Steering in computational science: mesoscale modelling and simulation

This paper outlines the benefits of computational steering for high performance computing applications. Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to illustrate the substantial improvements which computational steering offers in terms of resource efficiency and time to discover new physics. We discuss details of our current steering implementations and describe their future outlook with the advent of computational grids.Comment: 40 pages, 11 figures. Accepted for publication in Contemporary Physic

Phase-field-crystal models for condensed matter dynamics on atomic length and diffusive time scales: an overview

Here, we review the basic concepts and applications of the phase-field-crystal (PFC) method, which is one of the latest simulation methodologies in materials science for problems, where atomic- and microscales are tightly coupled. The PFC method operates on atomic length and diffusive time scales, and thus constitutes a computationally efficient alternative to molecular simulation methods. Its intense development in materials science started fairly recently following the work by Elder et al. [Phys. Rev. Lett. 88 (2002), p. 245701]. Since these initial studies, dynamical density functional theory and thermodynamic concepts have been linked to the PFC approach to serve as further theoretical fundaments for the latter. In this review, we summarize these methodological development steps as well as the most important applications of the PFC method with a special focus on the interaction of development steps taken in hard and soft matter physics, respectively. Doing so, we hope to present today's state of the art in PFC modelling as well as the potential, which might still arise from this method in physics and materials science in the nearby future.Comment: 95 pages, 48 figure

Study of random porous morphologies by means of statistical analysis and computer simulations of fluid dynamics

This thesis presents an investigation of porous media by means of simulation techniques and morphological analysis. As a basis for the investigation throughout this work, we use three- dimensional (3D) images of porous structures obtained by imaging techniques, in particular, fo- cused ion beam scanning electron microscopy (FIB-SEM) and confocal laser scanning microscopy (CLSM) for macroporous space, and scanning transmission electron microscopy (STEM) to re- solve mesopores. A set of different morphological methods (chord length distribution (CLD), medial axis analysis (MAA), estimations of geometric, branch and diffusive tortuosities) are applied to capture averaged descriptors of the reconstructed porous samples. Because fluid dy- namics is inherent in many applications of porous media, several techniques are deployed to simulate the fluid dynamics in the reconstructions of porous media. This work includes four chapters that cover three different topics associated with the investigation of fluid dynamics in porous media. Each chapter also represents a separate journal publication. In the first chapter, we perform hydrodynamic dispersion simulations to study the morphology- flow relationship in physical reconstructions of particulate beds as well as in computer-generated packings of monosized spheres. A combination of lattice-Boltzmann and random-walk parti- cle tracking (RWPT) methods were utilized to simulate the flow and mass transport, respec- tively. Based on mean chord length μ and standard deviation σ estimated for CLD, we present a morphological descriptor, σ/μ, that can predict the longitudinal dispersion coefficient for any morphological configuration of packed beds. In the second chapter, we introduce the overall hindrance factor expression, H(λ), that de- scribes transport limitations in mesoporous space of random silica monoliths in dependence of λ, the ratio of solute size to mean pore size. The presented H(λ) is obtained through diffusion simulations of finite-size tracers applying the RWPT technique in three reconstructions of mor- phologically similar porous silica. The expression can also be utilized to assess the hindered diffusion coefficient for any material with similar morphology. In the third chapter, we adopt the lattice-gas mean field density functional theory (MFDFT) to virtually reproduce adsorption/desorption processes in a mesopore network of one of the monoliths from the second chapter. We demonstrate a good qualitative agreement of simulated boundary curves with experimental isotherms with an H2 hysteresis loop obtained for nitrogen at 77 K. We also use 3D images of the phase distribution that can be provided by MFDFT for any relative pressure value in the range 0 < p/p0 ≤ 1 to reveal the relation between hysteresis and phase distribution. In the fourth chapter, we continue using the concept of exploration of phase distribution and perform MFDFT modeling in physically reconstructed geometrical models of two ordered (SBA-15, KIT-6) and one random mesoporous silicas. We conduct a short parametric study of the MFDFT model to find optimal agreement with experimental isotherms in the hysteresis region. We also present simulated boundary curves for both ordered structures with a clear H1 hysteresis loop and for the disordered material with type H2(a) hysteresis. The phase distribution analysis as well as the shape of scanning curves reveal a highly heterogeneous morphology of the random silica. Hence, pore blocking and cavitation phenomena are identified and analyzed

Coupling boundary conditions in continuum-particle approach for open systems: theoretical analysis and computational implementation

Adaptive Resolution Simulation (AdResS) is a multi-resolution method with open system characteristics for modelling atomistic-level systems. In AdResS, a high-resolution open system is in contact with a reservoir of particles and energy, and the system is recreating the thermodynamics and physics of the full atomistic system of reference. In this thesis, the fundamental characteristics of the AdResS method are studied to provide a better understanding of the statistical mechanics undergoing within open system. Among the most relevant results, it is worth underlining the equivalence of the grand potential, determined theoretically, with the pressure, calculated numerically for the same volume of the atomistically resolved region. Moreover, such analysis led to a straightforward calculation of the chemical potential of the liquid under investigation for a wide range of thermodynamic conditions. It has been shown that the pressure difference resulting from the abrupt change of resolutions is compensated by the energy provided by the external force (thermodynamic force) in AdResS. Moreover, the chemical potential of AdResS is related to the chemical potential of the full-atomistic simulation of reference by calculating different contributions corresponding to the abrupt change of resolutions. Next, a fluctuating hydrodynamics (FHD) solver is designed to capture the small-scale fluctuations in the continuum simulations by adding a stochastic flux term to the Navier-Stokes equation of the compressible flow. Then, this continuum solver is coupled to the previously developed AdResS simulator through a small interface region by employing a novel coupling algorithm according to the non-equilibrium AdResS simulation. To this aim, a set of pre-calculated thermodynamic forces is prepared and the information on the continuum side transfers to the particle subdomain by interpolating proper thermodynamic force. The AdResS-FHD coupling system is developed and tested for various cases with different conditions and showed satisfactory agreement with the results of the reference continuum and fully atomistic simulations.Die Adaptive Resolution Simulation (AdResS) ist eine Mehrfachauflösungsmethode mit Eigenschaften eines offenen Systems zur Modellierung von Systemen auf atomistischer Ebene. Bei AdResS steht ein hochaufl¨osendes offenes System in Kontakt mit einem Reservoir von Teilchen und Energie, und das System bildet die Thermodynamik und Physik des vollständigen atomistischen Bezugssystems nach. In dieser Arbeit werden die grundlegenden Eigenschaften der AdResS-Methode untersucht, um ein besseres Verständnis der statistischen Mechanik in einem offenen System zu ermöglichen. Zu den wichtigsten Ergebnissen gehört die Aquivalenz zwischen dem theoretisch ermittelten Großkanonischen Potential und dem numerisch berechneten Druck. Darüber hinaus führte diese Analyse zu einer einfachen Berechnung des chemischen Potenzials der untersuchten Flüssigkeit für ein breites Spektrum thermodynamischer Bedingungen. Es wurde gezeigt, dass der Druckunterschied, der sich aus der abrupten Anderung der Auflösung ergibt, durch die Energie kompensiert wird, die von der Äußeren Kraft (thermodynamische Kraft) in AdResS bereitgestellt wird. Als Nächstes wird ein fluktuierender hydrodynamischer (FHD) Solver entwickelt, um die kleinräumigen Fluktuationen in den Kontinuumssimulationen zu erfassen, indem ein stochastischer Flussterm zur Navier-Stokes-Gleichung der kompressiblen Strömung hinzugefügt wird. Anschließend wird dieser Kontinuumslöser mit dem zuvor entwickelten AdResS-Simulator durch eine kleine Schnittstellenregion gekoppelt, indem ein neuartiger Kopplungsalgorithmus entsprechend der Nicht-Gleichgewichts AdResS-Simulation eingesetzt wird. Zu diesem Ziel wird ein Satz von vorberechneten thermodynamischen Kräften vorbereitet und die Informationen auf der Kontinuumsseite werden durch Interpolation geeigneter thermodynamischer Kräfte auf das Partikel-Subdomain transferieren. Das AdResS-FHD-Kopplungssystem wurde für verschiedene Fälle mit unterschiedlichen Bedingungen entwickelt und getestet und zeigte zufriedenstellende Übereinstimmung mit den Ergebnissen der Referenzkontinuums- und vollständig atomistischen Simulationen

Flowing matter

This open access book, published in the Soft and Biological Matter series, presents an introduction to selected research topics in the broad field of flowing matter, including the dynamics of fluids with a complex internal structure -from nematic fluids to soft glasses- as well as active matter and turbulent phenomena.Flowing matter is a subject at the crossroads between physics, mathematics, chemistry, engineering, biology and earth sciences, and relies on a multidisciplinary approach to describe the emergence of the macroscopic behaviours in a system from the coordinated dynamics of its microscopic constituents.Depending on the microscopic interactions, an assembly of molecules or of mesoscopic particles can flow like a simple Newtonian fluid, deform elastically like a solid or behave in a complex manner. When the internal constituents are active, as for biological entities, one generally observes complex large-scale collective motions. Phenomenology is further complicated by the invariable tendency of fluids to display chaos at the large scales or when stirred strongly enough. This volume presents several research topics that address these phenomena encompassing the traditional micro-, meso-, and macro-scales descriptions, and contributes to our understanding of the fundamentals of flowing matter.This book is the legacy of the COST Action MP1305 “Flowing Matter”

Mesoscale fluid simulation with the Lattice Boltzmann method

PhDThis thesis describes investigations of several complex fluid effects., including hydrodynamic spinodal decomposition, viscous instability. and self-assembly of a cubic surfactant phase, by simulating them with a lattice Boltzmann computational model. The introduction describes what is meant by the term "complex fluid", and why such fluids are both important and difficult to understand. A key feature of complex fluids is that their behaviour spans length and time scales. The lattice Boltzmann method is presented as a modelling technique which sits at a "mesoscale" level intermediate between coarse-grained and fine-grained detail, and which is therefore ideal for modelling certain classes of complex fluids. The following chapters describe simulations which have been performed using this technique, in two and three dimensions. Chapter 2 presents an investigation into the separation of a mixture of two fluids. This process is found to involve several physical mechanisms at different stages. The simulated behaviour is found to be in good agreement with existing theory, and a curious effect, due to multiple competing mechanisms, is observed, in agreement with experiments and other simulations. Chapter 3 describes an improvement to lattice Boltzmann models of Hele-Shaw flow, along with simulations which quantitatively demonstrate improvements in both accuracy and numerical stability. The Saffman-Taylor hydrodynamic instability is demonstrated using this model. Chapter 4 contains the details and results of the TeraGyroid experiment, which involved extremely large-scale simulations to investigate the dynamical behaviour of a self-assembling structure. The first finite- size-effect- free dynamical simulations of such a system are presented. It is found that several different mechanisms are responsible for the assembly; the existence of chiral domains is demonstrated, along with an examination of domain growth during self-assembly. Appendix A describes some aspects of the implementation of the lattice Boltzmann codes used in this thesis; appendix B describes some of the Grid computing techniques which were necessary for the simulations of chapter 4. Chapter 5 summarises the work, and makes suggestions for further research and improvement.Huntsman Corporation Queen Mary University Schlumberger Cambridge Researc

Magnetic Hybrid-Materials

Externally tunable properties allow for new applications of suspensions of micro- and nanoparticles in sensors and actuators in technical and medical applications. By means of easy to generate and control magnetic fields, fluids inside of matrices are studied. This monnograph delivers the latest insigths into multi-scale modelling, manufacturing and application of those magnetic hybrid materials

Taking Magnetic Resonance into Industrial Applications

Magnetic resonance (MR) is a highly versatile technique with great potential for use in industrial applications; from the in situ study of unit operations to the optimisation of product properties. This thesis, concerned with the latter, is divided into two parts. Firstly, dynamic MR is applied to characterise the flow behaviour, or rheology, of process fluids. Such characterisation is typically performed using conventional rheometry methods operating offline, with an online, or inline, method sought for process control and optimisation. Until recently, MR was an unlikely choice for this application due to the requirement of high-field MR hardware. However, recent developments in low-field MR hardware mean that the potential of MR in such applications can now be realised. Since the implementation of MR flow imaging is challenging on low-field MR hardware, two new approaches to MR rheometry are described using pulsed field gradient (PFG) MR. A cumulant analysis of the PFG MR signal is first used to characterise the rheology of model power-law fluids, namely xanthan gum-in-water solutions, accurate to within 5% of conventional rheometry, the data being acquired in only 6% of the time required when using MR flow imaging. The second approach utilises a Bayesian analysis of the PFG MR signal to characterise the rheology of model Herschel--Bulkley fluids, namely Carbopol 940-in-water solutions; data are acquired in only 12% of the time required for analysis using MR flow imaging. The suitability of the Bayesian MR approach to study process fluids is demonstrated through experimental study on an alumina-in-acetic acid slurry used by Johnson Matthey. Secondly, MR imaging is used to provide insights into the origins and mechanisms of colloidal gel collapse. Many industrial products are colloidal gels, a space-spanning network of attractive particles with a yield stress. Colloidal gels are, however, known to undergo gravitational collapse after a latency period, thus limiting the shelf-life of products. This remains poorly understood, with a more detailed understanding of both fundamental interest and practical importance. To this end, MR imaging is applied offline to investigate the phase behaviour of colloidal gels. In particular, a comparison of the simulated and experimental phase diagrams suggests gravitational gel collapse to be gravity-driven. Furthermore, measurement of the colloid volume fraction using MR imaging indicates the formation of clusters of colloids at the top of the samples. Whether such clusters initiate gravitational gel collapse is yield stress-dependent; the gravitational stress exerted by a cluster must be sufficient to yield the colloidal gel.Johnson Matthe