Strontium titanate (SrTiO3) is regarded as an essential material for oxide electronics. One of its many remarkable features is subtle structural phase transition, driven by antiferrodistortive lattice mode, from a high-temperature cubic phase to a low-temperature tetragonal phase. Classical molecular dynamics (MD) simulation is an efficient technique to reveal atomistic features of phase transition, but its application is often limited by the accuracy of empirical interatomic potentials. Here, we develop an accurate deep potential (DP) model of SrTiO3 based on a machine learning method using data from first-principles density functional theory (DFT) calculations. The DP model has DFT-level accuracy, capable of performing efficient MD simulations and accurate property predictions. Using the DP model, we investigate the temperature-driven cubic-to-tetragonal phase transition and construct the in-plane biaxial strain-temperature phase diagram of SrTiO3. The simulations demonstrate that strain-induced ferroelectric phase is characterized by two order parameters, ferroelectric distortion and antiferrodistortion, and the ferroelectric phase transition has both displacive and order-disorder characters. This works lays the foundation for the development of accurate DP models of other complex perovskite materials.
The structural, dynamic, and vibrational properties during the heat transfer process in Si/Ge superlattices, are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat c…
The temperature-induced structural and electronic transformation in VO$_2$ between the monoclinic M1 and tetragonal rutile phases was studied by means of \textit{ab initio} molecular dynamics, based on density functional theory with Hubbard correction (DFT+U). Analysis of the dynamical processes associated with the structural transformation was carried out on the atomic scale by following the time evolution of dimerization amplitudes of vanadium atom chains and the twisting angle of vanadium dimers. The electronic transition was studied by tracing the changes in projected densities of states a…
The question on the dominant driving mechanism (displacive or order-disorder) at each structural phase transition of KNbO3 is investigated by means of molecular dynamics simulations. To this purpose, we first develop a shell model by determining its potential parameters in order to reproduce the ferroelectric instabilities obtained by first-principles total energy calculations. The phase diagram as a function of temperature is obtained through constant-pressure molecular dynamics simulations. The analysis of the dynamical structure factor and the microscopic dynamics of the particles in the di…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable), which parameterizes the changes in effective free energy during the transformation. Results are reported for bcc-to-hcp lattice transitions under pressure. We explore coarse-variable space to reconstruct an effective free-energy landscape quantifying the relative stability of different metastable basins and locate the onset, at a critical pressure, of the bcc-to…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach provides a means for constructing effective free-energy landscapes of structural transitions in condensed matter. The predictions of the approach for the thermodynamic melting point of a model silicon system are in excellent agreement with those of ''traditional'' techniques for melting-point calculations, as well as with literature values.
We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (electrodes with flat surfaces) to structurally realistic, experimentally representative junctions resulting from break junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larg…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straight…
We have studied the pressure-induced structural transition of ZnO nanocrystals using constant pressure molecular dynamics simulations for finite system. We have observed the transition from the fourfold coordination wurtzite to the sixfold coordination rocksalt structure, and the process of transition is strongly dependent on the morphology of the nanocrystals. It is found that the perfect faceted ZnO nanocrystals undergo wurtzite to rocksalt transition with a perfect fivefold h-MgO structure as the intermediate status. But for the faceted ones without perfect surface structure, as the number …
Direct observation of organic molecular nanocrystals and their evolution using electron microscopy is extremely challenging, due to their radiation sensitivity and complex structure. Here, we introduce 4D-scanning confocal electron diffraction (4D-SCED), which enables direct in situ observation of bulk heterojunction (BHJ) thin films. 4D-SCED combines confocal electron microscopy with a pixelated detector to record focused spot-like diffraction patterns with high angular resolution, using an order of magnitude lower dose than previous methods. We apply it to study an active layer in organic so…
It is now possible to routinely perform atomistic simulations at the microsecond timescale. In the present work, we exploit this for a model binary Lennard-Jones glass to study structural relaxation at a timescale spanning up to 80 microseconds. It is found that at these longer time-scales, significant mobility and relaxation occurs, demonstrating a reproducible relaxation trajectory towards a class of asymptotic structural states which are strongly heterogeneous. These structures are discussed both in terms of the ideal glass state and a production route towards novel amorphous crystalline na…
The effect of structural constriction on molecular mobility is investigated by broadband dielectric spectroscopy (BDS) within three types of molecular arrangements: monomers, oligomers and self-assembled monolayers (SAMs). While disordered monomers exhibit a variety of cooperative and local relaxation processes, the constrained nanodomains of oligomers and highly ordered structure of monolayers exhibit much hindered local molecular fluctuations. Particularly, in SAMs, motions of the silane headgroups are totally prevented whereas the polar endgroups forming the monolayer canopy show only one c…
In this work the coupled motion of two different phases of Σ5(210)[001] grain boundaries were investigated by molecular dynamics simulations of fcc Cu. The effect of interfacial structural phase transitions is shown to have a profound effect on both the shear strength and the nature of the coupled motion. Specifically, the motion of the two different phases is described by ideal coupling factors β<100> and β<110> that have different magnitudes and even signs. Additionally, the shear strength for the two inter- facial phases is observed to differ by up to 40 % at the lowest temperatures simulat…
We study the effect of temperature up to 1000K on the structure of dense molecular para-hydrogen and ortho-deuterium, using the path-integral Monte Carlo method. We find a structural phase transition from orientationally disordered hexagonal close packed (hcp) to an orthorhombic structure of Cmca symmetry before melting. The transition is basically induced by thermal fluctuations, but quantum fluctuations of protons (deuterons) are important in determining the transition temperature through effectively hardening the intermolecular interaction. We estimate the phase line between hcp and Cmca ph…
Epitaxial layers of the topological insulator Bi2Se3 have been grown by molecular beam epitaxy on laterally lattice-matched InP(111)B substrates. High resolution X-ray diffraction shows a significant improvement of Bi2Se3 crystal quality compared to layers deposited on other substrates. The measured full width at half maximum of the rocking curve is Delta omega=13 arcsec, and the (omega-2theta) scans exhibit clear layer thickness fringes. Atomic force microscope images show triangular twin domains with sizes increasing with layer thickness. The structural quality of the domains is confirmed on…
We study a calcium aluminosilicate glass of composition (SiO2)0.60(Al2O3)0.10(CaO)0.30 by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions diff…
The energetic landscape at the interface between electron donating and accepting molecular materials favors efficient conversion of intermolecular charge-transfer states (CTS) into free charge carriers in high-performance organic solar cells. Here, we elucidate how interfacial energetics, charge generation and radiative recombination are affected by structural ordering. We experimentally determine the CTS binding energy of a series of model, small molecule donor-acceptor blends, where the used acceptors (B2PYMPM, B3PYMPM and B4PYMPM) differ only in the nitrogen position of their lateral pyridi…
We study the structural and electronic properties of phase III of solid hydrogen using accurate many-electron theories and compare to state-of-the-art experimental findings. The atomic structures of phase III modelled by C2/c-24 crystals are fully optimized on the level of second-order perturbation theory, demonstrating that previously employed structures optimized on the level of approximate density functionals exhibit errors in the H$_2$ bond lengths that cause significant discrepancies in the computed quasi particle band gaps and vibrational frequencies compared to experiment. Using the new…
By employing $ab$ $initio$ molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure polymeric amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of three and four-coordinated carbons and two mixed molecular-nonmolecular forms were observed. Transformation from a-carbonia t…
The microscopic structure of two amorphous materials with extreme nonlinear optical properties has been studied. One of these materials exhibits second harmonic generation, while another material of similar molecular structure emits brilliant white light if being irradiated with a simple IR laser diode. Structural differences were investigated using X-ray scattering and EXAFS combined with molecular RMC. Transmission electron microscopy and scanning precession electron diffraction were used to understand specific structural differences on all length scales, from mesoscopic down to mutual molec…
The present study elucidates the correlation between the structural and optical properties of GaN nanowires grown on Si(111) substrate by plasma assisted molecular beam epitaxy (PA-MBE) technique under various growth conditions. GaN NWs exhibiting different shapes, sizes and distribution were grown at various substrate temperatures with same Ga-N (III-V) ratio of 0.4. We observe that sample grown at lower substrate temperature (~700 degC) results 2-dimensional island like structure with almost very little (~30%) circularity while increasing substrate temperature (>770 degC) leads to growth of …
Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes deviates from an Arrhenius law for both polymers. We demonstrate that mode-coupling theory captures some aspects of the glassy slowdown, but it does not enable a complete explanation of the dynamical behavior. When the temperature is decreased, spatially heterogeneous and cooperative translational dynamics are found to become more important for the structural…
The effective pair potentials of liquid nickel have been derived by means of the inverse self-consistent method from the experimental diffraction data. The potentials provide highly accurate coincidence of experimental and simulated structural properties. The statistical analysis of Voronoi polyhedral and Delaunau simplices has shown that in the vicinity of the melting point in the structure of liquid nickel there are relatively stable spatial polytetrahedral formations with local 5-folder symmetry. With temperature rise such formations evolve to isolate and compact ones with preserving of the…
We demonstrate the growth of thin films of molybdenum ditelluride and molybdenum diselenide on sapphire substrates by molecular beam epitaxy. In-situ structural and chemical analyses reveal stoichiometric layered film growth with atomically smooth surface morphologies. Film growth along the (001) direction is confirmed by X-ray diffraction, and the crystalline nature of growth in the 2H phase is evident from Raman spectroscopy. Transmission electron microscopy is used to confirm the layered film structure and hexagonal arrangement of surface atoms. Temperature dependent electrical measurements…
Establishing the composition-structure-property relationships for amorphous materials is critical for many important natural and engineering processes, including the dissolution of highly complex volcanic glasses. In this investigation, we performed force field molecular dynamics (MD) simulations to generate detailed structural representations for ten natural CaO-MgO-Al2O3-SiO2-TiO2-FeO-Fe2O3-Na2O-K2O glasses with compositions ranging from rhyolitic to basaltic. Based on the resulting atomic structural representations at 300 K, we have calculated the partial radial distribution functions, near…
We develop the elastically collective nonlinear Langevin equation theory of bulk relaxation of glass-forming liquids to investigate molecular mobility under compression conditions. The applied pressure restricts more molecular motion and therefore significantly slows-down the molecular dynamics when increasing the pressure. We quantitatively determine the temperature and pressure dependence of the structural relaxation time. To validate our model, dielectric spectroscopy experiments for three rigid and non-polymeric supramolecules are carried out at ambient and elevated pressures. The numerica…
In this investigation, force field-based molecular dynamics (MD) simulations have been employed to generate detailed structural representations for a range of amorphous quaternary CaO-MgO-Al2O3-SiO2 (CMAS) and ternary CaO-Al2O3-SiO2 (CAS) glasses. Comparison of the simulation results with select experimental X-ray and neutron total scattering and literature data reveals that the MD-generated structures have captured the key structural features of these CMAS and CAS glasses. Based on the MD-generated structural representations, we have developed two structural descriptors, specifically (i) aver…
We present a detailed study of charge transfer (CT) excited states for a large number of structural conformations in a light-harvesting Carotenoid-diaryl-Porphyrin-C60 (CPC60) molecular triad. The molecular triad undergoes a photoinduced charge transfer process exhibiting a large excited state dipole moment, making it suitable for application to molecular-scale opto-electronic devices. An important consideration is that the conformational flexibility of the CPC 60 triad impacts its dynamics in solvents. Since experimentally measured dipole moments for the triad of ~110 Debye (D) and ~160 Debye…
The structure-thermodynamic stability relationship in vitreous silica is investigated using machine learning and a library of 24,157 inherent structures generated from melt-quenching and replica exchange molecular dynamics simulations. We find the thermodynamic stability, i.e., enthalpy of the inherent structure ($e_{\mathrm{IS}}$), can be accurately predicted by both linear and nonlinear machine learning models from numeric structural descriptors commonly used to characterize disordered structures. We find short-range features become less indicative of thermodynamic stability below the fragil…
Realistic models of amorphous ZrO2 are generated in a ``melt-and-quench'' fashion using ab-initio molecular dynamics in a plane-wave pseudopotential formulation of density-functional theory. The structural properties of the resulting amorphous models are analyzed, with special attention to coordination statistics. The vibrational and dielectric properties of one of these models are then investigated from first principles using linear-response methods. The electronic dielectric constant and Born effective charges are found to be very similar to those of the crystalline phases. Encouragingly, th…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, partic…
Several static and dynamic properties of liquid silicon near melting have been determined from an orbital free {\em ab-initio} molecular dynamics simulation. The calculated static structure is in good agreement with the available X-ray and neutron diffraction data. The dynamical structure shows collective density excitations with an associated dispersion relation which closely follows recent experimental data. It is found that liquid silicon can not sustain the propagation of shear waves which can be related to the power spectrum of the velocity autocorrelation function. Accurate estimates hav…
We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the SCAN meta-GGA functional approximation, and carry out systematic comparisons with the results obtained from the GGA-level PBE functional, and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band ga…
A magneto-structural phase transition is investigated in single crystal CrN thin films grown by rf plasma molecular beam epitaxy on MgO(001) substrates. While still within the vacuum environment following MBE growth, $\it in-situ$ low-temperature scanning tunneling microscopy, and $\it in-situ$ variable low-temperature reflection high energy electron diffraction are applied, revealing an atomically smooth and metallic CrN(001) surface, and an $\it in-plane$ structural transition from 1$\times$1 (primitive CrN unit cell) to $\mathrm{\sqrt{2}\times\sqrt{2}-R45^\circ}$ with a transition temperatu…
Structural, vibrational and thermal properties of densified sodium silicate (NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of three-fold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp…
Temperature-driven structural phase transitions in SmNiO$_3$: insights from deep potential molecular dynamics simulations
Xi’an Jiaotong University（西安交通大学）；University of Science and Technology of China（中国科学技术大学）；Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）；Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences（中国科学院宁波材料技术与工程研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Eastern Institute of Technology（东方理工大学）；Changzhou Institute of Technology（常州工学院）
Growth-induced trade-off between polarity, electrical isolation, and structural quality in AlN grown on Si(111) by plasma-assisted molecular beam epitaxy
Paul-Drude-Institut für Festkörperelektronik (PDI), Leibniz-Institut im Forschungsverbund Berlin e.V.（柏林莱布尼茨研究联合体保罗·德鲁德固体电子学研究所）；Institute of Physics of Materials and CEITEC IPM, Czech Academy of Sciences（捷克科学院材料物理与CEITEC IPM研究所）；School of Electrical and Computer Engineering, Cornell University（康奈尔大学电气与计算机工程学院）
Based on density functional theory calculations, the structural and electronic properties of polythiophene in periodic and oligomer forms have been investigated. In particular, the effects of Li or Cl adsorption onto a monolayer and Li or Cl-intercalation into bulk or bilayer polythiophene are addressed using periodic calculations. The binding energy of Li or Cl adsorbed bulk or bilayer polythiophene is significantly larger than for the monolayer. The trends in the binding energy as a function of adsorbent remain the same for both the periodic and molecular cases. The band gap or HOMO-LUMO gap…
Polymeric nitrogen with single bonds can be created from the molecular form at high pressure and due to large energy difference between triple and single bonds it is interesting as energetic material. Its structure and properties are, however, still not well understood. We studied amorphous nitrogen by \textit{ab initio} simulations, employing molecular dynamics and evolutionary algorithms. Amorphous nitrogen was prepared at pressure of 120 GPa by quenching from hot liquid, by pressure-induced amorphization of molecular crystal and by evolutionary search. All three amorphous forms were found t…
We studied the structural and the electronic properties of ionized and neutral small Au clusters via plane wave pseudopotential calculations. All except the anionic heptamer favor one-dimensional zigzag structures or two-dimensional arrangements of triangles. The HOMO-LUMO (highest occupied molecular orbital - lowest unoccupied molecular orbital) gap, the ionization energy, and the electronic affinity exhibit even-odd variation as a function of the cluster size.
Very recently, it was demonstrated that the carrier mobility of a molecular monolayer dioctylbenzothienobenzothiophene (C8-BTBT) on boron nitride can reach 10 cm2/Vs, the highest among the previously reported monolayer molecular field-effect transistors. Here we show that the high-quality single crystal of the C8-BTBT monolayer may be the key origin of the record-high carrier mobility. We discover that the C8-BTBT molecules prefer layer-by-layer growth on both hexagonal boron nitride and graphene. The flatness of these substrates substantially decreases the C8-BTBT nucleation density and enabl…
The structural and electronic properties of a single pentacene molecule and a pentacene molecular crystal, an organic semiconductor, are examined by a first-principles method based on the generalized gradient approximation of density functional theory. Calculations were carried out for a triclinic unit cell containing two pentacene molecules. The bandwidths of the valence and conduction bands which determine the charge migration mechanism are found to depend strongly on the crystallographic direction. Along the triclinic reciprocal lattice vectors A and B which are orientated approximately per…
We used molecular dynamics simulations based on a potential model in analogy to the Tight Binding scheme in the Second Moment Approximation to simulate the effects of aluminum icosahedral grains (dispersoids) on the structure and the mechanical properties of an aluminum matrix. First we validated our model by calculating several thermodynamic properties referring to the bulk Al case and we found good agreement with available experimental and theoretical data. Afterwards, we simulated Al systems containing Al clusters of various sizes. We found that the structure of the Al matrix is affected by…
Porous carbons are used in a wide range of applications, including electrochemical double layer capacitors for energy storage, in which electrolyte ion properties under confinement are crucial for the performance of the systems. While many synthesis techniques lead to the presence of surface functional groups, their effect on the adsorption and diffusion of electrolyte ions is still poorly understood. In this study we investigate the effect of surface chemistry on dynamical and structural properties of adsorbed ions through molecular dynamics simulations of a neat ionic liquid in contact with …
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The simulations demonstrate significant local structural excitations as a function of increasing temperature and show that enthalpy rather than energy is primarily responsible for relaxation. The observed enthalpy changes are of the order seen in experiment, and can be correlated with the level of internal hydrostatic stress homogenization and icosahedral content within…
We use the ``isoconfigurational ensemble'' [Phys. Rev. Lett. {\bf 93}, 135701 (2004)] to analyze both dynamical and structural properties in simulations of a glass forming molecular liquid. We show that spatially correlated clusters of low potential energy molecules are observable on the time scale of structural relaxation, despite the absence of spatial correlations of potential energy in the instantaneous structure of the system. We find that these structural heterogeneities correlate with dynamical heterogeneities in the form of clusters of low molecular mobility.
Ionic liquids (ILs) feature a tailorable and wide range of structural, chemical and electronic properties that make this class of materials suitable to a broad variety of forefront applications in next-generation electronics. Yet, their intrinsic complexity call for special attention and experimental probes have still limitations in unraveling the interactions occurring both in the bulk IL and at the interface with the solid substrates used to build the devices. This works provides an atomistic insight into these fundamental interactions by molecular modeling to complement the information stil…
The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding -- a central concept to our understanding of the physical chemistry of water, biological systems and ma…
We study the electronic and structural properties of the low-temperature ordered phase of hydrogen-bonded molecular conductors, $κ$-D$_3$(Cat-EDT-TTF)$_2$ and its selenium-substituted analog $κ$-D$_3$(Cat-EDT-ST)$_2$, by means of first-principles density functional theory~(DFT) calculations. In these compounds, the charge ordering in the $π$-electron system is coupled with the ordering of the displacements in the deuteriums forming the hydrogen-bond, equally shared by two oxygens in the high-temperature phase. While the structural optimization within the standard DFT method based on the genera…
Mn-doped GaAs nanowires were grown in the self-catalytic growth mode on oxidized Si(100) surface by molecular beam epitaxy and characterized by scanning and transmission electron microscopy, Raman scattering, photoluminescence, cathodoluminescence, and electron transport measurements. The transmission electron microscopy studies evidenced the substantial accumulation of Mn inside the catalyzing Ga droplets at the top of the nanowires. Optical and transport measurements revealed that the limit of Mn content for self-catalysed growth of GaAs nanowires corresponds to the doping level, i.e., is mu…
