Coupled Reversible and Irreversible Bistable Switches Underlying TGF-\beta-induced Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) plays important roles in embryonic development, tissue regeneration and cancer metastasis. While several feedback loops have been shown to regulate EMT, it remains elusive how they coordinately modulate EMT response to TGF-\beta treatment. We construct a mathematical model for the core regulatory network controlling TGF-\beta-induced EMT. Through deterministic analyses and stochastic simulations, we show that EMT is a sequential two-step program that an epithelial cell first transits to partial EMT then to the mesenchymal state, depending on the strength and duration of TGF-\beta stimulation. Mechanistically the system is governed by coupled reversible and irreversible bistable switches. The SNAIL1/miR-34 double negative feedback loop is responsible for the reversible switch and regulates the initiation of EMT, while the ZEB/miR-200 feedback loop is accountable for the irreversible switch and controls the establishment of the mesenchymal state. Furthermore, an autocrine TGF-\beta/miR-200 feedback loop makes the second switch irreversible, modulating the maintenance of EMT. Such coupled bistable switches are robust to parameter variation and molecular noise. We provide a mechanistic explanation on multiple experimental observations. The model makes several explicit predictions on hysteretic dynamic behaviors, system response to pulsed stimulation and various perturbations, which can be straightforwardly tested.Comment: 32 pages, 8 figures, accepted by Biophysical Journa

Low-dimensional Material: Structure-property Relationship and Applications in Energy and Environmental Engineering

In the past several decades, low-dimensional materials (0D materials, 1D materials and 2D materials) have attracted much interest from both the experimental and theoretical points of view. Because of the quantum confinement effect, low-dimensional materials have exhibited a kaleidoscope of fascinating phenomena and unusual physical and chemical properties, shedding light on many novel applications. Despite the enormous success has been achieved in the research of low-dimensional materials, there are three fundamental challenges of research in low-dimensional materials: 1) Develop new computational tools to accurately describe the properties of low-dimensional materials with low computational cost. 2) Predict and synthesize new low-dimensional materials with novel properties. 3) Reveal new phenomenon induced by the interaction between low-dimensional materials and the surrounding environment. In this thesis, atomistic modelling tools have been applied to address these challenges. We first developed ReaxFF parameters for phosphorus and hydrogen to give an accurate description of the chemical and mechanical properties of pristine and defected black phosphorene. ReaxFF for P/H is transferable to a wide range of phosphorus and hydrogen containing systems including bulk black phosphorus, blue phosphorene, edge-hydrogenated phosphorene, phosphorus clusters and phosphorus hydride molecules. The potential parameters were obtained by conducting global optimization with respect to a set of reference data generated by extensive ab initio calculations. We extended ReaxFF by adding a 60° correction term which significantly improved the description of phosphorus clusters. Emphasis was placed on the mechanical response of black phosphorene with different types of defects. Compared to the nonreactive SW potential of phosphorene, ReaxFF for P/H systems provides a significant improvement in describing the mechanical properties of the pristine and defected black phosphorene, as well as the thermal stability of phosphorene nanotubes. A counterintuitive phenomenon was observed that single vacancies weaken the black phosphorene more than double vacancies with higher formation energy. Our results also showed that the mechanical response of black phosphorene is more sensitive to defects in the zigzag direction than that in the armchair direction. Since ReaxFF allows straightforward extensions to the heterogeneous systems, such as oxides, nitrides, the proposed ReaxFF parameters for P/H systems also underpinned the reactive force field description of heterogeneous P systems, including P-containing 2D van der Waals heterostructures, oxides, etc. Based on the evolutionary algorithm driven structural search, we proposed a new stable trisulfur dinitride (S3N2) 2D crystal that is a covalent network composed solely of S-N σ bonds. S3N2 crystal is dynamically, thermally and chemically stable as confirmed by the computed phonon spectrum and ab initio molecular dynamics simulations. GW calculations showed that the 2D S3N2 crystal is a wide, direct band-gap (3.92 eV) semiconductor with a small hole effective mass. The anisotropic optical response of 2D S3N2 crystal was revealed by GW-BSE calculations. Our result not only marked the prediction of the first 2D crystal composed of nitrogen and sulfur, but also underpinned potential innovations in 2D electronics, optoelectronics, etc. Inspired by the discovery of S3N2 2D crystal, we proposed a new 2D crystal, diphosphorus trisulfide (P2S3), based on the extensive evolutionary algorithm driven structural search. The 2D P2S3 crystal was confirmed to be dynamically, thermally and chemically stable by the computed phonon spectrum and ab initio molecular dynamics simulations. This 2D crystalline phase of P2S3 corresponds to the global minimum in the Born-Oppenheimer surface of the phosphorus sulfide monolayers with 2:3 stoichiometry. It is a wide band gap (4.55 eV) semiconductor with P-S σ bonds. The electronic properties of P2S3 structure can be tuned by stacking into multilayer P2S3 structures, forming P2S3 nanoribbons or rolling into P2S3 nanotubes, expanding its potential applications for the emerging field of 2D electronics. Then we showed that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO32- with n = 1-8 water molecules was investigated by ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal/mol as the number of water molecules increases from 1 to 6. Meanwhile, the degree of the hydrolysis of CO32- is significantly increased compared to the bulk water solution scenario. The incomplete hydration shells facilitate the hydrolysis of CO32- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO2 air capture driven by the humidity-swing. Instead, the pore-diffusion of ions is expected to be the time-limiting step in the humidity driven CO2 air capture. The effect of humidity on the speed of CO2 air capture was studied by conducting CO2 absorption experiment using IER with a high ratio of CO32- to H2O molecules. Our result is able to provide valuable insights to designing efficient CO2 air-capture sorbents. Lastly, the self-assembly mechanism of one-end-open carbon nanotubes (CNTs) suspended in an aqueous solution was studied by molecular dynamics simulations. It was shown that two one-end-open CNTs with different diameters can coaxially self-assemble into a nanocapsule. The nanocapsules formed were stable in aqueous solution under ambient conditions, and the pressure inside the nanocapsule was much higher than the ambient pressure due to the van der Waals interactions between two parts of the nanocapsule. The effects of the normalized radius difference, normalized inter-tube distance and aspect ratio of the CNT pairs were systematically explored. The electric field response of nanocapsules was studied with ab initio molecular dynamics simulations, which showed that nanocapsules can be opened by applying an external electric field, due to the polarization of carbon atoms. This discovery not only shed light on a simple yet robust nanocapsule self-assembly mechanism, but also underpinned potential innovations in drug delivery, nano-reactors, etc

Strong Cosmic Censorship in Charged de Sitter spacetime with Scalar Field Non-minimally Coupled to Curvature

We examine the stability and the strong cosmic censorship in the Reissner-Nordstrom-de Sitter (RN-dS) black hole by investigating the evolution of a scalar field non-minimally coupled to the curvature. We find that when the coupling parameter is negative, the RN-dS black hole experiences instability. The instability disappears when the coupling parameter becomes non-negative. With the increase of the coupling parameter, the violation of the strong cosmic censorship occurs at a larger critical charge ratio. But such an increase of the critical charge is suppressed by the increase of the cosmological constant. Different from the minimal coupling situation, it is possible to accommodate $\beta\ge1$ in the near extremal black hole when the scalar field is non-minimally coupled to curvature. The increase of the cosmological constant can allow $\beta\ge1$ to be satisfied for even smaller value of the coupling parameter. The existence of $\beta\ge1$ implies that the resulting curvature can continuously cross the Cauchy horizon.Comment: 14 pages, 4 figures, 5 table

基于词典的语料库词义标注 = Dictionary Based Corpus Sense Tagging

Master'sMASTER OF ART

Development of a Transferable Reactive Force Field of P/H Systems: Application to the Chemical and Mechanical Properties of Phosphorene

ReaxFF provides a method to model reactive chemical systems in large-scale molecular dynamics simulations. Here, we developed ReaxFF parameters for phosphorus and hydrogen to give a good description of the chemical and mechanical properties of pristine and defected black phosphorene. ReaxFF for P/H is transferable to a wide range of phosphorus and hydrogen containing systems including bulk black phosphorus, blue phosphorene, edge-hydrogenated phosphorene, phosphorus clusters and phosphorus hydride molecules. The potential parameters were obtained by conducting unbiased global optimization with respect to a set of reference data generated by extensive ab initio calculations. We extend ReaxFF by adding a 60{\deg} correction term which significantly improves the description of phosphorus clusters. Emphasis has been put on obtaining a good description of mechanical response of black phosphorene with different types of defects. Compared to nonreactive SW potential [1], ReaxFF for P/H systems provides a huge improvement in describing the mechanical properties the pristine and defected black phosphorene and the thermal stability of phosphorene nanotubes. A counterintuitive phenomenon is observed that single vacancies weaken the black phosphorene more than double vacancies with higher formation energy. Our results also show that mechanical response of black phosphorene is more sensitive to defects for the zigzag direction than for the armchair direction. Since ReaxFF allows straightforward extensions to the heterogeneous systems, such as oxides, nitrides, ReaxFF parameters for P/H systems build a solid foundation for the reactive force field description of heterogeneous P systems, including P-containing 2D van der Waals heterostructures, oxides, etc