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Traditionally, phase transitions are explored using a combination of macroscopic functional characterization and scattering techniques, providing insight into average properties and symmetries of the lattice but local atomic level mechanisms during phase transitions generally remain unknown. Here we explore the mechanisms of a phase transition between the trigonal prismatic and distorted octahedral phases of layered chalogenides in the MoS2 ReS2 system from the observations of local degrees of freedom, namely atomic positions by Scanning Transmission Electron Microscopy (STEM). We employ local crystallographic analysis based on machine learning of atomic environments to build a picture of the transition from the atomic level up and determine local and global variables controlling the local symmetry breaking. In particular, we argue that the dependence of the average symmetry breaking distortion amplitude on global and local concentration can be used to separate local chemical and global electronic effects on transition. This approach allows exploring atomic mechanisms beyond the traditional macroscopic descriptions, utilizing the imaging of compositional fluctuations in solids to explore phase transitions over a range of realized and observed local stoichiometries and atomic configurations., Comment: 5 figures, 20 pages including supplementary

Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with strong correlations, either in electronic behavior or chemical segregation. In these cases, the details of atomic arrangements are generally not explored and analyzed. The knowledge of the generative physics and chemistry of the material can obviate this problem, since defect configuration libraries as stochastic representation of atomic level structures can be generated, or parameters of mesoscopic thermodynamic models can be derived. To obtain such information for improved predictions, we use data from atomically resolved microscopic images that visualize complex structural correlations within the system and translate them into statistical mechanical models of structure formation. Given the significant uncertainties about the microscopic aspects of the material's processing history along with the limited number of available images, we combine model optimization techniques with the principles of statistical hypothesis testing. We demonstrate the approach on data from a series of atomically-resolved scanning transmission electron microscopy images of Mo$_x$Re$_{1-x}$S$_2$ at varying ratios of Mo/Re stoichiometries, for which we propose an effective interaction model that is then used to generate atomic configurations and make testable predictions at a range of concentrations and formation temperatures., 26 pages, 8 figures

The exceptional electronic, optical and chemical properties of two-dimensional materials strongly depend on the 3D atomic structure and crystal defects. Using Re-doped MoS2 as a model, here we develop scanning atomic electron tomography (sAET) to determine the 3D atomic positions and crystal defects such as dopants, vacancies and ripples with a precision down to 4 picometers. We measure the 3D bond distortion and local strain tensor induced by single dopants for the first time. By directly providing experimental 3D atomic coordinates to density functional theory (DFT), we obtain more truthful electronic band structures than those derived from conventional DFT calculations relying on relaxed 3D atomic models, which is confirmed by photoluminescence measurements. We anticipate that sAET is not only generally applicable to the determination of the 3D atomic coordinates of 2D materials, heterostructures and thin films, but also could transform ab initio calculations by using experimental 3D atomic coordinates as direct input to better predict and discover new physical, chemical and electronic properties., 44 pages, 18 figures

Molybdenum disulfide (MoS2) monolayers have attracted much attention for their novel optical properties and efficient light-matter interactions. When excited by incident laser, the optical response of MoS2 monolayers was effectively modified by elementary photo-excited excitons owing to their large exciton binding energy, which can be facilitated for the optical-controllable exciton-plasmon interactions. Inspired by this concept, we experimentally investigated active light control of surface plasmon resonance (SPR) in MoS2-Ag hybrid nanostructures. The white light spectra of SPR were gradually red-shifted by increasing laser power, which was distinctly different from the one of bare Ag nanostructure. This spectroscopic tunability can be further controlled by near-field coupling strength and polarization state of light, and selectively applied to the control of plasmonic dark mode. An analytical Lorentz model for photo-excited excitons induced modulation of MoS2 dielectric function was developed to explain the insight physics of this SPR tunability. Our study opens new possibilities to the development of all-optical controlled nanophotonic devices based on 2D materials., Comment: 27 pages, 6 figures

Prominent resonance Raman and photoluminescence spectroscopic differences between AA' and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom will be discussed.