A Practical Guide to Surface Kinetic Monte Carlo Simulations

This review article is intended as a practical guide for newcomers to the field of kinetic Monte Carlo (KMC) simulations, and specifically to lattice KMC simulations as prevalently used for surface and interface applications. We will provide worked out examples using the kmos code, where we highlight the central approximations made in implementing a KMC model as well as possible pitfalls. This includes the mapping of the problem onto a lattice and the derivation of rate constant expressions for various elementary processes. Example KMC models will be presented within the application areas surface diffusion, crystal growth and heterogeneous catalysis, covering both transient and steady-state kinetics as well as the preparation of various initial states of the system. We highlight the sensitivity of KMC models to the elementary processes included, as well as to possible errors in the rate constants. For catalysis models in particular, a recurrent challenge is the occurrence of processes at very different timescales, e.g. fast diffusion processes and slow chemical reactions. We demonstrate how to overcome this timescale disparity problem using recently developed acceleration algorithms. Finally, we will discuss how to account for lateral interactions between the species adsorbed to the lattice, which can play an important role in all application areas covered here.Comment: This document is the final Author's version of a manuscript that has been peer reviewed and accepted for publication in Frontiers in Chemistry. To access the final edited and published work see https://www.frontiersin.org/articles/10.3389/fchem.2019.00202/abstrac

Droplet motion on miniaturized ratchets

The main objective of this study is to evaluate the feasibility of using miniaturized asymmetric structures to move liquid droplets and understand the driving mechanism. We developed the fabrication process for large area topological ratchets with the period ranging from millimeter down to sub-micrometer using micromachining techniques. Non-wetting superhydrophobic surfaces were successfully fabricated using soft UV or thermal nanoimprint lithography, reactive ion etching by oxygen plasma, and chemical surface modification by fluorinated silane vapor deposition. An accurate and reproducible experimental setup equipped with high speed camera and automatic injection system was established. Image processing tools allowed us to obtain various critical information related droplet motion and behavior along the ratchets surface. Various influences on the motion such as the surface temperature, ratchets dimension, surface wettability, droplet volume, kind of liquid, initial impact speed of droplet, polymer additive, and surface slope were systematically investigated for miniaturized non-wetting asymmetric ratchets. It is observed that the droplet motion on the ratchets is strongly dependent on the ratchets dimensions as well as the surface temperature. Extremely fast water droplet motion was achieved from the sub-micrometer ratchets near the Leidenfrost temperature. Even though the Leidenfrost-miniaturized ratchets system can be considered as an efficient pumping and cooling component, further intensive study to reduce the operating temperature and drive the liquid motion within microchannel is required for the broad range of applications

Physical Models in Community Detection with Applications to Identifying Structure in Complex Amorphous Systems

We present an exceptionally accurate spin-glass-type Potts model for the graph theoretic problem of community detection. With a simple algorithm, we find that our approach is exceptionally accurate, robust to the effects of noise, and competitive with the best currently available algorithms in terms of speed and the size of solvable systems. Being a local measure of community structure, our Potts model is free from a resolution limit that hinders community solutions for some popular community detection models. It further remains a local measure on weighted and directed graphs. We apply our community detection method to accurately and quantitatively evaluate the multi-scale: multiresolution ) structure of a graph. Our multiresolution algorithm calculates correlations among multiple copies: replicas ) of the same graph over a range of resolutions. Significant multiresolution structures are identified by strongly correlated replicas. The average normalized mutual information and variation of information give a quantitative estimate of the best resolutions and indicate the relative strength of the structures in the graph. We further investigate a phase transition effect in community detection, and we elaborate on its relation to analogous physical phase transitions. Finally, we apply our community detection methods to ascertain the most natural complex amorphous structures in two model glasses in an unbiased manner. We construct a model graph for the physical systems using the potential energy to generate weighted edge relationships for all pairs of atoms. We then solve for the communities within the model network and associate the best communities with the natural structures in the physical systems

Machine learning high multiplicity matrix elements for electron-positron and hadron-hadron colliders

The LHC is a large-scale particle collider experiment collecting vast quantities of experimental data to study the fundamental particles, and forces, of nature. Theoretical predictions made with the SM can be compared with observables measured at experiments. These predictions rely on the use of Monte Carlo event generators to simulate events which demand the evaluation of a matrix element. For high multiplicity processes this can take up a significant portion of the time spent simulating an event. In this thesis, we explore the usage of machine learning to accelerate the evaluation of matrix elements by introducing a factorisation-aware neural network model. Matrix elements are plagued with singular structures in regions of phase-space where particles become soft or collinear, however, the behaviour of the matrix element in these limits is well-understood. By exploiting the factorisation property of matrix elements in these limits, the model can learn how to best represent the approximation of the matrix elements as a linear combination of singular functions. We examine the application of the model to e−e+ annihilation matrix elements at tree-level and one-loop level, as well as to leading order pp collisions where the acceleration of event generation is critical for current experiments

A Primer for Black Hole Quantum Physics

The mechanisms which give rise to Hawking radiation are revealed by analyzing in detail pair production in the presence of horizons. In preparation for the black hole problem, three preparatory problems are dwelt with at length: pair production in an external electric field, thermalization of a uniformly accelerated detector and accelerated mirrors. In the light of these examples, the black hole evaporation problem is then presented. The leitmotif is the singular behavior of modes on the horizon which gives rise to a steady rate of production. Special emphasis is put on how each produced particle contributes to the mean albeit arising from a particular vacuum fluctuation. It is the mean which drives the semiclassical back reaction. This aspect is analyzed in more detail than heretofore and in particular its drawbacks are emphasized. It is the semiclassical theory which gives rise to Hawking's famous equation for the loss of mass of the black hole due to evaporation $dM/dt \simeq -1/M^2$. Black hole thermodynamics is derived from the evaporation process whereupon the reservoir character of the black hole is manifest. The relation to the thermodynamics of the eternal black hole through the Hartle--Hawking vacuum and the Killing identity are displayed. It is through the analysis of the fluctuations of the field configurations which give rise to a particular Hawking photon that the dubious character of the semiclassical theory is manifest. The present frontier of research revolves around this problem and is principally concerned with the fact that one calls upon energy scales that are greater than Planckian and the possibility of a non unitary evolution as well. These last subjects are presented in qualitative fashion only, so that this review stops at the threshold of quantum gravity.Comment: An old review article on black hole evaporation and black hole thermodynamics, put on the archive following popular demand, 178 pages, 21 figures (This text differs in slightly from the published version

Molecular Dynamics Simulation of the Structure, Dynamics and Crystallization of Ionic Liquids under Confinement and Low Temperature

Ionic liquids (ILs) have sparked widespread interest due to their peculiar properties and the resulting possibility of manifold applications. In this dissertation, molecular dynamics (MD) simulations have been used to elucidate the dynamics, structure and crystallization of ionic liquids in the bulk and confinement. First we studied the properties of the ILs [dmim+][Cl-] and [emim+][NTf2-] when they are confined inside nanomaterials such as CMK-3, CMK-5 and an isolated amorphous carbon nanopipe (ACNP). The results indicate that the ions of the ILs form different layers inside these nanomaterials and their dynamics are slower due to the confinement. We also found significant differences in the densities and mobilities of ions caused by pore morphologies. Moreover, the presence of IL adsorbed in the outer surface of an uncharged ACNP in CMK-5 affects the dynamics and the density of an IL adsorbed inside the ACNP, and vice versa. Biased MD simulations have been performed to study the homogeneous nucleation of IL [dmim+][Cl-] from its supercooled liquid in the bulk, as well as the heterogeneous nucleation of the same IL near a graphitic surface. The string method in collective variables (SMCV) and Markovian milestoning with Voronoi tessellations, when used in combination with suitable order parameters proposed for molecular crystals, allow us to sketch a minimum free energy path (MFEP) connecting the supercooled liquid and crystal phases, and to determine the free energy and the rates involving in the nucleation processes. The physical significance of the configurations found along these MFEPs is discussed with the help of calculations based on classical nucleation theory, as well as simulation snapshots. Analogies and differences between both nucleation processes are analyzed and discussed. The simulation work described here is relevant to using ILs as electrolytes in energy-related devices, such as electrochemical double layer capacitors and dye-sensitized solar cells. Furthermore, nucleation of ILs is relevant to developing nanomaterials based on ILs

Ensemble-Based Coarse-Grained Molecular Dynamics Simulations of Multifunctional DNA Nanopores

Transmembrane pores are highly specialised nano-devices, with intrinsic specificity and gate-keeping properties that can be exploited in the field of nanobiotechnology. Recently, DNA-origami inspired transmembrane pores with tailorable surface chemistry and programmable dimensions have been rationally designed in an effort to overcome the limitations of protein-based membrane pores such as their fixed lumen size and limited structural repertoire. Ongoing experimental research into the potential applications of triethylene glycol-cholesterol DNA nanopores (DNPs) has been fruitful, with a particular emphasis on drug delivery and biosensing. In this thesis, I describe an ensemble-based coarse-grained MD protocol devised to probe the interactions between bilayer lipids and DNPs, and to determine the effect of membrane encapsulation and salt concentration on the dynamics, structure and conductance of these nanopores. Furthermore, I aim to elucidate the mechanisms by which DNPs mediate translocation of small molecules across lipid bilayers, and the energetics associated with these mechanisms with constant-velocity steered MD and umbrella sampling simulations. I have found that the DNP has no distinct lumen in bulk solution, where it adopts a bloated, amorphous structure with strained and constricted termini regardless of the salt conditions, with significant kinking and fraying of helices. However, salt conditions have a profound effect on the structure of a DNP as it spans a planar lipid bilayer, where it assumes a barrel-like structure with a defined lumen. Sites of constriction in the lumen of the membrane-spanning DNP present a significant barrier to translocation of fluorophores bearing dense negative charges

Microstructure of Systems with Competition

The micro-structure of systems with competition often exhibits many universal features. In this thesis, we study certain aspects of these structural features as well as the microscopic interactions using disparate exact and approximate techniques. This thesis can be broadly divided into two parts. In the first part, we use statistical mechanics arguments to make general statements about length and timescales in systems with two-point interactions. We demonstrate that at high temperatures, the correlation function of general O(n) systems exhibits a universal form. This form enables the extraction of microscopic interaction potentials from the high temperature correlation functions. In systems with long range interactions, we find that the largest correlation length diverges in the limit of high temperatures. We derive an exact form for the correlation function in large-n systems with general two-point interactions at finite temperatures. From this, we obtain some features of the correlation and modulation lengths in general systems in the large-n limit. We derive a new exponent characterizing modulation lengths: or times) in systems in which the modulation length: or time) either diverges or becomes constant as a parameter, such as temperature exceeds a threshold value. In the second part of this thesis, we study the micro-structure of a metallic glass system using molecular dynamics simulations. We use both classical and first principles simulation to obtain atomic configurations in the liquid as well as the glassy phase. We analyze these using standard methods of local structure analysis - calculation of pair correlation function and structure factor, Voronoi construction, calculation of bond orientational order parameters and calculation of Honeycutt indices. We show the enhancement of icosahedral order in the glassy phase. Apart from this, we also use the techniques of community detection to obtain the inherent structures in the system using an algorithm which allows us to look at arbitrary length-scales