Dissipative Particle Dynamics Research Articles

New strategy for structure rearrangement of thin-film composite (TFC) polyamide (PA) membranes and offering potential use in both aqueous and organic solvents

The purity of sodium hexafluorophosphate (NaPF6) is crucial for the preparation of electrolytes in manufacturing. We propose a simple process in order to induce membrane structure rearrangement process (SRP) by activating thin-film composite (TFC) membranes with polyamide (PA) structure and explore their potential green recycling application in concentrating sodium-ion batteries (SIBs) electrolyte. The method utilizes a solution containing polar aprotic solvent as the soaking and activating solution to swell and disintegrate the loosely cross-linked PA layer, and a non-solvent solidification solution complete the SRP, enhancing the permeability of the PA layer while maintaining high rejection rates for divalent ions. Subsequently, during the further treatment of the membrane surface in structure rearrangement, tert-butanol (TBA) is introduced into the aqueous solution to reconstruct the surface PA layer, further improving the permeability. The optimal D8010T10 achieved a permeation flux of 24.2 L m−2 h−1·bar−1, with rejection rates for sodium sulfate (Na2SO4), magnesium chloride (MgCl2), and magnesium sulfate (MgSO4) reaching 94.7 %, 98.4 %, and 99.1 % respectively. And the mechanism of SRP with different solvent is analyzed and explained through dissipative particle dynamics (DPD) simulations. This study provides a commercially viable approach for manufacturing high-performance membranes. The D8010T10 membrane achieves more than 90 % separation efficiency for sodium hexafluorophosphate (NaPF6) dissolved in different solvents, providing a potential solution for the concentration and recovery of NaPF6 in lab-scale, verified its potential use in the organic solvent nanofiltration (OSN) and a path way for waste membrane recycling and degrading use in the industry.

All-natural and triple-inspired Janus electrospun fibers with integrated functions for high-performance liquid food packaging

The liquid barrier is a central component of functional liquid packaging materials and is crucial for encapsulating liquid food. To develop high-performance liquid packaging materials for the long-term storage of liquid food, a strong and stable liquid barrier and the simultaneous integration of diverse functionalities must be realized. In this study, inspired by mussel adhesion proteins, nanoparticles are synthesized through oxidative self-polymerization. Furthermore, electrostatic spinning is used for creating multifunctional electrospun fibers for liquid food packaging, which is inspired by the superhydrophobicity of lotus leaf surface and structures of red blood cells. A unique Janus structure with a thin hydrophilic layer and a thick hydrophobic layer prevents liquid food penetration for 12 (EHN/KN electrospun fibers) and 17 days (KN/EHN electrospun fibers). The liquid infiltration mechanism of Janus electrospun fibers is elucidated using the multibody dissipative particle dynamics method, emphasizing their efficacy in avoiding liquid penetration. Moreover, multifunctional KN/EHN electrospun fibers exhibit remarkable characteristics such as water resistance (water contact angle > 150°), UV-blocking (∼100 %), degradability (70 days in soil), biosafety (∼100 %), antioxidation (> 90 %), antimicrobial (∼100 %), grapes and meat freshness retention properties. Thus, this study provides insights into sustainable, high-performance liquid food packaging for enhanced preservation.

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

Abstract 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 (DPD) simulation. The results show 
that domain formation can be replicated.

Dissipative particle dynamics for coarse-grained models.

We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully off-lattice method that allows straightforward incorporation of hydrodynamics at desired solvent viscosity, compressibility, and solute diffusivity with any particle-based solute model. Solutes interact with the solvent only through the DPD thermostat, which ensures that the equilibrium properties of the solute system are not affected by the introduction of the DPD solvent, while the thermostat coupling strength sets the desired solute diffusivity. Thus, DPDS can be used as a replacement for traditional molecular dynamics thermostats such as Nosé-Hoover and Langevin. We demonstrate the applicability of DPDS in the case of polymer dynamics and electroosmotic flow through a nanopore. The method should be broadly useful as a means to introduce hydrodynamic interactions to existing coarse-grained models of solutes and soft materials.

Dual targeting total saponins of Pulsatilla of natural polymer crosslinked gel beads with multiple therapeutic effects for ulcerative colitis

Oral colon targeted drug delivery system (OCTDDS) is desirable for the treatment of ulcerative colitis (UC). In this study, we designed a partially oxidized sodium alginate-chitosan crosslinked microsphere for UC treatment. Dissipative particle dynamics (DPD) was used to study the formation and enzyme response of gel beads from a molecular perspective. The formed gel beads have a narrow particle size distribution, a compact structure, low cytotoxicity and great colon targeting in vitro and in vivo. Animal experiments demonstrated that gel beads promoted colonic epithelial barrier integrity, decreased the level of pro-inflammatory factors, accelerated the recovery of intestinal microbial homeostasis in UC rats and restored the intestinal metabolic disorders. In conclusion, our gel bead is a promising approach for the treatment of UC and significant for the researches on the pathogenesis and treatment mechanism of UC.

Investigation of morphology and structure of drug-loaded PLA-b-PEO-b-PLA polymeric micelle: A dissipative particle dynamics simulations study.

The dissipative particle dynamics (DPD) simulation was used to study the morphologies and structures of the paclitaxel-loaded PLA-b-PEO-b-PLA polymeric micelle. We focused on the influences of PLA block length, PLA-b-PEO-b-PLA copolymer concentration, paclitaxel drug content on morphologies and structures of the micelle. Our simulations show that: (i) with the PLA block length increase, the self-assemble structure of PLA-b-PEO-b-PLA copolymers with paclitaxel vary between onion-like structure (core-middle layer-shell) to spherical core-shell structure. The PEO shell thins and the size of the PLA core increases. The onionlike structures are comprised of the PEO hydrophilic core, the PLA hydrophobic middle layer, and the PEO hydrophilic shell, the distribution of the paclitaxel drug predominantly occurs within the hydrophobic intermediate layer; (ii) The system forms a spherical core-shell structure when a small amount of the drug is added, and within a certain range, the size of the spherical structure increases as the drug amount increases. When the drug contents (volume fraction) cdrug = 10%, it can be observed that the PLA4-b-PEO19-b-PLA4 spherical structures connect to form rod-shaped structures. With the length of PLA block NPLA = 8, as the paclitaxel drug concentrations cdrug = 4%, PEO has been insufficient to completely encapsulate the PLA and paclitaxel drug beads. To enhance drug loading capacity while maintaining stability of the system in aqueous solution, the optimal composition for loading paclitaxel is PLA4-b-PEO19-b-PLA4; the drug content is not higher than 4%; (iii) The paclitaxel-loaded PLA4-b-PEO19-b-PLA4 micelle undergo the transition from onionlike (core-middle layer-shell) to spherical (core-shell) to rod-shaped and lamellar structure as the PLA4-b-PEO19-b-PLA4 copolymer concentration increases from ccp = 10% to 40%.

Understanding self-assembly mechanisms in supramolecular fiber materials through multiscale simulation

Supramolecular materials, assembled through non-covalent interactions, have emerged as a versatile and tunable platform for the development of advanced functional materials with tailored properties and applications. However, comprehending the interactions between self-assembled monomers at the molecular level, particularly when organized into fibrous structures, remains a considerable challenge. In this study, we discovered that solely relying on all-atomistic molecular dynamics simulations is insufficient to reproduce the self-assembly process and the formation of fibrous supramolecular structures. Thus, we combined dissipative particle dynamics (DPD) and all-atomistic molecular dynamic simulations to accurately simulate the fibrous supramolecular structures previously observed in experiments. These structures consist of benzene-1,3,5-tricarboxamide (BTA-EG4), 2-ureido-4 [1H]-pyrimidinone-ethylene glycol molecules (UPy-EG), and glycyrrhizic acid (GA) molecules, each exhibiting varying degrees of topology and planarity. Our analyses focused on elucidating the stability mechanism of these fibrous structures. Notably, we found that hydrogen bonds, π-π interactions and nonbonded interactions, especially Coulomb interaction between monomers and water molecules, play pivotal roles in stabilizing these fibrous structures. This study significantly contributes to our understanding of self-assembly mechanism in supramolecular fiber materials and opens avenues for extending this knowledge to other fibrous supramolecular architectures.

Cholesteric liquid crystal phase variations within nanotubes: an in-depth analysis of the influences of twist radius and molecular pitch

ABSTRACT This study investigates the self-assembly and phase transitions of cholesteric liquid crystals (CLCs) when confined in nanotubes, specifically focusing on the variations in their molecular structures. A dissipative particle dynamics method was used to investigate how the changes in helix radius ( r LC ) and pitch ( P ) affect the behaviour of the LCs. For pitches of 24, 12, and 6, the orientation order parameter ( P 2 ) showed distinct trends during cooling. Smaller helix radii resulted in isotropic to nematic to smectic phase transitions, whereas larger radii resulted in a novel smectic phase with spiral structures (Sm   s ). Circumferential local-order parameters ( P 2 r and P 2 z ) were introduced to better characterise the phases, and a disordered spiral-structure phase (Sm   s 2 ) with local perturbations was observed. The transitions between isotropic, nematic, and smectic phases, highlighting the influence of the pitch and helix radius, were observed from the phase diagrams. Smaller pitches and radii prevented the formation of stable structures; however, specific combinations induced characteristic spiral structures in the smectic phase. These results provide new insights into the self-assembly of confined CLCs, which have potential applications in the design of photonic devices and LC-based sensors. This study advances our understanding of phase control in quasi-one-dimensional systems and highlights the importance of molecular variations in liquid crystal behaviour.

Collapse and expansion kinetics of a single polyelectrolyte chain with hydrodynamic interactions.

We investigate the collapse and expansion dynamics of a linear polyelectrolyte (PE) with hydrodynamic interactions. Using dissipative particle dynamics with a bead-spring PE model, long-range electrostatics, and explicit ions, we examine how the timescales of collapse tcol and expansion texp depend on the chain length N and obtain scaling relationships tcol ∼ Nα and texp ∼ Nβ. For neutral polymers, we derive values of α = 0.94 ± 0.01 and β = 1.97 ± 0.10. Interestingly, the introduction of electrostatic interaction markedly shifts α to α ≈ 1.4 ± 0.1 for salt concentrations within c = 10-4 to 10-2M. A reduction in the ion-to-monomer size ratio noticeably reduces α. On the other hand, the expansion scaling remains approximately constant, β ≈ 2, regardless of the salt concentration or ion size considered. We find β > α for all conditions considered, implying that expansion is always slower than collapse in the limit of long polymers. This asymmetry is explained by distinct kinetic pathways of collapse and expansion processes.

Coarse-grained simulation of thermal conductivity of boron nitride/epoxy composites based on DPD and SPH method

In this study, thermal conductivity (TC) of BN/polymer composites is investigated utilizing dissipative particle dynamics (DPD) and smoothed-particle hydrodynamics (SPH) methods by establishing the coarse-grained (CG) models of boron nitride nanotube (BNNT) and boron nitride nanosheet (BNNS). The Iterative Boltzmann inversion (IBI) approach is employed to calculate the parameters of the potential function of the hexagonal boron nitride (h-BN) coarse grain model for DPD method. Mesoscopic simulations on the TC of BNNT/EP, BNNS/EP, and BNNT/BNNS/EP composites are performed using SPH and DPD simulations to investigate the effects of nanofiller ratio, aspect ratio, size, and orientation on TC. The CG models established for the BNNT and BNNS structures are proven to be efficient in DPD and SPH simulations for predicting the TC of h-BN/polymer composites. Furthermore, it is demonstrated that the TC of BNNT/BNNS/EP composites is superior to that of BNNT/EP and BNNS/EP composites at the same filler ratio due to the synergistic effect of BNNT and BNNS.

Simulating Brownian motion in thermally fluctuating viscoelastic fluids by using the smoothed profile method

To investigate the Brownian motion of individual particles suspended in viscoelastic fluids, the stochastic smoothed profile method (SPm) for direct numerical simulation is developed by extending deterministic SPm for suspensions in viscoelastic media. To simulate viscoelastic flow driven by thermal fluctuations in the suspending medium, the random stress in the fluid momentum equation as well as the random driving force for the conformation tensor in the Oldroyd-B model are incorporated according to the fluctuating hydrodynamics and fluctuating viscoelasticity formalisms. The thermal equilibrium and dynamical properties calculated by using numerical simulations successfully reproduce the analytic predictions, validating the direct simulation for the coupled fluctuating Navier–Stokes and Oldroyd-B equations and for the coupling between the stochastic viscoelastic medium and individual particles. As an application of the stochastic SPm, we investigate finite system-size effects under periodic boundary conditions (PBCs) on the passive microrheological relationship between the mean-square displacement (MSD) of a Brownian particle and the medium's dynamic modulus. Comparing the modulus that was microrheologically calculated from the MSD with the input modulus reveals that the effect of periodic image cell interaction appears not only in the long-time diffusive regime but also in the short-time region. A frequency-dependent finite system-size correction is implemented by phenomenologically extending the long-time diffusive regime correction, allowing passive microrheology analysis under PBCs. This result can be directly applied to other mesoscale numerical simulations including coarse-grained molecular dynamics and dissipative particle dynamics simulations.

Characterization of partial wetting by CMAS droplets using multiphase many-body dissipative particle dynamics and data-driven discovery based on PINNs

The molten sand that is a mixture of calcia, magnesia, alumina and silicate, known as CMAS, is characterized by its high viscosity, density and surface tension. The unique properties of CMAS make it a challenging material to deal with in high-temperature applications, requiring innovative solutions and materials to prevent its buildup and damage to critical equipment. Here, we use multiphase many-body dissipative particle dynamics simulations to study the wetting dynamics of highly viscous molten CMAS droplets. The simulations are performed in three dimensions, with varying initial droplet sizes and equilibrium contact angles. We propose a parametric ordinary differential equation (ODE) that captures the spreading radius behaviour of the CMAS droplets. The ODE parameters are then identified based on the physics-informed neural network (PINN) framework. Subsequently, the closed-form dependency of parameter values found by the PINN on the initial radii and contact angles are given using symbolic regression. Finally, we employ Bayesian PINNs (B-PINNs) to assess and quantify the uncertainty associated with the discovered parameters. In brief, this study provides insight into spreading dynamics of CMAS droplets by fusing simple parametric ODE modelling and state-of-the-art machine-learning techniques.

Mechanistic Study of the Effects of Surfactants and Asphaltenes on the Action of Emulsions with Different Water Contents: Based on Dissipative Particle Dynamics

Mechanistic Study of the Effects of Surfactants and Asphaltenes on the Action of Emulsions with Different Water Contents: Based on Dissipative Particle Dynamics

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.

Molecular Simulation Study of the Kinetics and Mechanism of Micellization of Charged and Uncharged Block Copolymer in Aqueous Solution: Polystyrene-Block-Poly(acrylic acid) PS-b-PAA

The micellization kinetics, dynamics, and diffusional properties of poly(styrene)-block-poly(acrylic acid) copolymer chains in salt-free aqueous solution have been investigated as a function of the copolymer composition (XPS ) for the cases of un-ionized (charge density f = 0) and ionized PAA blocks (charge density f = 1), for the first time to our knowledge via atomistic molecular dynamic simulations. The micelle formation mechanism was inspected by tracking the population of unimers and clusters across the simulation trajectory; it confirmed that the asymmetric copolymer micelle formation followed a combined approach of unimer insertion and cluster fusion mechanisms, while symmetric micelle formation followed the unimer insertion method exclusively. Micelle formation took a longer time for copolymers having charged (ionized) PAA blocks (f > 0) and relatively short PS blocks (number fraction of PS repeat units in copolymer XPS < 0.5) due to the presence of a greater number of hydrophobic groups, in agreement with the micellization kinetics observed for model copolymer micelles via DPD (Dissipative Particle Dynamics) simulation studies in literature. The conformational dynamics were studied using the relaxation of backbone dihedral angles and radius of gyration, for the core and corona blocks, respectively, showed that the PS blocks relaxed slower as compared to the soluble PAA blocks in solution due to their hydrophobic nature. The conformational relaxation time increased linearly for the PS blocks and was invariant for the PAA blocks with respect to XPS. The interaction dynamics of the PS-b-PAA copolymer micelles studied via the relaxation times of the PAA-PAA inter-chain (τHB,PP) and PAA-water inter-molecular hydrogen bonds (τHB,PW) showed the increase of τHB,PP, and the decrease of τHB,PW in solution with the increase in XPS. The PAA-water H-bond relaxes slower at f = 1 than that at f = 0 due to the stronger affinity of ionized PAA units with water molecules. The diffusivity of the copolymer chains decreased exponentially with an increase in XPS value, which is in agreement with the theoretical and experimental observations described in the literature.

Construction of Multiscale Dissipative Particle Dynamics (DPD) Models from Other Coarse-Grained Models.

We present a general scheme for converting coarse-grained models into Dissipative Particle Dynamics (DPD) models. We build the corresponding DPD models by analogy with the de novo DPD coarse-graining scheme suggested by Groot and Warren (J. Chem. Phys., 1997). Electrostatic interactions between charged DPD particles are represented though the addition of a long-range Slater Coulomb potential as suggested by González-Melchor et al. (J. Chem. Phys., 2006). The construction is illustrated by converting MARTINI models for various proteins into a DPD representation, but it not restricted to the usual potential form in the MARTINI model-viz., Lennard-Jones potentials. We further extended the DPD scheme away from the typical use of homogeneous particle sizes, therefore faithfully representing the variations in the particle sizes seen in the underlying MARTINI model. The accuracy of the resulting construction of our generalized DPD models with respect to several structural observables has been benchmarked favorably against all-atom and MARTINI models for a selected set of peptides and proteins, and variations in the scales of the coarse-graining of the water solvent.

Influence of the internal structure of straight microchannels on inertial transport behavior of particles

The rapid advancement of Micro-Electro-Mechanical Systems (MEMS) technology has established microfluidics as a pivotal field. This technology marks the onset of a new era in various applications, including drug testing, cell culture, and disease monitoring, underscoring its extensive practicality and potential for future exploration. This research delves into the intricate behavior of particle inertial migration within microchannels, particularly focusing on the impact of different channel structures and Reynolds numbers (Re). Our studies reveal that particles in microchannels with one-sided sharp-cornered microstructures migrate towards the sharp corner at a relative position of 0.4 under low flow rates, and towards the straight wall side at a relative position of 0.8 under high flow rates. The migration pattern of equilibrium positions varies with different arrangements of sharp-corner structures, achieving stability at the channel's center only when the sharp corners are symmetrically arranged on both sides. Our investigation into the shape of microstructures indicates that sharp-cornered structures generate a more stable secondary flow compared to rectangular and semi-circular structures, preventing particle aggregation at the outlet. To address the challenges associated with handling variable cross-section geometries and solid-wall boundaries in dissipative particle dynamics methods effectively, we have developed a dissipative particle dynamics model specifically for analyzing such microchannels. Building upon our previous research, this model introduces a conservative force coefficient for particles within the microstructured region and an interaction zone that only involves repulsive forces, aligning well with experimental outcomes. Through the study of microstructures’ geometric shapes, this paper offers guidance for designing microchannels for particle enrichment. Furthermore, the dissipative particle dynamics model established for the particle flow and solid structure interaction within microstructured channels provides insights into the mesoscale dynamics of liquid-solid two-phase flow and particle motion. In conclusion, this paper aims to enhance particle motion sample preparation techniques, thereby broadening the scope of microfluidic applications in the biomedical field.

Assessing the structural stability and drug encapsulation efficiency of poly(ethylene glycol)-poly(L-lactic acid) nanoparticles loaded with atorvastatin calcium: Based on dissipative particle dynamics

Block polymer micelles have been proven highly biocompatible and effective in improving drug utilization for delivering atorvastatin calcium. Therefore, it is of great significance to measure the stability of drug-loading nano micelles from the perspective of block polymer molecular sequence design, which would provide theoretical guidance for subsequent clinical applications. This study aims to investigate the structural stability of drug-loading micelles formed by two diblock/triblock polymers with various block sequences through coarse-grained dissipative particle dynamics (DPD) simulations. From the perspectives of the binding strength of poly(L-lactic acid) (PLLA) and polyethylene glycol (PEG) in nanoparticles, hydrophilic bead surface coverage, and the morphological alteration of nanoparticles induced by shear force, the ratio of hydrophilic/hydrophobic sequence length has been observed to affect the stability of nanoparticles. We have found that for diblock polymers, PEG3kda-PLLA2kda has the best stability (corresponding hydrophilic coverage ratio is 0.832), while PEG4kda-PLLA5kda has the worst (coverage ratio 0.578). For triblock polymers, PEG4kda-PLLA2kda-PEG4kda has the best stability (0.838), while PEG4kda-PLLA5kda-PEG4kda possesses the worst performance (0.731), and the average performance on stability is better than nanoparticles composed of diblock polymers.

Expression of Concern: Developed Molecular Dynamics method of Dissipative Particle Dynamics for the bench mark numerical simulation of fluid flow inside a rectangular chamber

Expression of Concern: Developed Molecular Dynamics method of Dissipative Particle Dynamics for the bench mark numerical simulation of fluid flow inside a rectangular chamber

Expression of Concern: Representing Fluid Particle Model to incorporate two non-central components for dissipation forces associated with random forces: A new integral algorithm in modified Dissipative Particle Dynamics method

Expression of Concern: Representing Fluid Particle Model to incorporate two non-central components for dissipation forces associated with random forces: A new integral algorithm in modified Dissipative Particle Dynamics method