Armchair Janus MoSSe Nanoribbon with Spontaneous Curling: A First-Principles Study

Based on density functional theory, we theoretically investigate the electronic structures of free-standing armchair Janus MoSSe nanoribbons (A-MoSSeNR) with width up to 25.5 nm. The equilibrium structures of nanoribbons with spontaneous curling are obtained by energy minimization in molecular dynamics (MD). The curvature is 0.178 nm−1 regardless of nanoribbon width. Both finite element method and analytical solution based on continuum theory provide qualitatively consistent results for the curling behavior, reflecting that relaxation of intrinsic strain induced by the atomic asymmetry acts as the driving force. The non-edge bandgap of curled A-MoSSeNR reduces faster with the increase of width compared with planar nanoribbons. It can be observed that the real-space wave function at the non-edge VBM is localized in the central region of the curled nanoribbon. When the curvature is larger than 1.0 nm−1, both edge bandgap and non-edge bandgap shrink with the further increase of curvature. Moreover, we explore the spontaneous curling and consequent sewing process of nanoribbon to form nanotube (Z-MoSSeNT) by MD simulations. The spontaneously formed Z-MoSSeNT with 5.6 nm radius possesses the lowest energy. When radius is smaller than 0.9 nm, the bandgap of Z-MoSSeNT drops rapidly as the radius decreases. We expect the theoretical results can help build the foundation for novel nanoscale devices based on Janus TMD nanoribbons.

Effective elasticity and persistence of strain in active filament-motor assemblies

Cross-linked, elastic, filamentous networks that are deformed by active molecular motors feature in several natural and synthetic settings. The effective active elasticity of these composite systems determines the length scale over which active deformations persist in fluctuating environments. This fundamental quantity has been studied in passive systems; however mechanisms determining and modulating this length-scale in active systems has not been clarified. Here, focusing on active arrayed filament-motor assemblies, we propose and analyze a minimal model in order to estimate the length scale over which imposed or emergent elastic deformations or stresses persist. We combine a mean-field continuum theory valid for weakly elastic assemblies with high dimensional Multi-Particle Collision (MPC) based Brownian simulations valid for moderate to strongly elastic and noisy systems. Integrating analytical and numerical results, we show that localized strains - steady or oscillatory - persist over well-defined length scales that dependent on motor activity, effective shear elasticity and filament extensibility. Extensibility is key even in very stiff filaments, and cannot be ignored when global deformations are considered. We clarify mechanisms by which motor derived active elasticity and passive shear elasticity of the filamentous backbone combine to effectively soften filaments. Surprisingly, the predictions of the mean-field theory agree qualitatively with results from stochastic discrete filament-motor model, even for moderately strong noise. We also find that athermal motor noise impacts the overall duty ratio of the motors and thereby the persistence length in these driven assemblies. Our study demonstrates how correlated activity in natural ordered active matter possesses a finite range of influence with clear testable experimental implications.

Incompatible Deformation Model of Rocks with Defects around a Thick-Walled Cylinder

Before the excavation of underground engineering, joints, fissures, and voids already exist in the rock—that is, there are defects in the rock. Due to the existence of these defects, the rock produces plastic deformation, which can lead to incompatible deformation. Therefore, the classic continuum theory cannot accurately describe the deformation of the rock. In this paper, a relationship between the strain tensor and metric tensor was studied by analyzing the three states of elastic plastic deformation, and the elasto-plastic incompatible model was built. Additionally, the stress and deformation of a thick-walled cylinder under hydrostatic pressure was investigated by using a finite element program written in the FORTRAN language. The results show that the plastic strain is associated with not only deviator stress but also the distribution of defects (represented by the incompatible parameter R). With the value of R increasing, the defects in the rock increased, but the elastic plastic stiffness matrix decreased. Thus, as more rock enters the plastic state, the deformation of the surrounding rock is enlarged.

Determination of Silicon Electrical Properties Using First Principles Approach

Silicon nanowires have attracted attention as basis for reconfigurable electronics. However, as the size decreases, the electronic properties of the nanowires vary as a result of confinement, strain and crystal topology effects. Thus, at the thin diameter regime the band gap of Silicon nanowires can no longer be derived from a simple extrapolation of the isotropic bulk behaviour. This study compares band gap parameters in sub 10nm nanowires obtained from first-principles density-functional band structure calculations with extrapolations using continuum theory in order to rationalize the changes of the overall conductance, resistance and band gap. The device consists of silicon nanowire of size between 1 nm to 6nm. The results indicate an increase of, both the energy gap and the resistance along with reduced conductivity for the thinnest wires and a dependence on the crystal orientation with gaps reaching up to 4.3 eV along <111>, 4.0 eV along <110>, and 3.7 along <100>.

Continuum Theory for Planar Cell Polarity

Planar Cell Polarity (PCP), characterized by asymmetric localization of proteins at the cell membrane within the epithelial plane, plays essential roles in embryonic development and physiological functions. The significance of PCP can be appreciated by the outcomes of PCP failure in the form of defects in neural tube formation, tracheal malfunctions, organ shape misregulation, hair follicle misalignment etc. Extensive experimental works on PCP in fruit fly Drosophila melanogaster have classified the proteins involved in PCP into two modules: 'core' module, acting locally by inter-cellular protein interactions, and, 'global' module, responsible for the alignment of cell polarities with that of the tissue axis. Despite the involvement of different molecular players, the asymmetric localization of the proteins of the two modules on cell membrane primarily involve inter-cellular dimer formations. We have developed a continuum model of the localization of PCP proteins on the cell membrane and its regulation via intra- and inter-cellular protein-protein interactions. We have identified the conditions for the asymmetric protein localization, or PCP establishment, for uniform and graded protein expression levels in the tissue. We have found that in the absence of any tissue level expression gradient the polarized state of the tissue is not stable against finite length perturbations which is also a property of the active polar matter. However, in the presence of tissue level expression gradients of proteins the polarized state remains stable. We have also looked at the influence of the loss of PCP proteins from a select regions of the tissue on the polarization of the cells outside of that region. This continuum theory of the planar cell polarity can be coupled with the active matter hydrodynamics to study the cell flows and their regulation by genetic machinery.

Self-generated oxygen gradients control collective aggregation of photosynthetic microbes

For billions of years, photosynthetic microbes have evolved under the variable exposure to sunlight in diverse ecosystems and microhabitats all over our planet. Their abilities to dynamically respond to alterations of the luminous intensity, including phototaxis, surface association and diurnal cell cycles, are pivotal for their survival. If these strategies fail in the absence of light, the microbes can still sustain essential metabolic functionalities and motility by switching their energy production from photosynthesis to oxygen respiration. For suspensions of motile C. reinhardtii cells above a critical density, we demonstrate that this switch reversibly controls collective microbial aggregation. Aerobic respiration dominates over photosynthesis in conditions of low light, which causes the microbial motility to sensitively depend on the local availability of oxygen. For dense microbial populations in self-generated oxygen gradients, microfluidic experiments and continuum theory based on a reaction–diffusion mechanism show that oxygen-regulated motility enables the collective emergence of highly localized regions of high and low cell densities.

Numerical Simulations of Polymers at the Nanoscale

<p>In this thesis we study a variety of nanoscale phenomena in certain polymer systems using a combination of numerical simulation methods and mathematical modelling. The problems considered are: (a) the mixing behaviour of polymeric fluids in micro- and nanofluidic devices, (b) capillary absorption of polymer droplets into narrow capillaries, and (c) modelling the phase separation and self-assembly behaviour in polymer systems with freely deforming boundaries. These problems are significant in nanotechnological applications of polymer-based systems. First, the mixing behaviour of a polymeric melt over two parallely patternedslip surfaces is considered. Using molecular dynamics (MD) simulations, it is shown that mixing is enhanced when the polymer chain size is smaller than the wavelength of the chemical pattern of the surfaces. An off-set in the upper and lowerwall patterns improved themixing in the centre of the channel. Application of a sinusoidally varying body force in addition to the patterned-slip conditions is shown to enhance mixing further, compared to a constant body force case, with some limitations. Simulation findings for the constant body force cases are in qualitative agreement with the continuum theory of Pereira [1]. However, in the case of a sinusoidally varying body force our simulations do not agree with the continuum theory. We explain the reasons for the discrepancy between the two and point out the deficiencies in the continuum theory in predicting the correct behaviour. Second, the capillary phenomena of polymer droplets in narrow capillaries is studied using MD simulations. It is demonstrated that droplets composed of longer chains require wider tubes for absorption and this result is in agreement with our continuum modelling. The observed capillary dynamics deviate significantly from the standard Lucas-Washburn description thus questioning its validity at the nanoscale. The metastable states during the capillary absorption in some cases cannot be explained using the existing models of capillary dynamics. Lastly, the phase separation process in polymer blends between both confined and unconfined boundaries is studied using Smoothed Particle Hydrodynamics (SPH). The SPH technique has the advantage of not using a grid to discretize the spatial domain, which makes it appealing when dealing with problems where the spatial domain can change with time. The applicability of the SPH method in describing phase separation in these systems is demonstrated. In particular, its ability to model freely deforming polymer blends is shown.</p>

Numerical Simulations of Polymers at the Nanoscale

<p>In this thesis we study a variety of nanoscale phenomena in certain polymer systems using a combination of numerical simulation methods and mathematical modelling. The problems considered are: (a) the mixing behaviour of polymeric fluids in micro- and nanofluidic devices, (b) capillary absorption of polymer droplets into narrow capillaries, and (c) modelling the phase separation and self-assembly behaviour in polymer systems with freely deforming boundaries. These problems are significant in nanotechnological applications of polymer-based systems. First, the mixing behaviour of a polymeric melt over two parallely patternedslip surfaces is considered. Using molecular dynamics (MD) simulations, it is shown that mixing is enhanced when the polymer chain size is smaller than the wavelength of the chemical pattern of the surfaces. An off-set in the upper and lowerwall patterns improved themixing in the centre of the channel. Application of a sinusoidally varying body force in addition to the patterned-slip conditions is shown to enhance mixing further, compared to a constant body force case, with some limitations. Simulation findings for the constant body force cases are in qualitative agreement with the continuum theory of Pereira [1]. However, in the case of a sinusoidally varying body force our simulations do not agree with the continuum theory. We explain the reasons for the discrepancy between the two and point out the deficiencies in the continuum theory in predicting the correct behaviour. Second, the capillary phenomena of polymer droplets in narrow capillaries is studied using MD simulations. It is demonstrated that droplets composed of longer chains require wider tubes for absorption and this result is in agreement with our continuum modelling. The observed capillary dynamics deviate significantly from the standard Lucas-Washburn description thus questioning its validity at the nanoscale. The metastable states during the capillary absorption in some cases cannot be explained using the existing models of capillary dynamics. Lastly, the phase separation process in polymer blends between both confined and unconfined boundaries is studied using Smoothed Particle Hydrodynamics (SPH). The SPH technique has the advantage of not using a grid to discretize the spatial domain, which makes it appealing when dealing with problems where the spatial domain can change with time. The applicability of the SPH method in describing phase separation in these systems is demonstrated. In particular, its ability to model freely deforming polymer blends is shown.</p>