Effect of surface roughness on slip flows in hydrophobic and hydrophilic microchannels by molecular dynamics simulation

The influences of surface roughness on the boundary conditions for a simple fluid flowing over hydrophobic and hydrophilic surfaces are investigated by molecular dynamics (MD) simulation. The degree of slip is found to decrease with surface roughness for both the hydrophobic and hydrophilic surfaces. The flow rates measured in hydrophobic channels are larger than those in hydrophilic channels with the presence of slip velocity at the walls. The simulation results of flow rate are correlated with the theoretical predictions according to the assumption of no slip boundary condition. The slip boundary condition also strongly depends on the shear rate near the surface. For hydrophobic surfaces, apparent fluid slips are observed on smooth and rough surfaces. For simple fluids flowing over a hydrophobic surface, the slip length increases linearly with shear rate for both the smooth and rough surfaces. Alternately, the slip length has a power law dependence on the shear rate for the cases of hydrophilic surfaces. It is observed that there is a no-slip boundary condition only when shear rate is low, and partial slip occurs when it exceeds a critical level.     

On the Atomic Velocities in Molecular and Langevin Dynamics Simulations of Soft-Sphere Systems

Abstract

Time dependent probability distributions of the changes of direction of atomic velocities are considered in order to examine in detail the shape of the trajectories obtained through molecular simulations. We have analysed the atomic motions obtained from molecular dynamics simulations of soft-sphere systems at three very different states, i.e. a dilute fluid, a liquid at high density, and a solid. The methodology has also been used to check the reliability of the velocity evolution obtained when it is assumed that a single particle obeys the generalized Langevin equation and the effect of the other particles is represented by friction and random forces.     

3-D numerical simulation of blood flow through models of the human aorta

A Spiral Computerized Tomography (CT) scan of the aorta were obtained from a single subject and three model variations were examined. Computational fluid dynamics modeling of all three models showed variations in the velocity contours along the aortic arch with differences in the boundary layer growth and recirculation regions. Further down-stream, all three models showed very similar velocity profiles during maximum velocity with differences occurring in the decelerating part of the pulse. Flow patterns obtained from transient 3-D computational fluid dynamics are influenced by different reconstruction methods and the pulsatility of the flow. Caution is required when analyzing models based on CT scans.     

Investigating the effects of wettability and gaseous nanobubbles on roughened wall–fluid interface using molecular dynamics simulation

This paper reports on the use of molecular dynamics (MD) simulation to investigate the coupling effects of wettability, surface roughness and interfacial nanobubbles (INBs) on wall–fluid interfaces. The fluid properties close to the wall–fluid interface, such as potential energy, density, diffusion coefficients of fluid molecules and effective slip length are simulated. In the cases without surface nanobubbles, regions with lower potential energy have a higher probability of hosting water molecules. The local translational and rotational diffusion coefficients of water within the cavities are strongly influenced by wettability but largely unaffected by hydrodynamic effects. In cases where INBs exist, variations in wettability result in distinctly different argon morphologies. Argon nanobubbles form a convex shape on Wenzel-like interfaces but a shallow concave shape on Cassie-like interfaces. The phenomenon of water molecules invading grooves tends to occur on Wenzel-like interfaces; however, this depends largely on the morphology of the grooves. The high mobility and high density of argon molecules indicate that the state of the argon molecules within the grooves may require further investigation. Our results also show that the effective slip length is significantly influenced by wall–fluid wettability as well as the morphology of INBs.     

Peripheral-layer viscosity and microstructural effects on the capillary-tissue fluid exchange

A theoretical investigation of capillary-tissue fluid exchange has been studied including the characteristics and influence of the boundaries and media through which the fluid flows. Filtration from a cylindrical capillary into the concentrically surrounding tissue space and flow from a capillary into the tissue across a thin membrane are analyzed in detail. In has been observed that the filtration efficiency of the functional unit decreases as the viscosity of the peripheral layer increases. Contrary to the results of Apelblat [17], the slip velocity at the porous boundary plays a dominant role in filtration efficiency. It has also been noticed that the filtration efficiency decreases as the slip velocity at the porous boundary increases.     

Peristaltic motion of Phan–Thien–Tanner fluid in the presence of slip condition

This investigation considers the peristaltic flow of a Phan–Thien–Tanner fluid in the presence of slip condition and induced magnetic field. By use of the long wavelength and low Reynolds number approximations, closed form series solutions for stream function, pressure gradient, magnetic force function, axial induced magnetic field, and current density were obtained. The pressure gradient and frictional forces per wavelength were computed by numerical integration. The velocity slip condition in terms of shear stress is taken into account. Graphical results show the comparison between no-slip and viscous fluid cases. Pumping and trapping phenomena are discussed.     

Simulating nanoscale functional motions of biomolecules

We are describing efficient dynamics simulation methods for the characterization of functional motion of biomolecules on the nanometer scale. Multivariate statistical methods are widely used to extract and enhance functional collective motions from molecular dynamics (MD) simulations. A dimension reduction in MD is often realized through a principal component analysis (PCA) or a singular value decomposition (SVD) of the trajectory. Normal mode analysis (NMA) is a related collective coordinate space approach, which involves the decomposition of the motion into vibration modes based on an elastic model. Using the myosin motor protein as an example we describe a hybrid technique termed amplified collective motions (ACM) that enhances sampling of conformational space through a combination of normal modes with atomic level MD. Unfortunately, the forced orthogonalization of modes in collective coordinate space leads to complex dependencies that are not necessarily consistent with the symmetry of biological macromolecules and assemblies. In many biological molecules, such as HIV-1 protease, reflective or rotational symmetries are present that are broken using standard orthogonal basis functions. We present a method to compute the plane of reflective symmetry or the axis of rotational symmetry from the trajectory frames. Moreover, we develop an SVD that best approximates the given trajectory while respecting the symmetry. Finally, we describe a local feature analysis (LFA) to construct a topographic representation of functional dynamics in terms of local features. The LFA representations are low-dimensional, and provide a reduced basis set for collective motions, but unlike global collective modes they are sparsely distributed and spatially localized. This yields a more reliable assignment of essential dynamics modes across different MD time windows.     

Characterization of load-length-velocity relationships of nine different skeletal muscles

A three-dimensional characterization of muscle load, length and velocity was obtained from nine muscles in the cat's hind limb through contractions where the muscles shortened against inertial-gravitational loads. A model based on the load-length characteristic and second-order dynamics describes shortening velocity related to load and length under these conditions. We conclude that this model describes well contraction velocity as function of length and load under inertial-gravitational load conditions, with correlation coefficients higher than 0.9 in most of the tested muscles.     

Hydrodynamic theory of swimming of flagellated microorganisms.

A theory of the type commonly used in polymer hydrodynamics is developed to calculate swimming properties of flagellated microorganisms. The overall shape of the particle is modeled as an array of spherical beads which act, at the same time, as frictional elements. The fluid velocity field is obtained as a function of the forces acting at each bead through Oseen-type, hydrodynamic interaction tensors. From the force and torque equilibrium conditions, such quantities as swimming velocity, angular velocity, and efficiency can be calculated. Application is made to a spherical body propelled by a helical flagellum. A recent theory by Lighthill, and earlier formulations based on tangential and normal frictional coefficients of a curved cylinder, CT and CN, are analyzed along with our theory. Although all the theories predict similar qualitative characteristics, such as optimal efficiency and the effect of fluid viscosity, they lead to rather different numerical values. In agreement with Lighthill, we found the formalisms based on CN and CT coefficients to be somewhat inaccurate, and head-flagellum interactions are shown to play an important role.     

A theoretical description of blood flow through the mitral orifice

A nonlinear differential equation describing the Doppler velocity profile for blood flow through the mitral valve has been derived. This equation is based on fluid dynamics and a simple, but comprehensive model of atrial and ventricular mechanics. A numerical solution to the equation is described and provides excellent agreement with Doppler velocity curves obtained clinically. One important result of the theory is that in patients with mitral stenosis, the slope of the clinically observed straight-line descent of the velocity profile is proportional to the mitral orifice area and inversely proportional to the atrioventricular compliance.     

Examination of nanoflow in rectangular slits

This paper presents simulations of 3D nanoscale flow in rectangular channel with molecular dynamics simulation method. Rectangular cross section is a frequently encountered geometric shape for nanoscale flow problems. For a given cross sectional height h, we change the width w of the rectangular cross section and analyze the influence of w/h on the flow characteristics. The distributions of density, temperature, boundary slip and flow velocity inside the rectangular cross section are investigated in detail. Liquid argon material and Lennard-Jones potential are used in the simulations. The simulation results are also compared with Navier–Stokes solutions for rectangular channel flows.     

Crossover from picosecond collective to single particle dynamics defines the mechanism of lateral lipid diffusion

It has been widely accepted that the thermally excited motions of the molecules in a cell membrane is the prerequisite for a cell to carry its biological functions. On the other hand, the detailed mapping of the ultrafast picosecond single-molecule and the collective lipid dynamics in a cell membrane remains rather elusive. Here, we report all-atom molecular dynamics simulations of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer over a wide range of temperature. We elucidate a molecular mechanism underlying the lateral lipid diffusion in a cell membrane across the gel, rippled, and liquid phases using an analysis of the longitudinal and transverse current correlation spectra, the velocity auto-correlation functions, and the molecules mean square displacements. The molecular mechanism is based on the anomalous ultrafast vibrational properties of lipid molecules at the viscous-to-elastic crossover. The macroscopic lipid diffusion coefficients predicted by the proposed diffusion model are in a good agreement with experimentally observed values. Furthermore, we unveil the role of water confined at the water-lipid interface in triggering collective vibrations in a lipid bilayer.     

Effect of various surface conditions on nanochannel flows past permeable walls

In this paper, effects of surface conditions on the gas flow in nanochannels with permeable walls have been investigated by molecular dynamics simulations. The hydrodynamic characteristics of the gas flow in nanochannels, including the density distributions, slip length and boundary friction coefficient, have been significantly influenced by the molecular interactions between gas molecules and wall atoms. The density layering phenomena are observed at the fluid–wall interface under a strong fluid–wall interaction (FWI). Particularly, there is a peak of the gas density on the permeable surface where the gas density is increased and about 3 times larger than the bulk one under the strong FWI. It indicates a strong non-continuum density distribution on the permeable surface and the step down in density from nanopores to the bulk region. On the other hand, the nanoscale vortices are produced in the nanopores. Moreover, the mass flux of gas flow in nanopores is reduced, and the hydrodynamic boundary has been shifted above the permeable surface further under the weak FWI. Slip characteristics on the permeable surface under various conditions are explored. It has been found that the slip length on the permeable surface may vary as a logarithmic function with the molecular mean free path. Apparently, the skin friction on the permeable surface is affected by the velocity slip. These results are significant in the understanding of nanoscale hydrodynamics.     

Dynamical clustering of red blood cells in capillary vessels

We have modeled the dynamics of a 3-D system consisting of red blood cells (RBCs), plasma and capillary walls using a discrete-particle approach. The blood cells and capillary walls are composed of a mesh of particles interacting with harmonic forces between nearest neighbors. We employ classical mechanics to mimic the elastic properties of RBCs with a biconcave disk composed of a mesh of spring-like particles. The fluid particle method allows for modeling the plasma as a particle ensemble, where each particle represents a collective unit of fluid, which is defined by its mass, moment of inertia, translational and angular momenta. Realistic behavior of blood cells is modeled by considering RBCs and plasma flowing through capillaries of various shapes. Three types of vessels are employed: a pipe with a choking point, a curved vessel and bifurcating capillaries. There is a strong tendency to produce RBC clusters in capillaries. The choking points and other irregularities in geometry influence both the flow and RBC shapes, considerably increasing the clotting effect. We also discuss other clotting factors coming from the physical properties of blood, such as the viscosity of the plasma and the elasticity of the RBCs. Modeling has been carried out with adequate resolution by using 1 to 10 million particles. Discrete particle simulations open a new pathway for modeling the dynamics of complex, viscoelastic fluids at the microscale, where both liquid and solid phases are treated with discrete particles. Figure A snapshot from fluid particle simulation of RBCs flowing along a curved capillary. The red color corresponds to the highest velocity. We can observe aggregation of RBCs at places with the most stagnant plasma flow.     

Investigation of interfacial mechanical properties of graphene-polymer nanocomposites

A series of graphene (GR) pull-out simulations based on molecular dynamics (MD) were carried out to investigate the interfacial mechanical properties between GR and a polymer matrix (polyethylene: PE). The effects of pull-out velocity, number of vacancy defect in GR and temperature on the interfacial mechanical properties of a GR/PE nanocomposite system were explored. The obtained results showed that the pull-out velocity and the temperature have significant influences on the interfacial mechanical properties for a perfect GR. Moderate vacancy defects in GR can effectively enhance the interfacial mechanical properties in GR-based polymer nanocomposites.     

Influence of enzymatic reactions on blood coagulation autowave

A model of blood coagulation has been investigated. The model includes 25 “reaction-diffusion” equations describing the space-time dynamics of distribution of blood coagulation factor concentrations. The one-dimensional statement of the problem is considered. The autowave velocity has been estimated based on the spatial distribution of blood coagulation factors obtained by numerical calculation of the problem. The dependence of the autowave velocity on diffusion coefficients of prothrombin, AT-III, thrombin, and thrombin bound to α²-macroglobulin is estimated.     

Heat Transfer Analysis for Stationary Boundary Layer Slip Flow of a Power-Law Fluid in a Darcy Porous Medium with Plate Suction/Injection

In this paper, we investigate the slip effects on the boundary layer flow and heat transfer characteristics of a power-law fluid past a porous flat plate embedded in the Darcy type porous medium. The nonlinear coupled system of partial differential equations governing the flow and heat transfer of a power-law fluid is transformed into a system of nonlinear coupled ordinary differential equations by applying a suitable similarity transformation. The resulting system of ordinary differential equations is solved numerically using Matlab bvp4c solver. Numerical results are presented in the form of graphs and the effects of the power-law index, velocity and thermal slip parameters, permeability parameter, suction/injection parameter on the velocity and temperature profiles are examined.     

Interaction parameters between carbon nanotubes and water in Dissipative Particle Dynamics

Flow of water past an array of single-walled carbon nanotubes (SWNTs) is simulated in this work to determine the interaction parameters of carbon nanotubes (CNTs) and water using Dissipative Particle Dynamics (DPD). For this flow configuration, results from molecular dynamics simulations by Walther et al. are available and can be used for validation (Phys. Rev. E, 2004, 062201). The hydrodynamic properties for SWNT (32, 0) with diameter of 2.5 nm were determined in different Reynolds number flows. A set of appropriate DPD parameters was found so that the drag coefficients of the CNT agreed well with the Stokes–Oseen analytical solution and the fluid slip length on the CNT wall was comparable with the Walther et al. results. It was also found that it is feasible to apply these parameters in longer length and time scales by increasing the number of water molecules grouped into each DPD bead and still maintain the hydrodynamic properties of CNTs as well as their hydrophobic surface character.     

Protein Collective Motions Coupled to Ligand Migration in Myoglobin

Ligand migration processes inside myoglobin and protein dynamics coupled to the migration were theoretically investigated with molecular dynamics simulations. Based on a linear response theory, we identified protein motions coupled to the transient migration of ligand, carbon monoxide (CO), through channels. The result indicates that the coupled protein motions involve collective motions extended over the entire protein correlated with local gating motions at the channels. Protein motions, coupled to opening of a channel from the distal pocket to a neighboring xenon site, were found to share the collective motion with experimentally observed protein motions coupled to a doming motion of the heme Fe atom upon photodissociation of the ligand. Analysis based on generalized Langevin dynamics elucidated slow and diffusive features of the protein response motions. Remarkably small transmission coefficients for rates of the CO migrations through myoglobin were found, suggesting that the CO migration dynamics are characterized as motions governed by the protein dynamics involving the collective motions, rather than as thermally activated transitions across energy barriers of well-structured channels.     

Molecular Dynamics Simulations for 1:1 Solvent Primitive Model Electrolyte Solutions

Abstract

Molecular dynamics (MD) simulations at constant temperature have been carried out for systems of 1:1 solvent primitive model (SPM) electrolyte solutions. Equilibrium thermodynamics, mean cluster size, self-diffusion coefficients, and collision frequencies were computed to examine the electrostatic effects on the structural and dynamical properties. Coherent ionic cluster motion was deduced from a cluster analysis and from the dependence of the velocity and force autocorrelation functions (FACFs). The resulting MD data for the collision frequencies and self-diffusivities of both ions and hard-spheres were shown to be in good agreement with the theoretical predictions.