DPD Simulations Research Articles

Dissipative particle dynamics with an effective pair potential from integral equation theory of molecular liquids.

We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency.

Mesoscale simulation and experimental studies of self-assembly behavior of a PLA-PEG-PLA triblock copolymer micelle for sustained drug delivery

Dissipative Particle Dynamic simulation (DPD) was employed to investigate PLA-PEG-PLA copolymer micelles to gain more understanding at the molecular level in addition to experimental studies. Critical micelle concentration (cmc), micelle size and small molecule encapsulation of these triblock copolymer micelles with different hydrophobic/hydrophilic (LA/EG) block ratios (2.56, 4.88 and 7.25 with fixed PEG length = 23 monomer units) were determined. Only the appropriated LA/EG block ratio (4.88 and 7.25) can induce the formation of spherical micelle in a dilute solution. The cmc and micelle size were decreased and increased, respectively, as a function of the LA/EG block ratio. Upon adding small solubilizate molecules, a larger micelle size was formed. Then, PLA-PEG-PLA with the same LA/EG block ratios as DPD simulation were synthesized and the micelle solution was prepared. Pyrene was used as the molecular probe to find the cmc by fluorescence spectroscopy. Light scattering was applied to determine the hydrodynamic radius (R H ) of these micelles. The cmc and RH were decreased and increased, respectively, with LA/EG ratio, qualitatively similar to the trends as simulation results. The behavior of these copolymer micelles to encapsulate the small solubilizate molecules was also studied by fluorescence technique. The partition coefficients of pyrene between the water phase and the micelle core were increased with a higher LA/EG block ratio similar to results from the simulation.

Efficient solvent-free dissipative particle dynamics for lipid bilayers.

We rigorously derived effective potentials for solvent-free DPD simulation of lipid bilayers. The derivation relies on an earlier developed hybrid particle/field method and is based on the idea that the solvent is always in local equilibrium on a coarse-grained time scale, given the instantaneous templates set by the self-assembly structure. By relating the parameters in the effective implicit-solvent potentials directly to the lipid-solvent interactions and membrane properties for the explicit solvent DPD model, we constitute an efficient and general procedure for reformulating any DPD membrane model in an implicit-solvent form. Here, we determined these membrane properties for two existing DPD models, via an analysis of membrane fluctuation spectra. Equivalent single-processor implicit- and explicit-solvent calculations show the trade-mark of implicit solvent simulation: a 20-fold reduction of the total simulation time for a system containing 92% solvent. This increased efficiency enabled us to realistically simulate the spontaneous formation of a ∼20 nm diameter vesicle on a single processor overnight. We believe that this work will contribute to an enhanced computational study of large vesicles and thus a better understanding of experimental liposome dynamics.

Molecular modeling of membrane tube pearling and the effect of nanoparticle adsorption.

The shape transformation of membrane tubes, also known as pearling, is thought to play an important role in a variety of cellular activities, like intracellular transport. Despite considerable experiments have investigating this phenomenon, the detailed molecular mechanism as well as how environmental factors affect the tube pearling instability is still ambiguous. In this work, we use computer simulation techniques to obtain a molecular-level insight into the tube pearling process. We find that the tube morphology is strongly determined by the water pressure inside membrane tubes. For example, the tube shrinkage and subsequent bending is observed when we decrease the inner water pressure. Contrarily, as we increase the inner water pressure, the tube pearling tends to occur in order to reduce the surface energy. Besides, our simulations show that the membrane tube pearling is regulated by the adsorption of nanoparticles (NPs) in two competing ways. One is that the NP adsorption can exert an additional membrane tension and thus promote the pearling and subsequent division of membrane tubes. On the other hand, the NP adsorption can locally rigidify the membrane and thus contrarily restrain the tube pearling. Therefore, the NP size, NP concentration and NP-membrane adhesion strength will collectively regulate the tube pearling process.

Nanotribology of biopolymer brushes in aqueous solution using dissipative particle dynamics simulations: an application to PEG covered liposomes in a theta solvent

We undertake the investigation of sheared polymer chains grafted onto flat surfaces to model liposomes covered with polyethylene glycol brushes as a case study for the mechanisms of efficient drug delivery in biologically relevant situations, for example, as carriers for topical treatments of illnesses in the human vasculature. For these applications, specific rheological properties are required, such as low viscosity at high shear rates, to improve the transport of the liposomes. Therefore, extensive non-equilibrium, coarse-grained dissipative particle dynamics simulations of polymer brushes of various lengths and shear rates are performed to obtain the average viscosity and the friction coefficient of the system as functions of the shear rate and polymerization degree under theta-solvent conditions, and we find that the brushes experience considerable shear thinning at large shear rates. The viscosity (η) and the friction coefficient (μ) are shown to obey the scaling laws η ∼ γ dot above (-0.31) and μ ∼ γ dot above (0.69) at high shear rates (γ dot above) in a theta solvent, irrespective of the degree of polymerization of brushes. These results confirm recent scaling predictions and reproduce very well trends in measurements of the viscosity at a high shear rate (γ dot above) of red blood cells in a liposome containing medium.

Evaporation-induced morphology pattern of triblock copolymer A5B10C5 in thin film: A multibody DPD simulation study

We used multibody dissipative particle dynamics method, by which the attractive and repulsive interactions can be effectively considered, to investigate the evaporation-induced morphology patterns of triblock copolymer A5B10C5 in thin film. With changing attractive interactions between solvent vapor and triblock copolymer that represent various selective solvents, lamellar morphology, sandwich lamellar morphology, spherical morphology and disorder morphology patterns of the thin films were obtained for both coil-coil-coil and rod-coil-coil chain architectures, respectively. The order parameter and the film thickness were calculated during the process for characterizing the film properties, and it was found that the rigid A-block of the triblock copolymer hinders the formation of an ordered structure.

Study on Synergistic Effect Between Wormlike Micelles and Hydrophobically Modified Poly(acrylic acid) in Salt Solution

The complex system of hydrophobically modified poly (acrylic acid) (HMPA) and wormlike micelles formed by sodium oleate in the presence of sodium acetate is investigated by apparent viscosity and rheological measurements. Addition of small amount of HMPA markedly enhances the viscosity of wormlike micelles, with further increase of HMPA concentration, a viscosity drop is observed. At high salinity, the complex system still remains strong viscoelastic and eliminates the limitation of susceptibility to salt for HMPA. DPD simulation results are in good agreement with experimental data, which provide theoretical confirmation for a synergistic mechanism between HMPA and wormlike micelles.

Micellization of linear A-b-(B-alt-C)n multiblock terpolymers in A-selective solvents

We used three-dimensional self-consistent field theory to investigate the micellization behavior of A-b-(B-alt-C)n multiblock terpolymers in the presence of a solvent that is selective to the terminal A-block. In particular, we focused on the effects of the incompatibility parameter between B and C, χBC, and the composition of the solvophilic A-block, fA, on the formation of micelles from ABC triblock and A(BC)3 multiblock terpolymers, respectively. We observed a general trend that a segmented packing of B- and C-layers along the axial direction of the micelles is favored than the coaxial packing with the increasing of χBC or decreasing of fA. The separation of B and C blocks within a micelle leads to the formation of a variety of multicompartment micelle morphologies, such as core–shell–corona spherical micelles, hamburgers, and bump-surface micelles, in the ABC triblock copolymers. In the A(BC)3 multiblock terpolymers, we discovered more fascinating micelles by implementing the SCFT simulation than by the DPD simulation. Besides the BC-segmented worm-like micelles, which have been found in the DPD simulation work, concentric multilayer spheres and vesicles can be formed by the solvent-induced effect when the solvophilic A-block is a majority component. The SCFT method provides an efficient way to screen promising molecular architectures for the ability to self-assemble into technologically promising hierarchical structures.

DPD Simulation of Protein Conformations: From α-Helices to β-Structures.

We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.

Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

We combine the statistical–mechanical 1D/3D-RISM-KH molecular theory of solvation with DFT electronic structure calculations and MD and coarse-grained DPD simulations, and apply them to study association phenomena in synthetic organic soft matter and biomolecular systems. This combined approach from electronic to molecular structure and coarse-graining allows us to address complex processes occurring in solution on very long timescales, such as protein–ligand binding, distributions of electrolyte solution species in ion channels, and oligomeric polyelectrolyte gelation. The statistics of rare events involving supramolecular solute and solvent is accounted for analytically within the 3D-RISM-KH molecular theory of solvation. The hybrid MD/3D-RISM-KH method for molecular dynamics of the biomolecule in the potential of mean force obtained with the molecular theory of solvation has been implemented in the Amber package. The 3D molecular theory of solvation also replaces MM/GB(PB)SA post-processing using empirical treatment of non-polar contributions with MM/3D-RISM-KH evaluation of the solvation thermodynamics. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as the GroEL chaperonin complex, GLIC ion channel, and 3D maps of ligand binding affinity of antiprion compound to mouse PrPC prion protein at once without phenomenological approximations. We apply the DFT/1D-3D-RISM-KH/DPD multiscale approach to investigate the structural and dynamical properties and gelation ability of oligomeric polyelectrolyte gelators, towards understanding of the gelation mechanism.

Modeling of polyethylene, poly(l-lactide), and CNT composites: a dissipative particle dynamics study

Dissipative particle dynamics (DPD), a mesoscopic simulation approach, is used to investigate the effect of volume fraction of polyethylene (PE) and poly(l-lactide) (PLLA) on the structural property of the immiscible PE/PLLA/carbon nanotube in a system. In this work, the interaction parameter in DPD simulation, related to the Flory-Huggins interaction parameter χ, is estimated by the calculation of mixing energy for each pair of components in molecular dynamics simulation. Volume fraction and mixing methods clearly affect the equilibrated structure. Even if the volume fraction is different, micro-structures are similar when the equilibrated structures are different. Unlike the blend system, where no relationship exists between the micro-structure and the equilibrated structure, in the di-block copolymer system, the micro-structure and equilibrated structure have specific relationships.

Microphase Separation of Phenylene Oligomers with Polymeric Side Chains: A Dissipative Particle Dynamics Study

The microphase-separated morphologies of p-phenylene oligomers with POx, PCL, PS, and PEO side chains are studied using DPD simulations. It is shown that the microphase-separated morphologies depend significantly on the degree of chemical incompatibility between the components as indicated by the Flory-Huggins interaction parameters. The good agreement of the microphase separated morphologies as simulated by DPD with the experimentally determined thin film morphologies suggests that DPD can produce convincing morphological information at the nanoscale. The results show that grafting of polymeric side chains can be an important tool to control the morphology of polymers with a rigid backbone.

Dissipative Particle Dynamics investigation of parameters affecting planar nanochannel flows

The method of Dissipative Particle Dynamics is applied to investigate the effect of the parameters involved in a nano-channel Poisseuille flow. The parameters considered here include (a) fluid/wall interactions, (b) wall material, (c) range of interaction of fluid particles and wall particles, and (d) external applied force. The computed macroscopic quantities include density, velocity, pressure and temperature profiles. Fluid particle localization near the solid wall is affected by the conservative force (fluid/wall interactions), the wall number density, and the range of atomic interactions (cut-off radius). The external driving force magnitude does not affect the number density distribution. Fluid velocity increases as the conservative force and the wall density increase and the cut-off radius decreases. Pressure distribution is mainly affected by the conservative force and the interaction cut-off radius. Temperature is uniform across most of the channel but presents an increase close to the solid walls especially when increasing the external driving force. We believe that the detailed knowledge of the fluid behaviour under variation of the system parameters obtained from the DPD simulations could be helpful in the design of nanodevices such as lab-on-a-chip devices and nanomixers.

Microphase separation in regular and random сopolymer melts by DPD simulations

Phase separation in melts of regular and random multiblock AB copolymers of equimolar composition and various mean block length was modeled using parallel dissipative particle dynamics simulations. Regular copolymers form well-shaped lamellas, strong and super-strong segregation regimes being identified. Microstructure formation in random copolymers with short blocks takes place at higher χ values and results in rough lamellas, the period of which is larger in comparison with the regular multiblocks. For random copolymers, increasing the mean block length deteriorates lamellar morphology and finally results in the formation of a bicontinuous structure. In a large simulation box, multidomain morphologies are observed.

Mesoscopic Simulations of Morphological Transitions of Stimuli-Responsive Diblock Copolymer Brushes

Using coarse-grained DPD simulations, we study the morphology of AB diblock copolymer brushes in selective solvents which are good for the anchored A blocks but poor (of varying degrees measured by the distance from the Θ-point, τB) for B blocks. Choosing appropriate polymer compositions given by the fraction of B blocks, fB, we find transitions between spherical and cylindrical micelles as well as inverted morphologies (perforated layer). We discuss the phase diagram in the fB−τB parameter space and analyze characteristic quantities of the structures obtained such as domain size, periodic spacing and brush height. The internal structure of the uniform (lamellar) structure is investigated in detail. The simulation results are compared with theoretical predictions and experimental observations.

GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating

A general purpose DPD simulation entirely implemented on GPU is presented in this paper, including cell-list updating, force calculation and integrating forward. The algorithm and optimization needed to obtain best performance of GPU is discussed. The performance benchmarks show that our implementation running on single GPU can be more than 20x faster than conventional implementation running on single CPU core and 10x faster than that running on 5 CPU cores.

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.

Simulation of vapor-liquid coexistence using dissipative particle dynamics

Due to a purely repulsive conservative interaction adopted in the traditional dissipative particle dynamics, the vapor-liquid coexistence phenomena or fluid flows with free surfaces could not be simulated. In the present study a recently proposed combination of short-range repulsive and long-range attractive interaction for DPD was investigated to explore its ability of simulating vapor-liquid coexistence or fluid flows with free surfaces. With this modified interaction, steady vapor-liquid interface could be obtained in DPD simulation, and the stress distribution across the vapor-liquid interface region was also discussed, which were found in accordance with those obtained by multibody DPD. Furthermore, surface tension of vapor-liquid interface was studied, and it was verified that Laplace’s law is satisfied in our simulation. Surface tensions obtained by theoretical method and Laplace’s law, respectively, are in agreement with each other.

DPD Simulations of PMMA‐Oleic Acid Mixture Behaviour in Organic Capped Nanoparticle Based Polymer Nanocomposite

AbstractDissipative Particle Dynamics has been used to investigate the different morphology of polymer nanocomposites. Such a study was addressed to the definition of a suitable tool for understanding the distribution of oleic acid (OA) capped nanoparticles embedded into poly‐methylmethacrylate (PMMA) matrix for the formation of nanocomposite materials. In particular, simulations of PMMA/OA mixtures at different composition have exhibited the self‐assembly of amphiphiles to form separated nanosized domains with different morphologies going from spheres, to tubules up to the formation of continuous planar sheets as the OA composition increases. On the other hand, simulations carried out on nanocomposite systems have shown that NPs do not perturb the observed phase behaviour of PMMA/OA mixtures. In fact, at low OA compositions nanoparticles are confined in the spherical lipid domains to form NP clusters, while at high OA composition NPs appear homogeneously distributed in the continuous lipid domain.

Mesoscopic study of cylindrical phases of poly(styrene)-poly(isoprene) copolymer: Order–order phase transitions by temperature control

Abstract Phase transitions of cylindrical structures of poly(styrene)–poly(isoprene) copolymer (PS–PI) toward spherical and gyroid structures were explored using DPD simulations and a coarse-grained model. Cylindrical phases were first obtained within a composition interval (“predominance region”) 0.2 f PS