquid (in an ideal model of an incompressible environment) is investigated. Also a nonlinear mathematical model of the device relating to the vibration technique, which is intended for intensification of technological processes, for example, the process of mixing, is considered. The action of these devices is based on the oscillations of elastic elements during the gas or liquid flow. The dynamic stability of the elastic element located on one wall of the flow channel with the subsonic flow of gas or liquid (in an ideal model of a compressible environment) is investigated. Both models are described by a coupled nonlinear system of differential equations for the unknown functions — the potential of the gas velocity and deformation of the elastic element. On the basis of the construction of functionals, we obtain the sufficient conditions of the stability, the imposed restrictions on the free-stream velocity of the gas, the flexural stiffness of the elastic element, and other parameters of the mechanical system. The examples of construction of the stability regions for particular parameters of the mechanical system are presented.
Simulating strongly correlated multiparticle systems in a truncated Hilbert space
Representing a strongly interacting multiparticle wave function in a finite product basis leads to errors. Simple rescaling of the contact interaction can preserve the low-lying energy spectrum and long-wavelength structure of wave functions in one-dimensional systems and thus correct for the basis set truncation error. The analytic form of the rescaling is found for a two-particle system where the rescaling is exact. A detailed comparison between finite Hilbert space calculations and exact results for up to five particles show that rescaling can significantly improve the accuracy of numerical calculations in various external potentials. In addition to ground-state energies, the low-lying excitation spectrum, density profile, and correlation functions are studied. The results give a promising outlook for numerical simulations of trapped ultracold atoms.
Structural Basis for the Rescue of Stalled Ribosomes: Structure of YaeJ Bound to the Ribosome
In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA{sub i}{sup fMet} and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.
Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
The thanatos (the Greek god of death)-associated protein (THAP) domain is a sequence-specific DNA-binding domain that contains a C2-CH (Cys-Xaa{sub 2-4}-Cys-Xaa{sub 35-50}-Cys-Xaa{sub 2}-His) zinc finger that is similar to the DNA domain of the P element transposase from Drosophila. THAP-containing proteins have been observed in the proteome of humans, pigs, cows, chickens, zebrafish, Drosophila, C. elegans, and Xenopus. To date, there are no known THAP domain proteins in plants, yeast, or bacteria. There are 12 identified human THAP domain-containing proteins (THAP0-11). In all human THAP protein, the THAP domain is located at the N-terminus and is {approx}90 residues in length. Although all of the human THAP-containing proteins have a homologous N-terminus, there is extensive variation in both the predicted structure and length of the remaining protein. Even though the exact function of these THAP proteins is not well defined, there is evidence that they play a role in cell proliferation, apoptosis, cell cycle modulation, chromatin modification, and transcriptional regulation. THAP-containing proteins have also been implicated in a number of human disease states including heart disease, neurological defects, and several types of cancers. Human THAP4 is a 577-residue protein of unknown function that is proposed to bind DNA in a sequence-specific manner similar to THAP1 and has been found to be upregulated in response to heat shock. THAP4 is expressed in a relatively uniform manner in a broad range of tissues and appears to be upregulated in lymphoma cells and highly expressed in heart cells. The C-terminal domain of THAP4 (residues 415-577), designated here as cTHAP4, is evolutionarily conserved and is observed in all known THAP4 orthologs. Several single-domain proteins lacking a THAP domain are found in plants and bacteria and show significant levels of homology to cTHAP4. It appears that cTHAP4 belongs to a large class of proteins that have yet to be fully functionally characterized. On the basis of prior work, we predicted that cTHAP4 is composed of a heme-binding nitrobindin domain, making THAP4 the only human THAP protein predicted to bind a cofactor. Nitrobindin, a recently characterized protein from Arabidopsis thaliana, is structurally similar and exhibits nitric oxide (NO)-binding properties that resemble the heme-binding nitrophorins. Nitrophorins use a heme moiety to store, transport, and release NO in a pH-specific manner. Although the exact function of nitrobindin is not fully known, the similarities between the well-characterized nitrophorins imply a role in NO transport, sensing, or metabolism. To better elucidate the possible function of THAP4, we solved the hemebound structure of cTHAP4 to a resolution of 1.79 {angstrom}.
Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes
A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd) with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)
How to spoil a good basis set for Rayleigh-Ritz calculations
For model quantum mechanical systems such as the harmonic oscillator and a particle in an impenetrable box, we consider the set of exact discrete spectrum functions and define the modified basis set by subtraction of the ground state wavefunction from all the other wavefunctions with some real weights. It is demonstrated that the modified set of functions is complete in the space of square integrable functions if and only if the series of the squared weights diverges. A similar, but nonequivalent criterion is derived for convergence of Rayleigh-Ritz ground state energy calculations to the exact ground state energy value with the basis set extension. Some numerical illustrations are provided which demonstrate a wide variety of possible situations for model systems.
Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria
Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. We show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.