Understanding and controlling the properties and dynamics of topological defects is a lasting challenge in the study of two-dimensional materials, and is crucial to achieve high-quality films required for technological applications. Here grain boundary structures, energies, and dynamics of binary two-dimensional materials are investigated through the development of a phase field crystal model that is parameterized to match the ordering, symmetry, energy and length scales of hexagonal boron nitride. Our studies reveal some new dislocation core structures for various symmetrically and asymmetrically tilted grain boundaries, in addition to those obtained in previous experiments and first-principles calculations. We also identify a defect-mediated growth dynamics for inversion domains governed by the collective atomic migration and defect core transformation at grain boundaries and junctions, a process that is related to inversion symmetry breaking in binary lattice.Topological defects, such as dislocations and grain boundaries (GBs), are known to be pivotal in controlling material properties. It is challenging to effectively capture the complexity of defects, given the nonequilibrium nature of material growth and evolution processes. Recent progress in the study of two-dimensional (2D) hexagonal materials, such as graphene, hexagonal boron nitride (h-BN), and transition metal dichalcogenides (TMDs), provides an excellent platform for the investigation of defect properties and dynamics. This is driven by the demand for controllable fabrication and synthesis of largescale, high-quality samples of these atomically thin systems, which mostly rely on vapor-phase heteroepitaxy techniques particularly chemical vapor deposition. Such large-area 2D epitaxial films are usually polycrystalline [1], with various types of defects found in both theoretical [2-5] and experimental [6-11] studies of 2D materials. Typical examples include penta-hepta (5|7) defects in graphene [6] and either penta-hepta or square-octagon (4|8) defects in h-BN [7][8][9] and TMD [10] sheets.Compared to 2D single-component materials such as graphene, in binary hexagonal materials (e.g., h-BN and TMDs) the inversion symmetry is broken in the corresponding binary honeycomb lattice. A much richer variety of GB configurations can be identified, some of which can significantly alter system electronic properties, as predicted by first-principles calculations [4,5] It is of great difficulty to effectively track or control the dynamics of defect formation over the relevant spatial and temporal scales, via either in situ experimental techniques or simulations. Experimentally the studies of defect dynamics mostly rely on the activation process of electron irradiation that generates migrating vacancies in the sample [8,14,15]. Most theoretical studies are based on atomistic methods particularly first-principles density functional theory (DFT) and molecular dynamics. While large progress has been made for identifying lowest-energy defect structures and their elect...

The formation and dynamics of a wide variety of binary two-dimensional ordered structures and superlattices are investigated through a phase field crystal model with sublattice ordering. Various types of binary ordered phases, the phase diagrams, and the grain growth dynamics and structural transformation processes, including the emergence of topological defects, are examined. The results are compared to the ordering and assembly of two-component colloidal systems. Two factors governing the binary phase ordering are identified, the coupling and competition between the length scales of two sublattices and the selection of average particle densities of two components. The control and variation of these two factors lead to the prediction of various complex binary ordered patterns, with different types of sublattice ordering for integer vs. noninteger ratios of sublattice length scales. These findings will enable further systematic studies of complex ordering and assembly processes of binary systems particularly binary colloidal crystals. arXiv:1908.09404v1 [cond-mat.soft]

TRIOBP is an actin-bundling protein. Mutations of TRIOBP are associated with human deafness DFNB28. In vitro, TRIOBP isoform 4 (TRIOBP-4) forms dense F-actin bundles resembling the inner ear hair cell rootlet structure. Deletion of TRIOBP isoforms 4 and 5 leads to hearing loss in mice due to the absence of stereocilia rootlets. The mechanism of actin bundle formation by TRIOBP is not fully understood. The amino acid sequences of TRIOBP isoforms 4 and 5 contain two repeated motifs, referred to here as R1 and R2. To examine the potential role of R1 and R2 motifs in F-actin binding, we generated TRIOBP-4 mutant proteins deleted for R1 and/or R2, and then assessed their actin-binding activity and bundle formation in vitro using actin cosedimentation assays, and fluorescence and electron microscopy. Cellular distributions of the TRIOBP-4 mutants were examined by confocal microscopy. We showed that deletion of both R1 and R2 motifs completely disrupted the actin binding/bundling activities of TRIOBP-4 and impaired its localization to cellular actin cytoskeleton structures. By contrast, TRIOBP-4, lacking only R2 motif, retained its F-actin bundling ability and remained localized to actin filaments in cells, similar to full length TRIOBP-4. On the contrary, the R1 motif-deleted TRIOBP-4 mutant, which mainly consists of the R2 motif, formed thin F-actin bundles in vitro but failed to colocalize to actin filaments in cells. These results indicate that R1 motif is the major actin-binding domain of TRIOBP-4, and the binding of R2 motif with actin filaments is nonspecific.

In this work the influence of film-substrate misorientation on the strain-induced ordering of graphene films on various metallic surfaces is examined using a mesoscopic continuum model and first-principles atomistic calculations. The periodicity and free energy of the moiré patterns that emerge are studied as a function of film-substrate adhesion strength for misfit strains far from and close to an incommensurate-commensurate phase transition. Interestingly the lowest energy states are found to be at small but finite misorientation even though these states have a higher domain wall density than the zero-misorientation states. First-principles density functional theory calculations are used to connect the results with experimental findings in graphene epitaxy. This combination of mesoscopic and atomistic approaches can be applied to the study of a wide range of strained 2D material systems including the III-Nitride monolayer systems.

Many clinically relevant forms of acute injury, such as stroke, traumatic brain injury, and myocardial infarction, have resisted treatments to prevent cell death following injury. The clinical failures can be linked to the currently used inductive models based on biological specifics of the injury system. Here we contrast the application of inductive and deductive models of acute cell injury. Using brain ischemia as a case study, we discuss limitations in inductive inferences, including the inability to unambiguously assign cell death causality and the lack of a systematic quantitative framework. These limitations follow from an overemphasis on qualitative molecular pathways specific to the injured system. Our recently developed nonlinear dynamical theory of cell injury provides a generic, systematic approach to cell injury in which attractor states and system parameters are used to quantitatively characterize acute injury systems. The theoretical, empirical, and therapeutic implications of shifting to a deductive framework are discussed. We illustrate how a deductive mathematical framework offers tangible advantages over qualitative inductive models for the development of therapeutics of acutely injured biological systems.

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Neuroprotection seeks to halt cell death after brain ischemia and has been shown to be possible in laboratory studies. However, neuroprotection has not been successfully translated into clinical practice, despite voluminous research and controlled clinical trials. We suggested these failures may be due, at least in part, to the lack of a general theory of cell injury to guide research into specific injuries. The nonlinear dynamical theory of acute cell injury was introduced to ameliorate this situation. Here we present a revised nonautonomous nonlinear theory of acute cell injury and show how to interpret its solutions in terms of acute biomedical injuries. The theory solutions demonstrate the complexity of possible outcomes following an idealized acute injury and indicate that a “one size fits all” therapy is unlikely to be successful. This conclusion is offset by the fact that the theory can (1) determine if a cell has the possibility to survive given a specific acute injury, and (2) calculate the degree of therapy needed to cause survival. To appreciate these conclusions, it is necessary to idealize and abstract complex physical systems to identify the fundamental mechanism governing the injury dynamics. The path of abstraction and idealization in biomedical research opens the possibility for medical treatments that may achieve engineering levels of precision.

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