拥挤剂粒子形状对大分子链成环动力学的影响

Using 3D Langevin dynamics simulations,we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure.The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders.By contrast,the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders.Notably,the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44.We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.     

The moving boundary node method: A level set-based,finite volume algorithm with applications to cell motility

Eukaryotic cell crawling is a highly complex biophysical and biochemical process, where deformation and motion of a cell are driven by internal, biochemical regulation of a poroelastic cytoskeleton. One challenge to built quantitative models that describe crawling cells is solving the reaction–diffusion–advection dynamics for the biochemical and cytoskeletal components of the cell inside its moving and deforming geometry. Here we develop an algorithm that uses the level set method to move the cell boundary and uses information stored in the distance map to construct a finite volume representation of the cell. Our method preserves Cartesian connectivity of nodes in the finite volume representation while resolving the distorted cell geometry. Derivatives approximated using a Taylor series expansion at finite volume interfaces lead to second order accuracy even on highly distorted quadrilateral elements. A modified, Laplacian-based interpolation scheme is developed that conserves mass while interpolating values onto nodes that join the cell interior as the boundary moves. An implicit time stepping algorithm is used to maintain stability. We use the algorithm to simulate two simple models for cellular crawling. The first model uses depolymerization of the cytoskeleton to drive cell motility and suggests that the shape of a steady crawling cell is strongly dependent on the adhesion between the cell and the substrate. In the second model, we use a model for chemical signalling during chemotaxis to determine the shape of a crawling cell in a constant gradient and to show cellular response upon gradient reversal.     

Analytical Solution for Peristaltic Transport of Viscous Nanofluid in an Asymmetric Channel with Full Slip and Convective Conditions

The peristaltic flow of nanofluids is a relatively new area of research. Scientists are of the opinion that the no-slip conditions at the boundaries are no longer valid and consequently, the first and the second order slip conditions should be addressed. In this paper, the effects of slip conditions and the convective boundary conditions at the boundary walls on the peristaltic flow of a viscous nanofluid are investigated for. Also, the exact analytical solutions are obtained for the model. The obtained results are presented through graphs and discussed. The results reveal that the two slip parameters have strong effects on the temperature and the nanoparticles volume fraction profiles. Moreover, it has been seen that the temperature and nanoparticles volume fraction profiles attain certain values when the first slip condition exceeds a specified value. However, no limit value for the second slip parameter has been detected. Further, the effects of the various emerging parameters on the flow and heat transfer characteristics have been presented.     

Physical model for the width distribution of axons

The distribution of widths of axons was recently investigated, and was found to have a distinct peak at an optimized value. The optimized axon width at the peak may arise from the conflicting demands of minimizing energy consumption and assuring signal transmission reliability. The distribution around this optimized value is found to have a distinct non-Gaussian shape, with an exponential “tail”. We propose here a mechanical model whereby this distribution arises from the interplay between the elastic energy of the membrane surrounding the axon core, the osmotic pressure induced by the neurofilaments inside the axon bulk, and active processes that remodel the microtubules and neurofilaments inside the axon. The axon’s radius of curvature can be determined by the cell’s control of the osmotic pressure difference across the membrane, the membrane tension or by changing the composition of the different components of the membrane. We find that the osmotic pressure, determined by the neurofilaments, seems to be the dominant control parameter.     

Reaction-limited sintering in nearly saturated environments

We study the shape and growth rate of necks between sintered spheres with dissolution–precipitation dynamics in the reaction-limited regime. We determine the critical shape that separates those initial neck shapes that can sinter from those that necessarily dissolve, as well as the asymptotic evolving shape of sinters far from the critical shape. We compare our results with past results for the asymptotic neck shape in closely related but more complicated models of surface dynamics; in particular, we confirm a scaling conjecture, originally due to Kuczinsky. Finally, we consider the relevance of this problem to the diagenesis of sedimentary rocks and other applications.     

Swinging and tumbling of fluid vesicles in shear flow

The dynamics of fluid vesicles in simple shear flow is studied using mesoscale simulations of dynamically triangulated surfaces, as well as a theoretical approach based on two variables: a shape parameter and the inclination angle, which has no adjustable parameters. We show that, between the well-known tank-treading and tumbling states, a new "swinging" state can appear. We predict the dynamic phase diagram as a function of the shear rate, the viscosities of the membrane and the internal fluid, and the reduced vesicle volume. Our results agree well with recent experiments.     

Coupling shape dynamics to matter gives spacetime

Shape dynamics is a metric theory of pure gravity, equivalent to general relativity, but formulated as a gauge theory of spatial diffeomporphisms and local spatial conformal transformations. In this paper we extend the construction of shape dynamics form pure gravity to gravity-matter systems and find that there is no fundamental obstruction for the coupling of gravity to standard matter. We use the matter gravity system to construct a clock and rod model for shape dynamics which allows us to recover a spacetime interpretation of shape dynamics trajectories.     

Power-law for axon diameters at branch point

Background

Axon calibers vary widely among different animals, neuron classes, and even within the same neuron. What determines the diameter of axon branches?

Results

We pursue the hypothesis that the axon caliber has evolved to minimize signal propagation delays, while keeping arbor volume to a minimum. For a general cost function, we show that the optimal diameters of mother and daughter branches at a bifurcation satisfy a power law. The derivation relies on the fact that the axon conduction speed scales as a power of axon diameter. Although available data are consistent with the law, there is a large spread in the data. Future experimental tests will determine whether this spread is due to biological variability or measurement error.

Conclusions

Minimization of arbor volume and signal propagation delay may have been an important factor in the evolution of the brain.

     

Chaos in intrinsic motion of nuclei and its role in dissipative collective dynamics

We shall discuss the role of chaotic intrinsic motion in dissipative dynamics of the collective coordinates for nuclear systems. Using the formalism of linear response theory, it will be shown that the dissipation in adiabatic collective motion depends on the degree of chaos in the intrinsic dynamics of a system. This gives rise to a shape dependent dissipation rate for collective coordinates when the intrinsic motion is described by the independent particle model in a nucleus. The shape dependent chaos parameter measuring the degree of chaos in the intrinsic dynamics of the nuclear system will be obtained using the interpolating Brody distribution of nearest neighbour spacings in the single particle energy spectrum. A similar shape dependence is also found to be essential for phenomenological dissipation rates used in fission dynamics calculations.     

平流层飞艇气动外形优化设计:螺旋桨的影响

建立综合螺旋桨影响的平流层飞艇气动外形优化设计平台.采用Hicks-Henne型函数法参数化艇身轮廓,发展IDW-TFI混合动网格技术实现变形网格高效生成;基于作用盘理论模拟螺旋桨,建立飞艇流场高效数值求解方法.以LOTTE飞艇作为初始外形,阻力系数最小为目标,飞艇体积作为约束条件,通过NLPQL算法寻优获得最佳艇身设计方案.优化后飞艇的尾部形状较平坦,艇身最大横截面位置前移,气动性能得到明显改善,其阻力系数相对于初始外形降低了26.88%.     

Mechano-chemical oscillations of a gel bead

We present a formalism which describes the spatio-temporal evolution of a gel submitted to an autocatalytic chemical reaction to which it is responsive. This theory is based on an extension of a hydrodynamical multi-diffusional approach of the gel dynamics, which is plunged into a chemically active mixture. Emergent and autonomous volume self-oscillation dynamics of the gel are obtained from the nonlinear coupling of the elastic deformation, the chemical kinetics and the transport phenomena, that take place in the system. We apply this formalism to a spherical bead of gel plunged in a Belouzov-Zhabotinsky oscillatory chemical reaction, for which Yoshida et al. have obtained numerous experimental results. The case of a gel immersed in an autocatalytic bistable chemical reaction is also considered. We show that such formalism describes the autonomous volume self-oscillation dynamics of the gel beads.     

Scroll wave dynamics in a model of the heterogeneous heart

Scroll waves are found in physical, chemical and biological systems and underlie many significant processes including life-threatening cardiac arrhythmias. The theory of scroll waves predicts scroll wave dynamics should be substantially affected by heterogeneity of cardiac tissue together with other factors including shape and anisotropy. In this study, we used our recently developed analytical model of the human ventricle to identify effects of shape, anisotropy, and regional heterogeneity of myocardium on scroll wave dynamics. We found that the main effects of apical-base heterogeneity were an increased scroll wave drift velocity and a shift towards the region of maximum action potential duration. We also found that transmural heterogeneity does not substantially affect scroll wave dynamics and only in extreme cases changes the attractor position.     

水中自然超空泡机理及减阻效应的非平衡分子动力学研究

应用非平衡分子动力学方法,对水中超空泡流形成机理及减阻效应进行了模拟研究.计算得到了流体密度分布、局部空化数分布、阻力系数及含气百分比等流场细节数据,结果显示空化数判据在分子层面仍然成立,局部低空化数区域与超空泡形成区域在空间上分离;超空泡形成和稳定主要受物体运动速度影响;空化器构型对空泡内含气率有较大影响;从云雾空化状态过渡到超空泡,物体表面摩擦力可以减小50%—90%.与数值模拟结果的对比表明非平衡分子动力学模拟适用于研究微观超空泡机理,能够经济有效地探讨超高速流体运动的一些自然规律. 关键词： 非平衡分子动力学 超空泡 高速流体 摩擦系数     

Numerical investigation of cavitation generated by an ultrasonic dental scaler tip vibrating in a compressible liquid

Bacterial biofilm accumulation around dental implants is a significant problem leading to peri-implant diseases and implant failure. Cavitation occurring in the cooling water around ultrasonic scaler tips can be used as a novel solution to remove debris without any surface damage. However, current clinically available instruments provide insufficient cavitation around the activated tip surface. To solve this problem a critical understanding of the vibro-acoustic behaviour of the scaler tip and the associated cavitation dynamics is necessary. In this research, we carried out a numerical study for an ultrasound dental scaler with a curved shape tip vibrating in water, using ABAQUS based on the finite element method. We simulated the three-dimensional, nonlinear and transient interaction between the vibration and deformation of the scaler tip, the water flow around the scaler and the cavitation formation and dynamics. The numerical model was well validated with the experiments and there was excellent agreement for displacement at the free end of the scaler. A systematic parametric study has been carried out for the cavitation volume around the scaler tip in terms of the frequency, amplitude and power of the tip vibration. The numerical results indicate that the amount of cavitation around the scaler tip increases with the frequency and amplitude of the vibration. However, if the frequency is far from the natural frequency, the cavitation volume around the free end decreases due to reduced free end vibration amplitude.     

Calculation of the shape of the magnetic domain wall

The equilibrium shape of the bowing of the magnetic domain wall, for an applied magnetic field and within the bulged domain wall Globus model, is obtained. We make the assumption of having a bowing corresponding to a volume of revolution and use calculus of variations to minimize the total energy with respect to the profile of the shape. It is found that the equilibrium shape corresponds to a spherical cap, in agreement with the assumption made for this shape in previous work.     

Shape dependent electronic structure and exciton dynamics in small In(Ga)As quantum dots

We present a study of the primary optical transitions and recombination dynamics in InGaAs self-assembled quantum nanostructures with different shape. Starting from the same quantum dot seeding layer, and depending on the overgrowth conditions, these new nanostructures can be tailored in shape and are characterized by heights lower than 2 nm and base lengths around 100 nm. The geometrical shape strongly influences the electronic and optical properties of these nanostructuctures. We measure for them ground state optical transitions in the range 1.25–1.35 eV and varying energy splitting between their excited states. The temperature dependence of the exciton recombination dynamics is reported focusing on the intermediate temperature regime (before thermal escape begins to be important). In this range, an important increase of the effective photoluminescence decay time is observed and attributed to the state filling and exciton thermalization between excited and ground states. A rate equation model is also developed reproducing quite well the observed exciton dynamics.     

Vacillating breathing and tumbling of vesicles under shear flow

The dynamics of vesicles under a shear flow are analyzed analytically in the small deformation regime. We derive two coupled nonlinear equations which describe the vesicle orientation in the flow and its shape evolution. A new type of motion is found, namely, a "vacillating-breathing" mode: the vesicle orientation undergoes an oscillation around the flow direction, while the shape executes breathing dynamics. This solution coexists with tumbling. Moreover, we provide an explicit expression for the tumbling threshold. A rheological law for a dilute vesicle suspension is outlined.