The thermodynamic and optical properties of germanium, silicon, diamond and gallium arsenide

Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β₂-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.

Switch of Thermal Expansions Triggered by Itinerant Electrons in Isostructural Metal Trifluorides

Manageable thermal expansion (MTE) of metal trifluorides can be achieved by introducing local structure distortion (LSD) in the negative thermal expansion ScF₃. However, an open issue is why isostructural TiF₃, free of LSD, exhibits positive thermal expansion. Herein, a combined analysis of synchrotron X-ray diffraction, X-ray pair distribution function, and rigorous first-principles calculations was performed to reveal the important role of itinerant electrons in mediating soft phonons and lattice dynamics. Metallic TiF₃ demonstrates itinerant electrons and a suppressed Grüneisen parameter γ ≈ -20, while insulating ScF₃ absence of itinerant electrons has a considerable γ ≈ -120. With increasing electron doping concentrations in ScF₃, soft phonons become hardened and the γ is repressed significantly, identical to TiF₃. The presented results update the thermal expansion transition mechanism in framework structure analogues and provide a practical approach to obtaining MTE without inducing sizable structure distortion.

Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting

In molecular dynamics (MD), neural network (NN) potentials trained bottom-up on quantum mechanical data have seen tremendous success recently. Top-down approaches that learn NN potentials directly from experimental data have received less attention, typically facing numerical and computational challenges when backpropagating through MD simulations. We present the Differentiable Trajectory Reweighting (DiffTRe) method, which bypasses differentiation through the MD simulation for time-independent observables. Leveraging thermodynamic perturbation theory, we avoid exploding gradients and achieve around 2 orders of magnitude speed-up in gradient computation for top-down learning. We show effectiveness of DiffTRe in learning NN potentials for an atomistic model of diamond and a coarse-grained model of water based on diverse experimental observables including thermodynamic, structural and mechanical properties. Importantly, DiffTRe also generalizes bottom-up structural coarse-graining methods such as iterative Boltzmann inversion to arbitrary potentials. The presented method constitutes an important milestone towards enriching NN potentials with experimental data, particularly when accurate bottom-up data is unavailable.

Intermediate Cu-O-Si Phase in the Cu-SiO2/Si(111) System: Growth, Elemental, and Electrical Studies

We investigate here the strain-induced growth of Cu at 600 °C and its interactions with a thermally grown, 270 nm-thick SiO₂ layer on the Si(111) substrate. Our results show clear evidence of triangular voids and formation of triangular islands on the surface via a void-filling mechanism upon Cu deposition, even on a 270 nm-thick dielectric. Different coordination states, oxidation numbers, and chemical compositions of the Cu-grown film are estimated from the core level X-ray photoelectron spectroscopy (XPS) measurements. We find evidence of different compound phases including an intermediate mixed-state of Cu-O-Si at the interface. Emergence of a mixed Cu-O-Si intermediate state is attributed to the new chemical states of Cu ^x+, O ^x , and Si ^x+ observed in the high-resolution XPS spectra. This intermediate state, which is supposed to be highly catalytic, is found in the sample with a concentration as high as ∼41%. Within the Cu-O-Si phase, the atomic percentages of Cu, O, and Si are ∼1, ∼86, and ∼13%, respectively. The electrical measurements carried out on the sample reveal different resistive channels across the film and an overall n-type semiconducting nature with a sheet resistance of the order of 10⁶ Ω.

Calculation of Mode Grüneisen Parameters Made Simple

A novel method to calculate mode Grüneisen parameters of a material from first principles is presented. This method overcomes the difficulties and limitations of existing approaches, based on the calculation of either third-order force constants or phonon frequencies at different volumes. Our method requires the calculation of phonon frequencies of a material at only the volume of interest, it is based on the second-order differentiation of a corrected stress tensor with respect to normal mode coordinates, and it yields simultaneously all the components of the mode Grüneisen parameters tensor. In this work, after discussing conceptual and technical aspects, the method is applied to silicon, aluminum, scandium fluoride, and a metallic alloy. These calculations show that our method is straightforward and it is suited to be applied to the broad class of materials prone to exhibit structural instabilities, or presenting anisotropy, or chemical and/or structural disorder.

On the role of intermolecular vibrational motions for ice polymorphs I: Volumetric properties of crystalline and amorphous ices

Intermolecular vibrations and volumetric properties are investigated using the quasiharmonic approximation with the TIP4P/2005, TIP4P/Ice, and SPC/E potential models for most of the known crystalline and amorphous ice forms that have hydrogen-disordering. The ice forms examined here cover low pressure ices (hexagonal and cubic ice I, XVI, and hypothetical dtc ice), medium pressure ices (III, IV, V, VI, XII, hydrogen-disordered variant of ice II), and high pressure ice (VII) as well as the low density and the high density amorphous forms. We focus on the thermal expansivities and the isothermal compressibilities in the low temperature regime over a wide range of pressures calculated via the intermolecular vibrational free energies. Negative thermal expansivity appears only in the low pressure ice forms. The sign of the thermal expansivity is elucidated in terms of the mode Grüneisen parameters of the low frequency intermolecular vibrational motions. Although the band structure for the low frequency region of the vibrational density of state in the medium pressure ice has a close resemblance to that in the low pressure ice, its response against volume variation is opposite. We reveal that the mixing of translational and rotational motions in the low frequency modes plays a crucial role in the appearance of the negative thermal expansivity in the low pressure ice forms. The medium pressure ices can be further divided into two groups in terms of the hydrogen-bond network flexibility, which is manifested in the properties on the molecular rearrangement against volume variation, notably the isothermal compressibility.

Electronic Property and Negative Thermal Expansion Behavior of Si136-xGex (x = 8, 32, 40, 104) Clathrate Solid Solution from First Principles

We present the electronic and vibrational studies on Si_136-xGe_x (x = 8, 32, 40, 104) alloys, using the local density approximation (LDA) scheme. We find that a “nearly-direct” band gap exists in the band structure of Si₁₀₄Ge₃₂ and Si₉₆Ge₄₀, when compared with the similarly reported results obtained using a different computational code. The calculated electronic density of state (EDOS) profiles for the valence band remain nearly identical and independent of the Ge concentration (x = 32, 40, 104) even though some variation is found in the lower conduction band (tail part) as composition x is tuned from 8 (or 40) to 104. The negative thermal expansion (NTE) phenomenon is explored using quasi-harmonic approximation (QHA), which takes the volume dependence of the vibrational mode frequencies into consideration, while neglecting the temperature effect on phonon anharmonicity. Determined macroscopic Grüneisen parameter trends show negative values in the low temperature regime (1 K < T < 115 K), indicating the NTE behavior found in Si₁₂₈Ge₈ is analogous to the experimental result for Si₁₃₆. Meanwhile, calculations for the ratio of the vibrational entropy change to the volume change at several characteristic temperatures reconfirm the existence of NTE in Si₁₂₈Ge₈ and Si₁₀₄Ge₃₂.

Interplay between Phonons and Anisotropic Elasticity Drives Negative Thermal Expansion in PbTiO_{3}

We use first-principles theory to show that the ingredients assumed to be essential to the occurrence of negative thermal expansion (NTE)-rigid unit phonon modes with negative Grüneisen parameters-are neither sufficient nor necessary for a material to undergo NTE. Instead, we find that NTE in PbTiO_{3} involves a delicate interplay between the phonon properties of a material (Grüneisen parameters) and its anisotropic elasticity. These unique insights open new avenues in our fundamental understanding of the thermal properties of materials and in the search for NTE in new materials classes.

Thermal expansion of diamond at low temperatures

Temperature variation of a lattice parameter of a synthetic diamond crystal (type IIa) was measured using high-energy-resolution x-ray Bragg diffraction in backscattering. A 2 order of magnitude improvement in the measurement accuracy allowed us to directly probe the linear thermal expansion coefficient at temperatures below 100 K. The lowest value measured was 2x10{-9} K-1. It was found that the coefficient deviates from the expected Debye law (T3) while no negative thermal expansion was observed. The anomalous behavior might be attributed to tunneling states due to low concentration impurities.

Observation of a Mott insulating ground state for Sn/Ge(111) at low temperature

We report an investigation on the properties of 0.33 ML of Sn on Ge(111) at temperatures down to 5 K. Low-energy electron diffraction and scanning tunneling microscopy show that the (3x3) phase formed at approximately 200 K, reverts to a new ((square root 3)x(square root 3))R30 degrees phase below 30 K. The vertical distortion characteristic of the (3x3) phase is lost across the phase transition, which is fully reversible. Angle-resolved photoemission experiments show that, concomitantly with the structural phase transition, a metal-insulator phase transition takes place. The ((square root 3)x(square root 3))R30 degrees ground state is interpreted as the formation of a Mott insulator for a narrow half-filled band in a two-dimensional triangular lattice.

Spectroscopic mode Grüneisen parameters for diamond

Room temperature measurements are reported of the first and second order Raman spectra of diamond in the hydrostatic pressure range 0-2.4 GPa. Values calculated from the data for the optic mode Grüneisen parameters have been fitted in terms of a simple lattice dynamical model for diamond involving volume dependent interatomic forces. The interpolated set of mode Grüneisen parameters are shown to be in substantial agreement with thermodynamic data. The simple model for the anharmonicity of the interatomic forces in the diamond group materials is shown to provide a qualitative explanation for the contrasting low temperature behaviour of the thermal expansion exhibited by these materials.