Quantum Molecular Dynamics Calculations Research Articles

A new set of atmosphere and evolution models for cool T–Y brown dwarfs and giant exoplanets

We present a new set of solar metallicity atmosphere and evolutionary models for very cool brown dwarfs and self-luminous giant exoplanets, which we term ATMO 2020. Atmosphere models are generated with our state-of-the-art 1D radiative-convective equilibrium code ATMO, and are used as surface boundary conditions to calculate the interior structure and evolution of 0.001–0.075 M⊙ objects. Our models include several key improvements to the input physics used in previous models available in the literature. Most notably, the use of a new H–He equation of state including ab initio quantum molecular dynamics calculations has raised the mass by ~1−2% at the stellar–substellar boundary and has altered the cooling tracks around the hydrogen and deuterium burning minimum masses. A second key improvement concerns updated molecular opacities in our atmosphere model ATMO, which now contains significantly more line transitions required to accurately capture the opacity in these hot atmospheres. This leads to warmer atmospheric temperature structures, further changing the cooling curves and predicted emission spectra of substellar objects. We present significant improvement for the treatment of the collisionally broadened potassium resonance doublet, and highlight the importance of these lines in shaping the red-optical and near-infrared spectrum of brown dwarfs. We generate three different grids of model simulations, one using equilibrium chemistry and two using non-equilibrium chemistry due to vertical mixing, all three computed self-consistently with the pressure-temperature structure of the atmosphere. We show the impact of vertical mixing on emission spectra and in colour-magnitude diagrams, highlighting how the 3.5−5.5 μm flux window can be used to calibrate vertical mixing in cool T–Y spectral type objects.

Interpretation of experiments on shock compression and isentropic expansion of uranium by quantum molecular dynamics simulations

In this work, results of quantum molecular dynamics calculations of thermodynamical properties of uranium are presented. The experiments on shock compression and subsequent isentropic expansion of porous samples of uranium are well described. Our first-principle calculations of the shock Hugoniot and release isentropes of uranium demonstrate good agreement with experimental measurements. In addition, unique information of temperature along experimental curves was obtained including supposed entries of isentropes into the two-phase liquid–gas region according to the hypothetical kinks on the experimental isentropes.

Calculation of electron-ion temperature equilibration rates and friction coefficients in plasmas and liquid metals using quantum molecular dynamics.

We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals, and hot solids. Promising results from this method were recently reported for various materials and physical conditions [Simoni and Daligault, Phys. Rev. Lett. 122, 205001 (2019)PRLTAO0031-900710.1103/PhysRevLett.122.205001]. Like other ab initio calculations, the approach offers a very useful comparison with the experimental measurements and permits an extension into conditions not covered by the experiments. The energy relaxation rate is related to the friction coefficients felt by individual ions due to their nonadiabatic interactions with electrons. Each coefficient satisfies a Kubo relation given by the time integral of the autocorrelation function of the interaction force between an ion and the electrons. These Kubo relations are evaluated using the output of quantum molecular dynamics calculations in which electrons are treated in the framework of finite-temperature density functional theory. The calculation presents difficulties that are unlike those encountered with the Kubo formulas for the electrical and thermal conductivities. In particular, the widely used Kubo-Greenwood approximation is inapplicable here. Indeed, the friction coefficients and the energy relaxation rate diverge in this approximation since it does not properly account for the electronic screening of electron-ion interactions. The inclusion of screening effects considerably complicates the calculations. We discuss the physically motivated approximations we applied to deal with these complications in order to investigate a widest range of materials and physical conditions. Unlike the standard method used for the electronic conductivities, the Kubo formulas are evaluated directly in the time domain and not in the energy domain, which spares one from needing to introduce an extraneous undetermined numerical parameter to account for the discrete character of the numerical density of states. We highlight interesting properties of the energy relaxation rate not shared by other electronic properties, in particular its self-averaging character. We then present a detailed parametric and convergence study with the numerical parameters, including the system size, the number of bands and k points, and the physical approximations for the dielectric function and the exchange-correlation energy.

Interpretation of pulse-heating experiments for rhenium by quantum molecular dynamics

We present quantum molecular dynamics calculations of thermophysical properties of solid and liquid rhenium in the vicinity of melting. We show that some pulse-heating experiments for rhenium can be independently described by the first-principle calculations. Our calculations predict significant volume change of about 6% at melting. We also provide our estimation of the enthalpy of fusion, which is about 33.6 kJ/mol.

Compression of liquid Ni and Co under extreme conditions explored by x-ray absorption spectroscopy

The compression of liquid nickel and cobalt has been investigated up to 102 and 83 GPa, respectively, by x-ray absorption spectroscopy at the Ni and Co $K$ edges, using laser-heated diamond anvil cell. A shortening of about 8%--10% of the metal bond distances is observed in the pressure range considered and the experimental results are confirmed by theoretical calculations. Ab initio quantum molecular dynamics calculations have been performed, providing a model pair distribution function for cobalt, used as a starting model in the extended x-ray absorption fine structure analysis. The specific volume of the liquid has also been estimated and compared to calculations in the literature. This work sets the basis for x-ray absorption spectroscopy studies of liquid metals under extreme conditions with potentially important implications for the understanding of Earth and planetary interiors.

Heat of fusion of rhenium from first-principle simulations and the Richards–Tammann relation

We present quantum molecular dynamics calculations of thermophysical properties of expanded solid and liquid rhenium in the vicinity of melting. The dependence of specific enthalpy on temperature and the value of the heat of fusion is in good agreement with dynamic heating experimental data and do not confirm the high value of the enthalpy of fusion obtained using the Richards-Tammann relation.

Theory of the electron-ion temperature relaxation rate spanning the hot solid metals and plasma phases.

We present a theory for the rate of energy exchange between electrons and ions-also known as the electron-ion coupling factor-in physical systems ranging from hot solid metals to plasmas, including liquid metals and warm dense matter. The paper provides the theoretical foundations of a recent work [J. Simoni and J. Daligault, Phys. Rev. Lett. 122, 205001 (2019)PRLTAO0031-900710.1103/PhysRevLett.122.205001], where first-principles quantum molecular dynamics calculations based on this theory were presented for representative materials and conditions. We first derive a general expression for the electron-ion coupling factor that includes self-consistently the quantum mechanical and statistical nature of electrons, the thermal and disorder effects, and the correlations between particles. The electron-ion coupling is related to the friction coefficients felt by individual ions due to their nonadiabatic interactions with the electrons. Each coefficient satisfies a Kubo relation given by the time integral of the autocorrelation function of the interaction force of an ion with the electrons. Exact properties and different representations of the general expressions are discussed. We then show that our theory reduces to well-known models in limiting cases. In particular, we show that it simplifies to the standard electron-phonon coupling formula in the limit of hot solids with lattice and electronic temperatures much greater than the Debye temperature, and that it extends the electron-phonon coupling formula beyond the harmonic phonon approximation. For plasmas, we show that the theory readily reduces to the well-known Spitzer formula in the hot plasma limit, to the Fermi "golden rule" formula in the limit of weak electron-ion interactions, and to other models proposed to go beyond the latter approximation. We explain that the electron-ion coupling is particularly well adapted to average atom models, which offer an effective way to include nonideal interaction effects to the standard models and at a much reduced computational cost in comparison to first-principles quantum molecular dynamics simulations.

TITAN: A Code for Modeling and Generating Electric Fields-Features and Applications to Enzymatic Reactivity.

We present here a versatile computational code named "elecTric fIeld generaTion And maNipulation (TITAN)," capable of generating various types of external electric fields, as well as quantifying the local (or intrinsic) electric fields present in proteins and other biological systems according to Coulomb's Law. The generated electric fields can be coupled with quantum mechanics (QM), molecular mechanics (MM), QM/MM, and molecular dynamics calculations in most available software packages. The capabilities of the TITAN code are illustrated throughout the text with the help of examples. We end by presenting an application, in which the effects of the local electric field on the hydrogen transfer reaction in cytochrome P450 OleTJE enzyme and the modifications induced by the application of an oriented external electric field are examined. We find that the protein matrix in P450 OleTJE acts as a moderate catalyst and that orienting an external electric field along the Fe─O bond of compound I has the biggest impact on the reaction barrier. The induced catalysis/inhibition correlates with the calculated spin density on the O-atom. © 2019 Wiley Periodicals, Inc.

Unraveling Photocatalytic Mechanism and Selectivity in PET‐RAFT Polymerization

AbstractThe photoredox catalysts pheophorbide a (PheoA) and zinc tetraphenylporphine (ZnTPP) under illumination display strong selectivity toward reversible addition–fragmentation chain transfer (RAFT) agents containing thiocarbonylthio groups, namely dithiobenzoates, xanthates, and trithiocarbonates. The underlying mechanism for the process—whether via energy or electron transfer from the photoexcited catalyst to RAFT agent—has remained unclear, as has the reason for the remarkable selectivity. Quantum chemistry and molecular dynamics calculations are utilized to provide strong evidence that none of the common energy‐transfer mechanisms (Förster resonance energy transfer; Dexter electron exchange; or internal conversion followed by vibrational energy transfer) are likely to facilitate polymerization, let alone explain the observed selectivities. In contrast, extensive quantum chemical characterizations of the excited‐state orbitals associated with the catalyst–RAFT agent complexes uncover a clear selectivity pattern associated with charge‐transfer states that is highly consistent with experimental findings. The results shed light on the intrinsic catalytic role of the photocatalysts and provide a strong indication that a reversible electron/charge‐transfer mechanism underpins the remarkable photocatalytic selectivity.

A New Equation of State for Dense Hydrogen–Helium Mixtures

Abstract We present a new equation of state (EOS) for dense hydrogen/helium mixtures that covers a range of densities from 10−8 to , pressures from 10−9 to 1013 GPa, and temperatures from 102 to 108 K. The calculations combine the EOS of Saumon, Chabrier & van Horn in the low-density, low-temperature molecular/atomic domain, the EOS of Chabrier & Potekhin in the high-density, high-temperature fully ionized domain, the limits of which differ for H and He, and ab initio quantum molecular dynamics calculations in the regime of intermediate density and temperature, characteristic of pressure dissociation and ionization. The EOS for the H/He mixture is based on the so-called additive volume law and thus does not take into account the interactions between the two species. A major improvement of the present calculations over existing ones is that we calculate the entropy over the entire density–temperature domain, a necessary quantity for calculations of stellar or planetary evolution. The EOS results are compared with existing experimental data, namely Hugoniot shock experiments for pure H and He, and with first-principles numerical simulations for both the single elements and the mixture. This new EOS covers a wide range of physical and astrophysical conditions, from Jovian planets to solar-type stars, and recovers the existing relativistic EOS at very high densities, in the domains of white dwarfs and neutron stars. All the tables are made publicly available.

Anharmonicity-induced first-order isostructural phase transition of zirconium under pressure

We have performed a detailed x-ray diffraction structural study of Zr under pressure and unambiguously identify the existence of a first-order isostructural bcc-to-bcc phase transition near 58 GPa. First-principles quantum molecular dynamics calculations support the existence of this phase transition, in excellent agreement with experimental results, triggered by anharmonic effects. Our results highlight the potential ubiquity of anharmonically driven isostructural transitions within the periodic table under pressure and call for follow-up experimental and theoretical studies.

Supercomputer Modeling of Dual-Site Acetylcholinesterase (AChE) Inhibition

Molecular docking is one of the most popular tools of molecular modeling. However, in certain cases, like development of inhibitors of cholinesterases as therapeutic agents for Alzheimer's disease, there are many aspects, which should be taken into account to achieve accurate docking results. For simple molecular docking with popular software and standard protocols, a personal computer is sucient, however quite often the results are irrelevant. Due to the complex biochemistry and biophysics of cholinesterases, computational research should be supported with quantum mechanics (QM) and molecular dynamics (MD) calculations, what requires the use of supercomputers. Experimental studies of inhibition kinetics can discriminate between dierent types of inhibition—competitive, non-competitive or mixed type—that is quite helpful for assessment of the docking results. Here we consider inhibition of human acetylcholinesterase (AChE) by the conjugate of MB and 2,8-dimethyl-tetrahydro-y-carboline, study its interactions with AChE in relation to the experimental data, and use it as an example to elucidate crucial points for reliable docking studies of bulky AChE inhibitors. Molecular docking results were found to be extremely sensitive to the choice of the X-ray AChE structure for the docking target and the scheme selected for the distribution of partial atomic charges. It was demonstrated that exible docking should be used with an additional caution, because certain protein conformational changes might not correspond with available X-ray and MD data.

Ab initio inspection of thermophysical experiments for molybdenum near melting

We present quantum molecular dynamics calculations of thermophysical properties of solid and liquid molybdenum in the vicinity of melting. Detailed analysis of available experimental isobaric expansion data and extensive comparison over a wide set of properties with results of first-principle calculations is presented, possible reasons of contradictions are discussed. Accurate calculation of zero isobar confirms the density of solid Mo measured by electrostatic levitation technique and the lowest density of molten Mo observed in pulse heating experiments, that gives a substantial volume change on melting of about 5.5%.

Origin of elliptic flow and its dependence on the equation of state in heavy ion reactions at intermediate energies

Recently it has been discovered that the elliptic flow, ${v}_{2}$, of composite charged particles emitted at midrapidity in heavy-ion collisions at intermediate energies shows the strongest sensitivity to the nuclear equation of state (EoS), which has been observed up to now within a microscopic model. This dependence on the nuclear EoS is predicted by quantum molecular dynamics (QMD) calculations [A. Le F\`evre et al.. Nucl. Phys. A 945, 112 (2016)], which show as well that the absorption or rescattering of in-plane emitted particles by the spectator matter is not the main reason for the EoS dependence of the elliptic flow at midrapidity but different density gradients (and therefore different forces) in the direction of the impact parameter ($x$ direction) as compared to the direction perpendicular to the reaction plan ($y$ direction), caused by the presence of the spectator matter. The stronger density gradient in the $y$ direction accelerates the particles more and creates therefore a negative ${v}_{2}$. When using a soft momentum-dependent EoS, the QMD calculations reproduce the experimental results.

Lithium–Iron (III) Fluoride Battery with Double Surface Protection

AbstractLithium–metal fluoride batteries promise significantly higher energy density than the state‐of‐the‐art lithium‐ion batteries and lithium–sulfur batteries. Unfortunately, commercialization of metal fluoride cathodes is prevented by their high resistance, irreversible structural change, and rapid degradation. In this study, a substantial boost in metal fluoride (MF) cathode stability by designing nanostructure with two layers of protective shells—one deposited ex situ and the other in situ is demonstrated. Such methodology achieves over 90% capacity retention after 300 charge–discharge cycles, producing the first report on FeF3 as a cathode material, where a very high capacity utilization in combination with excellent stability is approaching the level needed for practical applications of FeF3. The cathode solid electrolyte interphase (CEI) containing lithium oxalate and BF bond containing anions is found to effectively protect the cathode material from direct contact with electrolytes, thus greatly suppressing the dissolution of Fe. Quantum chemistry and molecular dynamics calculations provide unique insights into the mechanisms of CEI layer formation. As a result, this work not only demonstrates unprecedented performance, but also provides the reader with a better fundamental understanding of electrochemical behavior of MF cathodes and the positive impact observed with the application of a lithium bis(oxalato)borate salt in the electrolyte.

Quantum molecular dynamics of warm dense iron and a five-phase equation of state.

Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7-30g/cm^{3} and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014)10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

Consistent interpretation of experimental data for expanded liquid tungsten near the liquid-gas coexistence curve

We present quantum molecular dynamics calculations of thermodynamic properties of expanded liquid tungsten. Experiments on shock compression of porous tungsten and its subsequent expansion into different anvil materials are successfully reproduced. Special attention is paid to available isobaric expansion experimental data and theoretical estimations of the critical point. Density on our first-principles 1 kbar isobar of liquid tungsten is slightly higher than in most wire-explosion experiments and the slope of the isobar is more flat. The dependence of the specific enthalpy on temperature is in good agreement with dynamic heating experimental data. A special Monte Carlo analysis has been applied for the estimation of the liquid-gas coexistence curve and critical point parameters of tungsten. The result is close to an estimation obtained with Likalter's similarity relation.

Material equation of state by coupling static and dynamic loading

Materials can be experimentally characterized up to terapascal pressures by sending a laser-induced shock wave through a sample that is pre-compressed inside a diamond-anvil cell. Pre-compression expands the ability to control the initial condition, allowing access to thermodynamic states from the principal Hugoniot and enter into the 10 TPa to 100 TPa (0.1-1 Gbar) pressure range that is relevant to planetary science. We demonstrate here a laser-driven shock wave in a water sample that is pre-compressed in a diamond anvil cell. The compression factors of the dynamic and static techniques are multiplied. This approach allows access to a family of Hugoniot curves which span the P-T phase diagram of fluid water to high density. According to the loading characteristics of the SG-Ⅱ high-power laser, the traditional diamond anvil cell is improved and optimized, and a new diamond anvil cell target adapting to high power laser loading is developed. In order to adapt to laser shock, the diamond window should be thin (100 μm) enough so that the shock can propagate to the sample before the side rarefaction erodes too much the shock planarity. With a thickness of 100 mm over an aperture of 600 μm diameter, a pre-compressed water sample at 0.5 GPa can be obtained. The water is pre-compressed to 0.5 GPa by using the diamond anvil cell. Hugoniot curve is partially followed starting from pre-compression at a pressure of 0.5 GPa. Pressure, density, and temperature data for pre-compressed water are obtained in a pressure range from 150 GPa to 350 GPa by using the laser-driven shock compression technique. Our P-ρ-T data totally agree with the results from the model based on quantum molecular dynamics calculations. These facts indicate that this water model can be used as the standard for modeling interior structures of Neptune, Uranus, and exoplanets in the liquid phase in the multi-Mbar range and should improve our understanding of these types of planets.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman–Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo–Greenwood with the quantum molecular dynamics calculations.

The sacrificial inactivation of the blue-light photosensor cryptochrome from Drosophila melanogaster.

Drosophila melanogaster cryptochrome functions as the primary blue-light receptor that mediates circadian photo entrainment. Absorption of a photon leads to reduction of the protein-bound FAD via consecutive electron transfer along a conserved tryptophan tetrad resembling the signalling state required for conformational changes and induction of subsequent signalling cascades. However, how the initial photochemistry and subsequent dark processes leading to downstream signalling are linked to each other at the molecular level is still poorly understood. Here, we investigated in detail the initial photochemical events in DmCRY by time-resolved and stationary absorption spectroscopy combined with quantum chemical and molecular dynamics calculations. We resolved the early events along the conserved tryptophan tetrad and the final deprotonation of the terminal tryptophanyl radical cation. These initial events lead to conformational changes, such as the known C-terminal tail release, Trp decomposition, and finally FAD release providing evidence that DmCRY does not undergo a photocycle. We propose that light is a negative regulator of DmCRY stability even under in vitro conditions where the proteasomal machinery is missing, that is in line with its biological function, i.e. entrainment of the circadian clock.