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).     

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.     

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.     

Microphase separation of star-diblock copolymer melts studied by dissipative particle dynamics simulation

The microphase-separation behaviors of two types of star-diblock copolymers (A)₄(B)₄ and (AB)₄ are investigated through the dissipative particle dynamics (DPD). The simulated phase diagrams show similar ordered mesostructures as those of corresponding linear and cyclic ones, such as lamellas (LAM), perforated lamellas (PL), hexagonal (HEX) cylinders and body-centered-cubic (BCC) spheres, besides, a series of gyroid (GR) morphologies predicted by theoretical research have been identified. In the regions between the totally ordered and disordered phases, we have found some melted morphologies that can be thought as locally ordered, such as micelles (M), liquid rods (LR) and random network (RN), which have not been identified in relevant theoretical predictions. The simulated threshold for a totally ordered mesostructure to appear is higher than theoretical predictions, which can be ascribed mainly to the increasing fluctuation with finite chain length, and the star architecture can facilitate microphase separation, which is in agreement with the theoretical predictions. In addition, it is easier for the (A) _n (B) _n copolymers than for corresponding (AB) _n ones to trigger microphase separation under the same conditions. The relations between the root-mean-square radius of gyration (RMSGR) and the composition f _A in the two types of star copolymers are almost contrary, which can be attributed to the differences in their structural characteristics.     

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 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.     

Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and fluid particle model

We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-resolution molecular structures (see the Figure) found in complex fluids ranging from single micelle, colloidal crystals, large-scale colloidal aggregates up to the mesoscale processes of hydrodynamical instabilities in the bulk of colloidal suspensions. We can simulate different colloidal structures in which the colloidal beds are of comparable size to the solvent particles. This undertaking is accomplished with a two-level discrete particle model consisting of the MD paradigm with a Lennard-Jones (L-J) type potential for defining the colloidal particle system and DPD or FPM for modeling the solvent. We observe the spontaneous emergence of spherical or rod-like micelles and their crystallization in stable hexagonal or worm-like structures, respectively. The ordered arrays obtained by using the particle model are similar to the 2D colloidal crystals observed in laboratory experiments. The micelle shape and its hydrophobic or hydrophilic character depend on the ratio between the scaling factors of the interactions between colloid–colloid to colloid–solvent. Unlike the miscellar arrays, the colloidal aggregates involve the colloid–solvent interactions prescribed by the DPD forces. Different from the assumption of equilibrium growth, the two-level particle model can display much more realistic molecular physics, which allows for the simulation of aggregation for various types of colloids and solvent liquids over a very broad range of conditions. We discuss the potential prospects of combining MD, DPD, and FPM techniques in a single three-level model. Finally, we present results from large-scale simulation of the Rayleigh–Taylor instability and dispersion of colloidal slab in 2D and 3D. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00894-001-0068-3.Electronic Supplementary Material available.     

Molecular dynamics simulation of a myosin subfragment-1 docking with an actin filament

Myosins are typical molecular motor proteins, which convert the chemical energy of ATP into mechanical work. The fundamental mechanism of this energy conversion is still unknown. To explain the experimental results observed in molecular motors, Masuda has proposed a theory called the “Driven by Detachment (DbD)” mechanism for the working principle of myosins. Based on this theory, the energy used during the power stroke of the myosins originates from the attractive force between a detached myosin head and an actin filament, and does not directly arise from the energy of ATP. According to this theory, every step in the myosin working process may be reproduced by molecular dynamics (MD) simulations, except for the ATP hydrolysis step. Therefore, MD simulations were conducted to reproduce the docking process of a myosin subfragment-1 (S1) against an actin filament. A myosin S1 directed toward the barbed end of an actin filament was placed at three different positions by shifting it away from the filament axis. After 30 ns of MD simulations, in three cases out of ten trials on average, the myosin made a close contact with two actin monomers by changing the positions and the orientation of both the myosin and the actin as predicted in previous studies. Once the docking was achieved, the distance between the myosin and the actin showed smaller fluctuations, indicating that the docking is stable over time. If the docking was not achieved, the myosin moved randomly around the initial position or moved away from the actin filament. MD simulations thus successfully reproduced the docking of a myosin S1 with an actin filament. By extending the similar MD simulations to the other steps of the myosin working process, the validity of the DbD theory may be computationally demonstrated.     

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.     

Depletion phenomenon in diblock copolymer films: a dissipative particle dynamics simulation

A tentative simulation study has been carried out on the depletion phenomenon in diblock copolymer films through dissipative particle dynamics technology. Results indicate that a depletion layer appears in nearly all the systems with strong interaction between different components, accompanied with weak interaction between the component and the boundary. The system temperature plays a dominant role in the thickness of the depletion layer, on which the component fraction also has an effect to a certain extent. The findings can give support to relevant application processes.     

Microphase separation of graft-diblock copolymer by dissipative particle dynamics simulation

Microphase-separation behaviour of graft-diblock copolymers was investigated by the dissipative particle dynamics. Besides familiar totally ordered mesostructures, the simulated phase diagram also shows unfamiliar locally ordered mesostructures together with a few melted morphologies. The simulated order–disorder transition critical value is higher than the theoretically predicted value due mainly to the increasing fluctuation coming from finite chain length. The microphase-separation morphologies in graft-diblock copolymers shift away significantly from that of the corresponding linear ones with the same component volume fractions. Generally, it is more difficult to trigger microphase separation for graft-diblock copolymers than for their linear analogues, in good agreement with theoretical and experimental findings. The change of graft fraction has a significant effect on the microphase-separation behaviour of graft-diblock copolymers.     

Simulation of a Single Red Blood Cell Flowing Through a Microvessel Stenosis Using Dissipative Particle Dynamics

The motion and deformation of a single red blood cell flowing through a microvessel stenosis was investigated employing dissipative particle dynamics (DPD) method. The numerical model considers plasma, cytoplasm, the RBC membrane and the microvessel walls, in which a three dimensional coarse-grained spring network model of RBC’s membrane was used to simulate the deformation of the RBC. The suspending plasma was modelled as an incompressible Newtonian fluid and the vessel walls were regarded as rigid body. The body force exerted on the free DPD particles was used to drive the flow. A modified bounce-back boundary condition was enforced on the membrane to guarantee the impenetrability. Adhesion of the cell to the stenosis vessel surface was mediated by the interactions between receptors and ligands. Firstly, the motion of a single RBC in a microfluidic channel was simulated and the results were found in agreement with the experimental data cited by [1]. Then the mechanical behavior of the RBC in the microvessel stenosis was studied. The effects of the bending rigidity of membrane, the size of the stenosis and the driven body force on the deformation and motion of red blood cell were discussed.     

Heat transfer simulation using energy conservative dissipative particle dynamics

Dissipative particle dynamics with energy conservation (eDPD) was used to investigate conduction heat transfer in two dimensions under steady-state condition. Various types of boundary condition were implemented to the conduction domain. Besides, 2D conduction with internal heat generation was studied and the heat generation term was used to measure the thermal conductivity and diffusivity of the eDPD system. The boundary conditions used include both the Neumann and Dirichlet boundary conditions. The Neumann boundary condition was applied via adiabatic surfaces and surfaces exposed to convection heat transfer. The DPD simulations were compared to analytical solutions and finite-difference techniques. It was found that DPD appropriately predicts the temperature distribution in the conduction regime. Details of boundary condition implementation and thermal diffusivity measurement are also described in this paper.     

Mixed modes in opening of KcsA potassium channel from a targeted molecular dynamics simulation

Potassium channels conduct K⁺ flow selectively across the membrane through a central pore. During a process called gating, the potassium channels undergo a conformational change that opens or closes the ion-conducting pore. The potassium channel KcsA has been structurally determined in its closed state. However, the dynamic mechanism of the gating transition of the KcsA channel is still being investigated. Here, a targeted molecular dynamics simulation up to 150 ns is performed to investigate the detailed opening process of the KcsA channel with an open Kv1.2 structure serving as the target. The channel arrived at a self-determined quasi-stable state within 60 ns. The rigid-body and hinge-bending modes are observed mixed together in the remaining 90 ns long quasi-stable state. The mixed-mode movement seems come from the competition between the helix rigidity and the biased-applied gating force.     

Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation

An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ～1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen–phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.     

Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.     

Artificial biomembrane morphology: a dissipative particle dynamics study

Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamics simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a ‘net’, or at very low densities, a series of disparate ‘clumps’ similar to the micelles formed by lipids in nature. When the initial lipid density is high, a membrane forms, but due to the large number of lipids, the naturally formed membrane would be larger than the simulation box, leading to ‘rippling’ behavior as the excess repulsive force of the membrane interior overcomes the bending energy of the membrane. Once the density reaches a certain point however, ‘bubbles’ appear inside the membrane, reducing the rippling behavior and eventually generating a relatively flat, but thick, structure with micelles of water inside the membrane itself. Our simulations also demonstrate that the interaction parameter between individual lipids plays a significant role in the formation and behavior of lipid membrane assemblies, creating similar structures as the initial lipid density distribution. This work provides a comprehensive approach to the intricacies of lipid membranes, and offers a guideline to design biological or polymeric membranes through self-assembly processes as well as develop novel cellular manipulation and destruction techniques.     

DPD simulation of non-Newtonian electroosmotic fluid flow in nanochannel

We use the dissipative particle dynamics (DPD) method to simulate the non-Newtonian electroosmotic flow (EOF) through nanochannels. Contrary to a large amount of past computational efforts dedicated to the study of EOF profile, this work pays attention to the EOF of non-Newtonian fluids, which has been rarely touched in past publications. Practically, there are many MEMS/NEMS devices, in which the EOF behaviour should be treated assuming both non-continuum and non-Newtonian conditions. Therefore, our concern in this work is to simulate the EOF through nanochannels considering both non-Newtonian fluid properties and non-continuum flow conditions. We have chosen DPD as our working tool because it provides several important advantages comparing with the classical time consuming molecular dynamics method. Using the DPD method, we explore the effect of a few important fluid properties and nanochannel parameters on the EOF behaviour and the resulting flow rate magnitudes. Our investigation will result in a number of findings, which have not been reported in past research works.