Tensile properties of microtubules: A study by nonlinear molecular structural mechanics modelling

A nonlinear molecular structural mechanics (MSM) model is proposed in this paper for studying the tensile properties of microtubules (MTs). In the nonlinear MSM models, the interactions between tubulin monomers in MTs are treated as nonlinear axial and torsional springs, whose stiffness coefficients are extracted from all-atom molecular dynamics simulations. The Young's modulus and fracture properties of MTs under tension extracted from the present nonlinear MSM models are found to agree well with the existing simulation and experiment results, which shows the efficiency and accuracy of the proposed nonlinear MSM models. In addition, the nonlinear MSM models are also extended to investigate the tensile properties including Young's modulus and fracture strain of MTs possessing lattice defects. The results obtained from nonlinear MSM models are utilized to develop a predictive equation for quickly predicting the tensile properties of MTs with different lattice defect levels.     

Mechanistic model for the dielectric spectrum of a simple dielectric material

ABSTRACT

In this paper, we perform molecular dynamics simulations of a dielectric fluidic material composed of permanent molecular dipoles. The dielectric spectrum features two peaks at lower frequencies than the system phonon frequency. The primary peak is observed at all temperatures studied and shifts toward lower frequencies as the temperature decreases. During this shift, the secondary peak emerges with a higher peak frequency than the primary peak. The secondary peak amplitude increases as the temperature decreases. Both peaks are dependent on the wavevector; in the small wavevector regime, the primary peak is shifted to higher frequencies as the wavevector squared and the secondary peak amplitude increases as the wavevector increases, but shows no shift in frequency. From the polarisation balance equation, we propose a model for the dielectric spectrum. This captures the spectrum features, and we conjecture that the primary peak is due to dipole moment correlations (Debye-type) and the secondary peak is due to the correlation between the dipole moment and a microscopic local field.     

Dynamics of a Predator-Prey Model with Allee Effect and Herd Behavior

This paper deals with dynamics of a predator-prey model with Allee effect and herd behavior. We first study the stability of non-negative constant solutions for such system. We also establish the existence of Hopf bifurcation solutions for such predator-prey model. The stability and bifurcation direction of Hopf bifurcation solution in the case of spatial homogeneity are further discussed. At the same time, several examples are given by MATLAB. Finally, the numerical simulations of the system are carried out through MATLAB, which intuitively verifies and supplements the theoretical analysis results.     

Nonequilibrium Time Reversibility with Maps and Walks

Time-reversible dynamical simulations of nonequilibrium systems exemplify both Loschmidt’s and Zermélo’s paradoxes. That is, computational time-reversible simulations invariably produce solutions consistent with the irreversible Second Law of Thermodynamics (Loschmidt’s) as well as periodic in the time (Zermélo’s, illustrating Poincaré recurrence). Understanding these paradoxical aspects of time-reversible systems is enhanced here by studying the simplest pair of such model systems. The first is time-reversible, but nevertheless dissipative and periodic, the piecewise-linear compressible Baker Map. The fractal properties of that two-dimensional map are mirrored by an even simpler example, the one-dimensional random walk, confined to the unit interval. As a further puzzle the two models yield ambiguities in determining the fractals’ information dimensions. These puzzles, including the classical paradoxes, are reviewed and explored here.     

Tumor Hypoxia Heterogeneity Affects Radiotherapy: Inverse-Percolation Shell-Model Monte Carlo Simulations

Tumor hypoxia was discovered a century ago, and the interference of hypoxia with all radiotherapies is well known. Here, we demonstrate the potentially extreme effects of hypoxia heterogeneity on radiotherapy and combination radiochemotherapy. We observe that there is a decrease in hypoxia from tumor periphery to tumor center, due to oxygen diffusion, resulting in a gradient of radiative cell-kill probability, mathematically expressed as a probability gradient of occupied space removal. The radiotherapy-induced break-up of the tumor/TME network is modeled by the physics model of inverse percolation in a shell-like medium, using Monte Carlo simulations. The different shells now have different probabilities of space removal, spanning from higher probability in the periphery to lower probability in the center of the tumor. Mathematical results regarding the variability of the critical percolation concentration show an increase in the critical threshold with the applied increase in the probability of space removal. Such an observation will have an important medical implication: a much larger than expected radiation dose is needed for a tumor breakup enabling successful follow-up chemotherapy. Information on the TME’s hypoxia heterogeneity, as shown here with the numerical percolation model, may enable personalized precision radiation oncology therapy.     

横向磁场激励下铁磁梁式板的混沌运动分析

在磁体力分布的磁弹性理论模型和磁场准静态假定模式基础上，对于处在周期时变磁场 中的不可移简支铁磁梁式板非线性磁弹性动力特性进行定性与定量分析．首先利用磁场的摄 动技术和结构变形的模态法，导出了关于模态坐标的非线性动力方程；然后利用Ｍｅｌｎｉｋｏｖ方 法，从理论上给出这一磁弹性动力系统可能出现混沌运动的必要条件及参数范围；最后采用变 步长Ｒｕｎｇｅ－Ｋｕｔｔａ数值积分方法对其磁弹性相互作用的混沌现象进行了定量搜索与模拟，并 利用其轨迹的Ｐｏｉｎｃａｒｅ截面图与Ｌｉａｐｕｎｏｖ指数加以判断．结果表明磁弹性简支梁式板在横 向周期时变磁场中存在混沌吸引子，且在机械阻尼很小时其混沌吸引子表现出稠的特性．     

The Influence of Visual and Spatial Reasoning in Interpreting Simulated 3D Worlds

This paper explores the way in which young children (6 year olds) made sense of screen-based images on the computer. The participants were required to interpret 3D-like representations and relate these images to objects in their environment. Both static and relatively dynamic software programs were used in the investigation. Some of the children could not make links between the screen representation and the intended three-dimensional (3D) objects. It is argued that young children should be exposed to activities that establish explicit links between 2D and 3D objects ``away' from the computer before attempting the more difficult links required to interpret and represent 3D objects in ICT contexts. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular scale structure formation by folding

A conception of a structure formation suitable for nano-technology is proposed, which is programmable and suitable for mass production-like lithography. This conception utilizes the controlled folding of chains like the scan-lines of television. Its possibility and property were studied theoretically using the modeled chains consist of beads. By adopting the interaction among the beads which can distinguish the kind of the partner by its polarity and is chiral to break the chiral symmetry of the folded state, the special chains which have the unique ground states could be designed. In these ground states, the chains are folded like the scan-lines of television. The thermodynamic properties of the suggested chains were studied by the Monte Carlo simulations and the suggested chains showed the phase-transition-like behavior which is distinct compared to both the random chains and the chain that has only the non-specific attraction. The size dependence and the effects of adding the non-specific attraction and modifying the border of the folded conformation were also studied.     

Physical Analysis of a Possibility to Reach the 1.30-μm Emission from the GaAs-Based VCSELs with the InGaAs/GaAs Quantum-Well Active Regions and the Intentionally Detuned Optical Cavities

Physical aspects of an operation of the GaAs-based InGaAs/GaAs quantum-well (QW) VCSELs with the intentionally detuned optical cavities have been considered in the present paper using the comprehensive three-dimensional self-consistent optical–electrical–thermal-gain simulation. In GaAs-based structures, very good DBR resonator mirrors and a very efficient methods to confine radially both the current spreading and the electromagnetic field with the aid of oxide apertures may be applied. It has been found using the above simulation that even currently available immature technology enables manufacturing the above devices emitting radiation of wavelengths over 1.20 μm. In particular, while the room-temperature 1.30-μm lasing emission is still beyond possibilities of the InGaAs/GaAs QW VCSELs, these structures may offer analogous 1.25-μm emission, especially for the high-power and/or high-temperature operation.