Realistic Energies Research Articles

An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies.

An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)n conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid - harmonic oscillator approximations reaching 10 kcal mol-1.

Assessing realistic binding energies of some essential interstellar radicals with amorphous solid water. A fully quantum chemical approach

Assessing realistic binding energies of some essential interstellar radicals with amorphous solid water. A fully quantum chemical approach

Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase.

Phosphoenolpyruvate carboxylase (PEPC) is used in plant metabolism for fruit maturation or seed development as well as in the C4 and crassulacean acid metabolism (CAM) mechanisms in photosynthesis, where it is used for the capture of hydrated CO2 (bicarbonate). To find the yet unknown binding site of bicarbonate in this enzyme, we have first identified putative binding sites with nonequilibrium molecular dynamics simulations and then ranked these sites with alchemical free energy calculations with corrections of computational artifacts. Fourteen pockets where bicarbonate could bind were identified, with three having realistic binding free energies with differences with the experimental value below 1 kcal/mol. One of these pockets is found far from the active site at 14 Å and predicted to be an allosteric binding site. In the two other binding sites, bicarbonate is in direct interaction with the magnesium ion; neither sequence alignment nor the study of mutant K606N allowed to discriminate between these two pockets, and both are good candidates as the binding site of bicarbonate in phosphoenolpyruvate carboxylase.

Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions.

For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use spatial stochastic computer simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol is highly likely and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (-12kBT<∆G<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.

Predicting driving transferred energy without needing the hammer efficiency: three case studies

This study presents case studies on the implementation of an innovative method of calculating effective driving energy with no need to account for hammer efficiency. The approach is based on measurements of set and elastic rebound, as well as a site-specific parameter (λ) calibration. The study applied this method to steel piles located in the cities of Santos (SP), Itaguaí (RJ), and Óbidos (PA), with the latter site being built in the Amazon region, near the Amazon River. Following coefficient calibration, the effective driving energy estimation technique exhibited a strong correlation with realistic and accurate energies directly obtained from dynamic loading tests. The method provides a highly accurate means of calculating effectively transferred energy to piles due to hammer blows, without relying on knowledge of the driving system performance. In that way, it can be applied to all the piles at the site (100% of them), including those that are not tested. This optimized and agile approach represents a significant breakthrough in foundation engineering and an enhance of pile foundation quality control.

Astrochemical model to study the abundances of branched carbon-chain molecules in a hot molecular core with realistic binding energies

ABSTRACT Straight-chain (normal-propyl cyanide, $\rm {n-C_3H_7CN}$) and branched-chain (iso-propyl cyanide, $\rm {i-C_3H_7CN}$) alkyl cyanides are recently identified in the massive star-forming regions (Sgr B2(N) and Orion). These branched-chain molecules indicate that the key amino acids (side-chain structures) may also be present in a similar region. The process by which this branching could propagate towards the higher order (butyl cyanide, $\rm {C_4H_9CN}$) is an active field of research. Since the grain catalysis process could have formed a major portion of these species, considering a realistic set of binding energies are indeed essential. We employ quantum chemical calculations to estimate the binding energy of these species considering water as a substrate because water is the principal constituent of this interstellar ice. We find significantly lower binding energy values for these species than were previously used. It is noticed that the use of realistic binding energy values can significantly change the abundance of these species. The branching is more favourable for the higher order alkyl cyanides with the new binding energies. With the inclusion of our new binding energy values and one essential destruction reaction ($\rm {i-C_3H_7CN+H \rightarrow CH_3C(CH_3)CN + H_2}$, having an activation barrier of 947 K), abundances of $\rm {t-C_4H_9CN}$ dramatically increased.

Scaling of self-compression of near-IR femtosecond pulses in hollow-core fibers down to the single-cycle limit

We numerically investigate the scaling of self-compression processes with experimental parameters for near-infrared ultrashort pulses (30 fs) in gas-filled hollow-core fiber (HCF). These simulations over a wide-range of input pulse energies as well as filling gas pressures reveal a remarkable scaling of the self-compression process and dynamics. As a function of soliton order N, we identify the relation between the propagation distance after which self-compression in the HCF begins and the subsequent propagation length up to which the pulse remains maximally compressed; both these length scales decrease with an increase in N, the soliton order. Although previous investigations revealed pulse compression scaling laws which provide a good approximation for input pulse-widths ∼100 fs down to the limit where soliton fission begins to dominate the dynamics, these are not sufficiently accurate to describe the entire scaling dynamics. Instead, we identify a more generalized set of scaling laws by taking both third-order dispersion and the saturation of the compression factor due to soliton fission into account. These conclusions about scaling are robust: our simulations were carried out over a wide range of realistic input pulse energies and gas pressures as implemented in laboratories taking into account higher-order dispersive properties of the gaseous propagating medium. Therefore, given that these numerical investigations consider conditions typically applied in practice in laboratories, this work provides elegant design principles and guideposts relevant to realizing systems capable of achieving self-compression at substantially high pulse energies down to the few-cycle limit; they are of paramount importance in generating single as well as trains of attosecond pulses and acceleration strategies for electrons and ions in intense laser pulses.

The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs

AbstractThe nucleobase derivative 5‐aminouracil (AUr, C4H5N3O2) is of interest for its biological activity, yet the solid state structure of this compound has remained elusive owing to its propensity to crystallize as aggregates of microcrystalline particles. Here we report the first single‐crystal structure of AUr determined from synchrotron x‐ray diffraction data. An early crystal structure prediction effort, which assumed that AUr was rigid in the isolated molecule optimized conformation, provided several poor matches to the simulated PXRD pattern. Revisiting these crystal structures, by periodic electronic level modelling (PBE‐TS optimization) gave more realistic relative lattice energies, but a good match to the experimental powder pattern required using the experimental cell parameters. PXRD and Raman spectroscopy suggest that phase impurities may be present in the bulk crystallization product, though the identity of alternative polymorphs could not be confirmed on the basis of the data available.

SAFT-γ-Mie Cross-Interaction Parameters from Density Functional Theory-Predicted Multipoles of Molecular Fragments for Carbon Dioxide, Benzene, Alkanes, and Water.

Determining unlike-pair interaction parameters, whether for group contribution equation of state or molecular simulations, is a challenge for the prediction of thermodynamic properties. As the number of components and their respective complexity increase, it becomes impractical to fit all the unlike interactions. Lorentz-Berthelot combining rules work well for systems, where the main interactions are dispersion forces, but they do not account for electrostatics. In this work, we derive predictive combining rules within the SAFT-γ-Mie framework. In the resulting model, the unlike-pair interactions account for the effect of ionization energies, partial charges, dipole moments, and quadrupole moments. We then estimate these properties for molecular fragments using density functional theory calculations and demonstrate their use to obtain realistic cross-interaction energies without the need for experimental data. An open-source python package, Multipole Approach to Predictively Scale Cross-Interactions, is included to facilitate use of the methods presented in this work. A good qualitative agreement was obtained for all phase equilibria calculations of binary mixtures containing carbon dioxide with propane, hexane, benzene, and water, as well as mixtures of hexane and benzene. Finally, we discuss future improvements to our methodology, including the use of physical insights when fitting self-interaction parameters.

Self-Interaction-Corrected Random Phase Approximation.

The short-range correlation energy of the random phase approximation (RPA) is too negative and is often corrected by local or nonlocal methods. These beyond-RPA corrections usually lead to a mixed performance for thermodynamics and dissociation properties. RPA+ is an additive correction based on density functional approximations that often gives realistic total energies for atoms or solids. RPA+ adds a moderate correction to the ionization energies/electron affinities of RPA but does not yield an improvement beyond RPA for atomization energies of molecules. This incompleteness results in severely underestimated atomization energies just like in RPA. Exchange-correlation kernels within the Dyson equation could simultaneously improve atomization, ionization energies, and electron affinities, but their implementation is computationally less feasible in localized basis set codes. In preceding work ( Phys. Rev. A 100, 2019022515), two of the authors proposed a computationally efficient generalized RPA+ (gRPA+) that changes RPA+ only for spin-polarized systems by making gRPA+ exact for all one-electron densities. gRPA+ was found to yield a large improvement of ionization energies and electron affinities of light atoms over RPA, and a smaller improvement over RPA+. Within this work, we investigate to what extent this improvement transfers to atomization energies, ionization energies, and electron affinities of molecules, using a modified gRPA+ (mgRPA+) method that can be applied in codes with localized basis functions. We thereby aim to understand the applicability of beyond-RPA corrections based on density functional approximations.

Statistical Fluctuations of Energy Spectra in the Isobar A = 68 Nuclei

Statistical fluctuations of nuclear energy spectra for the isobar A = 68 were examined by means of the random matrix theory together with the nuclear shell model. The isobar A = 68 nuclei are suggested to consist of an inert core of 56Ni with 12 nucleons in f5p-space (2p3/2, 1f5/2 and 2p1/2 orbitals). The nuclear excitation energies, required by this work, were obtained through performing f5p-shell model calculations using the isospin formalism f5pvh interaction with realistic single particle energies. All calculations of the present study were conducted using the OXBASH code. The calculated level densities were found to have a Gaussian shape. The distributions of level spacing P(s) and statistic for the considered classes of states, obtained with full Hamiltonian of f5pvh (absence of the off-diagonal Hamiltonian) calculations, showed a chaotic (regular) behavior and coincided well with the distribution of Gaussian orthogonal ensemble (Poisson). Moreover, these distributions were independent of spin (J) and isospin (T)

Dielectric Skyrmions

We consider the dielectric Skyrme model proposed recently, with and without the addition of the standard pion mass term. Then we write down Bogomol'nyi-type energy bounds for both the massless and massive cases. We further show that, except for when taking the strict BPS limit, the Skyrmions are made of 3 orthogonal dipoles that can always be placed in their attractive channel and form bound states. Finally, we study the model numerically and discover that, long before realistic binding energies are reached, the Skyrmions become bound states of well-separated point-particle-like Skyrmions. By going sufficiently close to the BPS limit, we are able to obtain classical binding energies of realistic values compared with experiments.

Failure processes of cemented granular materials.

The mechanics of cohesive or cemented granular materials is complex, combining the heterogeneous responses of granular media, like force chains, with clearly defined material properties. Here we use a discrete element model simulation, consisting of an assemblage of elastic particles connected by softer but breakable elastic bonds, to explore how this class of material deforms and fails under uniaxial compression. We are particularly interested in the connection between the microscopic interactions among the grains or particles and the macroscopic material response. To this end, the properties of the particles and the stiffness of the bonds are matched to experimental measurements of a cohesive granular medium with tunable elasticity. The criterion for breaking a bond is also based on an explicit Griffith energy balance, with realistic surface energies. By varying the initial volume fraction of the particle assembles we show that this simple model reproduces a wide range of experimental behaviors, both in the elastic limit and beyond it. These include quantitative details of the distinct failure modes of shear-banding, ductile failure, and compaction banding or anticracks, as well as the transitions between these modes. The present work, therefore, provides a unified framework for understanding the failure of porous materials such as sandstone, marble, powder aggregates, snow, and foam.

Accurate bulk properties of nuclei from A=2 to ∞ from potentials with Δ isobars

We optimize $\Delta$-full nuclear interactions from chiral effective field theory. The low-energy constants of the contact potentials are constrained by two-body scattering phase shifts, and by properties of bound-state of $A=2$ to $4$ nucleon systems and nuclear matter. The pion-nucleon couplings are taken from a Roy-Steiner analysis. The resulting interactions yield accurate binding energies and radii for a range of nuclei from $A=16$ to $A=132$, and provide accurate equations of state for nuclear matter and realistic symmetry energies. Selected excited states are also in agreement with data.

Spectral fluctuations and thermalization in the f5p-shell space

Chaos against thermalization, which was earlier investigated in the sd-shell space, is examined in the f5p-shell space. The two-body residual interaction of f5pvh with realistic single-particle energies have been utilized for carrying out f5p-shell space calculations. The present study demonstrates that the spectral fluctuations computed with realistic single-particle energies are in accordance with the Gaussian orthogonal ensemble of random matrices. Besides, the equilibrium heating is extremely related with the progress of many-body quantum chaos. Moreover, the single-particle entropy of individual states in the mean field basis is dissimilar to the thermodynamic entropy determined from the level density. The present results, which are a check of the ideas of many-body quantum chaos in a different version of the nuclear shell model applied to another part of the periodic table, are fully confirming what was formerly achieved in the sd-shell space and in this way exhibit their generality.

Exploring the relationship between nuclear matter and finite nuclei with chiral two- and three-nucleon forces

We address the connection between the saturating behavior of infinite nuclear matter and the description of finite nuclei based on state-of-the-art chiral two- and three-nucleon forces. We observe that chiral two- and three-nucleon interactions (at N2LO and at N3LO) which have been found to predict realistic binding energies and radii for a wide range of finite nuclei (from p-shell nuclei up to nickel isotopes) are unable to saturate infinite nuclear matter. On the other hand, it has been shown that, when the fits of the cD and cE couplings of the chiral three-nucleon interactions include the constraint of nuclear matter saturation in addition to, as is typically the case, the triton binding energy, medium-mass nuclei are underbound and their radii are sytematically too large. We discuss this apparent inconsistency and perform test calculations for various scenarios to shed light on the issue.

Erratum: Simple self-interaction correction to random-phase-approximation-like correlation energies [Phys. Rev. A 100, 022515 (2019)

The random phase approximation (RPA) is exact for the exchange energy of a many-electron ground state, but RPA makes the correlation energy too negative by about 0.5 eV/electron. That large short-range error, which tends to cancel out of iso-electronic energy differences, is largely corrected by an exchange-correlation kernel, or (as in RPA+) by an additive local or semilocal correction. RPA+ is by construction exact for the homogeneous electron gas, and it is also accurate for the jellium surface. RPA+ often gives realistic total energies for atoms or solids in which spin-polarization corrections are absent or small. RPA and RPA+ also yield realistic singlet binding energy curves for H2 and N2, and thus RPA+ yields correct total energies even for spin-unpolarized atoms with fractional spins and strong correlation, as in stretched H2 or N2. However, RPA and RPA+ can be very wrong for spin-polarized one-electron systems (especially for stretched H2+), and also for the spin-polarization energies of atoms. The spin-polarization energy is often a small part of the total energy of an atom, but important for ionization energies, electron affinities, and the atomization energies of molecules. Here we propose a computationally efficient generalized RPA+ (gRPA+) that changes RPA+ only for spin-polarized systems by making gRPA+ exact for all one-electron densities, in the same simple semilocal way that the correlation energy densities of many meta-generalized gradent approximations are made self-correlation free. By construction, gRPA+ does not degrade the exact RPA+ description of jellium. gRPA+ is found to greatly improve upon RPA and RPA+ for the ionization energies and electron affinities of light atoms. Many versions of RPA with an approximate exchange-correlation kernel fail to be exact for all one-electron densities, and they can also be self-interaction corrected in this way.

Phase-field modeling of γ/γ″ microstructure formation in Ni-based superalloys with high γ″ volume fraction

The excellent mechanical properties of the Ni-based superalloy IN718 mainly result from coherent γ″ precipitates. Due to a strongly anisotropic lattice misfit between the matrix and the precipitate phase, the particles exhibit pronounced plate-shaped morphologies. Using a phase-field model, we investigate various influencing factors that determine the equilibrium shapes of γ″ precipitates, minimizing the sum of the total elastic and interfacial energy. Upon increasing precipitate phase fractions, the model predicts increasingly stronger particle-particle interactions, leading to shapes with significantly increased aspect ratios. Matching the a priori unknown interfacial energy density to fit experimental γ″ shapes is sensitive to the phase content imposed in the underlying model. Considering vanishing phase content leads to 30% lower estimates of the interfacial energy density, as compared to estimates based on realistic phase fractions of 12%. We consider the periodic arrangement of precipitates in different hexagonal and rectangular superstructures, which result from distinct choices of point-symmetric and periodic boundary conditions. Further, non-volume conserving boundary conditions are implemented to compensate for strains due to an anisotropic lattice mismatch between the γ matrix and the γ″ precipitate. As compared to conventional boundary conditions, this specifically tailored simulation configuration does not conflict with the system's periodicity and provides substantially more realistic total elastic energies at high precipitate volume fractions. The energetically most favorable superstructure is found to be a hexagonal precipitate arrangement.

Thermal Simulations of Temperature Excursions on the Athena X-IFU Detector Wafer from Impacts by Cosmic Rays

We present the design and implementation of a thermal model, developed in COMSOL, aiming to probe the wafer-scale thermal response arising from realistic rates and energies of cosmic rays at L2 impacting the detector wafer of Athena X-IFU. The wafer thermal model is a four-layer 2D model, where 2 layers represent the constituent materials (Si bulk and Si$_{3}$N$_{4}$ membrane), and 2 layers represent the Au metallization layer's phonon and electron temperatures. We base the simulation geometry on the current specifications for the X-IFU detector wafer, and simulate cosmic ray impacts using a simple power injection into the Si bulk. We measure the temperature at the point of the instrument's most central TES detector. By probing the response of the system and pulse characteristics as a function of the thermal input energy and location, we reconstruct cosmic ray pulses in Python. By utilizing this code, along with the results of the GEANT4 simulations produced for X-IFU, we produce realistic time-ordered data (TOD) of the temperature seen by the central TES, which we use to simulate the degradation of the energy resolution of the instrument in space-like conditions on this wafer. We find a degradation to the energy resolution of 7 keV X-rays of $\approx$0.04 eV. By modifying wafer parameters and comparing the simulated TOD, this study is a valuable tool for probing design changes on the thermal background seen by the detectors.

Giant Conductance Enhancement of Intramolecular Circuits through Interchannel Gating

Summary For neutral intramolecular circuits with two constitutionally identical branches, a maximum 4-fold increase in total conductance can be obtained according to constructive quantum interference (CQI). For charged intramolecular circuits, however, the strong electrostatic interactions entangle the quantum states of these two parallel pathways, thus introducing complicated transport behavior that warrants experimental investigation of the intramolecular circuit rules. Here, we report that a tetracationic cyclophane with parallel channels exhibits a 50-fold conductance enhancement compared with that of a single-channel control, an observation that supplements intramolecular circuit law in systems with strong Coulombic interactions. Flicker noise measurements and theoretical calculations show that strong electrostatic interactions between charged parallel channels—serving as the chemical gate to promote the effective conductance of each channel—and CQI boosts the total conductance of the two-channel circuit. The molecular design presented herein constitutes a proof-of-principle approach to charged intramolecular circuits that are desirable for quantum circuits and devices.