Coarse-grained Dissipative Particle Dynamics Research Articles

A Structure Independent Molecular Fragment Interfuse Model for Mesoscale Dissipative Particle Dynamics Simulation of Peptides.

There is a need to develop robust computational models for mesoscale simulation of the structure of peptides over large length scales toward the discovery of novel peptides for medical applications to address the issues of peptide aggregation, enzymatic degradation, and short half-life. The primary objective was to predict the structure and conformation of peptides whose native structures are not known. This work presents a new model for computation of interaction parameters between the beads in coarse-grained dissipative particle dynamics (DPD) simulation that is properly calibrated for amino acids, supports compressibility requirement of water molecules, and accounts for subtle differences in the structure of amino acids and the charge in the side chain of charged amino acids. This new model is referred to as Structure Independent Molecular Fragment Interfuse Model, abbreviated as SIMFIM, because it accounts for specific interactions between different beads, which represent molecular fragments of the amino acids, in calculating nonbonded interaction parameters in the absence of knowing the actual peptide structure. The electrostatic interactions are incorporated in this model by using a normal distribution of charges around the center of the beads to prevent the collapse of oppositely charged soft beads. The uniquely parameterized DPD force field in the SIMFIM model is optimized for a given peptide with respect to the degree of coarse-grained graining for simulating the peptide over long times and length scales. The SIMFIM model was tested in this work using four peptides, namely, TrpZip2, Rubrivinodin, Lihuanodin, and IC3-CB1/Gai peptides, whose structures were sourced from the Protein Data Bank. The SIMFIM model predicted radius of gyration (Rg) values for the peptides closer to the actual structures as compared to the conventional model, and there was less deviation between the predicted and actual structures of the peptides.

Instability of membranes containing ionizable cationic lipids: Effects of the repulsive range of headgroups and tail structures

The stability of membranes formed by ionizable cationic lipids, which constitute the primary components in lipid nanoparticles capable of endosomal escape, is explored using coarse-grained dissipative particle dynamics. Three types of ionizable model lipids with different tail structures are considered. Endosome acidification causes the ionization of lipids, leading to an increased repulsive range between their headgroups. When electrostatic repulsion is modeled as a conservative force with a long-range cutoff distance (rc,HH), the membrane and vesicle experience a loss of structural integrity and develop holes as rc,HH is beyond a critical value, which varies with the tail structure. When Coulombic repulsion is explicitly incorporated and intensified, a fully ionized lipid membrane undergoes a loss of structural integrity, displaying a qualitative similarity to the effect observed with the increase in rc,HH on the membrane stability. Qualitatively similar results are obtained for partially ionized membranes as the fraction of charged lipids increases. The stability of a mixed lipid membrane containing both ionizable and conventional lipids is also investigated. The disruption of the bilayer structure occurs for a sufficiently high charged fraction. The membrane instability can be attributed to the decrease in the packing parameter, which significantly deviates from unity as the interaction range increases.

Molecular Processes Leading to Shear Banding in Entangled Polymeric Solutions.

The temporal and spatial evolution of shear banding during startup and steady-state shear flow was studied for solutions of entangled, linear, monodisperse polyethylene C3000H6002 dissolved in hexadecane and benzene solvents. A high-fidelity coarse-grained dissipative particle dynamics method was developed and evaluated based on previous NEMD simulations of similar solutions. The polymeric contribution to shear stress exhibited a monotonically increasing flow curve with a broad stress plateau at intermediate shear rates. For startup shear flow, transient shear banding was observed at applied shear rates within the steady-state shear stress plateau. Shear bands were generated at strain values where the first normal stress difference exhibited a maximum, with lifetimes persisting for up to several hundred strain units. During the lifetime of the shear bands, an inhomogeneous concentration distribution was evident within the system, with higher polymer concentration in the slow bands at low effective shear rate; i.e., γ˙<τR-1, and vice versa at high shear rate. At low values of applied shear rate, a reverse flow phenomenon was observed in the hexadecane solution, which resulted from elastic recoil of the molecules within the slow band. In all cases, the shear bands dissipated at high strains and the system attained steady-state behavior, with a uniform, linear velocity profile across the simulation cell and a homogeneous concentration.

Dissipative particle dynamics simulations for biological systems: From protein structures to cell mechanics

<p indent="0mm">Dissipative particle dynamics (DPD) is a mesoscopic coarse-grained simulation method developed in recent years, which is an important method for studying the dynamic behaviors of soft matter and complex fluids. In this method, each DPD particle represents a coarse-grained virtual cluster of a set of atoms or groups of matter. The position and momentum of the DPD particle are updated in a continuous phase but spaced at discrete time steps. The coarse-grained DPD particles are subject to simplified pairwise interacting conservative, dissipative, and random forces. Especially, the dissipative force and random force in the DPD method act as a heat sink and a source, respectively, and the combined effect of these two forces act as a thermostat, which conserves momentum and thus provides the correct description of hydrodynamic interactions for the model system. In addition, a common choice of the soft repulsion for the conservative force allows using larger integration time steps in DPD simulations than that usually allowed in classical molecular dynamics (MD) simulations. Hence, compared with the MD method, the computational cost of the DPD simulation is significantly reduced due to the smaller number of modeled particles and the larger computational time step, enabling the simulations of the static and dynamic behaviors of complex fluids and soft matter systems at physically attractive length scale and time scale. Moreover, the particle-based framework of the DPD method enables people to easily incorporate additional physical features into the model systems and extend its application to complex systems. For these reasons, the DPD method and its extension have been successfully applied to numerous soft matter and complex fluid systems such as oil/water/surfactant systems, chemical morphology, microscopic morphology, phase separation, as well as dynamics and rheological properties of polymer solutions and colloidal suspensions. In this paper, we first introduce the theoretical formulation and parameterization of the DPD method. Then, we review recent advances in DPD modeling of biological systems, focusing on its applications at the molecular and cellular scales. At the molecular scale, we highlight examples of successful simulations of the protein structures and their interactions, the structure and dynamics of amphiphilic lipid molecule membranes (e.g., the self-assembly of lipid molecules, the structure and properties of lipid membranes, the fusion of lipid membranes, and the budding and fission of lipid membranes), the interaction of lipid membranes with protein molecules, and the interaction of nanoparticles with lipid membranes; at the cellular scale, we focus on the DPD modeling of blood cell flow and blood rheological behaviors in the blood microcirculatory systems, including the shape deformation and flow dynamics of red blood cells, the margination and adhesion dynamics of white blood cells, the margination and aggregation behaviors of platelets, the hemorheological behavior of blood flow, as well as the separation of circulating tumor cells from blood flow using microfluidic devices. Additionally, we compare the advantages and disadvantages of the microscale blood flow simulations between the continuum-based methods and particle-based methods, including the DPD method. Finally, we briefly present the development trends and application prospects of DPD modeling in biological systems.

Interactions of Crosslinked Polyacrylic Acid Polyelectrolyte Gels with Nonionic and Ionic Surfactants.

The morphology and stability of surfactant-loaded polyelectrolyte gels are of great interest for a variety of personal care, cosmetic, and pharmaceutical products. However, the mechanisms of surfactant interactions with gel-forming polymers are poorly understood and experimentally challenging. The aim of this work is to explore in silico the specifics of surfactant absorption within polyelectrolyte gels drawing on the examples of typical non-ionic octaethylene glycol monooctyl ether (C8E8) and anionic sodium dodecyl sulfate (SDS) surfactants and polyacrylic acid modified with hydrophobic sidechains mimicking the practically important Carbopol polymer. Using the systematically parameterized coarse-grained dissipative particle dynamics models, we generate and characterize the equilibrium conformations and swelling of the polymer films in aqueous solutions with the surfactant concentrations varied up to the critical micelle concentration (cmc). We discover the striking difference in interactions of Carbopol-like polymers with nonionic and ionic surfactants under mildly acidic conditions. The sorption of C8E8 within the polymer film is found substantial. As the surfactant concentration increases, the polymer film swells and, close to cmc, becomes unstable due to the formation and growth of water pockets filled with surfactant micelles. Sorption of SDS at the same bulk concentrations is found much lower, with only about 1% of surfactant mass fraction achieved at cmc. As the SDS concentration increases further, a lamellae structure is formed within the film, which remains stable. Reduced swelling and higher stability indicate better prospects of using SDS-type surfactants with Carbopol-based gels in formulations for detergents and personal care products.

High Adsorption of α-Glucosidase on Polymer Brush-Modified Anisotropic Particles Acquired by Electrospraying-A Combined Experimental and Simulation Study.

In this particular contribution, we aim to immobilize a model enzyme such as α-glucosidase onto poly(DMAEMA) [poly(2-dimethyl amino ethyl methacrylate)] brush-modified anisotropic (cup- and disc-shaped) biocompatible polymeric particles. The anisotropic particles comprising a blend of PLA [poly(lactide)] and poly(MMA-co-BEMA) [poly((methyl methacrylate)-co-(2-(2-bromopropionyloxy) ethyl methacrylate)] were acquired by electrospraying, a scalable and convenient technique. We have also demonstrated the role of a swollen polymer brush grafted on the surface of cup-/disc-shaped particles via surface-initiated atom transfer radical polymerization in immobilizing an unprecedentedly high loading of enzyme [441 mg/g (cup)-589 mg/g (disc) of particles, 15-20 times higher than that of the literature-reported system] as compared to non-brush-modified particles. Circular dichroism spectroscopy was used to predict the structural changes of the enzyme upon immobilization onto the carrier particles. An enormously high amount of enzymes with preserved activity (∼85 ± 13% for cups and ∼78 ± 15% for discs) was found to adhere onto brush-modified particles at pH 7 via electrostatic adsorption. These findings were further explored at the atomistic level using a coarse-grained dissipative particle dynamics simulation approach, which exhibited excellent correlation with experimental results. In addition, accelerated particle separation was also achieved via magnetic force-induced aggregation within 20 min (without a centrifuge) by incorporating magnetic nanoparticles into disc-shaped particles while electrojetting. This further strengthens the technical feasibility of the process, which holds immense potential to be applied for various enzymes intended for several applications.

Effects of metal-polymer complexation on structure and transport properties of metal-substituted polyelectrolyte membranes

Morphological and transport properties of hydrated metal-substituted Nafion membranes doped with metal ions of different valency and coordination strength are explored using coarse-grained dissipative particle dynamics simulations. To incorporate the effects of metal-polymer complexation, we introduce a novel metal ion complexation model, in which the charged central metal ion is surrounded by dummy sites that coordinate with ligands. The model parameters are determined by matching the metal–ligand running coordination numbers and the diffusion coefficients obtained from atomistic simulations and/or experiments. The increase of valency and coordination strength is found to strongly influence both the morphology and transport characteristics of the membrane at all hydration levels. The membrane segregation into hydrophobic and hydrophilic sub-phases is affected by metal-sulphonate coordination induced crosslinking at the hydrophilic/hydrophobic interface. The simulation results indicate that the interfacial crosslinking influences the interfacial tension and thereby affect the growth and coalescence of water clusters upon the increase of hydration. Multivalent complexation hinders water and ion mobility and causes anomalous sub-diffusion and dramatic decrease of the water permeability and ionic conductivity. Our DPD model is found efficient in elucidating the mechanisms of coordination-induced cross-linking and complexation and predicting on a semi-quantitative level the morphological and transport properties of metal-substituted Nafion membranes depending on the ion valency and coordination strength. The proposed model can be further advanced and adopted for other polyelectrolyte systems, such as sulfonated block-copolymers, polysaccharide solutions and composites, and biopolymer assemblies.

Critical Micelle Concentrations in Surfactant Mixtures and Blends by Simulation.

We explore the use of coarse-grained dissipative particle dynamics simulations to predict critical micelle concentrations (CMCs) in polydisperse surfactant mixtures and blends. By fitting pseudo-phase separation models (PSMs) to aqueous solutions of binary surfactant mixtures at selected compositions above the CMC, we avoid the need for expensive simulations of more complex multicomponent mixtures performed as a function of dilution. The approach is demonstrated for sodium laureth sulfate (SLES) surfactants with polydispersity in the ethoxylate spacer. For this system, we find a modest degree of cooperativity in micelle formation, which we attribute to the reduced repulsion between charged headgroups for surfactants with dissimilar ethoxylate spacer lengths. However, this is insufficient to explain the lowered CMC often observed in commercial SLES samples, which we attribute to the presence of small amounts of unsulfated alkyl ethoxylates and/or traces of salt.

Solubilization of Charged Porphyrins in Interpolyelectrolyte Complexes: A Computer Study.

Using coarse-grained dissipative particle dynamics (DPD) with explicit electrostatics, we performed (i) an extensive series of simulations of the electrostatic co-assembly of asymmetric oppositely charged copolymers composed of one (either positively or negatively charged) polyelectrolyte (PE) block A and one water-soluble block B and (ii) studied the solubilization of positively charged porphyrin derivatives (P) in the interpolyelectrolyte complex (IPEC) cores of co-assembled nanoparticles. We studied the stoichiometric mixtures of 137 AB and 137 AB chains with moderately hydrophobic A blocks (DPD interaction parameter ) and hydrophilic B blocks () with 10 to 120 P added (). The P interactions with other components were set to match literature information on their limited solubility and aggregation behavior. The study shows that the moderately soluble P molecules easily solubilize in IPEC cores, where they partly replace PE and electrostatically crosslink PE blocks. As the large P rings are apt to aggregate, P molecules aggregate in IPEC cores. The aggregation, which starts at very low loadings, is promoted by increasing the number of P in the mixture. The positively charged copolymers repelled from the central part of IPEC core partially concentrate at the core-shell interface and partially escape into bulk solvent depending on the amount of P in the mixture and on their association number, . If is lower than the ensemble average , the copolymer chains released from IPEC preferentially concentrate at the core-shell interface, thus increasing , which approaches . If , they escape into the bulk solvent.

Influence of pore morphology on the diffusion of water in triblock copolymer membranes.

Understanding the transport properties of water in self-assembled block copolymer morphologies is important for furthering the use of such materials as water-purifying membranes. In this study, we used coarse-grained dissipative particle dynamics simulations to clarify the influence of pore morphology on the self-diffusion of water in linear-triblock-copolymer membranes. We considered representative lamellar, cylindrical, and gyroid morphologies and present results for both the global and local diffusivities of water in the pores. Our results suggest that the diffusivity of water in the confined, polymer-coated pores differs from that in the unconfined bulk. Explicitly, in confinement, the mobility of water is reduced by the hydrodynamic friction arising from the hydrophilic blocks coating the pore walls. We demonstrate that in lamella and cylindrical morphologies, the latter effects can be rendered as a universal function of the pore size relative to the brush height of the hydrophilic blocks.

Quantification of Ostwald Ripening in Emulsions via Coarse-Grained Simulations.

Ostwald ripening is a diffusional mass transfer process that occurs in polydisperse emulsions, often with the result of threatening the emulsion stability. In this work, we design a simulation protocol that is capable of quantifying the process of Ostwald ripening at the molecular level. To achieve experimentally relevant time scales, the dissipative particle dynamics (DPD) simulation protocol is implemented. The simulation parameters are tuned to represent two benzene droplets dispersed in water. The coalescence between the two droplets is prevented via the introduction of membranes, which allow diffusion of benzene from one droplet to the other. The simulation results are quantified in terms of the changes in the droplet volume as a function of time. The results are in qualitative agreement with experiments. The agreement with the Lifshitz-Slyozov-Wagner theory becomes quantitative when the simulated solubility and diffusion coefficient of benzene-in-water are considered. The effect of two different surfactants was also investigated. In agreement with both experimental observations and theory, the addition of surfactants at moderate concentrations decreased the Ostwald ripening rate because of the reduction in the interfacial tension between benzene and water; as the surfactant film becomes dense, other phenomena are likely to further delay the Ostwald ripening. In fact, the results suggest that the surfactant that yields higher density at the benzene-water interface delayed more effectively Ostwald ripening. The formation of micelles can also affect the ripening rate, in qualitative agreement with experiments, although our simulations are not conclusive on such effects. Our simulations show that the coarse-grained DPD formalism is able to capture the molecular phenomena related to Ostwald ripening and reveal molecular level features that could help to understand experimental observations. The results could be useful for predicting and eventually controlling the long-term stability of emulsions.

Elucidating the Effects of Metal Complexation on Morphological and Rheological Properties of Polymer Solutions by a Dissipative Particle Dynamics Model

When a salt is added to a polymer solution, metal cations may coordinate with polymer ligands forming interchain and intrachain links. Metal coordination leads to drastic changes of polymer morphology, formation of clusters, and, ultimately, a sol–gel transition that affect the solution rheology. Although metal coordination is ubiquitous in polymeric systems, the physical mechanisms of coordination-induced morphological and rheological changes are still poorly understood due to the multiscale nature of this phenomenon. Here, we propose a coarse-grained dissipative particle dynamics (DPD) model to study morphological and rheological properties of concentrated solutions of polymers in the presence of multivalent cations that can coordinate the polymer ligands. The coordinating metal is introduced as a 3D complex of planar, tetrahedral, or octahedral geometry with the central DPD bead representing the metal cation surrounded at the vertices by either four or six dummy beads representing coordination sites, s...

Dissipative particle dynamics study on the temperature dependent interfacial tension in surfactant-oil-water mixtures

Effects of cationic (CATB) and anionic (SDBS) surfactants on the interfacial tension (IFT) of surfactant/oil/water system at different temperatures are predicted using coarse-grained dissipative particle dynamics (DPD) at the mesoscopic scale. The DPD repulsive interaction parameters, aij, as a function of temperature (T) are calculated from the T dependent Flory-Huggins parameter χ for different components using all-atom molecular dynamics (MD). This paper provides a method based on DPD dynamics to obtain linear correspondences between the Flory-Huggins parameter χ and the excess repulsion parameter Δa at different temperatures, which is a bridge between DPD and MD. The IFTs are measured in surfactant/oil/water systems at different temperatures to validate simulated results, they are in good agreement. Both experiments and simulations indicate that the interfacial tension decreases with an increase of temperature. Meanwhile, the interfacial information including equilibrated interface morphology, mean interfacial density and RMS end-to-end distance is obtained, by which the capacities of different surfactants to regulate oil-water interfacial properties at different temperatures are evaluated. Compared with CTAB and SDBS, SDBS has a good resistance to a higher temperature, and can maintain a lower interfacial tension in the range of 343–358 K. This indicates that the interfacial tension decreases with the increase of temperature in a certain range and the sensitivity of different surfactants to temperature is different. Furthermore, the impact of inorganic salt (NaCl) on interfacial properties of ionic surfactant (CTAB) is analyzed. It demonstrates that the modified DPD method is a good alternative to study the interfacial characteristics of surfactant/oil/water system at different temperatures.

Dissipative particle dynamics simulation parameters and interactions of a hydrogel

In this work, we report a parameterization procedure to compute the parameters of a hydrogel consisting of a hydrophilic polymer and a cross-linker. The system is parameterized so that coarse-grained dissipative particle dynamics (DPD) simulations can be performed. Proper computation of the simulation parameters is crucial in order to represent the inherent chemical nature of the hydrogel and to model the correct structure. The polymer is parameterized by considering different volumes for coarse-grained beads. Moreover, the hydrogen bond interactions should be represented and properly defined in the simulations. To that purpose, we use a recently introduced parameterization procedure that incorporates the attraction as a result of the hydrogen bond interactions between relevant beads. This paper serves as an example of how the realistic simulation parameters of a hydrophilic polymer can be straightforwardly computed by leading to a proper determination of the structure and properties. The computational background, the procedures and the results of the computation are reported and discussed in this paper.

Surfactants adsorption on crossing stripes and steps.

Using coarse-grained dissipative particle dynamics (DPD) simulations, we systematically study the effect of surface heterogeneity on surfactant adsorption. Here we investigate the adsorption and aggregation of surfactants on hydrophobic stripes crossing each other perpendicularly (i.e., crossing stripes) and on hydrophobic steps. The results are compared with those obtained for isolated stripes. We find that on crossing stripes of moderate stripe widths (e.g., L = 0.61LS, 1.22LS and 1.83LS, where LS is the length of one surfactant molecule) the crossing region hinders the formation of defect-free adsorbed surfactant structures. By increasing the stripe width and/or by increasing the length of one of the two perpendicularly crossing stripes (i.e., lowering the surface density of defects/intersections), the crossing region is found to have a weaker effect on the features of the adsorbed structures. Regarding surfactant adsorption on steps, our simulation results show that the self-assembled aggregates can be stretched along the step corner, and the resultant elastic deformation can hinder adsorption. This qualitative observation can facilitate a description of surfactant adsorption that takes into consideration also the deformation of the self-assembled film. As suggested by such a general model, increasing the convex angle of the step, increasing the size of the surfactant head groups, and changing other physical parameters can reduce the elastic energy penalty, and yield larger amounts of surfactants adsorbed. The results presented could assist in understanding and sometimes predicting surfactant adsorption on heterogeneous surfaces, suggest methods to formulate surfactant mixtures to control surface coverage on heterogeneous surfaces, and perhaps facilitate new methods for the fabrication of nano-structured surfaces.

Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals.

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.

Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes

Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.

Theoretical insight into the relationship between the structures of antimicrobial peptides and their actions on bacterial membranes.

Antimicrobial peptides with diverse cationic charges, amphiphathicities, and secondary structures possess a variety of antimicrobial activities against bacteria, fungi, and other generalized targets. To illustrate the relationship between the structures of these peptide and their actions at microscopic level, we present systematic coarse-grained dissipative particle dynamics simulations of eight types of antimicrobial peptides with different secondary structures interacting with a lipid bilayer membrane. We find that the peptides use multiple mechanisms to exert their membrane-disruptive activities: A cationic charge is essential for the peptides to selectively target negatively charged bacterial membranes. This cationic charge is also responsible for promoting electroporation. A significant hydrophobic portion is necessary to disrupt the membrane through formation of a permeable pore or translocation. Alternatively, the secondary structure and the corresponding rigidity of the peptides determine the pore structure and the translocation pathway.

Multiscale Modeling Approach toward the Prediction of Viscoelastic Properties of Polymers.

We report a multiscale modeling approach to study static and dynamical properties of polymer melts at large time and length scales. We use a bottom-up approach consisting of deriving coarse-grained models from an atomistic description of the polymer melt. We use the iterative Boltzmann inversion (IBI) procedure and a pressure-correction function to map the thermodynamic conditions of the atomistic configurations. The coarse-grained models are incorporated in the dissipative particle dynamics (DPD) method. The thermodynamic, structural, and dynamical properties of the cis-1,4-polybutadiene melt are very well reproduced by the coarse-grained DPD models with a significative computational gain. We complete this study by addressing the challenging question of the investigation of the shear modulus evolution. As expected from experiments, the stress correlation functions show behaviors that are dependent on the molecular weights defining unentangled and weakly entangled polymer melts.

Dissipative Particle Dynamics Simulations on the Structure of Heavy Oil Aggregates

Heavy oil is an extremely complex colloidal system where asphaltenes, as the core of micelles, are dispersed in the continuous phase of other saturated fractions. We used dissipative particle dynamics (DPD) to simulate the mesoscopic colloidal structure of heavy oil and to determine its effective factors. Coarse-grained DPD model molecules were constructed in accordance with molecular structures of the component fractions in heavy oil. A modification of the standard DPD program was used to calculate the motion of rigid polycyclic aromatic rings. The simulations show that the coarse-grained DPD models used in this paper predict the colloidal structure of heavy oil well. The ordered structure of micelles depends greatly on the molecular structure of asphaltenes. Higher ordered micelles contain highly fused aromatic rings whereas the alkyl side-chains exhibit dispersing behavior. Deflocculation of the resins was observed in the simulations. A critical concentration ratio for the resin and asphaltene exists. The coagulation of heavy oil occurs when the concentration ratio of resin and asphaltene is less than this critical value.