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At least 1,207 records · Page 67

Protein–Ligand Binding Free-Energy Calculations with ARROW–A Purely First-Principles Parameterized Polarizable Force Field

Protein–ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)–a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein–ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ~0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental Validation of Calorimetric Electron Capture Spectral Theory with 193 Pt

Using microcalorimeters, a high statistics, high-resolution calorimetric spectrum of electron capture in 163 Ho can be used to determine the neutrino mass. The spectral shape can be calculated from first principles with various assumptions and approximations. To determine the validity of these choices, the theoretical calculations must be compared to data from multiple isotopes. In this work, new calorimetric data for a 193 Pt-in-Pt absorber measured with a transition edge sensor are presented and compared to theoretical calculations and values from the literature.

74 ATOMIC AND MOLECULAR PHYSICS↗

Efficient calculation of carrier scattering rates from first principles

Abstract The electronic transport behaviour of materials determines their suitability for technological applications. We develop a computationally efficient method for calculating carrier scattering rates of solid-state semiconductors and insulators from first principles inputs. The present method extends existing polar and non-polar electron-phonon coupling, ionized impurity, and piezoelectric scattering mechanisms formulated for isotropic band structures to support highly anisotropic materials. We test the formalism by calculating the electronic transport properties of 23 semiconductors, including the large 48 atom CH 3 NH 3 PbI 3 hybrid perovskite, and comparing the results against experimental measurements and more detailed scattering simulations. The Spearman rank coefficient of mobility against experiment ( r s = 0.93) improves significantly on results obtained using a constant relaxation time approximation ( r s = 0.52). We find our approach offers similar accuracy to state-of-the art methods at approximately 1/500th the computational cost, thus enabling its use in high-throughput computational workflows for the accurate screening of carrier mobilities, lifetimes, and thermoelectric power.

97 MATHEMATICS AND COMPUTING↗

Towards cubic symmetry for Ir 4 + : Structure and magnetism of the antifluorite K 2 IrBr 6

Here, crystal structure, electronic state of Ir 4 + , and magnetic properties of the antifluorite compound K 2 IrBr 6 are studied using high-resolution synchrotron x-ray diffraction, resonant inelastic x-ray scattering (RIXS), thermodynamic and transport measurements, and ab initio calculations. The crystal symmetry is reduced from cubic at room temperature to tetragonal below 170 K and eventually to monoclinic below 122 K. These changes are tracked by the evolution of the noncubic crystal-field splitting Δ measured by RIXS. Nonmonotonic changes in Δ are ascribed to the competing effects of the tilt, rotation, and deformation of the IrBr 6 octahedra as well as tetragonal strain on the electronic levels of Ir 4 + . The Néel temperature of T N = 11.9 K exceeds that of the isostructural K 2 IrCl 6 , and the magnitude of frustration on the fcc spin lattice decreases. We argue that the replacement of Cl by Br weakens electronic correlations and enhances magnetic couplings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Point defect induced incommensurate dipole moments in the K Ca 2 Nb 3 O 10 Dion-Jacobson layered perovskite

Local structural distortions due to isolated atomic defects and defect complexes strongly affect the macroscopic properties of oxide ceramics. While the characterization of local defect structures is more common in simple AB O 3 perovskites, unambiguous determination of the same in layered perovskites is more difficult due to their complex crystal structures. In this study, we combined x-ray pair distribution function and density functional theory calculations to characterize the structure of cation-oxygen divacancy pairs in a Dion-Jacobson (D-J) layered perovskite. Our results indicate that local incommensurate dipole moments with polarization density in the range of ~ 0.1–17μC/cm 2 are created due to divacancy-induced structural distortions in the D-J phase K Ca 2 Nb 3 O 10 . This is comparable with defect dipole moments observed in well-known perovskite ferroelectrics. The current results imply that controlling the atomic defects can potentially lead to significant control of dielectric properties in D-J layered perovskites.

3-dimensional systems↗

16 O Electroweak Response Functions from First Principles

We present calculations of various electroweak response functions for the 16 O nucleus obtained using coupled-cluster theory in conjunction with the Lorentz integral transform method. We employ nuclear forces derived at next-to-leading order and next-to-next-to-leading order in chiral effective field theory and perform a Bayesian analysis to assess uncertainties. Our results are in good agreement with available electron-scattering data at |𝐪|≈326 MeV/c. Additionally, we provide several predictions for the weak response functions in the quasielastic peak region at |𝐪| =300 and 400 MeV/c, which are critical for long-baseline neutrino experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Persistence of deuterium and tritium nuclear spin-polarization in presence of high-frequency plasma waves

We present first-principles numerical calculations of the depolarization rate of spin-polarized deuterium and tritium nuclei in realistic tokamak plasmas, driven by resonant interactions with plasma waves. Backed up by first-of-a-kind linear and nonlinear simulations, we find that alpha particle-driven Alfvénic modes cause only negligible depolarization, which is contrary to expectations in prior literature. Other Alfvénic instabilities can in principle degrade polarization, but only under conditions unlikely to be realized on transport timescales. By combining full-orbit particle tracing with a dedicated depolarization solver, we demonstrate that wave-driven depolarization is surprisingly weak in SPARC and ITER-scale devices. These results provide strong evidence that spin-polarized fuel can maintain its polarization long enough to boost fusion reactivity, opening a viable path toward substantially enhanced performance in magnetic confinement fusion power plants.

Cook, James William Setchfield [UK Atomic Energy A↗

NiGa 2 O 4 interfacial layers in NiO/Ga 2 O 3 heterojunction diodes at high temperature

NiO/Ga 2 O 3 heterojunction diodes have attracted attention for high-power applications, but their high temperature performance and reliability remain underexplored. Here, we report the time evolution of the electrical properties in the widely studied p-NiO/n-Ga 2 O 3 heterojunction diodes and formation of NiGa 2 O 4 interfacial layers at high temperatures. Results of our thermal cycling experiment show an initial leakage current increase which stabilizes after sustained thermal load, due to reactions at the NiO–Ga 2 O 3 interface. High-resolution TEM microstructure analysis of the devices after thermal cycling indicates that the NiO–Ga 2 O 3 interface forms a ternary compound at high temperatures, and thermodynamic calculations suggest the formation of the spinel NiGa 2 O 4 layer between NiO and Ga 2 O 3 . First-principles defect calculations find that NiGa 2 O 4 shows low p-type intrinsic doping and hence can serve to limit electric field crowding at the interface. Vertical NiO/ Ga 2 O 3 diodes with intentionally grown 5 nm thin spinel-type NiGa 2 O 4 interfacial layers show an excellent device ON/OFF ratio of >10 10 (± 3 V), V ON of ~1.9 V, and increased breakdown voltage of ~1.2 kV for an initial unoptimized 300 lm diameter device. These p–n heterojunction diodes are promising for high-voltage, high temperature applications.

30 DIRECT ENERGY CONVERSION↗

Multiphase tin equation of state using density functional theory

In this work, we perform density functional theory (DFT) calculations of five solid phases and the liquid phase of tin. The calculations include cold curves of the five solid phases, phonon calculations in the quasiharmonic approximation over a range of volumes for each solid phase, and DFT-based molecular dynamics (DFT-MD) simulations of the liquid phase, including those of the melt curve using the Z method. Using the DFT results, we construct a tabular multiphase sesame equation of state for tin, referred to as sesame 2162. Comparisons to experimental data are made and show a high level of agreement in isobaric data, isothermal data, shock data, and phase boundary measurements, including measurements of the melt curve. The 2162 EOS will be useful for hydrodynamics simulations and has been designed with an eye toward hydrodynamics simulations that incorporate materials strength models and allow for modeling of the kinetics of phase transitions.

3-dimensional systems↗

Optical activity of solids from first principles

Within the framework of independent particle approximation, the optical activity tensor of solids is formulated as from different contributions: the magnetic dipole, electric quadrupole, and band dispersion terms. The first two terms have similar counterparts in the theory of finite systems, whereas the last term is unique for crystals. Further, the magnetic dipole and electric quadrupole transition moments are calculated with a sum-over-states formulation. We apply the formulation to calculate and analyze the optical rotation of elemental tellurium and the circular dichroism of the (6,4) carbon nanotube. Decomposed optical activity into different contributions is discussed. The calculated spectra agree well with experiments. As a showcase of achiral crystals, we calculate the optical activity of wurtzite GaN.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Anharmonicity and Phase Diagram of Magnesium Oxide in the Megabar Regime

With density functional molecular dynamics simulations, we computed the phase diagram of MgO from 50 to 2000 GPa up to 20000 K. Via thermodynamic integration (TDI), we derive the Gibbs free energies of the B1, B2, and liquid phases and determine their phase boundaries. With TDI and a pseudo-quasi-harmonic approach, we show that anharmonic effects are important and stabilize the B1 phase in particular. As a result, the B1-B2 transition boundary in the pressure-temperature plane exhibits a steep slope. We predict the B1-B2-liquid triple point to occur at approximately T= 10000 K and P = 370 GPa, which is higher in pressure than was inferred with quasi-harmonic methods alone. We predict the principal shock Hugoniot curve to enter the B2 phase stability domain but only over a very small range of parameters. Here, this may render it difficult to observe this phase with shock experiments because of kinetic effects.

3-dimensional systems↗

Role of Hydrogen-bonded Bimolecular Formic Acid–Formate Complexes for Formic Acid Decomposition on Copper: A Combined First-Principles and Microkinetic Modeling Study

Hydrogen bonding interactions alter the nanoscale reaction mechanisms of many chemistries. Yet, it remains unclear how they affect heterogeneously catalyzed decomposition of formic acid (FA), a reaction of intense interest since FA is a promising hydrogen carrier. In this work, we elucidate how hydrogen bonding affects the reaction mechanisms for FA decomposition on Cu(111) by combining first-principles density functional theory calculations to calculate reaction energetics, Latin-hypercube sampling to elucidate stable high-coverage adsorbate configurations, and coverage self-consistent mean-field microkinetic models to predict reaction kinetics. We demonstrate that hydrogen-bonded complexes of FA with formate (bimolecular FA–HCOO complexes) can play a dominant role in FA decomposition. Specifically, our first-principles calculations show that hydrogen bonding of FA with HCOO may stabilize the crucial monodentate HCOO intermediate and the transition states for HCOO decomposition, especially at low coverages. We predict that, depending on the reaction conditions, 40–80% of the reaction flux goes through pathways involving the bimolecular FA–HCOO complexes. Additionally, the active site for FA decomposition on Cu(111) involves a high coverage (~0.4 monolayers (ML)) of these complexes, which unexpectedly stabilize intermediates and transition states via van der Waals interactions. Our work provides molecular insights consistent with previous experimental observations on supported Cu/Al 2 O 3 catalysts. This paves the way toward the development of novel catalysts for FA decomposition as well as for other industrially important chemistries with intermediates capable of hydrogen bonding, such as ammonia electrooxidation and CO 2 hydrogenation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mirror neutron stars

The fundamental nature of dark matter is entirely unknown. A compelling candidate is twin Higgs mirror matter, invisible hidden-sector cousins of the Standard Model particles and forces. This predicts mirror neutron stars made entirely of mirror nuclear matter. Here we find their structure using realistic equations of state, robustly modified based on first-principle quantum chromodynamic calculations, for the first time. This allows us to predict their gravitational wave signals, demonstrating an impressive discovery potential and ability to probe dark sectors connected to the hierarchy problem.

79 ASTRONOMY AND ASTROPHYSICS↗

Elastic deformation of the gyro rotor in the relativity gyro experiment

The elastic deformation of a spinning sphere is calculated from first principles. Numerical results are quoted for a quartz sphere spinning at 200 Hz, the most likely configuration for the relativity gyro experiment. The difference in principal moments of inertia is also calculated for the spinning gyro.

Eby, P. B.↗

Anisotropic-strain-enhanced hole mobility in GaN by lattice matching to ZnGeN 2 and MgSiN 2

The key obstacle toward realizing integrated gallium nitride (GaN) electronics is its low hole mobility. Here, we explore the possibility of improving the hole mobility of GaN via epitaxial matching to II–IV nitride materials that have recently become available, namely, ZnGeN 2 and MgSiN 2 . We perform state-of-the-art calculations of the hole mobility of GaN using the ab initio Boltzmann transport equation. We show that effective uniaxial compressive strain of GaN along the [$1\bar{1}00$] by lattice matching to ZnGeN 2 and MgSiN 2 results in the inversion of the heavy hole band and split-off hole band, thereby lowering the effective hole mass in the compression direction. We find that lattice matching to ZnGeN 2 and MgSiN 2 induces an increase in the room-temperature hole mobility by 50% and 260% as compared to unstrained GaN, respectively. Further, examining the trends as a function of strain, we find that the variation in mobility is highly nonlinear; lattice matching to a hypothetical solid solution of Zn 0.75 Ge 0.75 Mg 0.25 Si 0.25 N 2 would already increase the hole mobility by 160%.

36 MATERIALS SCIENCE↗

Fast and Universal Kohn-Sham Density Functional Theory Algorithm for Warm Dense Matter to Hot Dense Plasma

Understanding many processes, e.g., fusion experiments, planetary interiors, and dwarf stars, depends strongly on microscopic physics modeling of warm dense matter and hot dense plasma. This complex state of matter consists of a transient mixture of degenerate and nearly free electrons, molecules, and ions. This regime challenges both experiment and analytical modeling, necessitating predictive ab initio atomistic computation, typically based on quantum mechanical Kohn-Sham density functional theory (KS-DFT). However, cubic computational scaling with temperature and system size prohibits the use of DFT through much of the warm dense matter regime. A recently developed stochastic approach to KS-DFT can be used at high temperatures, with the exact same accuracy as the deterministic approach, but the stochastic error can converge slowly and it remains expensive for intermediate temperatures (< 50 eV). Here we have developed a universal mixed stochastic-deterministic algorithm for DFT at any temperature. This approach leverages the physics of KS-DFT to seamlessly integrate the best aspects of these different approaches. We demonstrate that this method significantly accelerated self-consistent field calculations for temperatures from 3 to 50 eV, while producing stable molecular dynamics and accurate diffusion coefficients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗