Progress in particle-based multiscale and hybrid methods for flow applications

This work focuses on the review of particle-based multiscale and hybrid methods that have surfaced in the field of fluid mechanics over the last 20 years. We consider five established particle methods: molecular dynamics, direct simulation Monte Carlo, lattice Boltzmann method, dissipative particle dynamics and smoothed-particle hydrodynamics. A general description is given on each particle method in conjunction with multiscale and hybrid applications. An analysis on the length scale separation revealed that current multiscale methods only bridge across scales which are of the order of O(102)−O(103) and that further work on complex geometries and parallel code optimisation is needed to increase the separation. Similarities between methods are highlighted and combinations discussed. Advantages, disadvantages and applications of each particle method have been tabulated as a reference

Performance and degradation of Proton Exchange Membrane Fuel Cells: State of the art in modeling from atomistic to system scale

Jahnke, T. et al.Proton Exchange Membrane Fuel Cells (PEMFC) are energy efficient and environmentally friendly alternatives to conventional energy conversion systems in many yet emerging applications. In order to enable prediction of their performance and durability, it is crucial to gain a deeper understanding of the relevant operation phenomena, e.g., electrochemistry, transport phenomena, thermodynamics as well as the mechanisms leading to the degradation of cell components. Achieving the goal of providing predictive tools to model PEMFC performance, durability and degradation is a challenging task requiring the development of detailed and realistic models reaching from the atomic/molecular scale over the meso scale of structures and materials up to components, stack and system level. In addition an appropriate way of coupling the different scales is required. This review provides a comprehensive overview of the state of the art in modeling of PEMFC, covering all relevant scales from atomistic up to system level as well as the coupling between these scales. Furthermore, it focuses on the modeling of PEMFC degradation mechanisms and on the coupling between performance and degradation models.The research leading to this review has been partially supported by the European Union's Seventh Framework Program for the Fuel Cells and Hydrogen Joint Technology Initiative under the project PUMA MIND (grant agreement no 303419).Peer Reviewe

Advances in Molecular Simulation

Molecular simulations are commonly used in physics, chemistry, biology, material science, engineering, and even medicine. This book provides a wide range of molecular simulation methods and their applications in various fields. It reflects the power of molecular simulation as an effective research tool. We hope that the presented results can provide an impetus for further fruitful studies

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.Comment: review article, to appear in Rep. Prog. Phy

Rational design of nanofibrous materials

Making Carbon nanotubes a functional material for widespread use is a very cumbersome and challenging task. Not only do CNT materials require the tubes to be well dispersed and individualized rather than in bundles but resulting material has much poorer properties than expected due to insufficient load transfer between crossing CNT. This work tries to provide insight and solutions onto both of these problems, by employing computer simulations to reveal the dual nature of surfactant mediated forces on CNT. A generic coarse grain model has been used along with a dissipative particle dynamics thermostat and implicit solvent treatment. Results illustrate that depending on the bulk concentration of surfactants and their geometry, one can control the surfatantmediated forces on tubes being able to trigger both tube gluing or dispersion. Furthermore, an adsorption study elucidating the differences between surfactant adsorption on individual tubes and their bundles has been done. Surfactants follow a superlinear synergetic adsorption isothermon individual tubes,whereas adsorb via a Langmuir mechanism on their bundles. This work provides a solid framework of knowledge and insight regarding the nature of CNT and surfactants interaction and adsorption, providing rational arguments for the design of optimum CNT materials

Critical assessment of particle-infused fire suppression system in building structures

In the past decades, water droplet-based suppression systems (i.e. fire sprinklers, water mist) have been extensively utilized as building fire suppression systems. Nevertheless, current suppression systems operate under considerable design limitations due to high-rise structures and rapid increase in building complexity, such as pressure supply and water storages. Challenges can also be foreseen in suppressing water-reactive chemicals (i.e. alkali metals, hydrides) as the violent explosive reaction will be triggered. Therefore, it is vital to investigate potential suppression agents to cope with the increasing building fire risk associated with complex building materials and hazardous combustibles. A large eddy simulation (LES) model incorporated with novel user-defined functions (UDFs) to consider particle expansion and charring was proposed in this thesis. This model has been utilised to numerically study an experimental case to investigate the fire suppression behaviour of expandable graphite (EG) in building structures. This approach has provided an in-depth characterization of EG's thermophysical properties. This includes the expansion, barrier effect from char formation and the decomposition of EG. It was discovered that EG is more effective in fire suppression compared to natural graphite. Among the diameter range of EG (400 µm - 1000 µm), the smaller diameter of EGs tend to be efficient in suppressing metallic fire. The WALE SGS model has provided the most accurate temperature prediction among other SGS models, with average relative errors of 7.71% and 8.93%. The novel multiphase model was comprehensively validated by material testing and other experiments, and proven to be an effective tool to investigate particle-infused suppression in a structural fire. Moreover, the thermophysical properties (i.e. pyrolysis kinetics) of graphite have also been characterized through Molecular Dynamics (MD) simulations. The extracted Arrhenius kinetics parameters (i.e. activation energy) were compared to the experimental results, with an averaged relative discrepancy between 1.71 % - 5.38 %. The species breakdown analysis from the ReaxFF simulation will also further explore the feasibility of MD as a practical approach to analyse graphite's pyrolysis and chemical reaction mechanisms. The MD simulations have improved the understanding of particle pyrolysis and volatile emission during the oxidation of graphite and provided insights into the future of multiscale simulations

Importance of molecular interactions in colloidal dispersions

We review briefly the concept of colloidal dispersions, their general properties and some of their most important applications, as well as the basic molecular interactions that give rise to their properties in equilibrium. Similarly, we revisit Brownian motion and hydrodynamic interactions associated with the concept of viscosity of colloidal dispersion. It is argued that the use of modern research tools, such as computer simulations, allows one to predict accurately some macroscopically measurable properties by solving relatively simple models of molecular interactions for a large number of particles. Lastly, as a case study, we report the prediction of rheological properties of polymer brushes using state of the art, coarse grained computer simulations, which are in excellent agreement with experiments.Comment: 8 pages, 10 figure

Application of computer simulation approaches to study the structure and properties of polymeric systems

The study at the nanoscopic level of the polymeric systems is a keystone for a deeper understanding of their internal structure and properties, not only at nanometric scale but also at macroscopic level. The disciplines involved in this scientific field are diverse, including areas such as chemistry, physics, material science, biology and statistics among others. The aforementioned fields converge in a scientific and technologic central branch called nanotechnology. In the last decades, nanotechnology based on polymeric systems has aroused a great interest among the scientific community, as is clearly evidenced by the huge amount of scientific publications and applications developed within this area. However, the experimental complexity for the development of new devices and the economical limitations devoted to this end are barriers that let us think about the use of alternative approaches in this scientific field. In the face of this endeavors, the application of computer simulation methodologies to must be taken into account. The principal focus of this Thesis is the study at the atomic and molecular level of some polymeric systems through theoretical methodologies based on quantum and classical mechanics formalisms. Such methods allow us to support and understand some chemical and physical observables as well as to analyze and describe these systems at their structural level. Within the framework of the application of the atomic and molecular simulation methodologies, this Thesis could be divided mainly in three main research lines: Conducting Polymers, Polymeric Cation Exchange Membranes, and Dendrimers and Dendronized Polymers The first one focusses on evaluating the detection ability of different conducting polymers when they interact with dopamine or morphine with the final aim of developing a sensor based on these materials. The examination of conducting polymers sensitivity to the analyte detection was carried out via inspection of their ability to form secondary interactions (i.e. weak and strong hydrogen bonds, p-stacking interactions), which was examined using quantum mechanical calculations. Second line is devoted to the application of atomistic molecular dynamics simulation for the investigation of the influence of the electric field strength and the temperature in the dynamical and structural properties of cationic exchange membranes. These investigations were focused on the analysis of hydronium transport mechanism, internal structural rearrangements of the membrane and the characteristics of the hydration shell surrounding the diffused hydronium ions. The last working line of this Thesis is centered on the study at electronic and atomic level of dendritic molecules and dendronized polymers through both quantum and classical mechanics formalisms. The structural properties and molecular interactions occurring in a particular class of dendronized polymers were analyzed. On one side, through a characterization of the inter and intramolecular non bonded interactions of two interacting polymer chains in an attempt to relate atomistic information to the rheological response of these large cylindrical-shape objects. On the other side, studying the internal structure and solvent absorption ability of these systems positively charged and comparing them with their neutral analogues. Finally, studies of both dendrimers and dendronized polymers based on all-thiophene dendrons trough quantum mechanics and molecular dynamics were performed. The electronic properties of symmetric and unsymmetric all-thiophene dendrimers containing up to 45 thiophene rings in neutral and oxidized state was investigated. On the other hand, the internal organization of second and third generation macromonomers and dendronized polymers based on all-thiophene dendrons was studied using density functional theory calculations and classical molecular dynamics simulations, respectively.El estudio a nivel nanoscópico de sistemas poliméricos es un punto clave para la comprensión de su estructura atómica y de sus propiedades, no solamente a escala nanométrica sino también a nivel macroscópico. Las disciplinas involucradas en este campo son diversas e incluyen áreas tales como la química, física, ciencia de materiales y estadística, entre otras. Todos estos campos convergen en una rama científica y tecnológica denominada nanotecnología. En los últimos años, el uso de sistemas poliméricos dentro del campo de la nanotecnología ha suscitado un gran interés dentro de la comunidad científica, tal como queda manifiesto debido al gran número de publicaciones científicas y aplicaciones desarrolladas. Sin embargo tanto el grado de complejidad que implica el desarrollo de nuevos dispositivos dentro de esta disciplina como las limitaciones económicas existentes para estos fines, han hecho que los métodos de simulación molecular sean una herramienta clave para continuar avanzando en esta línea de investigación. El propósito de esta Tesis es el estudio de algunos sistemas poliméricos a nivel atómico y molecular mediante métodos teóricos basados en mecánica cuántica y clásica. Dichos métodos nos han permitido corroborar y entender propiedades físico-químicas a la vez que analizar y describir estos sistemas a nivel estructural. Dentro del marco de la aplicación de métodos de simulación atomístico y molecular, esta tesis puede dividirse en tres líneas de trabajo: Polímeros Conductores, Membranas Poliméricas de Intercambio Catiónico, y Polímeros Dendríticos. En la primera línea se ha evaluado, a partir de estudios cuánticos, la capacidad de detección de diversos polímeros conductores al interactuar con morfina o dopamina; con el objetivo final de desarrollar sensores basados en dichos materiales. Los análisis de sensibilidad de estos polímeros para la detección de dichos analitos se llevaron a cabo mediante el estudio de la capacidad que presentan estos sistemas para formar interacciones secundarias (i.e. puentes de hidrógeno y p-stacking). En segundo lugar se han llevado a cabo estudios atomísticos basados en dinámica molecular para estudiar la influencia de la intensidad del campo eléctrico y de la temperatura en las propiedades dinámicas y estructurales que tienen lugar en membranas de intercambio catiónico. Estas investigaciones se centraron en el análisis de los mecanismos de transporte de los iones hidronio, los cambios sufridos a nivel estructural dentro de la membrana y la caracterización de la capa de hidratación que rodea los a los iones difundidos. La última línea de trabajo está centrada en el estudio tanto a nivel electrónico como atomístico de moléculas dendríticas y polímeros dendronizados mediante mecánica cuántica y clásica. Se llevaron a cabo análisis de las propiedades estructurales así como de las interacciones moleculares que tienen lugar en una clase particular de polímeros dendronizados. Por un lado, mediante la caracterización de las interacciones inter e intramoleculares de dos cadenas poliméricas interpenetradas con el objetivo de establecer la relación existente entre la información atomística obtenida y las propiedades viscoelásticas propias de estos objetos cilíndricos. Por otro lado, mediante un estudio comparativo de estos sistemas en estado neutro y cargado para determinar como la distribución de carga afecta a su estructura interna y a su capacidad de absorción en disolución. Finalmente, se han estudiado dendrímeros y polímeros dendronizados basados en dendrones de tiofeno. Se investigaron propiedades electrónicas de estructuras simétricas y asimétricas de dendrímeros con hasta 45 anillos de tiofeno en estado neutro y oxidado. Además, se analizó la organización interna de macromonómeros basados en dendrones de tiofeno de 2ª y 3ª generación así como de sus correspondientes polímeros mediante cálculos de teoría de funcional de densidad y mediante simulaciones de dinámica molecular, respectivamente.Postprint (published version