The combined hydrodynamic and thermodynamic effects of immobilized proteins on the diffusion of mobile transmembrane proteins

2019 ◽  
Vol 877 ◽  
pp. 648-681
Author(s):  
Rohit R. Singh ◽  
Ashok S. Sangani ◽  
Susan Daniel ◽  
Donald L. Koch
Keyword(s):  
Percolation Threshold ◽  
Stokes Equations ◽  
Volume Fraction ◽  
Transmembrane Proteins ◽  
Hydrodynamic Interactions ◽  
Steric Effects ◽  
Two Dimensional ◽  
Long Time ◽  
Short Time ◽  
Mobile Protein

The plasma membranes of cells are thin viscous sheets in which some transmembrane proteins have two-dimensional mobility and some are immobilized. Previous studies have shown that immobile proteins retard the short-time diffusivity of mobile particles through hydrodynamic interactions and that steric effects of immobile proteins reduce the long-time diffusivity in a model that neglects hydrodynamic interactions. We present a rigorous derivation of the long-time diffusivity of a single mobile protein interacting hydrodynamically and thermodynamically with an array of immobile proteins subject to periodic boundary conditions. This method is based on a finite element method (FEM) solution of the probability density of the mobile protein diffusing with a position-dependent mobility determined through a multipole solution of Stokes equations. The simulated long-time diffusivity in square arrays decreases as the spacing in the array approaches the particle size in a manner consistent with a lubrication analysis. In random arrays, steric effects lead to a percolation threshold volume fraction above which long-time diffusion is arrested. The FEM/multipole approach is used to compute the long-time diffusivity far away from this threshold. An approximate analysis of mobile protein diffusion through a network of pores connected by bonds with resistances determined by the FEM/multipole calculations is then used to explore higher immobile area fractions and to evaluate the finite simulation cell size scaling behaviour of diffusion near the percolation threshold. Surprisingly, the ratio of the long-time diffusivity to the spatially averaged short-time diffusivity in these two-dimensional fixed arrays is higher in the presence of hydrodynamic interactions than in their absence. Finally, the implications of this work are discussed, including the possibility of using the methods developed here to investigate more complex diffusive phenomena observed in cell membranes.

scholarly journals Natural convection melting of nano-enhanced phase change material in a cavity with finned copper profile

2018 ◽  
Vol 240 ◽  
pp. 01006 ◽  
Author(s):  
Nadezhda Bondareva ◽  
Mikhail Sheremet
Keyword(s):  
Heat Transfer ◽  
Natural Convection ◽  
Stokes Equations ◽  
Volume Fraction ◽  
Melting Process ◽  
Navier Stokes ◽  
Two Dimensional ◽  
Navier Stokes Equations ◽  
Dimensional Approximation ◽  
Change Material

Present study is devoted to numerical simulation of heat and mass transfer inside a cooper profile filled with paraffin enhanced with Al2O3 nanoparticles. This profile is heated by the heat-generating element of constant volumetric heat flux. Two-dimensional approximation of melting process is described by the Navier-Stokes equations in non-dimensional variables such as stream function, vorticity and temperature. The enthalpy formulation has been used for description of the heat transfer. The influence of volume fraction of nanoparticles and intensity of heat generation on melting process and natural convection in liquid phase has been studied.

Three-dimensional impulsive vortex formation from slender orifices

2011 ◽  
Vol 666 ◽  
pp. 506-520 ◽  
Author(s):  
F. DOMENICHINI
Keyword(s):  
Stokes Equations ◽  
Intermediate Phase ◽  
Vortex Formation ◽  
Three Dimensional ◽  
Navier Stokes ◽  
Two Dimensional ◽  
Navier Stokes Equations ◽  
Vortex Ring Formation ◽  
Long Time ◽  
Definition Of

The vortex formation behind an orifice is a widely investigated phenomenon, which has been recently studied in several problems of biological relevance. In the case of a circular opening, several works in the literature have shown the existence of a limiting process for vortex ring formation that leads to the concept of critical formation time. In the different geometric arrangement of a planar flow, which corresponds to an opening with straight edges, it has been recently outlined that such a concept does not apply. This discrepancy opens the question about the presence of limiting conditions when apertures with irregular shape are considered. In this paper, the three-dimensional vortex formation due to the impulsively started flow through slender openings is studied with the numerical solution of the Navier–Stokes equations, at values of the Reynolds number that allow the comparison with previous two-dimensional findings. The analysis of the three-dimensional results reveals the two-dimensional nature of the early vortex formation phase. During an intermediate phase, the flow evolution appears to be driven by the local curvature of the orifice edge, and the time scale of the phenomena exhibits a surprisingly good agreement with those found in axisymmetric problems with the same curvature. The long-time evolution shows the complete development of the three-dimensional vorticity dynamics, which does not allow the definition of further unifying concepts.

scholarly journals Metastability and rapid convergence to quasi-stationary bar states for the two-dimensional Navier–Stokes equations

2013 ◽  
Vol 143 (5) ◽  
pp. 905-927 ◽  
Author(s):  
Margaret Beck ◽  
C. Eugene Wayne
Keyword(s):  
Decay Rate ◽  
Stokes Equations ◽  
Navier Stokes ◽  
Two Dimensional ◽  
Navier Stokes Equation ◽  
Navier Stokes Equations ◽  
Optimal Decay ◽  
Optimal Decay Rate ◽  
Long Time ◽  
High Reynolds

Quasi-stationary, or metastable, states play an important role in two-dimensional turbulent fluid flows, where they often emerge on timescales much shorter than the viscous timescale, and then dominate the dynamics for very long time intervals. In this paper we propose a dynamical systems explanation of the metastability of an explicit family of solutions, referred to as bar states, of the two-dimensional incompressible Navier–Stokes equation on the torus. These states are physically relevant because they are associated with certain maximum entropy solutions of the Euler equations, and they have been observed as one type of metastable state in numerical studies of two-dimensional turbulence. For small viscosity (high Reynolds number), these states are quasi-stationary in the sense that they decay on the slow, viscous timescale. Linearization about these states leads to a time-dependent operator. We show that if we approximate this operator by dropping a higher-order, non-local term, it produces a decay rate much faster than the viscous decay rate. We also provide numerical evidence that the same result holds for the full linear operator, and that our theoretical results give the optimal decay rate in this setting.

scholarly journals Well-Posedness and Long-Time Behavior of Solutions for Two-Dimensional Navier-Stokes Equations with Infinite Delay and General Hereditary Memory

2021 ◽  
Author(s):  
Yasi Zheng ◽  
Wenjun Liu ◽  
Yadong Liu
Keyword(s):  
Stokes Equations ◽  
Infinite Delay ◽  
Navier Stokes ◽  
Time Behavior ◽  
Two Dimensional ◽  
Navier Stokes Equations ◽  
Bounded Absorbing Set ◽  
Long Time ◽  
The One ◽  
Class Of Functions

We address the dynamics of two-dimensional Navier-Stokes models with infinite delay and hereditary memory, whose kernels are a much larger class of functions than the one considered in the literature, on a bounded domain. We prove the existence and uniqueness of weak solutions by means of Faedo-Galerkin method. Moreover, we establish the existence of global attractor for the system with the existence of a bounded absorbing set and asymptotic compact property.

EARLY TIME PROPERTIES OF TIME EVOLUTION IN TWO-DIMENSIONAL SUBSPACE AND CP VIOLATION PROBLEM

1993 ◽  
Vol 08 (21) ◽  
pp. 3721-3745 ◽  
Author(s):  
K. URBANOWSKI
Keyword(s):  
Time Evolution ◽  
Early Time ◽  
Dimensional Subspace ◽  
Effective Hamiltonian ◽  
Two Dimensional ◽  
Matrix Elements ◽  
The Matrix ◽  
Long Time ◽  
Time Region ◽  
Short Time

Approximate formulae are given for the effective Hamiltonian H||(t) governing the time evolution in a subspace ℋ|| of the state space ℋ. The properties of matrix elements of H||(t) and the eigenvalue problem for H||(t) are discussed in the case of two-dimensional ℋ||. The eigenvectors of H||(t) for the short time region are found to be different from those for the long time region. The decay law of particles described by the eigenvectors of H||(t) is shown to have the form of the exponential function multiplied by some time-independent factor, equal to 1 only in the case of the [Formula: see text]-invariant theory. Some general properties of the matrix elements of H||(t) are tested in the Lee model.

scholarly journals Unsteady hybrid nanoparticle-mediated magneto-hemodynamics and heat transfer through an overlapped stenotic artery: Biomedical drug delivery simulation

2021 ◽  
pp. 095441192110260
Author(s):  
Jayati Tripathi ◽  
Buddakkagari Vasu ◽  
Osman Anwar Bég ◽  
Rama Subba Reddy Gorla
Keyword(s):  
Drug Delivery ◽  
Blood Flow ◽  
Stokes Equations ◽  
Volume Fraction ◽  
Hybrid Nanoparticles ◽  
Navier Stokes ◽  
Hybrid Nanofluid ◽  
Two Dimensional ◽  
Governing Equations ◽  
Navier Stokes Equations

Two-dimensional laminar hemodynamics through a diseased artery featuring an overlapped stenosis was simulated theoretically and computationally. This study presented a mathematical model for the unsteady blood flow with hybrid biocompatible nanoparticles (Silver and Gold) inspired by drug delivery applications. A modified Tiwari-Das volume fraction model was adopted for nanoscale effects. Motivated by the magneto-hemodynamics effects, a uniform magnetic field was applied in the radial direction to the blood flow. For realistic blood behavior, Reynolds’ viscosity model was applied in the formulation to represent the temperature dependency of blood. Fourier’s heat conduction law was assumed and heat generation effects were included. Therefore, the governing equations were an extension of the Navier–Stokes equations with magneto-hydrodynamic body force included. The two-dimensional governing equations were transformed and normalized with appropriate variables, and the mild stenotic approximation was implemented. The strongly nonlinear nature of the resulting dimensionless boundary value problem required a robust numerical method, and therefore the FTCS algorithm was deployed. Validation of solutions for the particular case of constant viscosity and non-magnetic blood flow was included. Using clinically realistic hemodynamic data, comprehensive solutions were presented for silver, and silver-gold hybrid mediated blood flow. A comparison between silver and hybrid nanofluid was also included, emphasizing the use of hybrid nanoparticles for minimizing the hemodynamics. Enhancement in magnetic parameter decelerated the axial blood flow in stenotic region. Colored streamline plots for blood, silver nano-doped blood, and hybrid nano-doped blood were also presented. The simulations were relevant to the diffusion of nano-drugs in magnetic targeted treatment of stenosed arterial diseases.

Self-diffusion in sheared suspensions

1996 ◽  
Vol 312 ◽  
pp. 223-252 ◽  
Author(s):  
Jeffrey F. Morris ◽  
John F. Brady
Keyword(s):  
Volume Fraction ◽  
Diffusion Tensor ◽  
Hard Spheres ◽  
Strain Tensor ◽  
The Self ◽  
Hydrodynamic Interactions ◽  
Spherical Particles ◽  
Tagged Particle ◽  
Self Diffusion ◽  
Long Time

Self-diffusion in a suspension of spherical particles in steady linear shear flow is investigated by following the time evolution of the correlation of number density fluctuations. Expressions are presented for the evaluation of the self-diffusivity in a suspension which is either raacroscopically quiescent or in linear flow at arbitrary Peclet number $Pe = \dot{\gamma}a^2/2D$, where $\dot{\gamma}$ is the shear rate, a is the particle radius, and D = kBT/6πa is the diffusion coefficient of an isolated particle. Here, kB is Boltzmann's constant, T is the absolute temperature, and η is the viscosity of the suspending fluid. The short-time self-diffusion tensor is given by kBT times the microstructural average of the hydrodynamic mobility of a particle, and depends on the volume fraction $\phi = \frac{4}{3}\pi a^3n$ and Pe only when hydrodynamic interactions are considered. As a tagged particle moves through the suspension, it perturbs the average microstructure, and the long-time self-diffusion tensor, D∞s, is given by the sum of D0s and the correlation of the flux of a tagged particle with this perturbation. In a flowing suspension both D0s and D∞ are anisotropic, in general, with the anisotropy of D0s due solely to that of the steady microstructure. The influence of flow upon D∞s is more involved, having three parts: the first is due to the non-equilibrium microstructure, the second is due to the perturbation to the microstructure caused by the motion of a tagged particle, and the third is by providing a mechanism for diffusion that is absent in a quiescent suspension through correlation of hydrodynamic velocity fluctuations.The self-diffusivity in a simply sheared suspension of identical hard spheres is determined to O(øPe3/2) for Pe ≤ 1 and ø ≤ 1, both with and without hydro-dynamic interactions between the particles. The leading dependence upon flow of D0s is 0.22DøPeÊ, where Ê is the rate-of-strain tensor made dimensionless with $\dot{\gamma}$. Regardless of whether or not the particles interact hydrodynamically, flow influences D∞s at O(øPe) and O(øPe3/2). In the absence of hydrodynamics, the leading correction is proportional to øPeDÊ. The correction of O(øPe3/2), which results from a singular advection-diffusion problem, is proportional, in the absence of hydrodynamic interactions, to øPe3/2DI; when hydrodynamics are included, the correction is given by two terms, one proportional to Ê, and the second a non-isotropic tensor.At high ø a scaling theory based on the approach of Brady (1994) is used to approximate D∞s. For weak flows the long-time self-diffusivity factors into the product of the long-time self-diffusivity in the absence of flow and a non-dimensional function of $\bar{P}e = \dot{\gamma}a^2/2D^s_0(\phi)$. At small $\bar{P}e$ the dependence on $\bar{P}e$ is the same as at low ø.

The effect of hydrodynamic interactions on the tracer and gradient diffusion of integral membrane proteins in lipid bilayers

1994 ◽  
Vol 258 ◽  
pp. 167-190 ◽  
Author(s):  
Stuart J. Bussell ◽  
Daniel A. Hammer ◽  
Donald L. Koch
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Stokes Equations ◽  
Thin Sheet ◽  
Three Dimensional ◽  
Integral Membrane Proteins ◽  
Area Fraction ◽  
Hydrodynamic Interactions ◽  
Low Viscosity ◽  
Long Time

Biological membranes can be considered two-dimensional fluids with suspended integral membrane proteins (IMPs). We have calculated the effect of hydrodynamic interactions on the various diffusion coefficients of IMPs in lipid bilayers. The IMPs are modelled as hard cylinders of radius a immersed in a thin sheet of viscosity μ and thickness h bounded by a fluid of low viscosity μ′. We have ensemble averaged the N-body Stokes equations to the pair level and have renormalized them following the methods of Batchelor (1972) and Hinch (1977). The lengthscale for the hydrodynamic interactions is λa = μh / μ′, Which is O (100a), and the slow decay of the interactions introduces new features in the renormalizations compared to the analogous analyses for three-dimensional suspensions of spheres.We have calculated the asymptotic limits for the short- and long-time tracer diffusivities, Ds and Dl, respectively, and for the gradient diffusivity, Dg, for ϕ [Lt ] 1 and λ [Gt ] 1, where ϕ is the IMP area fraction and λ = μh / (μ′a). The diffusivities are \begin{eqnarray*} D_s/D_0 &=& 1-2\phi[1-(1+\ln (2)-9/32)/(\ln(\lambda)-\gamma)], D_l/D_0 &=& D_s/D_0 - 0.07/(\ln(\lambda)-\gamma), D_g/D_0 &=& 1+\phi[-7+(6\ln(2)+7/16+0.37)/(\ln(\lambda)-\gamma)], \end{eqnarray*} where D0 is the diffusivity in the limit of zero area fraction, and γ = 0.577216 is Euler's constant. The results for Dl and Ds differ only slightly. The decrease in Dg/Do as ϕ increases contrasts with the result for spheres for which Dg/Do > 1.

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