Viscometric flow for a many-body dissipative particle dynamics (MDPD) fluid with Lees–Edwards boundary condition

Viscometric properties of polymer are explored by the many-body dissipative particle dynamics (MDPD) using Lees–Edwards boundary conditions. The equation of state for the MDPD system is modified by fitting the density correction to different values of the cut-off radius. Due to the many-body interactions in MDPD, the viscosity contributed from the conservative force increases considerably with increasing repulsive coefficient, density and cut-off radius, and cannot be ignored compared to the ‘standard’ DPD case. The influence of these parameters on the MDPD viscosity is investigated, and we propose an equation to predict the viscosity in MDPD model. Additionally, the dumbbell polymer suspension model is investigated in the MDPD fluid, and the relations concerning first normal stress difference and shear rate, the relaxation time and spring constant, are consistent to theoretical works. We conclude that the MDPD model can be used to investigate the dynamics of non-Newtonian droplets.     

Effect of Electrostatic Interaction in the Formation of Dust-Acoustic Shock Wave with Fluctuating Dust Charge

A theoretical investigation on the effect of electrostatic interaction on dust acoustic wave (DAW) has been carried out in weakly nonlinear limit in strongly coupled regime with fluctuating dust charge. The generalized hydrodynamic set of equations is employed in the hydrodynamic limit. The dust?dust electrostatic interaction couples with dust charge fluctuation, as well as the viscosity of the medium, and provides the dissipative effect, which leads to the formation of shock wave in such a system. The novel feature of the present work is that, in the presence of charge fluctuation, the effective electrostatic temperature starts affecting the behavior and also enhancing the formation of monotonic shock wave. In this investigation, the dissipative effect arising due to charge fluctuation is dominant in comparison to the viscosity of the medium in the presence of electrostatic temperature.     

Simulation of Suspensions in Constricted Geometries by Dissipative Particle Dynamics

We investigate the flow of a suspension through a constriction by means of the mesoscopic technique known as dissipative particle dynamics (DPD). The dispersed phase was modeled as a set of soft spheres interacting through a conservative force while suspended and continuum phases interact via DPD forces. It is shown that a Poiseuille steady state is achieved in the presence of bounding walls and under a pressure gradient in a cylindrical pipe. Flow geometry in the laminar regime is explored and discussed for periodic conditions in the presence of a cylindrical narrowing or constriction.     

Linear Augmentation for Stabilizing Stationary Solutions: Potential Pitfalls and Their Application

Linear augmentation has recently been shown to be effective in targeting desired stationary solutions, suppressing bistablity, in regulating the dynamics of drive response systems and in controlling the dynamics of hidden attractors. The simplicity of the procedure is the main highlight of this scheme but questions related to its general applicability still need to be addressed. Focusing on the issue of targeting stationary solutions, this work demonstrates instances where the scheme fails to stabilize the required solutions and leads to other complicated dynamical scenarios. Examples from conservative as well as dissipative systems are presented in this regard and important applications in dissipative predator—prey systems are discussed, which include preventative measures to avoid potentially catastrophic dynamical transitions in these systems.     

Dynamics of the Coiled-Coil Unfolding Transition of Myosin Rod Probed by Dissipation Force Spectrum

The motor protein myosin II plays a crucial role in muscle contraction. The mechanical properties of its coiled-coil region, the myosin rod, are important for effective force transduction during muscle function. Previous studies have investigated the static elastic response of the myosin rod. However, analogous to the study of macroscopic complex fluids, how myosin will respond to physiological time-dependent loads can only be understood from its viscoelastic response. Here, we apply atomic force microscopy using a magnetically driven oscillating cantilever to measure the dissipative properties of single myosin rods that provide unique dynamical information about the coiled-coil structure as a function of force. We find that the friction constant of the single myosin rod has a highly nontrivial variation with force; in particular, the single-molecule friction constant is reduced dramatically and increases again as it passes through the coiled-uncoiled transition. This is a direct indication of a large free-energy barrier to uncoiling, which may be related to a fine-tuned dynamic mechanosignaling response to large and unexpected physiological loads. Further, from the critical force at which the minimum in friction occurs we determine the asymmetry of the bistable landscape that controls uncoiling of the coiled coil. This work highlights the sensitivity of the dissipative signal in force unfolding to dynamic molecular structure that is hidden to the elastic signal.     

Acoustical response of hair receptors in insects

Summary A detailed mechanical model is developed to account for the behaviour of hair-like acoustical sensory receptors in insects. For the small hair diameters commonly found, it is concluded that the force acting on the moving hair is caused almost entirely by the viscosity of the air, as analyzed long ago by Stokes. The result of this viscous force is to provide a bending moment about the base of the hair that is proportional to the acoustic particle velocity but that lags behind it by about 135°. In addition the viscous force increases the moment of inertia of the hair by a large and frequency dependent addition, and provides a viscous damping term of sufficient magnitude to reduce the Q value to near unity.The measurements of Tautz (1977) on the thoracic hairs of the caterpillarBarathra brassicae are discussed in detail in terms of the model. Many of these observations are well accounted for, though a few discrepancies remain.This work is part of a programme in biological acoustics supported by the Australian Research Grants Committee.     

Blood flow: Theory,effective viscosity and effects of particle distribution

A study is made of blood flow by assuming that the blood constitutes a suspension of cells in plasma instead of a simple homogeneous fluid. A macroscopic theory governing the motion of plasma in a plasma-cell system is derived from the local volume averaging method for a system without mass transfer between the phases, and its characteristic length is much larger than the size of the cells. The equations governing the motion of the local averaged fluid quantities include one additional term in the equation of motion and two additional terms in the energy equation. These terms represent, respectively, the force exerted upon the fluid by the particles, and the rate of heat transfer and work kone upon the fluid by the particles. The theory is applied to obtain the effective viscosity as the explicit function of the volume concentration of the cells by assuming that the cells behave like rigid spherical particles with slip-collision, and the plasma is an compressible Newtonian fluid. Comparison with existing experimental results shows a good agreement. The theory is also used to obtain the effects of cell distribution upon the overall effective viscosity in a circular tube. The quantitative result shows that there is a decrease in overall effective viscosity as the concentration of cells increases toward the center of the tube, and the overall effective viscosity is smaller than the flow with evenly distributed cells.     

Effects of flowing RBCs on adhesion of a circulating tumor cell in microvessels

Adhesion of circulating tumor cells (CTCs) to the microvessel wall largely depends on the blood hydrodynamic conditions, one of which is the blood viscosity. Since blood is a non-Newtonian fluid, whose viscosity increases with hematocrit, in the microvessels at low shear rate. In this study, the effects of hematocrit, vessel size, flow rate and red blood cell (RBC) aggregation on adhesion of a CTC in the microvessels were numerically investigated using dissipative particle dynamics. The membrane of cells was represented by a spring-based network connected by elastic springs to characterize its deformation. RBC aggregation was modeled by a Morse potential function based on depletion-mediated assumption, and the adhesion of the CTC to the vessel wall was achieved by the interactions between receptors and ligands at the CTC and those at the endothelial cells forming the vessel wall. The results demonstrated that in the microvessel of \(15\,\upmu \hbox {m}\) diameter, the CTC has an increasing probability of adhesion with the hematocrit due to a growing wall-directed force, resulting in a larger number of receptor–ligand bonds formed on the cell surface. However, with the increase in microvessel size, an enhanced lift force at higher hematocrit detaches the initial adherent CTC quickly. If the microvessel is comparable to the CTC in diameter, CTC adhesion is independent of Hct. In addition, the velocity of CTC is larger than the average blood flow velocity in smaller microvessels and the relative velocity of CTC decreases with the increase in microvessel size. An increased blood flow resistance in the presence of CTC was also found. Moreover, it was found that the large deformation induced by high flow rate and the presence of aggregation promote the adhesion of CTC.     

Metastable region of phase diagram: optimum parameter range for processing ultrahigh molecular weight polyethylene blends

Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is very difficult to obtain a UHMWPE/NMWP blend which may demonstrate both two-phase morphology and thick interface. In this work, dissipative particle dynamics simulations and Flory-Huggins theory are applied in predicting the optimum NMWP and the corresponding conditions, wherein the melt flowability of UHMWPE can be improved while its mechanical properties can also be retained. As is indicated by dissipative particle dynamics simulations and phase diagram calculated from Flory-Huggins theory, too small Flory-Huggins interaction parameter (χ) and molecular chain length of NMWP (N(NMWP)) may lead to the formation of a homogeneous phase, whereas very large interfacial tension and thin interfaces might also appear when parameters N(NMWP) and χ are too large. When these parameters are located in the metastable region of the phase diagram, however, two-phase morphology occurs and interfaces of the blends are extremely thick. Therefore, metastable state is found to be advisable for both the viscosity reduction and mechanical property improvement of the UHMWPE/NMWP blends.     

Salting-out in the aqueous single-protein solution: the effect of shape factor

A molecular-thermodynamic model is developed to describe salt-induced protein precipitation. The protein-protein interaction goes through the potential of mean force. An equation of state is derived based on the generalized van der Waals partition function. The attractive term including the potential of mean force is perturbed by the statistical mechanical perturbation theory. The precipitation behaviors are studied by calculating the partition coefficient with various conditions such as the ionic strength and the shape of protein. Our results show that the protein shape plays a significant role in the protein precipitation behavior.     

Molecular simulation study of cooperativity in hydrophobic association

To investigate the cooperativity of hydrophobic interactions, the potential of mean force of two- and three-molecule methane clusters in water was determined by molecular dynamics simulations using two methods: umbrella-sampling with the weighted histogram analysis method and thermodynamic integration. Two water models, TIP3P and TIP4P, were used, while each methane molecule was modeled as a united atom. It was found that the three-body potential of mean force is not additive, i.e., it cannot be calculated as a sum of two-body contributions, but requires an additional three-body cooperative term. The cooperative term, which amounts to only about 10% of the total hydrophobic association free energy, was found to increase the strength of hydrophobic association; this finding differs from the results of earlier Monte Carlo studies with the free energy perturbation method of Rank and Baker (1997). As in the work of Rank and Baker, the solvent contribution to the potential of mean force was found to be well approximated by the molecular surface of two methane molecules. Moreover, we also found that the cooperative term is well represented by the difference between the molecular surface of the three-methane cluster and those of all three pairs of methane molecules. In addition, it was found that, while there is a cooperative contribution to the hydrophobic association free energy albeit a small one, the errors associated with the use of pairwise potentials are comparable to or larger than this contribution.     

The coordination of protein motors and the kinetic behavior of microtubule--a computational study

Utilizing the mechanical energy converted from chemical energy through hydrolysis of ATP, motor proteins drive cytoskeleton filaments to move in various biological systems. Recent technological advance has shown the potential of the motor proteins for powering future nano-bio-mechanical systems. In order to effectively use motor proteins as a biological motor, the interaction between the protein motors and bio-filaments needs to be well clarified, since such interaction is largely influenced by many factors, such as the coordination among the motors, their dynamic behavior, physical properties of microtubules, and the viscosity of solution involved, etc. In this study, a two-dimensional model was proposed to simulate the motion of a microtubule driven by protein motors based on a dissipative particle dynamics (DPD) method with attempt to correlate the microtubule's kinetic behavior to the coordination among protein motors.     

Lysozyme-lysozyme and lysozyme-salt interactions in the aqueous saline solution: a new square-well potential

We investigate lysozyme-lysozyme and lysozyme-salt interactions in electrolyte solutions using a molecular-thermodynamic model. An equation of state based on the statistical mechanical perturbation theory is applied to describe the interactions. The perturbation term includes a new square-well potential of mean force, which implies the information about the lysozyme surface and salt type. The attractive energy of the potential of mean force is correlated with experimental cloud-point temperatures of lysozyme in various solution conditions. The same attractive energy is used to predict osmotic pressure of a given system with no additional parameters. The new potential shows a satisfactory improvement in understanding the interactions between lysozymes in aqueous salt solutions.     

A model for estimating the medium properties of Avicel to ethanol conversion

Simultaneous saccharification and fermentation received an increasing level of attention over recent decades, with the primary focus on the development of improved enzyme and organism performance. Little literature is available on the effects of the various fermentation components on the apparent dynamic viscosity of the fermentation broth for use in reactor design and analysis. This work investigates density and settling properties of Avicel PH-101 particles and the effects of base medium composition, yeast concentration and cellulose particles on the apparent dynamic viscosity of the fermentation mixture. Dynamic viscosity measurements were obtained using a rotational viscometer equipped with a DG 26.7 double gap concentric cylinder measuring system. Results indicated that Avicel particles experience a greater drag force compared to similar sized spherical particles and have a measured density of 1,605.7 kg m^?3. The Ostwäld-de Waele formulation was used to describe the dynamic viscosity of the particles due to it shear-thinning nature. Correlation between the predicted particle effects and experimental results deviated with a root mean square error of 8.46 %.     

Dissipative resonance. An analytical solution with fixed boundaries

A simple one-dimensional model is presented in which the dissipative resonance phenomenon takes place. An analytical solution for steady-state oscillations occurring in the system due to the external periodic force was obtained. An analytical solution describing the dynamics of the particles-acceptors of the external force is also presented. Some common properties of such systems are considered. The method can be used to explore a wide class of models in which the dissipative resonance occurs and which can be used to describe the mechanisms of action of weak electromagnetic fields to biological and physiochemical objects.     

Heat exchange in dusty plasma

The effect of the charge of a dust grain on the exchange of its heat with plasma particles and with neutral gas particles in an anisotropic dusty plasma with dissipative flows is discussed. It is shown, in particular, that nonuniform heating of the grain surface gives rise to the radiometric force, which may be stronger than the ion wind force. Also, the grain charge causes the thermophoretic force to change its sign.     

Measuring the force production of the hormogonia of Mastigocladus laminosus

The cyanobacterium Mastigocladus laminosus forms hormogonia, which glide slowly away from the parent colony by extruding slime out of nozzles. Using video microscopy, we observed hormogonia embedded in and moving through 1-4% agar solutions with an average velocity of 0.5 microm/s. Agar is non-Newtonian and is subject to shear-thinning so that its viscosity greatly increases at low shear rates. We measured the viscosity of these agar solutions at the very low shear rates appropriate for gliding hormogonia and found it to vary from 1 to 52 million centipoise. Then, by applying a Newtonian drag coefficient for a 100-microm-long, cigar-shaped hormogonium, we found that it produced a force of several million pN. A typical hormogonium has 10-100 thousand 9-nm-wide slime extrusion nozzles. Wolgemuth et al. have proposed hydration-driven swelling of the polyelectrolyte slime ejected from these nozzles as the force production mechanism, and our experiment found a large nozzle force that was consistent with this hypothesis. Average single nozzle force depended on viscosity, being large when the viscosity was high: 71 pN in 3% and 126 pN in 4% agar.     

Characterization and modelling of the musculoarticular complex mechanical behavior in passive conditions. Effects of cyclic and static stretching

This work aims to model the mechanical behavior of the musculoarticular complex (MAC). First, the implementation and the validation of original methodologies have enabled to assess elasticity, viscosity and friction of the MAC. The effects of cyclic and static stretching on these properties were then assessed. Changes in MAC mechanical properties induced by static stretching could mainly be explained by an acute increase in muscle lengths, while dissipative properties and stiffness of the MAC are only modified after cyclic stretching. Our results enable to suggest and discuss about some mechanisms probably implied in these adaptations. Finally, a rheological model was proposed and validated to model the mechanical behavior and the adaptations induced by cyclic and static stretching assessed in our studies. This model could then be used to simulate the effects of specific protocols performed for instance in sports or functional rehabilitation.     

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions

The non-polar component of the potential of mean force of dimerization of alanine dipeptide has been calculated in explicit solvent by free energy perturbation. We observe that the calculated PMF is inconsistent with a non-polar hydration free energy model based solely on the solute surface area. The non-linear behavior of the solute-solvent van der Waals energy is primarily responsible for the non-linear dependence of the potential of mean force with respect to the surface area. The calculated potential of mean force is reproduced by an implicit solvent model based on a solvent continuum model for the solute-solvent van der Waals interaction energy and the surface area for the work of forming the solute cavity.     

QCM-D sensitivity to protein adsorption reversibility

Using a quartz crystal microbalance with dissipative monitoring (QCM-D) we have determined the adsorption reversibility and viscoelastic properties of ribonuclease A adsorbed to hydrophobic self-assembled monolayers. Consistent with previous work with proteins unfolding on hydrophobic surfaces, high protein solution concentrations, reduced adsorption times, and low ammonium sulfate concentrations lead to increased adsorption reversibility. Measured rigidity of the protein layers normalized for adsorbed protein amounts, a quantity we term specific dissipation, correlated with adsorption reversibility of ribonuclease A. These results suggest that specific dissipation may be correlated with changes in structure of adsorbed proteins.