Dissipative particle dynamics simulations for biological tissues: rheology and competition

In this work, we model biological tissues using a simple, mechanistic simulation based on dissipative particle dynamics. We investigate the continuum behavior of the simulated tissue and determine its dependence on the properties of the individual cell. Cells in our simulation adhere to each other, expand in volume, divide after reaching a specific size checkpoint and undergo apoptosis at a constant rate, leading to a steady-state homeostatic pressure in the tissue. We measure the dependence of the homeostatic state on the microscopic parameters of our model and show that homeostatic pressure, rather than the unconfined rate of cell division, determines the outcome of tissue competitions. Simulated cell aggregates are cohesive and round up due to the effect of tissue surface tension, which we measure for different tissues. Furthermore, mixtures of different cells unmix according to their adhesive properties. Using a variety of shear and creep simulations, we study tissue rheology by measuring yield stresses, shear viscosities, complex viscosities as well as the loss tangents as a function of model parameters. We find that cell division and apoptosis lead to a vanishing yield stress and fluid-like tissues. The effects of different adhesion strengths and levels of noise on the rheology of the tissue are also measured. In addition, we find that the level of cell division and apoptosis drives the diffusion of cells in the tissue. Finally, we present a method for measuring the compressibility of the tissue and its response to external stress via cell division and apoptosis.     

Dissipative particle dynamics simulation of a gold nanoparticle system

Dissipative particle dynamics (DPD) was carried out to study systems containing gold atoms, organic ether (oligohydroquinonyl ether terminated with a thiol group) and organic solvents. The components in the simulated system are very different in size and chemical nature. Our simulation showed that the reproduction of the macroscopic experimental phase separation, properly dividing the polymeric molecule into beads, selecting the size of gold bead, and choosing the appropriate interaction parameters between beads are crucial. In addition, the solvent effect was the dominant factor for the formation of spherical aggregates of Au atoms and organic ether molecules. We report the interaction strengths between the solvent and gold clusters. Our work has demonstrated that DPD methods can be applied to the study of complex meso-scale systems.     

Dissipative particle dynamics of non-spherical particles using a Gaussian density model

The Gaussian density molecular model has been adapted for dissipative particle dynamics. The model, when combined with a soft potential, is shown to be a very flexible mesoscale model exhibiting a wide range of phase behaviour. The soft potential allows relatively large time steps to be used and hence a more rapid equilibration. In addition, the model can be used to study both uniaxial and biaxial systems. We have undertaken a number of pilot studies and have demonstrated that the Gaussian model is able to identify nematic–isotropic phase transitions in liquid crystals and the formation of ordered discotic phases.     

Dissipative particle dynamics simulation of the relaxation behaviour of a triblock copolymer supramolecular network

Since block copolymers self-assemble into various nanostructures and these are widely used in soft materials such as cosmetics and paints, these continue to be the subjects of fundamental studies that progress new technologies. ABA triblock copolymers self-organise into supramolecular networks in which crosslinked structures change upon heating and other external stimulation. Supramolecular networks that consist of ABA triblock copolymers have three components: bridges, loops and dangles. These supramolecular networks have structural regions (clusters) in which end blocks of polymer chains are aggregated and connected by the internal blocks of the polymer chains. Despite of the importance of relaxation behaviour during the measurement and control of polymer materials, the molecular-level behaviour of these systems has not been addressed. We observed pull-out phenomenon that the ends of these polymers detach from clusters, and estimated characteristic detachment times by counting the number of detachments and compared it with the time of longest relaxation in that system.     

Molecular dynamics simulations of SOPS and sphingomyelin bilayers containing cholesterol

We performed a molecular dynamics simulation of an asymmetric bilayer that contained different lipid mixtures in its outer and inner leaflets. The outer leaflet contained a mixture of sphingomyelin (SM) with cholesterol and the inner leaflet a mixture of stearoyl-oleoyl-phosphatidylserine (SOPS) with cholesterol. For comparison purposes, we also performed two simulations on symmetric bilayers: the first simulation was performed on a bilayer containing a binary mixture of SOPS with cholesterol; the second contained a mixture of SM with cholesterol. We studied the hydrogen-bonding network of the bilayers in our simulations and the difference in the network properties in the monolayers either with SM or SOPS. We observed that in the asymmetric bilayer the properties of monolayers were the same as in the corresponding monolayers in the symmetric bilayers.     

Dissipative particle dynamics simulation on the meso-scale structure of diblock copolymer under cylindrical confinement

The meso-scale structure of symmetric diblock copolymer under cylindrical confinement is studied by dissipative particle dynamics (DPD). The simulation results show that coiled cylindrical geometry is favored in the presence of larger cylinder radius (R/L ₀>～1.5), and the number of rings depends on the cylinder radius. Because of the cylinder wall's selectivity, each block can form the central core, but only the preferential block forms the outmost layer. An approximately linear relationship exists between structure transition point, which is approximately in proportion to the 3/5 exponential of chain length of copolymer and number of layers. As the cylinder radius is decreased, a helical morphology is found. Lamellae parallel to the underside of the cylinder appear when the cylinder radius is made smaller (R/L ₀ < ～1.1).     

Detailed molecular dynamics simulations of model biological membranes containing cholesterol

Detailed molecular dynamics simulations performed to study the nature of lipid raft domains that appear in model membranes are reviewed in this paper. The described simulations were performed on hydrated bilayers containing binary mixtures of cholesterol with phospholipids and also on ternary mixtures containing cholesterol, a phospholipid with a high main transition temperature T_m, and a phospholipid with a low transition temperature T_m. These simulations provide qualitative and semi-quantitative information about cholesterol-lipid interactions and also a testing ground for major assumptions made to explain the nature of lipid rafts in model membranes.     

Structural analysis of telechelic polymer solution using dissipative particle dynamics simulations

A telechelic polymer is an amphiphilic polymer that can form micellar structures when dissolved in water. A telechelic polymer solution shows viscoelastic behaviour owing to the formation of characteristic networks, i.e. loops, bridges and dangling chains. For industrial purposes, telechelic polymers have many applications as thickening agents, such as in paints and cosmetics. Thus, it is desirable to predict and control the rheological properties of telechelic polymers. However, detailed studies at the molecular level have not yet been performed. In this study, I use the dissipative particle dynamics (DPD) method to investigate the relationship between the characteristic structural properties and the molecular structure in telechelic polymer solutions. I show that the morphology of telechelic polymer solutions depends on the concentration and chain length, the distribution of the end-to-end distance, the mean square end-to-end distance, the mean square radius of gyration and the time-averaged mean square displacement. Although an effect of entanglement is important for properties of polymer melts, the polymer chain composed of DPD particles cannot reproduce it. Therefore, I compare telechelic polymer solutions with and without the segmental repulsive potential (SRP), which can simulate the effect of entanglement in DPD simulations. The results indicate that it is necessary to include the SRP in DPD simulations to correctly analyse the behaviour of telechelic polymer solutions.     

Dissipative particle dynamics simulation of the soft micro actuator using polymer chain displacement in electro-osmotic flow

ABSTRACT

In this research, the numerical simulation of a soft polymer micro actuator performance has been investigated using the dissipative particle dynamics method in electro-osmotic flow. Effective factors including electro-osmotic flow and polymer chain parameters have been studied. First of all, considering a wide range of electro-osmotic parameters, the validation of analytical results is carried out in a simple micro channel. The electric field and zeta potential changes are linearly related to the flow rate, and the kh parameter behaves nonlinearly to around the kh?=?10. In the following, a convergent–divergent channel is used for the soft micro actuator simulation in which a polymer chain as a heart of actuation is embedded in the middle. As the main control parameter, the direction of the electric field is changed every 4?s, and it leads to a reciprocating motion. The numerical results indicate that the displacement of the soft polymer chain will be increased by enhancing the electric field, the number of beads, decreasing the harmonic bond coefficient and also exposing more length of a polymer chain in front of fluid flow. The results of this study may be useful for some future applications such as artificial fibres and muscles.     

Effect of the angular potential on the temperature control in dissipative particle dynamics simulations

Angular potentials in dissipative particle dynamics (DPD) simulation can describe the rigidity of rod segments in the rod–coil block copolymers and cause system instability monitored by the kinetic temperature. We studied the influence of the bending constant of angular potentials on the temperature control of the DPD simulation system by our defined two parameters, deviation temperature δ _T and standard deviation SD _T . Small bending constants have no obvious influence on the temperature control. For the large bending constants, a relation of δ _T  = a? ^b Δt ^c is constructed. Based on this relation, we can give the appropriate parameters to balance the requirement of the temperature control and the rigid formation of rod-like blocks correctly.     

Molecular dynamics and dissipative particle dynamics simulations for prediction of miscibility in polyethylene terephthalate/polylactide blends

The miscibility of polyethylene terephthalate (PET)/polylactide (PLA) blends is studied through atomistic molecular dynamics (MD) and mesoscale dissipative particle dynamics (DPD) simulation. Five PET/PLA blends (with the weight ratio at 90/10, 70/30, 50/50, 30/70 and 10/90) as well as pure PET and PLA are examined. The solubility parameter values obtained by using the MD simulation are in good agreement with the reference data. The Flory–Huggins parameters, χ, which are computed for different blends and determined from the cohesive energy densities, with the radial distribution functions g(r) of the inter-molecular atoms, suggest that PET is completely miscible with PLA over the entire composition range. This is further proved by the mesoscopic morphologies of PET/PLA blends. All the simulation results are qualitatively consistent with the experimental results, and demonstrate that the modelling strategies in this study may serve as a powerful tool for predicting miscibility and mesoscopic morphology of polymer blends.     

Rheological properties of suspensions containing cross-linked starch nanoparticles prepared by spray and vacuum freeze drying methods

The rheological behavior of suspensions containing vacuum freeze dried and spray dried starch nanoparticles was investigated to explore the effect of these two drying methods in producing starch nanoparticles which were synthesized using high pressure homogenization and mini-emulsion cross-linking technique. Suspensions containing 10% (w/w) spray dried and vacuum freeze dried nanoparticles were prepared. The continuous shear viscosity tests, temperature sweep tests, the frequency sweep and creep-recovery tests were carried out, respectively. The suspensions containing vacuum freeze dried nanoparticles showed higher apparent viscosity within shear rate range (0.1-100s(-1)) and temperature range (25-90°C). The suspensions containing vacuum freeze dried nanoparticles were found to have more shear thinning and less thixotropic behavior compared to those containing spray dried nanoparticles. In addition, the suspensions containing vacuum freeze dried particles had stronger elastic structure. However, the suspensions containing spray dried nanoparticles had more stiffness and greater tendency to recover from the deformation.     

Molecular dynamics simulations of opioid peptide analogs containing multiple conformational restrictions.

Molecular dynamics simulations were performed on the potent and slightly mu-receptor selective cyclic dermorphin analog H-Tyr-D-Orn-Phe-Glu-NH2 as well as on analogs containing a conformationally restricted phenylalanine derivative in place of Phe in the 3 position of the peptide sequence. Peptides studied included the potent and highly mu-selective analogs H-Tyr-D-Orn-Aic-Glu-NH2 (Aic = 2-aminoindan-2-carboxylic acid), H-Tyr-D-Orn-Atc-Glu-NH2 (Atc = 2-aminotetralin-2-carboxylic acid) and H-Tyr-D-Orn-D-Atc-Glu-NH2, and the weakly active analog H-Tyr-D-Orn-Tic-Glu-NH2 (Tic = tetrahydroisoquinoline-3-carboxylic acid). Four different starting conformations were chosen for each peptide, and after equilibration each simulation was allowed to proceed for 100 picoseconds at 600 degrees K. The 14-membered ring structures in the Phe-, Aic-, L- and D-Atc-containing analogs showed moderate structural flexibility, while the peptide ring in the Tic-containing analog was more rigid. As theoretically predicted, the phi 3 and psi 3 angles of the Aic-, L- and D-Atc-containing analogs were limited to values of either about +50 degrees or -50 degrees during almost the entire period of the simulations. In the Tic-containing analog the phi 3 and psi 3 angles were 0 degrees and 90 degrees, respectively, and did not change for the entire duration of the simulation. The side chains of the constrained amino acids showed limited movement, but transitions between the allowed conformations did occur on the time scale of the simulations.(ABSTRACT TRUNCATED AT 250 WORDS)     

Computational fluid dynamics simulations of particle deposition in large-scale, multigenerational lung models

Computational fluid dynamics (CFD) has emerged as a useful tool for the prediction of airflow and particle transport within the human lung airway. Several published studies have demonstrated the use of Eulerian finite-volume CFD simulations coupled with Lagrangian particle tracking methods to determine local and regional particle deposition rates in small subsections of the bronchopulmonary tree. However, the simulation of particle transport and deposition in large-scale models encompassing more than a few generations is less common, due in part to the sheer size and complexity of the human lung airway. Highly resolved, fully coupled flowfield solution and particle tracking in the entire lung, for example, is currently an intractable problem and will remain so for the foreseeable future. This paper adopts a previously reported methodology for simulating large-scale regions of the lung airway (Walters, D. K., and Luke, W. H., 2010, "A Method for Three-Dimensional Navier-Stokes Simulations of Large-Scale Regions of the Human Lung Airway," ASME J. Fluids Eng., 132(5), p. 051101), which was shown to produce results similar to fully resolved geometries using approximate, reduced geometry models. The methodology is extended here to particle transport and deposition simulations. Lagrangian particle tracking simulations are performed in combination with Eulerian simulations of the airflow in an idealized representation of the human lung airway tree. Results using the reduced models are compared with those using the fully resolved models for an eight-generation region of the conducting zone. The agreement between fully resolved and reduced geometry simulations indicates that the new method can provide an accurate alternative for large-scale CFD simulations while potentially reducing the computational cost of these simulations by several orders of magnitude.     

Rheology of polymers in many-body dissipative particle dynamics simulations: Schmidt number effect

The Schmidt number effect on the rheology of finitely extensible nonlinear elastic chains (FENE) in many-body dissipative particle dynamics (MDPD) is investigated in this work. We find that the Schmidt number, ranging from (10¹) to (10³), has limited influence on the polymer properties, such as its radius of gyration (R_g), diffusion coefficient (D) and relaxation time (τ). The simulation results follow Zimm model's predictions well. The hydrodynamic interaction strength parameter h* demonstrates that the full hydrodynamic interaction can be simulated for Schmidt number from (10⁰-10⁶) in MDPD. Next, the rheology of FENE polymers is studied using Lees-Edward boundary condition in shear flow. The shear-thinning and normal stress difference are measured and analysed with MDPD; meanwhile, the volume fraction, solvent quality and chain length are varied to explore their effects on the extent of the Newtonian region. Finally, the non-Newtonian droplet is firstly simulated in MDPD. Its maximum spreading diameter is measured for both Newtonian and non-Newtonian droplet with Weber number (We) ranging from 4.37 to 109.2 on hydrophilic, moderate and hydrophobic surfaces, respectively. The fluid shear-thinning property increases at high shear rate and is further enhanced on more hydrophobic surface, from the maximum spreading diameter results. The non-Newtonian (FENE) droplet can be now well simulated in MDPD and this provides additional insight to further research concerning polymer-solvent-surface interactions, which is crucial in various applications.     

Evaluation of viscosities of aqueous two-phase systems containing protein

The dynamic viscosities of aqueous polyethylene glycol, aqueous bovine serum albumin, and polyethylene glycol-bovine serum albumin-water solutions were measured at temperatures of 15, 20, 25, 30 and 35 degree C. To estimate the viscosity values of polyethylene glycol-bovine serum albumin-water solutions, a one parameter Grunberg-like model which was satisfactorily used earlier by the present author for polyethylene glycol-dextran-water solutions was employed. The disposable parameter a for our temperature range was estimated as 3.71. The relative errors varying from 0.29 to 18.98 in absolute value indicates that the Grunberg-like model works perfectly for polymer-protein solutions as well.     

Dissipative particle dynamics simulation on the properties of the oil/water/surfactant system in the absence and presence of polymer

Dissipative particle dynamics is used to simulate the oil/water/surfactant system in the absence and presence of polymer. Structural properties, interfacial properties, and their dependence on the surfactant concentration, polymer concentration and oil/water ratio were investigated. The snapshots illustrate the variation of the structure of oil/water/surfactant system. In the presence of polymer, the interface is supersaturated at a lower surfactant concentration. The end-to-end distance increases with surfactant concentration and polymer chains but shows weak dependence on the oil/water ratio. The peak of density grows higher with surfactant concentration, but it is not affected by oil/water ratio. The density profiles of polymer grow higher with polymer chains, indicating that most of the polymer chains stay at the interface for stability. Interfacial thickness shows an adsorption of polymer/surfactant complexes at the interface, where the polymer is in an extended conformation at the interface. The formation of polymer/surfactant complexes is favourable for the decrease of oil/water interfacial tension.