Dissipative particle dynamics simulation of flow in periodically grooved three-dimensional nano- and micro-channels

This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.Nonequillibrium flow in three-dimensional grooved nano- and micro-channels is investigated using the Dissipative Particle Dynamics simulation method. Roughness is introduced by periodically placing rectangular protruding elements on the upper channel wall. The protrusion length and height are varied and their effect on the flow is examined. The computed macroscopic quantities of practical interest include density, velocity, pressure, and temperature profiles as well as relations between the friction factor and the Reynolds number. When compared to the smooth channel case, lower flow velocities are observed in the central part of the channel for all cases studied. This reduction of velocities becomes more pronounced as the protrusion height increases. For the micro-channel, density, pressure and temperature remain almost constant in the central part of the channel and their pattern near and inside the cavities depend on the protrusion shape. In the nanochannel case, lower temperatures and pressures are observed for all grooved channels relative to the smooth channel case. For all channel cases studied the calculated friction factor decreases as Reynolds number increases, following a power law relation

Influence of Fibrinogen Deficiency on Clot Formation in Flow by Hybrid Model

International audienceIn this work we develop the 2D model suggested in [32] in order to study the impact of fibrinogen concentration and the fibrin polymer production rate on clot growth in flow. The model is based on the method of Dissipative Particle Dynamics describing blood plasma flow and platelet suspension and on a system of partial differential equations describing blood coagulation regulatory network. We study the influence of parameters on clot development and on its final size

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

International audienceThe paper is devoted to mathematical modelling of clot growth in bloodflow. Great complexity of the hemostatic system dictates the need of usage of themathematical models to understand its functioning in the normal and especially inpathological situations. In this work we investigate the interaction of blood flow,platelet aggregation and plasma coagulation. We develop a hybrid DPD–PDE modelwhere 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 partialdifferential equations. Modelling results confirm the potency of the scenario of clotgrowth where at the first stage of clot formation platelets form an aggregate due toweak inter-platelet connections and then due to their activation. This enables the formationof the fibrin net in the centre of the platelet aggregate where the flow velocity issignificantly 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 vesseland the increase of flow shear rate at the surface of the clot. Its outer part is detachedby the flow revealing the inner part covered by fibrin. This fibrin cap does not allownew platelets to attach at the high shear rate, and the clot stops growing. Dependenceof the final clot size on wall shear rate and on other parameters is studied

Implementation of fluid dynamics simulator in meso-scale with the DPD method

Orientador: Luiz Otávio Saraiva FerreiraDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia MecânicaResumo: Este trabalho tem como objetivo principal a implementação do motor de simulação de um framework de simulação com partículas, o motor de simulação utilizará o método DPD (Dissipative Particle Dynamics), baseando-se no paradigma de programação orientada a objeto (POO) e no uso de estruturas de dados otimizadas. O motor de simulação foi escrito em linguagem C++. A concepção do sistema foi realizada de forma a facilitar e promover a reutilização e manutenção do código. Buscou-se, também, a flexibilidade e generalização através do uso da linguagem Python na geração dos arquivos de entrada correspondentes a distribuição espacial das partículas, sendo utilizada a linguagem de marcação XML (eXtensible Markup Language) na estruturação dos arquivos resultantes da simulação. No final, o motor de simulação é avaliado aplicando o problema do fluxo de um fluído entre placas paralelas e o resultado comparado com os resultados obtidos no simulador Hoomd-BlueAbstract: This work aims the implementation of the simulation of a simulation framework with particle engine, the simulation engine will use DPD (Dissipative Particle Dynamics) method, based on the paradigm of object oriented programming (OOP) and use optimized data structures. The simulation engine is written in C language ++. The system design was performed in order to facilitate and promote the reuse and maintainability of the code. Also, we sought flexibility and generalization through the use of Python in the generation of the input files corresponding to the spatial distribution of particles, (eXtensible Markup Language) XML markup being used in structuring the files resulting from the simulation. At the end, the simulation engine is the problem of applying rated flow of a fluid between parallel plates and the result compared with the results obtained in the simulation Hoomd-BlueMestradoMecanica dos Sólidos e Projeto MecanicoMestre em Engenharia Mecânic

Rheological characterization of polymers via dissipative particle dynamics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008.Includes bibliographical references (p. 191-200).Dissipative particle dynamics (DPD) is a mesoscale simulation technique which uses soft potentials between large particles to reproduce liquid behavior. In form, DPD is similar to molecular dynamics, as all matter is represented by point particles which interact with each other via, pairwise forces. The method was first introduced in the early 1990's, and has since undergone a number of refinements which have put it on a firm thermodynamic footing. DPD is notable for the flexibility it presents the modeler for building complex fluid systems. DPD has been used to study simple molecular liquids, polymer and colloid solutions, and phase behavior of block copolymer melts. Recently, a number of workers have used DPD to study the flow of polymer solutions in various geometries such as microchannels, pores, and sudden contractions. While these types of flows are well-suited to DPD's relative strengths, an important step has been skipped. Before the results of these complex flows can be accepted, it is necessary to demonstrate that the rheological predictions made by DPD are generally reliable. The principle aim of this thesis is to demonstrate that the rheology of polymer solutions can be simulated successfully with DPD. The rheology of a solution of DPD dumbbells using a FENE spring force law is studied in the first part of this thesis via simulation of steady shear flow and steady planar elongational flow. The rheological results are compared to dilute Brownian dynamics simulations of the same FENE dumbbell model. The level of coarse-graining of the DPD fluid is varied by changing the length of the DPD dumbbell relative to the particle size, while maintaining a constant extensibility parameter. Broadly speaking, the viscosity, first normal stress coefficient, and dumbbell extension in shear flow calculated with DPD are in agreement with the BD results. The two methods are not perfectly alike however, and two systematic differences between the DPD and BD results are observed. An excluded volume effect which occurs naturally in DPD and is not present in the BD simulations results in elevated viscosity and dumbbell extension in the zero-shear-rate regime.(cont.) The effect is more powerful in DPD dumbbells which are more coarse-grained. At high shear rates in the power-law regime, DPD systematically overpredicts the rate of shear-thinning, with the greatest deviation occurring in the most coarse-grained dumbbells. This is hypothesized to be a result of hydrodynamic interaction which comes naturally out of DPD's explicit treatment of the solvent. The HI effect is analyzed using the Giesekus anisotropic drag tensor. Shortly after its introduction, the complaint was made that DPD's dynamic results are suspect because it has a very low, gas-like Schmidt number, meaning that momentum and mass are transported through the DPD medium at similar rates. This is in contrast with physical liquids, which have large Schmidt numbers. The use of the Lowe-Anderson formulation of DPD allows the Schmidt number of a solution to be varied for the same polymer model. Shear flow simulations of identical dumbbells under different Schmidt number conditions give results in excellent agreement with each other, indicating that the Schmidt number is not an important factor in determining polymer rheology with DPD. Steady planar elongational flow is simulated for the first time in DPD using the Kraynik and Reinelt boundary conditions, which are periodic in both space and time, allowing for simulations of planar elongational flow for an unlimited period of time. The planar elongational flow results of FENE dumbbells are also in agreement with BD, butshow the same systematic deviations observed in shear flow. The second portion of this thesis examines a more complex polymer solution using DPD, with simulations of semidilute solutions of longer N = 20 bead-spring chain polymers undergoing shear and planar elongational flow. In addition to concentration effects, the importance of the solvent quality is also examined with simulations of polymer solutions in both good and theta solvents. In order to capture concentration dependency, a spring -spring repulsion force is added to the DPD model to prevent polymer springs from passing though each other. A strong concentration dependence on the longest relaxation time is observed.(cont.) In planar elongational flow, each solution goes through a coil-stretch transition at the theoretically predicted strain rate De = 0.5. In shear flow, the rheological results are in qualitative agreement with theory, showing a plateau at low De, and a transition into a shear-thinning regime beginning at De = 1. While the planar elongational flow results show clear dependence on the solution relaxation time, the shear results show a mixed dependence on the overall solution relaxation time, which reflects the concentration dependence, and the relaxation rate of an isolated chain, suggesting that only some aspects of the shear rheology are affected by the concentration. The conclusion of this thesis is that DPD is able to faithfully reproduce reliable rheological behavior with bead-spring polymer models. We find however, that the computational costs associated with the explicit simulation of the solvent put DPD at a disadvantage for systematic rheology studies when compared to Brownian dynamics. The high costs of the spring-spring repulsion force implementation are particularly limiting. In complex systems where DPD's natural flexibility in molecular architecture and chemistry make it the best choice, rheological results can now be accepted with more confidence.by Theis Forman Clarke.Ph.D