Modelling of the in-stent thrombus formation by dissipative particle dynamics.

BACKGROUND: Stent implantation is a highly efficacious intervention for the treatment of coronary atherosclerosis. Nevertheless, stent thrombosis and other post-operative complications persist, and the underlying mechanism of adverse event remains elusive. METHODS: In the present study, a dissipative particle dynamics model was formulated to simulate the motion, adhesion, activation, and aggregation of platelets, with the aim of elucidating the mechanisms of in-stent thrombosis. FINDINGS: The findings suggest that stent thrombosis arises from a complex interplay of multiple factors, including endothelial injury resulting from stent implantation and alterations in the hemodynamic milieu. Furthermore, the results suggest a noteworthy association between in-stent thrombosis and both the length of the endothelial injured site and the degree of stent malposition. Specifically, the incidence of stent thrombosis appears to rise in tandem with the extent of the injured site, while moderate stent malposition is more likely to result in in-stent thrombosis compared to severe or minor malposition. INTERPRETATION: This study offers novel research avenues for investigating the plasticity mechanism of stent thrombosis, while also facilitating the clinical prediction of stent thrombosis formation and the development of more precise treatment strategies.

Transport Properties of Aqueous Methane Solutions and Blocking Behavior of Intelligent-Responsive Temporary Plugging Agent in a Switchable Nano-channel: A Dissipative Particle Dynamics Simulation Study.

Intelligent-responsive temporary plugging agents (TPAs) have great potential in the field of oil and gas resource extraction due to their self-adaptability to the environment. However, the transport mechanism of oil and gas molecules, such as aqueous methane solution in intelligent-responsive TPA-modified nano-channels and the blocking behavior of TPA, have not been verified yet. In this work, dissipative particle dynamics simulations (DPD) are conducted to investigate the velocity distribution and the force characteristics of aqueous methane solutions under different driving velocities, as well as the blocking effect of TPA to the flow of solution. Simulation results indicate that aqueous methane solution primarily concentrates in the uncovered area of the TPA and diffuses into the TPA-covered area when the nano-channel is closed. The velocity distribution of the flowing solution in the open nano-channel follows a subparabolic pattern. Methane molecules in the closed nano-channel show sharp oscillations in velocity and force profiles, which can be mitigated by increasing the methane concentration. The designed TPA effectively blocks fluid flow but its head and tail are vulnerable to the shear forces from the fluid. This study enhances the understanding of the nanoflows in the wellbores during the extraction of oil and natural gas resources.

Experimental and Computational Evaluation of Self-Assembled Morphologies in Diblock Janus Bottlebrush Copolymers.

Diblock Janus-type "A-branch-B" bottlebrush copolymers (di-JBBCPs) consist of a backbone with alternating A and B side chains, in contrast to the side chain arrangement of conventional bottlebrush copolymers. As a result, A and B blocks of di-JBBCPs can microphase-separate perpendicular to the backbone, which is located at the interface between the two blocks. A reparametrized dissipative particle dynamics (DPD) model is used to theoretically investigate the self-assembly of di-JBBCPs and to compare with the experimental results of a range of polystyrene-branch-polydimethylsiloxane di-JBBCPs. The experimentally formed cylinder, gyroid, and lamellar morphologies showed good correspondence with the model phase diagram, and the effect of changing volume fraction and backbone length is revealed. The DPD model predicts a bulk-stable perforated lamella morphology together with two unconventional spherical phases, the Frank-Kasper A15 spheres and the hexagonally close-packed spheres, indicating the diversity of morphologies available from complex BCP molecular architectures.

Effect of Cosolvent on the Vesicle Formation Pathways under Solvent Exchange Process: A Dissipative Particle Dynamics Simulation.

The effective control over the vesicle formation pathways is vital for tuning its function. Recently, a liquid-liquid phase-separated intermediate (LLPS) is observed before a vesicular structure during the solvent exchange self-assembly of block copolymers. Though the understanding of polymer structures and chemical compositions on the competition between LLPS and micellization has made some progress, little is known about the role of cosolvent on it. In this study, the influence of cosolvent on the vesicle formation pathways is investigated by using dissipative particle dynamics. The results show that the range of water fraction within which the LLPS is favored will be highly dependent on the affinity difference of cosolvent to water and to polymer repeat units. The change of the cosolvent-water interaction and the water fraction impact the distribution of cosolvent in the polymer domain, the miscibility between the components in the system as well as the chain conformations, which finally induce different self-assembly behaviors. Our findings would be helpful for understanding the LLPS and controlling the morphologies of diblock polymers in solutions for further applications.

Dissipative Particle Dynamics Simulation of the Sensitive Anchoring Behavior of Smectic Liquid Crystals at Aqueous Phase.

Rational design of thermotropic liquid crystal (LC)-based sensors utilizing different mesophases holds great promise to open up novel detection modalities for various chemical and biological applications. In this context, we present a dissipative particle dynamics study to explore the unique anchoring behavior of nematic and smectic LCs at amphiphile-laden aqueous-LC interface. By increasing the surface coverage of amphiphiles, two distinct anchoring sequences, a continuous planar-tilted-homeotropic transition and a discontinuous planar-to-homeotropic transition, can be observed for the nematic and smectic LCs, respectively. More importantly, the latter occurs at a much lower surface coverage of amphiphiles, demonstrating an outstanding sensitivity for the smectic-based sensors. The dynamics of reorientation further reveals that the formation of homeotropic smectic anchoring is mainly governed by the synchronous growth of smectic layers through the LCs, which is significantly different from the mechanism of interface-to-bulk ordering propagation in nematic anchoring. Furthermore, the smectic LCs have also been proven to possess a potential selectivity in response to a subtle change in the chain rigidity of amphiphiles. These simulation findings are promising and would be valuable for the development of novel smectic-based sensors.

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.

Effect of cytosol viscosity on the flow behavior of red blood cell suspensions in microvessels.

OBJECTIVE: The flow behavior of blood is strongly affected by red blood cell (RBC) properties, such as the viscosity ratio C between cytosol and suspending medium, which can significantly be altered in several pathologies (e.g. sickle-cell disease, malaria). The main objective of this study is to understand the effect of C on macroscopic blood flow properties such as flow resistance in microvessels, and to link it to the deformation and dynamics of single RBCs. METHODS: We employ mesoscopic hydrodynamic simulations to investigate flow properties of RBC suspensions with different cytosol viscosities for various flow conditions in cylindrical microchannels. RESULTS: Starting from a dispersed cell configuration which approximates RBC dispersion at vessel bifurcations in the microvasculature, we find that the flow convergence and development of RBC-free layer (RBC-FL) depend only weakly on C, and require a convergence length in the range of 25D-50D, where D is channel diameter. In vessels with D≤20µm , the final resistance of developed flow is nearly the same for C = 5 and C = 1, while for D=40µm , the flow resistance for C = 5 is about 10% larger than for C = 1. The similarities and differences in flow resistance can be explained by viscosity-dependent RBC-FL thicknesses, which are associated with the viscosity-dependent dynamics of single RBCs. CONCLUSIONS: The weak effect on the flow resistance and RBC-FL explains why RBCs can contain a high concentration of hemoglobin for efficient oxygen delivery, without a pronounced increase in the flow resistance. Furthermore, our results suggest that significant alterations in microvascular flow in various pathologies are likely not due to mere changes in cytosolic viscosity.

Simultaneous polymerization and adhesion under hypoxia in sickle cell disease.

Polymerization and adhesion, dynamic processes that are hallmarks of sickle cell disease (SCD), have thus far been studied in vitro only separately. Here, we present quantitative results of the simultaneous and synergistic effects of adhesion and polymerization of deoxygenated sickle hemoglobin (HbS) in the human red blood cell (RBC) on the mechanisms underlying vasoocclusive pain crisis. For this purpose, we employ a specially developed hypoxic microfluidic platform, which is capable of inducing sickling and unsickling of RBCs in vitro, to test blood samples from eight patients with SCD. We supplemented these experimental results with detailed molecular-level computational simulations of cytoadherence and biorheology using dissipative particle dynamics. By recourse to image analysis techniques, we characterize sickle RBC maturation stages in the following order of the degree of adhesion susceptibility under hypoxia: sickle reticulocytes in circulation (SRs) → sickle mature erythrocytes (SMEs) → irreversibly sickled cells (ISCs). We show that (i) hypoxia significantly enhances sickle RBC adherence; (ii) HbS polymerization enhances sickle cell adherence in SRs and SMEs, but not in ISCs; (iii) SRs exhibit unique adhesion dynamics where HbS fiber projections growing outward from the cell surface create multiple sites of adhesion; and (iv) polymerization stimulates adhesion and vice versa, thereby establishing the bidirectional coupling between the two processes. These findings offer insights into possible mechanistic pathways leading to vasoocclusion crisis. They also elucidate the processes underlying the onset of occlusion that may involve circulating reticulocytes, which are more abundant in hemolytic anemias due to robust compensatory erythropoiesis.

Dissipative Particle Dynamics Aided Design of Drug Delivery Systems: A Review.

A nanocarrier drug delivery system, effectively assisting to improve the solubility, bioavailability, and targeting of drugs in the human body, is a crucial means for treating cancer and other diseases. However, drug carriers usually possess multiple components and complex microstructures, and studies on the formation mechanism and internal structural details of nanocarriers are still incomplete by experimental methods. In order to overcome this adversity, the dissipative particle dynamics (DPD) simulation has been widely used owing to its unique simulation time-space scale and satisfying computing efficiency. In the past decades, more and more kinds of complex nanocarriers with various structures have been successfully characterized, and influencing factors in mounting numbers have also been parametrized. Not only emphasizing on the self-assembly structure of nanocarriers, but the application area of DPD simulation has also become a complete system covering from the synthesis and preparation to interaction with the biomembrane. This article reviews the application of DPD simulations in drug delivery systems. We have established the connection between existing studies and proposed some outlooks for the further combination between DPD simulation and the design of a drug delivery system.

Harnessed Dopant Block Copolymers Assist Decorating Membrane Pores: A Dissipative Particle Dynamics Study.

Self-assembly of asymmetric block copolymers (BCPs) around active pore edges has emerged as an important strategy to produce smart membranes with tunable pathways for solute transport. However, thus far, it is still challenging to manipulate pore shape and functionality for directional transformation under external stimuli. Here, a versatile strategy by mesoscale simulations to design stimuli-responsive pores with various edge decorations in hybrid membranes is reported. Dopant BCPs are used as decorators to stabilize pore edges and extend their function in reconfiguring pores in response to repeated membrane stretching/shrinking caused by external stimuli. The decoration morphologies are predictable since the assemblies of dopant BCPs around pore edges are closely related to their self-assemblies in solution. The coassembly between different BCPs in the hybrid membrane for the control of pore morphology is featured, and the parameter settings, including block incompatibility and molecular architecture for the construction of a specific pore, are determined. Results show that harnessed dopant BCPs in the hybrid membrane can enhance pore formation and induce directional pore shape and functionality transformation. Diversified pore decorations exhibit potential that can be further explored in selective solute transport and the design of stimuli-responsive smart nanodevices.

Directed Self-Assembly of Patchy Microgels into Anisotropic Nanostructures.

Multi-geometry nanostructures with high-order, complex, and controllable geometries have attracted extensive attention in the development of functional nanomaterials. A simple and versatile strategy is proposed to construct various anisotropic nanostructures through the directed self-assembly (DSA) of patchy microgels. A general criterion for interaction parameters is developed by the variance analysis method to achieve the formation of 1D nanorods by the single directional DSA process, and 2D or 3D polymorphs including V/T/h/cross shapes, multiple arms, multi-directional bending, single/multiple rings, nanocages, etc., by the multi-directional DSA process of binary microgel blends. At the optimum interaction parameters, the nanorods exhibit the quickest formation process and the most thermodynamically stable geometry, while the various 2D or 3D assemblies exhibit controlled jointing behaviors for versatile assembly geometries. The number of recognition sites on the patchy microgel surface guides the aggregation modes of microgels during the DSA process. These assemblies can bear large curvature variance with the increase of shear rates due to the high flexibility and the ability of adjusting orientation spontaneously. The DSA behavior of patchy microgels differs from the traditional self-assembly process of block copolymers, which may open a new route for guiding the formation of controllable nanoparticle architectures.

Modeling Clot Formation of Shear-Injured Platelets in Flow by a Dissipative Particle Dynamics Method.

The regions with high non-physiological shear stresses (NPSS) are inevitable in blood-contacting medical devices (BCMDs) used for mechanically assisted circulatory support. NPSS can cause platelet activation and receptor shedding potentially resulting in the alteration of hemostatic function. In this study, we developed a dissipative particle dynamics model to characterize clot formation (platelet-collagen and inter-platelet adhesion) of NPSS-traumatized blood at a vascular injury site. A rectangular tube of 50 × 50 × 200 µm with an 8 × 8 µm collagen-coated area was modeled as a small blood vessel and perfusion with blood. Clot formation dynamics during perfusion was simulated. NPSS-traumatized blood was modeled to have more activated platelet and fewer adhesion receptors with weakened inter-platelet binding. Computational results showed that clots grew at a faster rate while the structure of the clots was less stable and collapsed more frequently for NPSS-traumatized blood compared with normal blood. The finding that NPSS-traumatized platelets could result in quicker but more easily breakable blood clots at injury sites may explain why increased risks of thrombotic and bleeding complications occurred concurrently in patients implanted with BCMDs.

Micellar polymerization: Computer simulations by dissipative particle dynamics.

Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular-weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc.

Transdermal Cubic Phases of Metformin Hydrochloride: In Silico and in Vitro Studies of Delivery Mechanisms.

Transdermal delivery is one of important controlled drug release strategies for drug development. Cubic phases are the assemblies of amphiphilic molecules in water with the hydrophilic-hydrophobic interpenetrating network for transdermal delivery of both hydrophilic and hydrophobic drugs. However, many details about the transdermal delivery of drugs from cubic phases remain unclear. Here, metformin hydrochloride (Met) cubic phases were prepared with glyceryl monooleate (GMO), ethanol, and water. The cubic structure was identified with the polarizing light microscopy and small-angle X-ray scattering method. Dissipative particle dynamics (DPD) was used for building the microstructures of the cubic phases to explore the mechanism of drug release that mainly depended on drug diffusion from the water channels of cubic phases in accordance with the Higuchi equation of in vitro release experiments. The coarse-grained model and molecular docking method showed that GMO could enhance drug permeation through the skin by disturbing the interaction between Met and the skin proteins, and increasing the fluidity of skin lipids, which was confirmed with the Fourier transform infrared spectroscopy, Langmuir monolayer, and immunohistochemistry. Furthermore, in vitro permeation experiments showed the high Met transdermal improvement of cubic phases. Cubic phases are an ideal transdermal delivery system of Met. In silico methods are very useful for analyzing the molecular mechanisms of transdermal formulations.

Interaction pathways between soft lipid nanodiscs and plasma membranes: A molecular modeling study.

Lipid nanodisc, a model membrane platform originally synthesized for study of membrane proteins, has recently been used as the carrier to deliver amphiphilic drugs into target tumor cells. However, the central question of how cells interact with such emerging nanomaterials remains unclear and deserves our research for both improving the delivery efficiency and reducing the side effect. In this work, a binary lipid nanodisc is designed as the minimum model to investigate its interactions with plasma membranes by using the dissipative particle dynamics method. Three typical interaction pathways, including the membrane attachment with lipid domain exchange of nanodiscs, the partial membrane wrapping with nanodisc vesiculation, and the receptor-mediated endocytosis, are discovered. For the first pathway, the boundary normal lipids acting as ligands diffuse along the nanodisc rim to gather at the membrane interface, repelling the central bola lipids to reach a stable membrane attachment. If bola lipids are positioned at the periphery and act as ligands, they diffuse to form a large aggregate being wrapped by the membrane, leaving the normal lipids exposed on the membrane exterior by assembling into a vesicle. Finally, by setting both central normal lipids and boundary bola lipids as ligands, the receptor-mediated endocytosis occurs via both deformation and self-rotation of the nanodiscs. All above pathways for soft lipid nanodiscs are quite different from those for rigid nanoparticles, which may provide useful guidelines for design of soft lipid nanodiscs in widespread biomedical applications.

Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations.

Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD-region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard-Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose-Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self-diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc.

Salt Responsive Morphologies of ssDNA-Based Triblock Polyelectrolytes in Semi-Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length.

A comprehensive study is reported on the effect of salt concentration, polyelectrolyte block length, and polymer concentration on the morphology and structural properties of nanoaggregates self-assembled from BAB single-strand DNA (ssDNA) triblock polynucleotides in which A represents polyelectrolyte blocks and B represents hydrophobic neutral blocks. A morphological phase diagram above the gelation point is developed as a function of solvent ionic strength and polyelectrolyte block length utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations. As the solvent ionic strength increases, the self-assembled DNA network structures shrinks considerably, leading to a morphological transition from a micellar network to worm-like or hamburger-shape aggregates. This study provides insight into the network morphology and its changes by calculating the aggregation number, number of hydrophobic cores, and percentage of bridge chains in the network. The simulation results are corroborated through cryogenic transmission electron microscopy on the example of the self-assembly of ssDNA triblocks.

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

Modelling of platelet-fibrin clot formation in flow with a DPD-PDE method.

The paper is devoted to mathematical modelling of clot growth in blood flow. Great complexity of the hemostatic system dictates the need of usage of the mathematical models to understand its functioning in the normal and especially in pathological situations. In this work we investigate the interaction of blood flow, platelet aggregation and plasma coagulation. We develop a hybrid DPD-PDE model where dissipative particle dynamics (DPD) is used to model plasma flow and platelets, while the regulatory network of plasma coagulation is described by a system of partial differential equations. Modelling results confirm the potency of the scenario of clot growth where at the first stage of clot formation platelets form an aggregate due to weak inter-platelet connections and then due to their activation. This enables the formation of the fibrin net in the centre of the platelet aggregate where the flow velocity is significantly reduced. The fibrin net reinforces the clot and allows its further growth. When the clot becomes sufficiently large, it stops growing due to the narrowed vessel and the increase of flow shear rate at the surface of the clot. Its outer part is detached by the flow revealing the inner part covered by fibrin. This fibrin cap does not allow new platelets to attach at the high shear rate, and the clot stops growing. Dependence of the final clot size on wall shear rate and on other parameters is studied.

Effect of Sodium Dodecyl Sulfate Adsorption on the Behavior of Water inside Single Walled Carbon Nanotubes with Dissipative Particle Dynamics Simulation.

Dissipative particle dynamics (DPD) simulations were utilized to investigate the ability of sodium dodecyl sulfate (SDS) to adsorb inside a single-walled, arm-chair carbon nanotube (SWCNT), as well as the effect of surfactant on the properties of water inside the SWCNT. The diameter of the SWCNT varied from 1 to 5 nm. The radial and axial density profiles of water inside the SWCNTs were computed and compared with published molecular dynamics results. The average residence time and diffusivity were also calculated to show the size effect on mobility of water inside the SWCNT. It was found that nanotubes with diameter smaller than 3 nm do not allow SDS molecules to enter the SWCNT space. For larger SWCNT diameter, SDS adsorbed inside and outside the nanotube. When SDS was adsorbed in the hollow part of the SWCNT, the behavior of water inside the nanotube was found to be significantly changed. Both radial and axial density profiles of water inside the SWCNT fluctuated strongly and were different from those in bulk phase. In addition, SDS molecules increased the retention of water beads inside SWCNT (d ≥ 3nm) while water diffusivity was decreased.