Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful computational method for fundamental research in science branches such as biology, chemistry, biomedicine and physics over the past 60 years. Powered by rapidly advanced supercomputing technologies in recent decades, MD has entered the engineering domain as a first-principle predictive method for material properties, physicochemical processes, and even as a design tool. Such developments have far-reaching consequences, and are covered for the first time in the present paper, with a focus on MD for combustion and energy systems encompassing topics like gas/liquid/solid fuel oxidation, pyrolysis, catalytic combustion, heterogeneous combustion, electrochemistry, nanoparticle synthesis, heat transfer, phase change, and fluid mechanics. First, the theoretical framework of the MD methodology is described systemically, covering both classical and reactive MD. The emphasis is on the development of the reactive force field (ReaxFF) MD, which enables chemical reactions to be simulated within the MD framework, utilizing quantum chemistry calculations and/or experimental data for the force field training. Second, details of the numerical methods, boundary conditions, post-processing and computational costs of MD simulations are provided. This is followed by a critical review of selected applications of classical and reactive MD methods in combustion and energy systems. It is demonstrated that the ReaxFF MD has been successfully deployed to gain fundamental insights into pyrolysis and/or oxidation of gas/liquid/solid fuels, revealing detailed energy changes and chemical pathways. Moreover, the complex physico-chemical dynamic processes in catalytic reactions, soot formation, and flame synthesis of nanoparticles are made plainly visible from an atomistic perspective. Flow, heat transfer and phase change phenomena are also scrutinized by MD simulations. Unprecedented details of nanoscale processes such as droplet collision, fuel droplet evaporation, and CO2 capture and storage under subcritical and supercritical conditions are examined at the atomic level. Finally, the outlook for atomistic simulations of combustion and energy systems is discussed in the context of emerging computing platforms, machine learning and multiscale modelling

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth

Optimizing flame synthesis of carbon nanotubes: experimental and modelling perspectives

Synthesis of carbon nanotubes in flames has become highly attractive due to its rapid, inexpensive, and simple method of production. The study of flame synthesis of carbon nanotubes revolves around the control of flame and catalyst parameters to increase the synthesis efficiency and to produce high quality nanotubes. The control parameters include flame temperature, concentration of carbon source species, catalyst type, equivalence ratio, and fuel type. Carbon nanotubes which are produced with rapid growth rate and possess high degree of purity and alignment are often desired. The present study reviews various optimization techniques from the advanced studies of chemical vapour deposition which are applicable for the synthesis of nanotubes in flames. The water-assisted and catalyst free synthesis are seen as possible candidates to improve the growth rate, alignment, and purity of the synthesized nanotubes. The state-of-the-art of the flame synthesis modelling at particle and flame scales are reviewed. Based on the thorough review of the recent experimental findings related to the catalytic growth of nanotube, possible refinement of the existing particle scale model is discussed. The possibility of two-way coupling between the two scales in computational fluid dynamics may be a major contribution towards the optimization of the flame synthesis

Ono: an open platform for social robotics

In recent times, the focal point of research in robotics has shifted from industrial ro- bots toward robots that interact with humans in an intuitive and safe manner. This evolution has resulted in the subfield of social robotics, which pertains to robots that function in a human environment and that can communicate with humans in an int- uitive way, e.g. with facial expressions. Social robots have the potential to impact many different aspects of our lives, but one particularly promising application is the use of robots in therapy, such as the treatment of children with autism. Unfortunately, many of the existing social robots are neither suited for practical use in therapy nor for large scale studies, mainly because they are expensive, one-of-a-kind robots that are hard to modify to suit a specific need. We created Ono, a social robotics platform, to tackle these issues. Ono is composed entirely from off-the-shelf components and cheap materials, and can be built at a local FabLab at the fraction of the cost of other robots. Ono is also entirely open source and the modular design further encourages modification and reuse of parts of the platform

Development of High Fidelity Soot Aerosol Dynamics Models using Method of Moments with Interpolative Closure

The method of moments with interpolative closure (MOMIC) for soot formation and growth provides a detailed modeling framework maintaining a good balance in generality, accuracy, robustness, and computational efficiency. This study presents several computational issues in the development and implementation of the MOMIC-based soot modeling for direct numerical simulations (DNS). The issues of concern include a wide dynamic range of numbers, choice of normalization, high effective Schmidt number of soot particles, and realizability of the soot particle size distribution function (PSDF). These problems are not unique to DNS, but they are often exacerbated by the high-order numerical schemes used in DNS. Four specific issues are discussed in this article: the treatment of soot diffusion, choice of interpolation scheme for MOMIC, an approach to deal with strongly oxidizing environments, and realizability of the PSDF. General, robust, and stable approaches are sought to address these issues, minimizing the use of ad hoc treatments such as clipping. The solutions proposed and demonstrated here are being applied to generate new physical insight into complex turbulence-chemistry-soot-radiation interactions in turbulent reacting flows using DNS

Reactive Molecular Dynamics of Fuel Oxidation and Catalytic Reactions

The present research employs the ReaxFF (a force field for reactive systems) molecular dynamics simulation method to investigate the detailed microscopic modelling for complex chemistry of fuel oxidation and catalytic reactions on graphenebased nanomaterials at the atomic level. Specifically, in total, four different systems are studied in detail. Firstly, the fundamental reaction mechanisms of hydrous ethanol oxidation in comparison with the ethanol oxidation under fuel-air condition is investigated. The results indicate that it is the addition of water that promotes the OH production due to the chemical effect of H2O leading to the enhancement of ethanol oxidation and reduction of CO production. Secondly, the fundamental study on mechanisms of thermal decomposition and oxidation of aluminium hydride is conducted. It is found that the thermal decomposition and oxidation of aluminium hydride proceed in three distinctive stages ((1) Pre-diffusion; (2) Core-shell integration; (3) Post-diffusion, and (I) Oxygen adsorption; (II) Fast dehydrogenation; (III) Al oxidation), respectively. Thirdly, the catalytic mechanisms and kinetics of methane oxidation assisted by Platinum/graphene-based catalysts are studied. Platinumdecorated functionalized graphene sheet is reported to be the most effective catalyst among all the involved nanoparticle candidates and it improves the catalytic activity by dramatically lowering the activation energy by approximately 73% compared with pure methane oxidation. Fourthly, the initiation mechanisms of JP-10 pyrolysis and oxidation with functionalized graphene sheets in comparison with normal JP-10 reactions are revealed. The results suggest that both pyrolysis and oxidation of JP-10 are advanced and enhanced in the presence of functionalized graphene sheets. Additionally, the functional groups also participate in various intermediate reactions to further enhance the pyrolysis and oxidation of JP-10. In summary, the new findings from the present research could contribute to the design and improvement of the future high-performance energy and propulsion systems, especially for the promising graphene-containing fuel/propellant formulations

Numerical study of surface tension driven convection in thermal magnetic fluids

Microgravity conditions pose unique challenges for fluid handling and heat transfer applications. By controlling (curtailing or augmenting) the buoyant and thermocapillary convection, the latter being the dominant convective flow in a microgravity environment, significant advantages can be achieved in space based processing. The control of this surface tension gradient driven flow is sought using a magnetic field, and the effects of these are studied computationally. A two-fluid layer system, with the lower fluid being a non-conducting ferrofluid, is considered under the influence of a horizontal temperature gradient. To capture the deformable interface, a numerical method to solve the Navier???Stokes equations, heat equations, and Maxwell???s equations was developed using a hybrid level set/ volume-of-fluid technique. The convective velocities and heat fluxes were studied under various regimes of the thermal Marangoni number Ma, the external field represented by the magnetic Bond number Bom, and various gravity levels, Fr. Regimes where the convection were either curtailed or augmented were identified. It was found that the surface force due to the step change in the magnetic permeability at the interface could be suitably utilized to control the instability at the interface.published or submitted for publicationis peer reviewe