Enhanced effect of dimension of receptor-ligand complex and depletion effect on receptor-mediated endocytosis of nanoparticles

We present an extended analytical model including the depletion effect and the dimension of ligand-receptor complex,aiming to elucidate their influences on endocytosis of spherocylindrical nanoparticles(NPs). It is found that the dimension of ligand-receptor complex(δ) and the depletion effect interrelatedly govern the optimal conditions of NP endocytosis. The endocytosis phase diagram constructed in the space of NP radius and relative aspect ratio indicates that the endocytosis of NP is enhanced evidently by reducing the optimal radius and the threshold radius of endocytosed NP. Meanwhile, through thermodynamic and kinetic analysis of the diffusion of receptors, the dependence of diffusion length on depletion effect and the dimension of ligand-receptor complex can be identified in great detail. For small aspect ratio, diffusion length decreases with increasing concentration c of small bioparticles in cellular environment. Endocytosis speed corresponding to large radius R and high concentration c of small bioparticles strongly depends on the increasing(2 r-δ). These results may show some highlights into the conscious design of NPs for diagnostic agents and therapeutic drug delivery applications.     

Reverse depletion effects and the determination of ligand density on some spherical bioparticles

In cell environments crowded with macromolecules, the depletion effects act and assist in the assembly of a wide range of cellular structures, from the cytoskeleton to the chromatin loop, which are well accepted. But a recent quantum dot experiment indicated that the dimensions of the receptor–ligand complex have strong effects on the size-dependent exclusion of proteins in cell environments. In this article, a continuum elastic model is constructed to resolve the competition between the dimension of the receptor–ligand complex and depletion effects in the endocytosis of a spherical virus-like bioparticle. Our results show that the depletion effects do not always assist endocytosis of a spherical virus-like bioparticle; while the dimension of the ligand–receptor complex is larger than the size of a small bioparticle in cell environments, the depletion effects do not work and reverse effects appear. The ligand density covered on the virus can be identified quantitatively.     

Phase diagram and phase transitions of the adsorbate system S/Ru(0001): a Monte Carlo study of a lattice gas model

We investigate the phase diagram and the critical properties of the adsorbate system sulphur/ruthenium(0001) in the coverage region 0 < Θ < 1/3 using Monte Carlo simulations of a lattice gas model on a triangular lattice. From experiments it is known that for low coverages an island phase appears in the phase diagram of this system at low temperatures. To capture this feature we include in our lattice gas model a weak third neighbour attraction in addition to the repulsive first and second neighbour forces. The phase diagram obtained from simulations of this model is in very good agreement with the experimental phase diagram. The critical properties of the lattice gas model are found to be compatible with the results of experiments on the system sulphur/ruthenium(0001). Finer details of the phase diagram, e. g. the location of tricritical points, which may be difficult to assess experimentally will also be discussed.     

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.     

Effect of monomer geometry on the fractal structure of colloidal rod aggregates

The fractal structure of clusters formed by diffusion-limited aggregation of rodlike particles is characterized over three decades of the scattering vector q, and displays an unexpected dependence on the aspect ratio of the constituent monomers. Monte Carlo simulations of aggregating Brownian rods corroborate the experimental finding that the measured fractal dimension is an increasing function of the monomer aspect ratio. Moreover, increasing the rod aspect ratio eliminates the structural distinction between diffusion- and reaction-limited cluster aggregation that is observed for spheres.     

Phase diagram of hard colloidal platelets: a theoretical account

We construct the complete liquid crystal phase diagram of hard plate-like cylinders for variable aspect ratio using Onsager's second virial theory and employing the Parsons–Lee decoupling approximation to account for higher-body interactions in the isotropic and nematic fluid phases. The stability of the solid (columnar) state at high packing fraction is included by invoking a simple equation of state based on a Lennard–Jones–Devonshire cell model which has proven to be quantitatively reliable over a large range of packing fractions. By employing an asymptotic analysis based on the Gaussian approximation we are able to show that the nematic–columnar transition is universal and independent of particle shape. The predicted phase diagram is in qualitative agreement with simulation results.     

Variable nanoparticle-cell adhesion strength regulates cellular uptake

In receptor-mediated endocytosis, cells exercise biochemical control over the mechanics of adhesion to engulf foreign particles, featuring a variable adhesion strength. Here we present a thermodynamic model with which we elucidate that the variable adhesion strength critically governs the cellular uptake, yielding an uptake phase diagram in the space of ligand density and particle size. We identify from the diagram an endocytosed phase with markedly high uptake, encompassed by a lower and an upper phase boundary that are set, respectively, by the enthalpic and entropic limits of the adhesion strength. The phase diagram may provide useful guidance to the rational design of nanoparticle-based therapeutic and diagnostic agents.     

Population dynamics on random networks: simulations and analytical models

We study the phase diagram of the standard pair approximation equations for two different models in population dynamics, the susceptible-infective-recovered-susceptible model of infection spread and a predator-prey interaction model, on a network of homogeneous degree k. These models have similar phase diagrams and represent two classes of systems for which noisy oscillations, still largely unexplained, are observed in nature. We show that for a certain range of the parameter k both models exhibit an oscillatory phase in a region of parameter space that corresponds to weak driving. This oscillatory phase, however, disappears when k is large. For k = 3, 4, we compare the phase diagram of the standard pair approximation equations of both models with the results of simulations on regular random graphs of the same degree. We show that for parameter values in the oscillatory phase, and even for large system sizes, the simulations either die out or exhibit damped oscillations, depending on the initial conditions. We discuss this failure of the standard pair approximation model to capture even the qualitative behavior of the simulations on large regular random graphs and the relevance of the oscillatory phase in the pair approximation diagrams to explain the cycling behavior found in real populations.     

Yang-Lee zeros of the Potts model

The Yang-Lee zeros of the three-component ferromagnetic Potts model in one dimension in the complex plane of an applied field are determined. The phase diagram consists of a triple point where three phases coexist. Emerging from the triple point are three lines on which two phases coexist and which terminate at critical points (Yang-Lee edge singularity). The zeros do not all lie on the imaginary axis but along the three two-phase lines. The model can be generalized to give rise to a tricritical point which is a new type of Yang-Lee edge singularity. Gibbs phase rule is generalized to apply to coexisting phases in the complex plane.Supported in part by the National Science Foundation under Grant No. DMR-81-06151.     

中等半径比反向旋转圆Couette系统流动稳定性的实验和数值研究

圆Couette系统已成为研究从层流转捩为湍流以及有限几何尺寸对图案选择影响的范例.本文以实验和计算机模拟方法研究中等半径比圆Couette系统的稳定性.考察同轴独立旋转圆筒之间的粘性不可压缩流体运动，推广了经典的Rayleigh离心不稳定性理论，导出稳定性判据，用来定量地确定稳定界限.实验采用了流动显示和激光散射技术.仪器有半径比η=0.699，形状比Γ=18.流动状态相图中的显著特征是新的首次失稳态：当外筒静止或反向旋转时，首次失稳出现具有非零方位角波数的螺旋涡流，在轴向和方位角方向为行进波，而并非与时间无关的Taylor涡.初步实验所得的转捩Reynolds数与数值计算结果一致.实验室和数值实验显示出半径比对图案形成和转捩序列的影响. 关键词：     

Continuum theory of retroviral capsids

We present a self-assembly phase diagram for the shape of retroviral capsids, based on continuum elasticity theory. The spontaneous curvature of the capsid proteins drives a weakly first-order transition from spherical to spherocylindrical shapes. The conical capsid shape which characterizes the HIV-1 retrovirus is never stable under unconstrained energy minimization. Only under conditions of fixed volume and/or fixed spanning length can the conical shape be a minimum energy structure. Our results indicate that, unlike the capsids of small viruses, retrovirus capsids are not uniquely determined by the molecular structure of the constituent proteins but depend in an essential way on physical constraints present during assembly.     

The analysis of a novel 3-D autonomous system and circuit implementation

This Letter presents a new three-dimensional autonomous system with four quadratic terms. The system with five equilibrium points has complex chaotic dynamics behaviors. It can generate many different single chaotic attractors and double coexisting chaotic attractors over a large range of parameters. We observe that these chaotic attractors were rarely reported in previous work. The complex dynamical behaviors of the system are further investigated by means of phase portraits, Lyapunov exponents spectrum, Lyapunov dimension, dissipativeness of system, bifurcation diagram and Poincaré map. The physical circuit experimental results of the chaotic attractors show agreement with numerical simulations. More importantly, the analysis of frequency spectrum shows that the novel system has a broad frequency bandwidth, which is very desirable for engineering applications such as secure communications.     

Phase diagram of optimal paths

We show that by choosing appropriate distributions of the randomness the search for optimal paths links diverse problems of disordered media, such as directed percolation, invasion percolation, and directed and nondirected spanning polymers. We also introduce a simple and efficient algorithm, which solves the d-dimensional model numerically in O(N(1+df/d)) steps, where df is the fractal dimension of the path. Using extensive simulations in two dimensions, we identify the phase boundaries of the directed polymer universality class. A new strong-disorder phase occurs where the optimum paths are self-affine with parameter-dependent scaling exponents. Furthermore, the phase diagram contains directed and nondirected percolation as well as the directed random walk models at specific points and lines.     

Effect of unequal injection rates and different hopping rates on asymmetric exclusion processes with junction

In this paper, the effects of unequal injection rates and different hopping rates on the asymmetric simple exclusion process (ASEP) with a 2-input 1-output junction are studied by using a simple mean-field approach and extensive computer simulations. The steady-state particle currents, the density profiles, and the phase diagrams are obtained. It is shown that with unequal injection rates and different hopping rates, the phase diagram structure is qualitatively changed. The theoretical calculations are in good agreement with Monte Carlo simulations.     

Quantum oscillations in confined and degenerate Fermi gases. II. The phase diagram and applications of half-vicinity model

For part I see DOI: 10.1016/j.physleta.2018.02.006. Size and density dependent quantum oscillations appear in Fermi gases under strong confinement and degeneracy conditions. We provide a universal recipe that explicitly separates oscillatory regime from non-oscillatory (stationary) one. A phase diagram representing stationary and oscillatory regimes on degeneracy-confinement space is proposed. Analytical expressions of phase transition interfaces are derived. The critical point, which separates entirely stationary and oscillatory regions, is determined and its dependencies on aspect ratios are examined for anisometric domains. Accuracy of the half-vicinity model and the phase diagram are verified through the quantum oscillations in electronic heat capacity and its ratio to entropy.     

A kinetic theory and benchmark predictions for polymer-dispersed, semi-flexible macromolecular rods or platelets

The goals of this paper are: to present a mean-field kinetic theory for the hydrodynamics of macromolecular high aspect ratio rods or platelets dispersed in a polymeric solvent; and, to apply the formalism to predict the impact due to a polymeric versus viscous solvent on the classical Onsager isotropic-nematic equilibrium phase diagram and on the monodomain response to imposed steady shear. The kinetic theory coupling between the nanoscale rods or platelets and the polymeric solvent is incorporated through a mean-field potential that reflects the enormous particle-polymer surface area and the particle-polymer interactions across this interfacial area. To determine predictions of this theory on the equilibrium and sheared monodomain phase diagrams, we present a reduction procedure which approximates the coupled Smoluchowski equations for the polymer chain probability distribution function (PDF) and the nano-particle orientational PDF in favor of a coupled system of equations for the rank 2 second-moment tensors for each PDF. The reduced model consists of an 11-dimensional dynamical system, which we solve using continuation software (AUTO) to predict the modified Onsager equilibrium phase diagram and the modified Doi-Hess shear phase diagram due to the physics of polymer-particle surface interactions.     

Phase diagrams of magnetic nanotubes

Analytical expressions for the total magnetic energy of two characteristic internal configurations of nanometric tubes are calculated. A magnetic phase diagram with respect to the aspect ratio of the tubes is obtained which allows a discussion about the possibility of getting ensembles of nanotubes with low coercive fields. A comparison with recently reported coercive fields of three different cobalt nanotube arrays agrees well with the phase diagram derived here.     

The Asymmetric Exclusion Process: Comparison of Update Procedures

The asymmetric exclusion process (ASEP) has attracted a lot of interest not only because of its many applications, e.g., in the context of the kinetics of biopolymerization and traffic flow theory, but also because it is a paradigmatic model for nonequilibrium systems. Here we study the ASEP for different types of updates, namely random-sequential, sequential, sublattice-parallel, and parallel. In order to compare the effects of the different update procedures on the properties of the stationary state, we use large-scale Monte Carlo simulations and analytical methods, especially the so-called matrix-product Ansatz (MPA). We present in detail the exact solution for the model with sublattice-parallel and sequential updates using the MPA. For the case of parallel update, which is important for applications like traffic flow theory, we determine the phase diagram, the current, and density profiles based on Monte Carlo simulations. We furthermore suggest an MPA for that case and derive the corresponding matrix algebra.     

Simulation of phase boundaries using constrained cell models

Despite impressive advances, precise simulation of fluid-fluid and fluid-solid phase transitions still remains a challenging task. The present work focuses on the determination of the phase diagram of a system of particles that interact through a pair potential, ?(r), which is of the form ?(r)?=?4?[(σ/r)(2n)?-?(σ/r)(n)] with n?=?12. The vapor-liquid phase diagram of this model is established from constant-pressure simulations and flat-histogram techniques. The properties of the solid phase are obtained from constant-pressure simulations using constrained cell models. In the constrained cell model, the simulation volume is divided into Wigner-Seitz cells and each particle is confined to moving in a single cell. The constrained cell model is a limiting case of a more general cell model which is constructed by adding a homogeneous external field that controls the relative stability of the fluid and the solid phase. Fluid-solid coexistence at a reduced temperature of 2 is established from constant-pressure simulations of the generalized cell model. The previous fluid-solid coexistence point is used as a reference point in the determination of the fluid-solid phase boundary through a thermodynamic integration type of technique based on histogram reweighting. Since the attractive interaction is of short range, the vapor-liquid transition is metastable against crystallization. In the present work, the phase diagram of the corresponding constrained cell model is also determined. The latter is found to contain a stable vapor-liquid critical point and a triple point.     

Operation and physics potential of Tevatron Run 2

We consider a lattice scalar field model with higher derivative terms in the action whose phase diagram contains a tricritical point which is also a triple point between the paramagnetic, ferromagnetic and antiferromagnetic phases. The continuum limit is defined by approching the tricritical point from the paramagnetic side. Contrary to the lattice tricritical g₆ϕ⁶ model we can do a perturbative computation in dimension four. The non-perturbative aspect of the theory relies on the dispersion relation which has the particular feature of having several minima similar to the propagator of lattice fermions. It is shown that this new model is perturbatively renormalizable and provides a non trivial mass spectrum. The positive norm Hilbert space and the unitarity of the time evolution operator in Minkowski space is established by means of the reflection positivity property.