Model Perturbation Theory Research Articles

Density split statistics: Cosmological constraints from counts and lensing in cells in DES Y1 and SDSS data

We derive cosmological constraints from the probability distribution function (PDF) of evolved large-scale matter density fluctuations. We do this by splitting lines of sight by density based on their count of tracer galaxies, and by measuring both gravitational shear around and counts-in-cells in overdense and underdense lines of sight, in Dark Energy Survey (DES) First Year and Sloan Digital Sky Survey (SDSS) data. Our analysis uses a perturbation theory model (see companion paper Friedrich at al.) and is validated using N-body simulation realizations and log-normal mocks. It allows us to constrain cosmology, bias and stochasticity of galaxies w.r.t. matter density and, in addition, the skewness of the matter density field. From a Bayesian model comparison, we find that the data weakly prefer a connection of galaxies and matter that is stochastic beyond Poisson fluctuations on <=20 arcmin angular smoothing scale. The two stochasticity models we fit yield DES constraints on the matter density $\Omega_m=0.26^{+0.04}_{-0.03}$ and $\Omega_m=0.28^{+0.05}_{-0.04}$ that are consistent with each other. These values also agree with the DES analysis of galaxy and shear two-point functions (3x2pt) that only uses second moments of the PDF. Constraints on $\sigma_8$ are model dependent ($\sigma_8=0.97^{+0.07}_{-0.06}$ and $0.80^{+0.06}_{-0.07}$ for the two stochasticity models), but consistent with each other and with the 3x2pt results if stochasticity is at the low end of the posterior range. As an additional test of gravity, counts and lensing in cells allow to compare the skewness $S_3$ of the matter density PDF to its LCDM prediction. We find no evidence of excess skewness in any model or data set, with better than 25 per cent relative precision in the skewness estimate from DES alone.

Perturbation Theory/Machine Learning Model of ChEMBL Data for Dopamine Targets: Docking, Synthesis, and Assay of New l-Prolyl-l-leucyl-glycinamide Peptidomimetics.

Predicting drug-protein interactions (DPIs) for target proteins involved in dopamine pathways is a very important goal in medicinal chemistry. We can tackle this problem using Molecular Docking or Machine Learning (ML) models for one specific protein. Unfortunately, these models fail to account for large and complex big data sets of preclinical assays reported in public databases. This includes multiple conditions of assays, such as different experimental parameters, biological assays, target proteins, cell lines, organism of the target, or organism of assay. On the other hand, perturbation theory (PT) models allow us to predict the properties of a query compound or molecular system in experimental assays with multiple boundary conditions based on a previously known case of reference. In this work, we report the first PTML (PT + ML) study of a large ChEMBL data set of preclinical assays of compounds targeting dopamine pathway proteins. The best PTML model found predicts 50000 cases with accuracy of 70-91% in training and external validation series. We also compared the linear PTML model with alternative PTML models trained with multiple nonlinear methods (artificial neural network (ANN), Random Forest, Deep Learning, etc.). Some of the nonlinear methods outperform the linear model but at the cost of a notable increment of the complexity of the model. We illustrated the practical use of the new model with a proof-of-concept theoretical-experimental study. We reported for the first time the organic synthesis, chemical characterization, and pharmacological assay of a new series of l-prolyl-l-leucyl-glycinamide (PLG) peptidomimetic compounds. In addition, we performed a molecular docking study for some of these compounds with the software Vina AutoDock. The work ends with a PTML model predictive study of the outcomes of the new compounds in a large number of assays. Therefore, this study offers a new computational methodology for predicting the outcome for any compound in new assays. This PTML method focuses on the prediction with a simple linear model of multiple pharmacological parameters (IC50, EC50, Ki, etc.) for compounds in assays involving different cell lines used, organisms of the protein target, or organism of assay for proteins in the dopamine pathway.

First Principles Computation on the Photovoltaic and Thermoelectric Properties of MAPbI3-xClx Perovskites

This research employs the first principles computation to simulate the chlorine (Cl) doping effect with different proportion (x value) on the photovoltaic and thermoelectric properties of bulk mixed halide methyl-ammonium lead perovskites (MAPbI3-xClx). In the study, the density functional theory (DFT) and Boltzmann transport equation (BTE) are applied to calculate the optical band gaps, electrical conductivity , carrier thermal conductivity , and Seebeck coefficient S. The density functional perturbation theory (DFPT) and Debye model are used to calculate the phonon thermal conductivity . Tuning the greatest thermoelectric figure of merit (ZT) with suitable solar absorbance range is the major target for our solar thermoelectric chip design. The simulation results reveal that doping Cl will increase the electronic conductivity, phonon thermal conductivity, and causes a blue shift in the light absorption. The main contribution to the total thermal conductivity is mainly from optical phonons, and the main absorbance wavelength locates in the ultraviolet and visible light region (40nm &lt; &lt; 700nm). When x=0.25, MAPbI2.75Cl0.25 achieves the optimized tuning for both light absorption coefficient α and figure of merit ZT in our simulation cases.

Electric-field-induced changes of magnetic moments and magnetocrystalline anisotropy in ultrathin cobalt films

In this study, the microscopic origins of the voltage-controlled magnetic anisotropy (VCMA) in 3d-ferromagnetic metals are revealed. Using in-situ X-ray fluorescence spectroscopy that provides a high quantum efficiency, electric-field-induced changes in orbital magnetic moment and magnetic dipole Tz terms in ultrathin Co films are demonstrated. An orbital magnetic moment difference of 0.013{\mu}B. was generated in the presence of electric fields of +(-)0.2 V/nm. The VCMA of Co was properly estimated by the induced change in orbital magnetic moment, according to the perturbation theory model. The induced change in magnetic dipole Tz term only slightly contributed to the VCMA in 3d-ferromagnetic metals.

Electronic structures of Al–Si clusters and the magic number structure Al8Si4

ABSTRACTThe low-energy structures of Al8Sim (m = 1–6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al–Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al–Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si–Si, Si–Al and Al–Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory

The current molecular docking study provided the Free Energy of Binding (FEB) for the interaction (nanotoxicity) between VDAC mitochondrial channels of three species (VDAC1-Mus musculus, VDAC1-Homo sapiens, VDAC2-Danio rerio) with SWCNT-H, SWCNT-OH, SWCNT-COOH carbon nanotubes. The general results showed that the FEB values were statistically more negative (p < 0.05) in the following order: (SWCNT-VDAC2-Danio rerio) > (SWCNT-VDAC1-Mus musculus) > (SWCNT-VDAC1-Homo sapiens) > (ATP-VDAC). More negative FEB values for SWCNT-COOH and OH were found in VDAC2-Danio rerio when compared with VDAC1-Mus musculus and VDAC1-Homo sapiens (p < 0.05). In addition, a significant correlation (0.66 > r2 > 0.97) was observed between n-Hamada index and VDAC nanotoxicity (or FEB) for the zigzag topologies of SWCNT-COOH and SWCNT-OH. Predictive Nanoparticles-Quantitative-Structure Binding-Relationship models (nano-QSBR) for strong and weak SWCNT-VDAC docking interactions were performed using Perturbation Theory, regression and classification models. Thus, 405 SWCNT-VDAC interactions were predicted using a nano-PT-QSBR classifications model with high accuracy, specificity, and sensitivity (73–98%) in training and validation series, and a maximum AUROC value of 0.978. In addition, the best regression model was obtained with Random Forest (R2 of 0.833, RMSE of 0.0844), suggesting an excellent potential to predict SWCNT-VDAC channel nanotoxicity. All study data are available at https://doi.org/10.6084/m9.figshare.4802320.v2.

Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry.

Wave functions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included a posteriori. In this Article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allows us to describe both static/nondynamic and dynamic electron correlation effects. Specifically, our perturbation theory models combine a diagonal and off-diagonal zero-order Hamiltonian, a single-reference and multireference dual state, and different excitation operators used to construct the projection manifold. We benchmark all proposed models as well as an a posteriori Linearized Coupled Cluster correction on top of AP1roG against CR-CC(2,3) reference data for reaction energies of several closed-shell molecules that are extrapolated to the basis set limit. Moreover, we test the performance of our new methods for multiple bond breaking processes in the homonuclear N2, C2, and F2 dimers as well as the heteronuclear BN, CO, and CN+ dimers against MRCI-SD, MRCI-SD+Q, and CR-CC(2,3) reference data. Our numerical results indicate that the best performance is obtained from a Linearized Coupled Cluster correction as well as second-order perturbation theory corrections employing a diagonal and off-diagonal zero-order Hamiltonian and a single-determinant dual state. These dynamic corrections on top of AP1roG provide substantial improvements for binding energies and spectroscopic properties obtained with the AP1roG approach, while allowing us to approach chemical accuracy for reaction energies involving closed-shell species.

Ab initio many-body perturbation theory and no-core shell model**Supported by National Key Basic Research Program of China (2013CB834402), National Natural Science Foundation of China (11235001, 11320101004, 11575007) and the CUSTIPEN (China-U.S. Theory Institute for Physics with Exotic Nuclei) funded by the U.S. Department of Energy, Office of Science (DE-SC0009971)

In many-body perturbation theory (MBPT) we always introduce a parameter Nshell to measure the maximal allowed major harmonic-oscillator (HO) shells for the single-particle basis, while the no-core shell model (NCSM) uses NmaxℏΩ HO excitation truncation above the lowest HO configuration for the many-body basis. It is worth comparing the two different methods. Starting from “bare” and Okubo-Lee-Suzuki renormalized modern nucleon-nucleon interactions, NNLOopt and JISP16, we show that MBPT within Hartree-Fock bases is in reasonable agreement with NCSM within harmonic oscillator bases for 4He and 16O in “close” model space. In addition, we compare the results using “bare” force with the Okubo-Lee-Suzuki renormalized force.

Vibrational transitions in hydrogen bonded bimolecular complexes – A local mode perturbation theory approach to transition frequencies and intensities

The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded bimolecular complexes with donors such as alcohols, amines and acids. We have applied the modified model to a series of complexes of different hydrogen bond type and complex energy. We found that the differences between local mode (LM) and LMPT calculated fundamental XH-stretching transition wavenumbers and oscillator strengths were correlated with the strength of the hydrogen bond. Overall, we have found that the LMPT model in most cases predicts transition wavenumbers within 20cm−1 of the experimental values.

The large-scale three-point correlation function of the SDSS BOSS DR12 CMASS galaxies

We report a measurement of the large-scale 3-point correlation function of galaxies using the largest dataset for this purpose to date, 777, 202 Luminous Red Galaxies in the Sloan Digital Sky Survey Baryon Acoustic Oscillation Spectroscopic Survey (SDSS BOSS) DR12 CMASS sample. This work exploits the novel algorithm of Slepian & Eisenstein (2015b) to compute the multipole moments of the 3PCF in $\mathcal{O}(N^2)$ time, with $N$ the number of galaxies. Leading-order perturbation theory models the data well in a compressed basis where one triangle side is integrated out. We also present an accurate and computationally efficient means of estimating the covariance matrix. With these techniques the redshift-space linear and non-linear bias are measured, with 2.6% precision on the former if $\sigma_8$ is fixed. The data also indicates a $2.8\sigma$ preference for the BAO, confirming the presence of BAO in the 3-point function.

KdotPsoft: Modelling and Simulation of Semiconductors and Device Physics

We introduce a new platform called KdotPsoft, to model and simulate semiconductor quantum wells (QWs) and multiple QW (MQW) systems. It is suitable to design and study quantum cascaded lasers, vertical-cavity surface-emitting laser, etc in conjunction with experiment and fabrication. For fundamental physics and device physics applications, KdotPsoft is an ideal platform to model, simulate and study semiconductors QWs and MQW structures for fundamental physics and device physics applications. It can study MQW based structures such as quantum cascaded lasers (QCL), vertical-cavity surface-emitting laser (VCSEL), etc. KdotPsoft is based on the 16-band k·p perturbation theory model and it supports all conventional semiconductor materials, and also can works for dilute nitride and bismide doped semiconductors. As a demonstration, we will show a study an example case of lattice matched GaNBiAs/GaAs QWs and show its major results, such as the energy dispersion curves, optical gain spectra and electron-hole wave-functions. At a larger scale, it can be used to comprehensively study the band lineups, energy dispersion relation, DOS, polarization-dependent transition matrix element strengths, optical gain/absorption spectra, spontaneous emission rate, radiative current density, electric field effects on the QW, etc. Advanced users may note that the development of the platform was done using Fortran and Python. We will strive to make KdotPsoft available as a independent platform or a Matlab toolbox in the future.

Experimental-Theoretic Approach to Drug-Lymphocyte Interactome Networks with Flow Cytometry and Spectral Moments Perturbation Theory

We can combine experimental techniques like Flow Cytometry Analysis (FCA) with Chemoinformatics methods to predict the complex networks of interactions between organic compounds and targets in the immune system. In this work, we determined experimentally the values of EC50 = 17.82 μg/mL and Cytotoxicity = 20.6 % for the anti-microbial / anti-parasite drug Dermofural over Balb/C CD9 lymphocytes using flow cytometry. After that, we developed a new Perturbation-theory model for Drug-Cell Target Interactome in Lymphocytes based on dispersion-polarization moments of drug structure. The models correctly classifies 34591 out of 42715 (Accuracy = 80.9%) cases of perturbations in assay endpoints of 11492 drugs (including both train and validation series). Each endpoint correspond to one out of 2616 assays, 38 molecular and cellular targets, 77 standard type measures, in four possible (human and rodents).

Neutron scattering study of the terminating protons in the basic structural units of non-graphitising and graphitising carbons

The proton-related fine structure of inelastic neutron spectra of glassy carbon, pure anthracite coal, furnace black and activated carbon has been evaluated using periodic density-functional perturbation theory models of graphene sheets with isolated (H1), vicinal hydrogen (H2) and mixed (H1, H2) termination. Significant differences in the out-of-plane aryl C-H bending/wagging mode region were observed which are not simply numerically correlated with the hydrogen content but with the fine structure of the carbons of different origin and production technology. The basic structural units in glassy carbon type 1 appear to be more uniform than in other carbons, H1 and H2 terminations seems to occur in distinct domains and a mixture of the types is sparse. The neutron spectra of type 2 material and of acetylene blacks of low hydrogen content show similarity to the spectrum of pure graphite, however, transmission electron microscopy reveals distinct differences in morphology at the nanoscale.

Rho resonance parameters from lattice QCD

We perform a high-precision calculation of the phase shifts for $\pi$-$\pi$ scattering in the I = 1, J = 1 channel in the elastic region using elongated lattices with two mass-degenerate quark favors ($N_f = 2$). We extract the $\rho$ resonance parameters using a Breit-Wigner fit at two different quark masses, corresponding to $m_{\pi} = 226$MeV and $m_{\pi} = 315$MeV, and perform an extrapolation to the physical point. The extrapolation is based on a unitarized chiral perturbation theory model that describes well the phase-shifts around the resonance for both quark masses. We find that the extrapolated value, $m_{\rho} = 720(1)(15)$MeV, is significantly lower that the physical rho mass and we argue that this shift could be due to the absence of the strange quark in our calculation.

Masses of higher spin fields onAdS4and conformal perturbation theory

We study the breaking of gauge symmetry for higher spin theory on AdS_4 dual to the 3d critical O(N) vector model. It was argued that the breaking is due to the change of boundary condition for a scalar field through a loop effect and the Goldstone modes are bound states of a scalar field and higher spin field. The masses of higher spin fields were obtained from the anomalous dimensions of dual currents at the leading order in 1/N, and we reproduce them from the O(N) vector model in the conformal perturbation theory. The anomalous dimensions can be computed from the bulk theory using Witten diagrams, and we show that the bulk computation reduces to the boundary one in the conformal perturbation theory. With this fact our computation provides an additional support for the bulk interpretation.

The response electron–electron repulsion energy and energy component analysis in CC/MBPT methods

Molecular properties are computed as responses to perturbations (energy derivatives) in coupled-cluster (CC)/many-body perturbation theory (MBPT) models. Here, the CC/MBPT energy derivative with respect to a general two-electron (2-e) perturbation is assembled from gradient theory for 2-e property evaluation, including the electron repulsion energy. The correlation energy (∆E) is shown to be the sum of response kinetic (∆T), electron–nuclear attraction (∆V), and electron repulsion (∆V ee ) energies. Thus, evaluation of total V ee for energy component analysis is simple: For total energy (E), total 1-e responses T and V, and nuclear–nuclear repulsion energy (V NN ), V ee = E − V NN − T − V is the true 2-e response value. Component energy analysis is illustrated in an assessment of steric repulsion in ethane’s rotational barrier. Earlier SCF-based results (Bader et al. in J Am Chem Soc 112:6530, 1990) are corroborated: The higher-energy eclipsed geometry is favored versus staggered in the two repulsion energies (V NN and V ee ), while decisively disfavored in electron–nuclear attraction energy (V). Our best quality calculations (CCSD/cc-pVQZ) attain practical Virial Theorem compliance (i.e., agreement among the kinetic energy, potential energy, and total energy representations) in assigning 2.70 ± 0.06 to the barrier height; −195.80 kcal/mol is assigned to the drop in “steric” repulsion upon going to the eclipsed geometry. Steric repulsion is not responsible for any fraction of the ~3 kcal/mol barrier.

Benchmarking semiempirical, Hartree–Fock, DFT, and MP2 methods against the ionization energies and electron affinities of short- through long-chain [n]acenes and [n]phenacenes

Vertical and adiabatic ionization energies (IEs) and electron affinities (EAs) were calculated for the n = 1–10 [n]acenes using a wide range of semiempirical, Hartree–Fock, density functional, and second-order Moller–Plesset perturbation theory model chemistries. None of the model chemistries examined was able to accurately predict the IEs or EAs for both short- through long-chain [n]acenes, as well as for extrapolations to the polymeric limit, when compared to available experimental and benchmark theoretical data. Except for 6-31G(d), the choice of the basis set does not affect B3LYP results significantly. Analogous calculations using a suite of eight modern and (or) popular density functionals for the n = 1–10 [n]phenacenes revealed similar problems in estimating the IEs and EAs of these compounds, with the sole exception of the M062X functional for adiabatic IEs and potentially the APFD, B3LYP, and MN12SX functionals for adiabatic EAs. The poor IE/EA prediction performance for the parent [n]acenes and [n]phenacenes may extend to their substituted derivatives and heteroatom-substituted analogs. Consequently, caution should be exercised in the application of non-high-level calculations for estimating the IE/EA of these important classes of materials.

Perturbation theory model of reactivity and enantioselectivity of palladium-catalyzed Heck–Heck cascade reactions

A new multi-output PT-QSRR model to correlate and predict the enantioselectivity and yield of Heck–Heck cascade reactions has been developed.

Ab initiodownfolding for electron-phonon-coupled systems: Constrained density-functional perturbation theory

The problem of electron-phonon interactions in strongly correlated systems is addressed by a new method which establishes a rigorous link between \textit{ab initio} density functional perturbation theory and low-energy model Hamiltonians. This allows the construction of model Hamiltonians for strongly correlated systems in a predictable and quantitative way, with respect to material oriented applications, especially where both electron-electron and electron-phonon couplings have the same magnitude. This could lead either to a competition or a cooperation between the two interactions, and stabilize interesting phases such as superconductivity in fullerenes.

Taylor's Series and Dispersion Relation Analyses of the Vector Pion Form Factor and their Comparison with Perturbative and Non Perturbative Calculations

The first three coefficients of the Taylor's series expansion of the vevtor pion form factor as a function of the momentum transfer are evaluated using the experimental data on the pion form factor and the P-wave \(\pi\pi\) phase shifts. The real part of the form factor as a function of energy is also calculated by dispersion relation. Comparisons there results with Chiral Perturbation Theory and unitarized models are given.