Particle Dynamics Method Research Articles

Self-Assembly of Janus Type Amphiphilic Dendrimers from Dissipative Particle Dynamics Simulation

The self-assembly of Janus type amphiphilic dendrimers has been studied extensively through experiments and computer simulations, while most of the simulations assume that Janus molecules are connected by covalent bonds, disregarding the noncovalent interaction which evokes the particular dynamic self-assembly regulation. This paper investigates the dynamic self-assembly behavior of Janus type amphiphilic dendrimers through the dissipative particle dynamics (DPD) method. A series of coarse-grained models of Janus type amphiphilic dendrimers with different hydrophobic-hydrophilic ratios were constructed to simulate the static self-assembly, and then the dynamic self-assembly was carried out through introducing a chemical bonding reaction to simulate the non-covalent interaction between the two different parts of Janus type dendrimers. The control of reaction rate was accomplished by modifying the reaction probability to adjust the dynamic self-assembly process. The results indicate that the introduction of non-covalent interaction changes the self-assembly behavior of some models and generates different dynamic self-assembly structures. It can also be deduced that the reaction rate exerts influence on the structure of dynamic self-assembly.

Develop dissipative particle dynamics method to study the fluid flow and heat transfer of Ar and O2 flows in the micro- and nanochannels with precise atomic arrangement versus molecular dynamics approach

Fluid atomic behavior is an important factor for industrial applications. Computer simulations based on simple models predict Poiseuille flow for these atomic structures with the presence of external force. In this work, we describe the dynamical properties of Ar and O2 flows with precise atomic arrangement via dissipative particle dynamics (DPD) and molecular dynamics (MD) simulation approaches. In these methods, each model is represented by using Large-scale Atomic/Molecular Massively Parallel Simulator package. Simulation results show that maximum rate for velocity of Ar flow in platinum and copper microchannels is 0.100 (unit less)/0.091 A ps−1 and 0.121 (unit less)/0.105 A ps−1 by using DPD/MD approach. This atomic parameter changes to 0.111 (unit less)/0.102 A ps−1 and 0.125 (unit less)/0.108 A ps−1 for O2 fluid with mentioned approaches. By decreasing the microchannel size, the maximum rate of velocity reaches to 0.101 (unit less)/0.099 A ps−1 and maximum temperature rate decreases to 485 (unit less)/440 K with DPD/MD approaches. These calculated parameters can be used in industrial application designing for some processes such as heat transfer in structures. It was seen that the developed DPD approach was able to simulate the fluid flow and heat transfer of various types of fluids at micro- and nanoscales with suitable accuracy versus MD.

Modeling the design of the scaler for thermochemical treatment of beet ships before extracting sucharose

The extraction of sucrose is a key process in sugar beet production that determines its efficiency. This process is significantly accelerated by a complex thermal, electrical and chemical effect on beet tissue in the process of its preparation and is carried out in scalders of various designs. The design parameters of the scalder can be estimated using mathematical modeling methods. When developing the model, a finite element approach was used by representing complex bodies in the form of a large number of separate elements of the same type and the method of particle dynamics. In the simulation, a number of coefficients were introduced related to splitting the chips into separate spherical elements: mЭ, cС, dЭС, cИС. Reference and experimental data were used to calculate them. The mathematical model is implemented in the form of a system of differential and algebraic equations, for the processing of which a computer program in the Object Pascal language has been developed. The developed model makes it possible to vary a large number of design and technological parameters of the scalder and mechanical and geometric parameters of beet chips, and to determine indicators characterizing the efficiency of thermochemical processing of chips. The angle of inclination of the nozzle in the vertical plane, length and diameter of the nozzle were chosen as design parameters. The efficiency of the scalder design was evaluated by the mass of beet chips accumulated on the nozzle and the contact time of the beet chips with the inner surfaces of the scalder. In the course of a computer experiment, it was found that an increase in the angle of inclination of the nozzles at different lengths and diameters significantly reduces the mass of accumulated chips and the time of contact of the chips with the surface of the scalder. The resulting model is intended for the design of prototypes of the scalder.

Simulation of the effect of mucociliary clearance on the bronchial distribution of inhaled radon progenies and related cellular damage using a new deposition and clearance model for the lung

Most of the current dosimetry models of inhaled short-lived radon decay products assume uniform activity distributions along the bronchial airways. In reality, however, both deposition and clearance patterns of inhaled radon progenies are highly inhomogeneous. Consequently, a new deposition-clearance model has been developed that accounts for such inhomogeneities and applied together with biophysical models of cell death and cell transformation. The scope of this study was to apply this model which is based on computational fluid and particle dynamics methods, in an effort to reveal the effect of mucociliary clearance on the bronchial distribution of deposited radon progenies. Furthermore, the influence of mucociliary clearance on the spatial distribution of biological damage due to alpha-decay of the deposited radon progenies was also studied. The results obtained demonstrate that both deposition and clearance of inhaled radon progenies are highly non-uniform within a human airway bifurcation unit. Due to the topology of the carinal ridge, a slow clearance zone emerged in this region, which is the location where most of the radio-aerosols deposit. In spite of the slow mucus movement in this zone, the initial degree of inhomogeneity of the activity due to the nonuniform deposition decreased by a factor of about 3 by considering the effect of mucociliary clearance. In the peak of the airway bifurcation, the computed cell death and cell transformation probabilities were lower when considering deposition and clearance simultaneously, compared to the case when only deposition was considered. However, cellular damage remained clustered.

Simulation of liquid transfer between the plate and the groove

The transfer of the liquid from groove to plate is significantly affected by the breakup process of liquid bridge, which is the core problem of gravure. In this paper, many-body dissipative particle dynamics method (MDPD) is used to simulate the behaviors of the stretching liquid cylinder between the plate and the groove, and the influence of surface wettability, stretching velocity and groove structure on the liquid cylinder rupture and the transfer rate of liquid are studied. The results show that both of the slipping velocity of the contact line on the plate and the thinning velocity of the liquid cylinder determine the breakup state of the liquid bridges and the liquid transfer rate from the groove to the plate. In the cases with the same surface wettability, at high hydrophilicity surface, the transfer rate increases firstly and then decreases with the increase of the stretching velocity. In the cases with different surface wettability of the plate and the groove, reducing the stretching velocity and the inclination angle of the groove are helpful to pull the liquid out of the groove and increase the transfer rate, and it could also be achieved by increasing the wettability of the plate and decreasing the wettability of the groove. This study provides some new insights into the effects of surface wettability, stretching velocity and groove structure on the dynamics of breakup process and liquid transfer in stretching.

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 × 200µm with an 8 × 8µm 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.

Numerical simulation of heat transfer in a parallel plate channel and promote dissipative particle dynamics method using different weight functions

In this paper heat transfer in a channel with parallel plates has been studied using Dissipative Particle Dynamics with energy conservation (eDPD). To simulate and present different thermal flows in finite geometries, a computer program was developed. The thermal boundary condition of the wall is assumed to be a constant temperature. Each particle in contact with the wall achieves the wall temperature. Also periodic boundary condition in the direction of the flow of the solution domain and no-slip boundary condition on the walls have been considered. The no-slip boundary condition is possible by freezing the layers of particles on the walls and applying bounce-back reflection. The results show dimensionless temperature and velocity profiles perpendicular to the direction of the flow along the channel. Finally, in this research it is tried to endeavored the fluctuations near the wall and promote the method by proposing different weight functions. Four different weight functions were used and the results on the velocity and temperature profiles were investigated. All of the results in the present work were compared and verified with the previous results.

Molecular theory of the tilting transition and computer simulations of the tilted lamellar phase of rod-coil diblock copolymers.

Symmetric rod-coil diblock copolymers have been simulated using the method of dissipative particle dynamics in the broad range of the Flory-Huggins parameter. It has been found that the tilted lamellar phase appears to be the most stable one at strong segregation. The rod-coil copolymer tilt angle and orientational order parameters have been determined as functions of the segregation strength. The density functional theory of rod-coil diblock copolymers has been generalized to the case of the tilted lamellar phase and used to study the stability of the orthogonal lamellar phase with respect to tilt. The orthogonal phase indeed appears to be unstable in the broad region of the parameter space in the case of relatively strong segregation. It has also been shown that the transition into the tilted lamellar phase is determined by a strong coupling between two independent tilt order parameters.

Coarse-graining, compressibility, and thermal fluctuation scaling in dissipative particle dynamics employed with pre-determined input parameters

In this study, a Dissipative Particle Dynamics (DPD) method is employed with its input parameters directly determined from the fluid properties, such as the fluid mass density, water compressibility, and viscosity. The investigation of thermal fluctuation scaling requires constant fluid properties, and this proposed DPD version meets this requirement. Its numerical verifications in simple or complex fluids under viscometric or non-viscometric flows indicate that (i) the level of thermal fluctuations in the DPD model for both types of fluids is consistently reduced with an increase in the coarse-graining level and (ii) viscometric or non-viscometric flows of a model fluid at different coarse-graining levels have a similar behavior. Furthermore, to reduce the compressibility effect of the DPD fluid in simulating incompressible flows, a new simple treatment is presented and shown to be very effective.

MD simulation studies of the physical and mechanical properites of P3HT-based blends

In this research, the physical and mechanical properties of semi-crystalline polymerpoly-(3-hexylthiophene-2,5-diyl)-based blends were investigated. The volume versus temperature curves of polymerpoly-(3-hexylthiophene-2,5-diyl)/methano-fullerene derivative[6]-phenyl-C64-butyricacidmethyl ester (P3HT:PCBM) and polymerpoly-(3-hexylthiophene-2,5-diyl)/DOCN-PPV (P3HT/CNPh-PPV) were plotted; however, we obtained one single temperature for each curve between glass transition temperatures of the compounds, which could be considered a good indicator of miscibility. In addition, the Coesif energy density of P3HT, PCBM, and CNPh-PPV were calculated and used to obtain the solubility parameters δP3HT, δPCBM, and δCNPh-PPV. The interaction parameter χ was calculated and used in the investigation and we confirmed the miscibility of our polymer systems. By using the dissipative particle dynamic method, the morphologies of P3HT/PCBM and P3HT/CNPh-PPV were enhanced.

Dissipative particle dynamics for systems with polar species: Interactions in dielectric media.

In this work, we develop a method for simulating polar species in the dissipative particle dynamics (DPD) method. The main idea behind the method is to treat each bead as a dumb-bell, i.e., two sub-beads kept at a fixed distance, instead of a point-like particle. The relation between the bead dipole moment and the bulk dielectric permittivity was obtained. The interaction force of single charges in polar liquid showed that the effective dielectric permittivity is somewhat smaller than that obtained for the bulk case at large separation between the charges. In order to understand the reasons behind the observed drop in the dielectric permittivity, we calculate the electric field of an isolated charge in a polar liquid; no permittivity drop is observed for this case. We can assume that the behavior observed for the force is due to the fact that the probing point is always associated with the charged bead, which is a force center, which essentially leads to a non-homogeneous density distribution around it on average; this is not the case when the field is measured. The interaction of a single charge with an interface between two liquids with different permittivities was studied after that; the model is found to correctly reproduce the "mirror image" effects. Finally, we show why it is necessary to treat the polar species in DPD explicitly by investigating the behavior of a charged colloidal particle at a liquid-liquid interface.

Gold clusters morphology on LiNbO3 (0001) surfaces with opposite polarization direction

Gold clusters are considered as widely used catalyst for chemical industry, but the efficiency of catalyst has been limited by the aggregation of the gold atoms, since the active sites are only located on the surface of the catalyst particles. In this paper the surface distribution of gold clusters influenced by spontaneous polarization and temperature is discussed. The morphology of the gold particle on different ferroelectric surface was simulated by the dissipative particle dynamics method, and the results are examined by pulsed laser deposition and Atomic Force Microscopy. The negatively poled surface with temperature adjustment could grow more dispersed gold clusters and offer a new progress to select the ferroelectric materials as the substrates for metal catalyst.

Estimation of the Diffusion Coefficient of Doxorubicin Molecules in a Water Solution in the Volume of a Porous Carrier Medium

An experimental investigation of the phenomenon of diffusion of the solution components in nanosized pores is extremely difficult and in certain cases impossible. An effective approach to obtaining qualitative and quantitative estimates of the diffusion process characteristics is computer simulation. Relying on the method of dissipative particle dynamics, a nanoscale numerical model is proposed for estimating the value of diffusion coefficient of the dissolved substance molecules in the pores of different sizes. An aqueous solution of doxorubicin, an antitumor antibiotic, in the pores of hydroxyapatite (a promising carrier medium for solving the problems of targeted administration of highly toxic drugs) is considered as a model system. Using the proposed model, the diffusion coefficient of doxorubicin in the pores of different linear sizes is evaluated at different volume concentrations of the antibiotic. In particular, it is found out that with an increase in the pore size the diffusion coefficient of doxorubicin increases by an order of magnitude and, starting from the pore size of 300 nm, it attains saturation. An increase in the antibiotic concentration from 0.1 to 5% gives rise to a decrease in the diffusion coefficient by more than a factor of 1.5. The developed model can be applied for solving the problems of predicting the release rate of the solution components (including drug molecules) from the pore volume of different solid-phase carrier media.

VORTEX DEVICES OF THE DIESEL AIR SUPPLY SYSTEM: MATHEMATICAL MODEL OF AERODYNAMIC PROCESSES

Introduction. The calculation of effective indicators of the vortex ejector used in the diesel air supply system is a pressing task as it allows significantly reducing time for determination of rational design parameters at the design stage. One of the modifications of the particle dynamics method is a promising direction, allowing with high physical adequacy, “from the first principles,” to model aerodynamic processes in vortex devices. Therefore, the purpose of the paper is to develop a mathematical model of a vortex ejector.Materials and methods. The paper discussed a method of the mathematical simulation of ejection and ejection flows in a vortex ejector. The proposed modification of the particle dynamics method allowed describing aerodynamic processes with the help of simple laws of classical dynamics, and modeling them with the help of software of the Delphi 7 System. The author presented differential equations, which were solved by the Runge-Kutt method of the second order. As a result of the solution, the authors determined paths of air elements movement in the vortex ejector, which allowed estimating effective parameters of vortex devices.Results. To study the model, the author developed a program with the possibility to set geometric parameters of the vortex ejector in the interface window and to display the current values of the process parameters.Discussion and conclusions. Proposed mathematical model and computer program make it possible to quantify efficiency of vortex devices at their design stage. The advantage of the proposed mathematical model lies in more accurate calculation of vortex flow parameters from the vortex ejector design and physical properties of ejecting and ejecting flows.Financial transparency: the author has no financial interest in the presented materials or methods. There is no conflict of interest.

Investigation of Magneto Hydro-Dynamics Effects on a Polymer Chain Transfer in Micro-Channel Using Dissipative Particle Dynamics Method

In this paper, the effect of Magneto Hydro-Dynamics (MHD) on a polymer chain in the micro channel is studied by employing the Dissipative Particle Dynamics simulation (DPD) method. First, in a simple symmetric micro-channel, the results are evaluated and validated for different values of Hartmann (Ha) Number. The difference between the simulation and analytical solution is below 10%. Then, two types of polymer chain including short and long polymer chain are examined in the channel and the effective parameters such as Ha number, the harmony bond coefficient or spring constant (K), and the length of the polymer chain (N) are studied in the MHD flow. It is shown that by increasing harmony bond constant to 10 times with Ha = 20, the reduction of about 80% in radius of gyration squared, and half in polymer length compared to Ha = 1 would occur for both test cases. For short and long length of polymer, proper transfer of a polymer chain through MHD particles flow is observed with less perturbations (80%) and faster polymer transfer in the symmetric micro-channel.

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.

Multiscale design, interaction mechanism and performance of CL-20/Al energetic composites with embedded structure.

In order to design and prepare hexanitrohexaazaisowurtzitane/aluminum (CL-20/Al) composites, the contact state of CL-20 with aluminum particles under different mixed solvent contents were calculated with the method of dissipative particle dynamics (DPD). Then the modified attachment energy (AE) model was applied to predict the morphologies of CL-20 in ethyl acetate, hexane and ethyl acetate/hexane mixed solvents. Furthermore, the morphologies, the surface element distribution, the sensitivity and the energy performance of CL-20/Al composites prepared with the solvent/non-solvent method were characterized, and the interaction mechanism were also obtained. The results achieved show that phase separation phenomenon becomes obvious with the decrease of ethyl acetate/n-hexane mixed solvent content. CL-20/aluminum particles will form the composites of aluminum particles embedded in CL-20 crystal when the solvent content is zero. The order of modified attachment energies for ethyl acetate/hexane mixed solvents on CL-20 faces is (011) > (110) > (101) ≈ (11−1) ≈ (10−1) > (002). Besides that, the crystalline morphology of CL-20 in acetate/hexane mixed solvents is spindle-shaped. There are many Al particles embedded in CL-20 crystals of CL-20/Al composites prepared by using solvent/non-solvent method. The calculated results agree well with the experimental results. In CL-20/Al composites, aluminum particles interact with CL-20 mainly through hydrogen bond and strong van der Waals force. The sensitivity of CL-20/Al composites decreased obviously compared with pure CL-20 and mechanical mixing composites. Besides, the CL-20/Al composites with embedded structure can increase the explosion reaction temperature to 791.2 K, which has obvious energy advantage compared with CL-20/Al physical mixture.

Encapsulation and release of drug nanoparticles in functional polymeric vesicles.

We investigated the co-assembly of amphiphilic diblock copolymers in solutions containing drugs and functional nanoparticles using the dissipative particle dynamics (DPD) method. By controlling the size and the concentration of the functional nanoparticles, the length of the hydrophobic blocks, and the interaction parameters between the hydrophobic block/solvent and the functional nanoparticles, we obtained the desired aggregates to load drugs. The aggregates loaded with drugs can be disk-like micelles, sphere-like micelles and vesicles with functional nanoparticles on the surface. When the solvent environment changes, the drugs loaded in the functional vesicles can release into the solvent. The release content is critically dependent on the repulsive interaction between the drugs and the solvent. The dynamic curve of drug release is obtained. The result is in agreement with the experiments about drug release. Our studies showed that we can precisely control the formation of functional vesicles to load and release drugs. Loading drugs in the process of self-assembly and controlling the release have broad potential in the field of clinical medicine and adding functional nanoparticles can be of great help in drug delivery and medical diagnosis.

Effect of grafting density on the self-assembly of side-chain discotic liquid crystalline polymers with triphenylene discogens.

The self-assembly of triphenylene (TP)-based side-chain discotic liquid crystalline polymers (SDLCPs) with different grafting densities was investigated by using the dissipative particle dynamics (DPD) method. We explored the coupling effect between the main chain and the side-chain TP discogens with various length alkyl tails, and how the rigidity of the main chain, grafting density and spacer lengths affect the self-assembled morphologies of SDLCPs. By changing the above factors, we have obtained nine phases. It is deduced that a moderate grafting density, a polymer backbone with sufficient length and alkyl tails with medium length ensure SDLCPs form ordered columnar mesophases. It is worth noting that double columnar phases (Colne-Col and Colh-Col) were obtained with high grafting densities and sufficiently long backbones. All these results provide an effective basis and helpful guidance for the in-depth research of such kinds of fascinating organic semiconducting materials, SDLCPs, from the perspective of grafting density.

Evaluation of computational errors in a red blood cell model of the dissipative particle dynamics method

Evaluation of computational errors in a red blood cell model of the dissipative particle dynamics method