DPD Simulations Research Articles

DPD simulation to reproduce lipid membrane microdomains based on fragment molecular orbital calculations

Lipid domains play a critical role in signal transduction and transport across cell membranes. The formation of domains in “HLC” ternary lipid bilayers composed of high transition temperature (high-Tm) lipids, low-Tm lipids, and cholesterol (Chol) has been extensively studied as a raft-like system. Recently, experiments were performed to control the formation of submicron domains in LLC lipid bilayers containing low-Tm phosphatidylethanolamine (PE), low-Tm phosphatidylcholine (PC), and Chol by manipulating the presence or absence of Chol. The formation of microdomains in this LLC mixture was replicated by dissipative particle dynamics simulation. The results show that domain formation can be replicated.

Photomodulated phase-separation kinetics in block copolymer melts: a DPD simulation study

ABSTRACT We study phase-separation kinetics of symmetric diblock copolymer (BCP) melt in 3 d subjected to sequential light on/off cycles. The incompatible blocks of each BCP chain are connected by a photosensitive bond, which undergoes breakage during photo-illumination (on-cycle) and recombination during the off-cycle. We set a shorter fixed time limit for each on-cycles and focus on analysing how the much longer duration of the light off-cycles affects the segregation kinetics. We explore two scenarios for each off-cycle time variation: one with equal and another with increasing durations. For both cases, we determine the rate constants for bond formation and degradation reactions and assess their influence on the dynamical scaling functions and the growth scale of evolving morphologies. The average domain size typically exhibits diffusive growth ( R ( t ) ∼ t 1 / 3 ) for a couple of cycles in the beginning. However, the domain growth nearly freezes during the rest of the cycles, resulting in bicontinuous and nearly frozen isotropic morphologies.

PH-induced morphological transition of aggregates formed by miktoarm star polymers in dilute solution: a mesoscopic simulation study.

The self-assembly of miktoarm star polymers μ-A i (B(D)) j C k in a neutral solution and the pH-responsive behaviors of vesicles and spherical micelles in an acidic solution have been investigated by DPD simulation. The results show that the self-assembled morphologies can be regulated by the lengths of pH-responsive arm B and hydrophilic arm C, leading to the formation of vesicles, discoidal micelles, and spherical micelles in a neutral solution. The dynamic evolution pathways of vesicles and spherical micelles are categorized into three stages: nucleation, coalescence, and growth. Subsequently, the pH-responsive behaviors of vesicles and spherical micelles have been explored by tuning the protonation degree of pH-responsive arm B. The vesicles evolves from nanodisks to nanosheets, then to nanoribbons, as the protonation degree increases, corresponding to a decrease in pH value, while the spherical micelles undergoes a transition into worm-like micelles, nanosheets, and nanoribbons. Notably, the electrostatic interaction leads the counterions to form a regular hexagonal pattern in nanosheets, while an alternative distribution of charged beads has been observed in nanoribbons. Furthermore, the role of the electrostatic interaction in the morphological transition has been elucidated through the analysis of the distribution of positive and negative charges, as well as the electrostatic potential for associates.

Injectable thermogel constructed from self-assembled polyurethane micelle networks for 3D cell culture and wound treatment.

Injectable hydrogels have attracted significant interest in the biomedical field due to their minimal invasiveness and accommodation of intricate scenes. Herein, we developed an injectable polyurethane-based thermogel platform by modulating the hydrophilic-hydrophobic balance of the segmented components with pendant PEG. The thermogelling behavior is achieved by a combination of the bridging from the hydrophilic PEG and the percolated network from the hydrophobic micelle core. Firstly, the thermogelation mechanism of this system was demonstrated by both DPD simulation and experimental investigation. The gelling temperature could be modulated by varying the solid content, the component of soft segments, and the length of the pendant PEG. We further applied 3D printing technology to prepare personalized hydrogel structures. This integration highlights the adaptability of our thermogel for fabricating complex and patient-specific constructs, presenting a significant advance in the field of regenerative medicine and tissue engineering. Subsequently, in vitro cell experiments demonstrated that the thermogel had good cell compatibility and could promote the proliferation and migration of L929 cells. Impressively, A549 cells could be expediently in situ parceled in the thermogel for three-dimensional cultivation and gain lifeful 3D cell spheres after 7 days. Further, in vivo experiments demonstrated that the thermogel could promote wound healing with the regeneration of capillaries and hair follicles. Ultimately, our study demonstrates the potential of hydrogels to prepare personalized hydrogel structures via 3D printing technology, offering innovative solutions for complex biomedical applications. This work not only provides a fresh perspective for the design of injectable thermogels but also offers a promising avenue to develop thermoresponsive waterborne polyurethane for various medical applications.

Architectural control over morphologies of bottlebrush block copolymer superstructures

The morphology of superstructures formed by bottlebrush block copolymers in the melt can be tuned by changing the side chain length or/and their grafting density at constant volume fractions of the blocks. This feature enables fabrication of microphase separated bulk structures and mesoporous materials thereof with spherical or cylindrical domains (precursors of the mesopores), with high porosity unattainable for materials produced from conventional linear block copolymers. These paradigms are proven by DPD simulations that allow constructing morphological phase diagrams of the melt of block copolymers comprising one linear and one bottlebrush block and comparing the simulation results to the predictions of the mean field analytical theory. While the binodal lines separating the stability regions of spherical and cylindrical domains predicted by the theory perfectly match the simulation results, the simulation indicates appearance of a gyroid phase around the theoretical binodal separating the stability ranges of cylinders and lamellae. The results of our work provide guidelines for macromolecular design of novel composite and mesoporous materials with a wide spectrum of potential applications.

Effect of amphiphilic polymers on phase separating binary mixtures: A DPD simulation study.

We present the phase separation dynamics of a binary (AB), simple fluid (SF), and amphiphilic polymer (AP) mixture using dissipative particle dynamics simulation at d = 3. We study the effect of different AP topologies, including block copolymers, ring block copolymers (RCP), and miktoarm star polymers, on the evolution morphologies, dynamic scaling functions, and length scale of the AB mixture. Our results demonstrate that the presence of APs leads to significantly different evolution morphologies in SF. However, the deviation from dynamical scaling is prominent, mainly for RCP. Typically, the characteristic length scale for SF follows the power law R(t) ∼ tϕ, where ϕ is the growth exponent. In the presence of high AP, we observe diffusive growth (ϕ → 1/3) at early times, followed by saturation in length scale (ϕ → 0) at late times. The extent of saturation varies with constraints imposed on the APs, such as topology, composition ratio, chain length, and stiffness. At lower composition ratios, the system exhibits inertial hydrodynamic growth (ϕ → 2/3) at asymptotic times without clearly exhibiting the viscous hydrodynamic regime (ϕ → 1) at earlier times in our simulations. Our results firmly establish the existence of hydrodynamic growth regimes in low surfactant-influenced phase separation kinetics of binary fluids and settle the related ambiguity in d = 3 systems.

Effectiveness of DPD Simulations to Predict the Dynamics of Polymer Chains in Solutions at Equilibrium and Steady Shear Flows

AbstractThe suitability of dissipative particle dynamics simulations is investigated to predict the dynamics of polymer chains in dilute polymer solutions. The authors find that the predictions depend on the value of the repulsive parameter for bead‐bead pairwise interactions used in the DPD simulations (aij). For all systems, the chain sizes and the relaxation time spectrum are analyzed. For aij = 0, theta solvent behaviour is obtained, whereas the dynamics at equilibrium agrees well with the predictions of the Zimm model. For higher values of aij, the static properties of the chain show good solvent behaviour. However, the scaling laws for the chain dynamics at equilibrium show wide variations, with consistent results obtained only at an intermediate value of aij = 25. At higher values of the repulsive parameter (aij ⩾ 25), the simulations are also able to predict the abrupt cut‐off in the relaxation spectrum, which has been observed earlier in experiments of dilute solutions. To verify further, the chain dynamics in shear flow using DPD simulations is studied. Specifically, the variation of the chain is analysed stretch and end‐over‐end tumbling with shear rates. Overall, the trends obtained from DPD simulations agree well with those observed in earlier BD simulations.

DPD simulation of the reciprocating translocation behaviour of polymer chain in a microchannel under variable external force

ABSTRACT In this study, an investigation has been carried out regarding the reciprocating translocation (i.e. back and forth motion) of a polymer chain in a microchannel. External force is one of the important factors in the movement of the polymer chain. In this investigation, variable forces are applied to the polymer chain and all fluid particles in which at a certain time, the direction of the force and the movement will change in this simulation. The behaviour and the properties of the chain, such as the radius of gyration, the centre of mass velocity and the amount of translocation, have been examined in this reciprocating movement. Based on the present results, when employing a longer polymer chain and especially applying the force on the polymer and fluid particles, due to the inertia effect, it would not be easily possible to stop the polymer chain. Consequently, changing the direction of polymer motion would not instantly occur by changing the force direction. In fact, some amount of displacement and lost time (LT) (around 6 dissipative particle dynamics units out of a total time of 40) will be associated with the case of applying force on just a polymer chain and imposing variable external force on all particles, LT has increased dramatically (dimensionless LT parameter is around 50%). The present method is a suitable tool for simulating the variable movement of polymer for the design of micro-actuators or polymer sensors.

A statistic study on raspberry vesicles: Formation and properties

This paper gives a statistic study on the formation of ABC raspberry vesicles under bulk swelling with DPD simulations. All vesicles formed through a disc wrap-up process, i.e. a disc micelle wraps up to form a vesicle. The lifetimes of the disc micelles before they become vesicles can be characterized as short and long (tfastandtslow). Vesicles formed with tfast have a high loading efficiency and a wide size distribution. Most of them have low membrane permeability. They resist structural deformation under shear due to their high bending rigidity. Vesicles formed with tslow have a narrow size distribution. They are small, and have low loading efficiency. A large portion of them have permeable membranes with low bending rigidity and structural defects. Shear could restructure these vesicles, and hence modify their permeability. Adjusting the repulsion between solvophobic polymers and solvents impacts on lifetimes of disc micelles. A reduction in such repulsion favours tslow. The knowledge obtained can be used to design raspberry vesicles of desired size, loading and cargo release properties.

Computing dissipative particle dynamics interactions to render molecular structure and temperature-dependent properties of simple liquids

Simulating structural and thermodynamical properties of liquids has always been a challenge. Typical examples of liquids that demonstrate particular structure and properties are water and the low molecular weight alcohols, for which hydrogen bond interactions lead to their distinctive properties, such as cage-like structures and temperature-dependent properties. Modeling these materials at the coarse-grained level is even a bigger challenge due to the loss of atomistic-level interactions. Nevertheless, one is interested in mimicking these typical properties at the coarse-grained level due to the relevance of these systems in complex environments, for which fully atomistic simulations still remain a challenge. In this paper, we introduce a mesoscopic level parameterization of DPD interactions to study the particular structural and thermodynamic properties of liquid water, methanol, ethanol and 1-propanol. The conservative repulsive DPD interactions are explicitly computed by a bottom-up parameterization, in which experimental thermodynamics data are used. A previously developed statistical mechanics approach is used to compute the hydrogen bond strength. The transport properties, such as viscosity, and thermodynamical properties, such as isothermal compressibility, are found to agree reasonably well with experimental data. Moreover, the structure as characterized by the radial distribution function and angular distributions of three neighboring molecules are in line with the atomistic simulations performed in this work. Furthermore, the temperature-dependency of the repulsive DPD interactions is modeled by incorporating the experimental isothermal compressibilities at different temperatures. The effect of the temperature on the hydrogen bond strengths is considered as well and the structural properties are predicted via the DPD simulations. In general, our work can be viewed as an attempt to model systems by the DPD simulations, where hydrogen bonds play a crucial role. The computed parameterization of DPD interactions is believed to pave the way towards extending the current applicability of DPD method to more complex systems.

DPD Simulation on the Transformation and Stability of O/W and W/O Microemulsions.

The dissipative particle dynamics simulation method is adopted to investigate the microemulsion systems prepared with surfactant (H1T1), oil (O) and water (W), which are expressed by coarse-grained models. Two topologies of O/W and W/O microemulsions are simulated with various oil and water ratios. Inverse W/O microemulsion transform to O/W microemulsion by decreasing the ratio of oil-water from 3:1 to 1:3. The stability of O/W and W/O microemulsion is controlled by shear rate, inorganic salt and the temperature, and the corresponding results are analyzed by the translucent three-dimensional structure, the mean interfacial tension and end-to-end distance of H1T1. The results show that W/O microemulsion is more stable than O/W microemulsion to resist higher inorganic salt concentration, shear rate and temperature. This investigation provides a powerful tool to predict the structure and the stability of various microemulsion systems, which is of great importance to developing new multifunctional microemulsions for multiple applications.

Dual-responsive zwitterion-modified nanopores: a mesoscopic simulation study.

In this work, dissipative particle dynamics simulation was carried out to investigate the intelligent switching effect of nanopores grafted by the zwitterionic polymer brushes poly(carboxybetaine) with excellent antifouling properties. The result shows that with different grafting densities and grafting lengths, zwitterionic polymer brushes show typical pH- and salt-responsiveness features. When the grafting density is greater than 0.2 accompanying a grafting length of 40, pH has a significant effect on the structure and pore size of the nanopores, that is, the pore remains open under neutral condition and exhibits a switching effect under acidic condition. Similarly, the size of the nanopore can be tuned by altering the grafting density and polymer chain length under salt-concentration-responsive conditions. Differently, compared with the pH effect, the salt concentration has an obvious impact on the switching effect, i.e., responsiveness emerges with a lower grafting density and length. This work provides molecular level mechanism and theoretical guidance for the design of smart nanopores modified by zwitterionic polymer brushes, as well as plays an important role in the construction of nanopores with antifouling and pH/salt-responsive properties.

Dissipative particle dynamics simulation study on ATRP-brush modification of variably shaped surfaces and biopolymer adsorption.

We present a dissipative particle dynamics (DPD) simulation study on the surface modification of initiator embedded microparticles (MPs) of different shapes via atom transfer radical polymerization (ATRP) brush growth. The surface-initiated ATRP-brush growth leads to the formation of a more globular MP shape. We perform the comparative analysis of ATRP-brush growth on three different forms of particle surfaces: cup surface, spherical surface, and flat surface (rectangular/disk-shaped). First, we establish the chemical kinetics of the brush growth: the monomer conversion and the reaction rates. Next, we discuss the structural changes (shape-modification) of brush-modified surfaces by computing the radial distribution function, spatial density distribution, radius of gyration, hydrodynamic radius, and shape factor. The polymer brush-modified particles are well known as the carrier materials for enzyme immobilization. Finally, we study the biopolymer adsorption on ATRP-brush modified particles in a compatible solution. In particular, we explore the effect of ATRP-brush length, biopolymer chain length, and concentration on the adsorption process. Our results illustrate the enhanced biopolymer adsorption with increased brush length, initiator concentration, and biopolymer concentration. Most importantly, when adsorption reaches saturation, the flat surface loads more biopolymers than the other two surfaces. The experimental results verified the same, considering the disk-shaped flat surface particles, cup-shaped particles, and spherical particles.

Micellar phase control of poly(acrylic-acid-co-acrylonitrile) polymeric micelles via upper critical solution temperature: Removal process of organic molecules

Micellar phase control of thermoresponsive polymeric micelles (PAA-co-PAN) via upper critical solution temperature (UCST) in aqueous environment was explored using DPD simulations. Performing a thermal scan we show that above its UCST a stable micellar system is generated. When the temperature decreases below the UCST (304 K), the colloidal system becomes thermodynamically unstable generating hydrophobic particles with PAN-core and PAA-shell. A notable effect is the generation of a cloud point and this polymeric multiphase behaviour is used to show the removal of methylene-blue dye from a solution. The stages of the removal process via cloud point are shown in detail.

Investigation of morphology, micelle properties, drug encapsulation and release behavior of self-assembled PEG-PLA-PEG block copolymers: A coarse-grained molecular simulations study

Targeted drug delivery has become one of the key fields of personalized medicine. Developing candidate drug delivery agents requires a thorough understanding of the drug carrier materials by means of structure, drug encapsulation and release properties. To this aim, coarse-grained DPD simulations are employed to study the morphology, drug encapsulation and release of a particular amphiphilic block copolymer system. Extent of the drug encapsulation and release are observed to be mainly affected from copolymer concentration in the mixture. Mean aggregation number and average micelle volume are observed to increase as drug is encapsulated in the micelles. In addition, the shape of micelles is characterized as mainly spherical. It is observed that the drug release follows a pseudo-Fickian diffusion model and can be represented by the Korsmeyer-Peppas model. Furthermore, the diffusion rate of the drug molecules is observed to increase mainly in the release-phase. Our simulations can be viewed as a computational attempt to model the drug encapsulation and release by mimicking real experimental conditions, while yielding results on the structure and dynamics of the polymeric carrier. The results can be anticipated to find applications in understanding and controlling the parameters to design candidate drug delivery micelles at the molecular level.

A new approach to thermal responsivity and hydrodynamics of poly(N-isopropylacrylamide) in aqueous solution: all-atom and mesoscopic simulations

In this study, the impact of chemical and physical characteristics of poly(N-isopropylacrylamide) (PNIPAm) in water on its thermoresponsive behavior and aggregation was investigated via all-atom and mesoscopic simulations. The calculated dimensional and spatial parameters of the PNIPAm proved the existence of a critical chain length consisting of 15 repeating units (1697 g mol−1) which beyond it the PNIPAm conformations depend on the temperature. The influence of chain length on the interfacial behaviors and non-bonded interactions of PNIPAm in water indicated that the thermoresponsive behavior of the PNIPAm chain is independent of the chain length, from interactional aspect. Interestingly, the interactional barriers against the PNIPAm temperature dependency was correlated to the polymer intramolecular interactions and their contribution to heat capacity (C p-intra ). The simulation results indicated the highest barrier energy against the polymer bending at the critical chain length with C p-intra = 1.0189 kcal mol−1. Additionally, the influence of the chain length on its aggregation mechanism in water was evaluated using DPD simulation to correlate the PNIPAm spatial shape to dynamics and frictional solvent forces acting on the solute. According to the simulation results, the PNIPAm has an innate ability for chain aggregation. The higher and less aggregation intensity was occurred for the chain with shorter and longer length than the critical chain length, respectively. The presented studies can be used to design PNIPAm block with a proper molecular weight for preparing an efficient copolymer with chain network formation ability in water.

Investigation of ibuprofen loading in PEG–PLGA–PEG micelles by coarse-grained DPD simulations

Investigation of ibuprofen loading in PEG–PLGA–PEG micelles by coarse-grained DPD simulations

Development of the analytical method using DPD simulation for molten fuel behaviour in a sodium-cooled fast reactor

Development of the analytical method using DPD simulation for molten fuel behaviour in a sodium-cooled fast reactor

Numerical simulation of blood flow modeled as a fluid- particulate mixture

ABSTRACT A continuum model for the transport of red blood cells (RBC) inside arteries and capillaries of small diameters is proposed. The pressure and velocity fields are solved using the Navier-Stokes equations while the distribution of the RBC volume fraction, namely, hematocrit is obtained by solving the particle transport equation arising from the diffusive flux model. The momentum and hematocrit transport equations are coupled through a hematocrit-dependent blood viscosity model. The coupled equations are numerically solved using a 3D unstructured finite volume method. The proposed model predicts the shear induced diffusion of RBCs where RBCs migrate from the wall to the center of the blood vessel leading to a cell free layer (CFL) near the wall. Three geometries with sizes of the order of 40 µm have been considered for the present work. For flow inside a tube, results in terms of the concentration distribution and cell-free layer from the present continuum model show a good match with experiments and DPD simulations. For flow inside a tube with a constriction it is found that hematocrit depletion is greater downstream of the neck of the constriction. In addition, the effect of hematocrit loading on its distribution is correctly predicted. Finally, for a flow inside a tube with a bifurcation the average hematocrit concentration is found to be higher for the branch with the higher flow rate, thereby complying with the well-known bifurcation law.

Towards extreme scale dissipative particle dynamics simulations using multiple GPGPUs

A multi-GPGPU development for Mesoscale Simulations using the Dissipative Particle Dynamics method is presented. This distributed GPU acceleration development is an extension of the DL_MESO package to MPI+CUDA in order to exploit the computational power of the latest NVIDIA cards on hybrid CPU–GPU architectures. Details about the extensively applicable algorithm implementation and memory coalescing data structures are presented. The key algorithms’ optimizations for the nearest-neighbour list searching of particle pairs for short range forces, exchange of data and overlapping between computation and communications are also given. We have carried out strong and weak scaling performance analyses with up to 4096 GPUs. A two phase mixture separation test case with 1.8 billion particles has been run on the Piz Daint supercomputer from the Swiss National Supercomputer Center. With CUDA aware MPI, proper GPU affinity, communication and computation overlap optimizations for multi-GPU version, the final optimization results demonstrated more than 94% efficiency for weak scaling and more than 80% efficiency for strong scaling. As far as we know, this is the first report in the literature of DPD simulations being run on this large number of GPUs. The remaining challenges and future work are also discussed at the end of the paper.