David Kauzlarić

A dissipative particle dynamics model of carbon nanotubes

A mesoscale dissipative particle dynamics model of single wall carbon nanotubes (CNTs) is designed and demonstrated. The coarse-grained model is produced by grouping together carbon atoms and by bonding the new lumped particles through pair and triplet forces. The mechanical properties of the simulated tube are determined by the bonding forces, which are derived by virtual experiments. Through the introduction of van der Waals interactions, tube–tube interactions were studied. Owing to the reduced number of particles, this model allows the simulation of relatively large systems. The applicability of the presented scheme to model CNT based mechanical devices is discussed.

Smoothed particle hydrodynamics simulation of shear-induced powder migration in injection moulding

We present the application of the smoothed particle hydrodynamics (SPH) discretization scheme to Phillips’ model for shear-induced particle migration in concentrated suspensions. This model provides an evolution equation for the scalar mean volume fraction of idealized spherical solid particles of equal diameter which is discretized by the SPH formalism. In order to obtain a discrete evolution equation with exact conservation properties we treat in fact the occupied volume of the solid particles as the degree of freedom for the fluid particles. We present simulation results in two- and three-dimensional channel flow. The two-dimensional results serve as a verification by a comparison to analytic solutions. The three-dimensional results are used for a comparison with experimental measurements obtained from computer tomography of injection moulded ceramic microparts. We observe the best agreement of measurements with snapshots of the transient simulation for a ratio Dc/Dη=0.1 of the two model parameters.

SYMPLER: SYMbolic ParticLE simulatoR with grid-computing interface ☆

Abstract We present the main design concepts of the object-oriented particle dynamics code SYMPLER. With this freely available software, simulations can be performed ranging from microscopic classical molecular dynamics up to the Lagrangian particle-based discretisation of macroscopic continuum mechanics equations. We show how the runtime definition of arbitrary degrees of freedom and of arbitrary equations of motion allows for modular and symbolic computation with high flexibility. Arbitrary symbolic expressions for inter-particle forces can be defined as well as fluxes of arbitrarily many additional scalar, vectorial or tensorial degrees of freedom. The integration in a high performance grid computing environment makes huge geographically distributed computational resources accessible to the software by an easy-to-use interface. Program summary Program title: SYMPLER Catalogue identifier: AERQ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERQ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 221255 No. of bytes in distributed program, including test data, etc.: 1805954 Distribution format: tar.gz Programming language: C++. Computer: Any system operatable with Linux. Operating system: Linux, MacOS. Has the code been vectorised or parallelised?: Experimental OpenMP parallelisation for usually up to 8 cores, the grid-version can use hundreds of cores. RAM: tens of MB to several GB, depending on problem. Classification: 7.7, 12, 16.1, 16.3, 16.13, 23. External routines: GSL, libxml2; optional: libsdl, OpenMP, libjama, libtnt, libsuperlu Nature of problem: A unified flexible and modular simulation tool allowing for the investigation of structural, thermodynamic, and dynamical properties of fluids and solids from microscopic over mesoscopic up to macroscopic time and length scales with suitable particle based simulation methods such as molecular dynamics, dissipative particle dynamics or smoothed particle hydrodynamics. The user should be enabled to freely define his own physical models without the need for recoding or code extensions. Solution method: SYMPLER provides flexibility to the user by 1. a modular object oriented structure that is passed to the user level and allows easy switching among different integration algorithms, particle interaction forces, boundary conditions, etc. 2. an arbitrary number of particle-species for the simulation of complex multi-component systems 3. an arbitrary number of additional user-defined degrees of freedom per particle-species 4. symbolic definition of runtime-compiled mathematical expressions for particle interactions 5. import of CAD-geometries 6. a flexible choice of available computational cores through a grid-computing interface, amongst others. Restrictions: Classical deterministic and stochastic Newtonian dynamics. Unusual features: Symbolic runtime-compiled user-defined expressions. Additional comments: The current version and all future updates to the code are also found at http://sympler.org . Running time: Some benchmarks are given in the paper. The running time is problem dependent and ranges from seconds to days.

Smoothed particle hydrodynamics-based numerical investigation on sessile, oscillating droplets

Forced oscillations in sessile droplets can be exploited in electrowetting mixing of fluid fractions. The necessary complex flows and large shape deformations require a numerical investigation of fluid dynamics in the transient regime. We provide a means to characterize oscillations qualitatively and quantitatively with the goal to examine and to classify flow patterns occurring inside. A superposition of different harmonic excitation patterns gives the possibility to control the convective flow. In this investigation, we apply a generic and accurate multi-phase smoothed particle hydrodynamics model to a two-dimensional three-phase flow and consider an oscillating droplet sitting on a substrate and immersed in a fluidic phase. These vibrations are investigated in two ways: the analysis of a step response due to an abrupt change of the contact angle is applied to identify the resonance frequencies. Secondly, the time evolution of the shape of the droplet in terms of harmonic functions is determined. Their amplitudes are examined in the time and frequency domain. This gives the possibility to relate resonance frequencies to mode shapes and to detect a coupling between them. Our approach is successfully applied to different numerical case studies.

Constrained simulations of flow in haemodynamic devices: towards a computational assistance of magnetic resonance imaging measurements

Cardiovascular diseases, mostly related to atherosclerosis, are the major cause of death in industrial countries. It is observed that blood flow dynamics play an important role in the aetiology of atherosclerosis. Especially, the blood velocity distribution is an important indicator for predisposition regions. Today magnetic resonance imaging (MRI) delivers, in addition to the morphology of the cardiovascular system, blood flow patterns. However, the spatial resolution of the data is slightly less than 1 mm and owing to severe restrictions in magnetic field gradient switching frequencies and intensities, this limit will be very hard to overcome. In this paper, constrained fluid dynamics is applied within the smoothed particle hydrodynamics formalism to enhance the MRI flow data. On the one hand, constraints based on the known volumetric flow rate are applied. They prove the plausibility of the order of magnitude of the measurements. On the other hand, the higher resolution of the simulation allows one to determine in detail the flow field between the coarse data points and thus to improve their spatial resolution.

Dissipative particle dynamics of diffusion-NMR requires high Schmidt-numbers

We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. After a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered.

Markovian equations of motion for non-Markovian coarse-graining and properties for graphene blobs

We obtain Markovian equations of motion for a many body system of interacting coarse-grained (CG) variables and additional fluxes. The investigated CG variables belong to the special family of linear combinations of atomistic degrees of freedom. The system of Markovian equations of motion approximates Moris exact non-Markovian generalized Langevin equation and is easy to solve by computer simulation. All parameters of the equations can be obtained from equilibrium molecular dynamics simulations of the investigated microscopic system. These parameters are either equal to the famous static covariances from Moris continued fraction or they represent generalized constant friction matrices. We propose two different ways to compute these friction matrices based on Moris continued fraction. Finally, some of the parameters are computed numerically for the special case of centre of mass variables in the graphene lattice and it is found that the CG variables interact with their additional fluxes in a spatially very local way.

Top-down vs. bottom-up coarse-graining of graphene and CNTs for nanodevice simulation

We present and compare two approaches for the coarse-graining (CG) of models for graphene and carbon nanotubes (CNTs). Such models are required to enable mechanical device simulation on mesoscopic time and length scales hardly reachable by the molecular dynamics method. The first is a heuristic top-down approach while the second performs a rigorous bottom-up CG based upon an atomistic description. Both models belong to the family of dissipative particle dynamics. The top-down model already allows to analyze CNT self assembly and the temperature dependent resonance behavior of resonators. Correct relaxation time-scales required, e.g., for the Q-factor of resonator-devices are hard to adjust in this model. Therefore, a statistical projection-operator based bottom-up approach was investigated. This model allows to reproduce the correct time scales of autocorrelation functions on a CG-level. For correct cross-correlations and hence the correct decay of eigenmodes, further improvements are necessary.