Role of Interactions and Correlations on Collective Dynamics of Molecular Motors Along Parallel Filaments

Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest molecules of their filament while performing any mechanical work. These interactions modify the microscopic level properties of motor proteins. In this work, a new version of two-channel totally asymmetric simple exclusion process, that incorporates the intra-channel interactions in a thermodynamically consistent way, is proposed. As the existing approaches for multi-channel systems deviate from analyzing the combined effect of inter and intra-channel interactions, a new approach known as modified vertical cluster mean field is developed. The approach along with Monte Carlo simulations successfully encounters some correlations and computes the complex dynamic properties of the system. Role of symmetry of interactions and inter-channel coupling is observed on the phase diagrams, maximal particle current and its corresponding optimal interaction strength. Surprisingly, for all values of coupling rate and most of the interaction splittings, the optimal interaction strength corresponding to maximal current belongs to the case of weak repulsive interactions. Moreover, for weak interaction splittings and with an increase in the coupling rate, the optimal interaction strength tends towards the known experimental results. The effect of coupling as well as interaction energy is also measured for correlations. They are found to be short-range and weaker for repulsive and weak attractive interactions while they are long-range and stronger for large attractions.     

Molecular dynamics simulation of zirconia melting

The melting point for the tetragonal and cubic phases of zirconia (ZrO₂) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over the tetragonal phase at high temperatures, ReaxFF also gives approximately the correct melting point, around 2900 K, whereas the Lewis-Catlow estimate is above 6000 K.     

Equation of state of a Fermi gas in the BEC-BCS crossover: a quantum Monte Carlo study

We calculate the equation of state of a two-component Fermi gas with attractive short-range interspecies interactions using the fixed-node diffusion Monte Carlo method. The interaction strength is varied over a wide range by tuning the value a of the s-wave scattering length of the two-body potential. For a>0 and a smaller than the inverse Fermi wave vector our results show a molecular regime with repulsive interactions well described by the dimer-dimer scattering length a(m)=0.6a. The pair correlation functions of parallel and opposite spins are also discussed as a function of the interaction strength.     

Acetylene on Cu(111): imaging a molecular surface arrangement with a constantly rearranging tip

Acetylene on Cu(111) is investigated by scanning tunnelling microscopy (STM); a surface pattern previously derived from diffraction measurements can be validated, if the variation of the STM image transfer function through absorption of an acetylene molecule onto the tip apex is taken into account. Density functional theory simulations point to a balance between short-range repulsive interactions of acetylene/Cu(111) associated with surface stress and longer range attractive interactions as the origin of the ordering.     

Fluctuation-induced casimir forces in granular fluids

We numerically investigate the behavior of driven noncohesive granular media and find that two fixed large intruder particles, immersed in a sea of small particles, experience, in addition to a short-range depletion force, a long-range repulsive force. The observed long-range interaction is fluctuation-induced and we propose a mechanism similar to the Casimir effect that generates it: The hydrodynamic fluctuations are geometrically confined between the intruders, producing an unbalanced renormalized pressure. An estimation based on computing the possible Fourier modes explains the repulsive force and is in qualitative agreement with the simulations.     

An accurate and efficient method for treating aerodynamic interactions of cloud droplets

Motivated by a need to improve the representation of short-range interaction forces in hybrid direct numerical simulation of interacting cloud droplets, an efficient method for treating the aerodynamic interaction of two spherical particles settling under gravity is developed. An effort is made to ensure the accuracy of our method for any inter-particle separation by considering three separation ranges. The first is the long-range interaction where a multipole method is applied. After a decomposition into six simple configurations, explicit formulae for drag forces and torques are derived from an approximate Force–Torque–Stresslet (FTS) formulation. The FTS formulation is found to be accurate when the separation distance normalized by the average radius is larger than 5. The second range concerns the short-range interaction where the interaction force could be very large. Leading-order lubrication expansions are employed for this range and are found to be accurate when the normalized separation is less than about 0.01. Finally, for the intermediate range where no simple method is available, a third-order polynomial fitting is proposed to bridge the treatments for long-range and short-range interactions. After optimizing the precise form of polynomial fitting and matching locations, the force representation is found to be highly accurate when compared with the exact solution for Stokes flows. Using this method, collision efficiencies of cloud droplets sedimenting under gravity have been calculated. It is shown that the results of collision efficiency are in excellent agreement with results based on the exact Stokes flow solution. Collision efficiency results are also compared to previous results to further illustrate the accuracy of our calculations. The effects of particle rotation and the attractive van der Waals force on the collision efficiency are also studied. The efficient force representation developed here is more general than the usual lubrication expansion and thus can serve as a better approach to correct unresolved short-range interactions in particle-resolved simulations.     

Dynamic properties of Lennard-Jones fluids and liquid metals

The dependence of the dynamic properties of liquid metals and Lennard-Jones fluids on the characteristics of the interaction potentials is analyzed. Molecular-dynamics simulations of liquids in analogous conditions but assuming that their particles interact either through a Lennard-Jones or a liquid-metal potential were carried out. The Lennard-Jones potentials were chosen so that both the effective size of the particles and the depth of the potential well were very close to those of the liquid-metal potentials. In order to investigate the extent to which the dynamic properties of liquids depend on the short-range attractive interactions as well as on the softness of the potential cores, molecular-dynamics simulations of the same systems but assuming purely repulsive interactions with the same potential cores were also performed. The study includes both single-particle dynamic properties, such as the velocity autocorrelation functions, and collective dynamic properties, such as the intermediate scattering functions, the dynamic structure factors, the longitudinal and transverse current correlations, and the transport coefficients.     

Island nucleation in thin-film epitaxy: A first-principles investigation

We describe a theoretical study of the role of adsorbate interactions in island nucleation and growth, using Ag/Pt(111) heteroepitaxy as an example. From density-functional theory, we obtain the substrate-mediated Ag adatom pair interaction and we find that, past the short range, a repulsive ring is formed about the adatoms. The magnitude of the repulsion is comparable to the diffusion barrier. In kinetic Monte Carlo simulations, we find that the repulsive interactions lead to island densities over an order of magnitude larger than those predicted by nucleation theory and thus identify a severe limitation of its applicability.     

Theoretical investigation of high-pressure phase transitions in Mg1-xSrxO

The stability of Mg_1-xSr_xO solid solution has been analyzed using charge transfer interaction potential (CTIP) model as well as density functional theory-based ab initio approach with Perdew–Burke–Ernzerhof (PBE) type parameterized generalized gradient approximation. The present CTIP model consists of long-range part as modified coulomb interactions and charge transfer forces whereas short-range part includes the van der Waals as well as Hafemeister Flygare type overlap repulsive interactions effective up to next nearest neighbor ions. The present study finds that under the influence of pressure host binary oxides as well as their solid solutions undergo B1→B2 structural phase transition in the pressure range of 54–495 GPa. The variation of ground state properties and transition pressures have also been analyzed as a function of Sr composition. The observed results for the end point members are in agreement to their experimental counterparts and the deviations have been discussed in terms of interactions taken into consideration in two approaches.     

带凹槽的微通道中液滴运动数值模拟

运用改进的耗散粒子动力学方法模拟了液滴在由凹槽所构成的粗糙表面微通道内的运动行为.改进的耗散粒子动力学方法采用新近提出的一种短程排斥、长程吸引相互作用势能函数,从而可以模拟带有自由面的流体,如液滴等.模拟了新势能函数下液滴与固体壁面的静态接触角,并用2次多项式拟合了"接触角-a_wf/a_f"变化曲线.研究了液滴在带凹槽的微通道中运动时,微通道壁面浸润性、外场力、液滴温度对液滴流动特性的影响.研究表明壁面浸润性和外场力对液滴流动特性的影响较大,液滴温度对液滴流动特性的影响较小.研究结果对运用耗散粒子动力学方法模拟并分析微流体在复杂微通道的流动有一定的参考价值.     

Influence of surface affinity of planar walls on effective interaction between the wall and colloids

Using density functional theory, we investigate the effective interaction between a big colloid immersed in a sea of small colloids and a wall which has different affinity to the small colloids. Steele 10-4-3 potential is introduced to mimic both short-range repulsive and long-range attractive interactions between the wall and the small colloids. It is found that the surface affinity of the wall has a significant influence on the effective interaction. In the short-range repulsive case, the repulsion greatly enhances the big colloid-wall effective attraction, which sensitively depends on the concentration of small colloids, and is not sensitive to the repulsive strength. In the long-range attractive case, both the concentration of small colloids and the attractive strength have great effect on the effective interaction, and with an increase of the attractive strength, a strong repulsion may be induced when the big colloid is close to the wall. In low density limit of small colloids, the present results agree well with those of the Asakura and Oosawa(AO) approximation.     

Liquid–vapour transition of the long range Yukawa fluid

Two liquid state theories, the self-consistent Ornstein–Zernike equation (SCOZA) and the hierarchical reference theory (HRT) are shown, by comparison with Monte Carlo simulations, to perform extremely well in predicting the liquid–vapour coexistence of the hard-core Yukawa (HCY) fluid when the interaction is long range. The long range of the potential is treated in the simulations using both an Ewald sum and hyperspherical boundary conditions. In addition, we present an analytical optimized mean field theory which is exact in the limit of an infinitely long-range interaction. The work extends a previous one by C. Caccamo, G. Pellicane, D. Costa, D. Pini, and G. Stell, Phys. Rev. E 60, 5533 (1999) for short-range interactions.     

Geometry estimation of planar swarm patterns

Phenomena of coupled individuals or particles aggregating to form cohesive patterns are ubiquitous in nature and human society. Estimation of the pattern geometry is of interest in many cases. This Letter considers a planar swarm system consisting of finite particles with long-range attractive and short-range repulsive interactions. An analytical approach is presented to evaluate the relative distance of neighboring particles and the diameter of the swarm pattern. The method is based on a scale transformation on minimum interaction potential condition of the steady state of the system, and can give conditions determining distance between neighboring particles in the steady state pattern as well as the size of it, under certain distribution assumptions. Numerical simulations are also carried out to show effectiveness of the approach.     

Thermodynamics of pseudo-hard body mixtures

Thermodynamic properties of binary mixtures of hard spheres of various size and pseudo-hard bodies, mimicking the short-range non-additive repulsive interactions in realistic models of water, have been determined over the entire concentration range using standard NVT Monte Carlo simulations. Virial coefficients of the mixture have also been computed. Having no other theoretical tool currently available, a perturbed virial expansion is examined with respect to its potential to estimate/predict the properties of the mixture without resorting to any fitting of simulation data. The perturbed virial expansion is found to perform quite accurately for the mixtures containing larger spheres, whereas for small spheres dissolved in water the result is only qualitatively correct.     

Explicit propagators for a random walker and unidirectionality on linear chains

Explicit propagators are given for a diffusing particle (motor) moving on a linear chain of either infinity or finite length with reflecting ends. Each chain contains a number of thermally accessible barriers and/or potential wells (active sites). All particle interactions with its environment are considered to be short-range and are described by repulsive/attractive delta function potentials. By employing perturbation expansion, closed analytical expressions for the spatio-temporal evolution of the probability density function of the motor are derived, and are valid up to second order with respect to the expansion parameter u, which denotes the strength of interaction between motor and active sites. The mean displacement for two different chains is calculated indicating in both cases that the organization of the motion is done through the interplay of interaction intensities and their positions.     

Pressure Induced Phase Transition in Sn1−xMn x Te*

We have investigated the pressure induced phase transition (B1 M B2) and other related properties of semimagnetic semiconductor (SMS) Sn 1 m x Mn x Te (0 h x h 0.70), using the three-body potential (TBP) approach. The lattice energy, according to this approach, consists of the long range Coulomb as well as three-body interaction and short range (SR) van der Waals (vdW) due to dipole-dipole interactions, and overlap repulsive interactions, effective up to the next nearest neighbours. The calculated phase transition pressure shows linear decrease as a function of Mn composition ( x ).     

Free cooling phase-diagram of hard-spheres with short- and long-range interactions

We study the stability, the clustering and the phase-diagram of free cooling granular gases. The systems consist of mono-disperse particles with additional non-contact (long-range) interactions, and are simulated here by the event-driven molecular dynamics algorithm with discrete (short-range shoulders or wells) potentials (in both 2D and 3D). Astonishingly good agreement is found with a mean field theory, where only the energy dissipation term is modified to account for both repulsive or attractive non-contact interactions. Attractive potentials enhance cooling and structure formation (clustering), whereas repulsive potentials reduce it, as intuition suggests. The system evolution is controlled by a single parameter: the non-contact potential strength scaled by the fluctuation kinetic energy (granular temperature). When this is small, as expected, the classical homogeneous cooling state is found. However, if the effective dissipation is strong enough, structure formation proceeds, before (in the repulsive case) non-contact forces get strong enough to undo the clustering (due to the ongoing dissipation of granular temperature). For both repulsive and attractive potentials, in the homogeneous regime, the cooling shows a universal behaviour when the (inverse) control parameter is used as evolution variable instead of time. The transition to a non-homogeneous regime, as predicted by stability analysis, is affected by both dissipation and potential strength. This can be cast into a phase diagram where the system changes with time, which leaves open many challenges for future research.     

Long range interactions between micro spheres and alloy surfaces in water changed by ion implantation

Ion implantation was adopted to change the surface potentials of samples made of aluminum bronze. The interactions between the SiO₂ particles and the sample surfaces in water were changed from attractive to repulsive. According to the surface element integration method, this interaction was simulated and the electrostatic double layer force was considered to be the dominated factor. This long range repulsive interaction was proved to have effect on preventing micro particles approaching the alloy surface by the fluorescent particles adhesion experiment, and the technology of ion implantation may have potential applications in adhesion resistance and abrasion reduction for alloys running in water.     

基于范德瓦尔斯表面张力模式液滴撞击疏水壁面过程的研究

液滴撞击疏水壁面过程的研究在介观流体力学和微流体作用材料科学的研究中具有重要的理论意义和工程价值. 论文在SPH方法中引入范德瓦尔斯状态方程处理液滴表面张力, 考虑流体粒子之间远程吸引, 近程排斥的内部作用力, 提出了流体粒子与疏水壁面粒子间势能函数与表面张力相结合的作用模式. 通过模拟真空条件下两个静止的等体积液滴相互融合的过程, 验证了计算模式在模拟液滴的表面张力中的有效性. 采用该模式模拟的液滴撞击疏水壁面过程, 不仅能够有效地模拟液滴撞击壁面后的变形过程, 而且清晰地模拟出液滴的回弹、腾空以及二次撞壁现象的完整过程. 模拟结果与液滴撞击疏水壁面的实验结果以及VOF模拟结果符合较好, 表明本文所提出的表面张力和疏水壁面作用力处理模式对模拟液滴撞壁过程具有实际应用价值.     

Dynamics of thin free liquid films stabilized with ionic surfactants

To study the dynamics of free liquid films which are stabilized with ionic surfactants, an electrohydrodynamic theory is developed. The long-range interaction forces, namely the repulsive force arising from the overlap of diffuse electric double layers and the attractive Van der Waals-London force, are described by the Maxwell stress tensor with its related field equations and the Van der Waals potential. The short-range surface force has a normal Laplace component and a tangential surface tension gradient component. The total set of first-order equations and their boundary conditions, which describes the capillary waves on the surfaces and the induced flow motion in the film, has been solved. The dispersion relation for the “squeezing mode” is obtained. The cases of no-slip condition and the long-wavelength limit have been studied in more detail. The testability of the dispersion relation using laser beat spectroscopy is reported.