Bridging the length and time scales: from ab initio electronic structure calculations to macroscopic proportions

Density functional theory (DFT) primarily provides a good description of the electronic structure. Thus, DFT primarily deals with length scales as those of a chemical bond, i.e. 10^-10 meter, and with time scales of the order of atomic vibrations, i.e. 10^-13 seconds. However, several interesting phenomena happen and/or become observable on different scales, namely meso- or macroscopic lengths and on time scales of seconds or even minutes. To bridge the gap between 10^-13 seconds and a second or between 10^-10 meter and 10 and more nano meters is one of the important challenges we are facing today. In this paper we show how we are overcoming these time and size problems for the example of crystal growth and the evolution of nano-scale structures. The key is a kinetic Monte Carlo approach with detailed input from DFT calculations of the relevant atomistic processes.Comment: 13 pages, 5 figures, to be published in Comments on Condens. Matt. Phys. (1998). Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Ab-initio study of the anomalies in the He atom scattering spectra of H/Mo(110) and H/W(110)

Helium atom scattering (HAS) studies of the H-covered Mo(110) and W(110) surfaces reveal a twofold anomaly in the respective dispersion curves. In order to explain this unusual behavior we performed density functional theory calculations of the atomic and electronic structure, the vibrational properties, and the spectrum of electron-hole excitations of those surfaces. Our work provides evidence for hydrogen adsorption induced Fermi surface nesting. The respective nesting vectors are in excellent agreement with the HAS data and recent angle resolved photoemission experiments of the H-covered alloy system Mo_0.95Re_0.05(110). Also, we investigated the electron-phonon coupling and discovered that the Rayleigh phonon frequency is lowered for those critical wave vectors. Moreover, the smaller indentation in the HAS spectra can be clearly identified as a Kohn anomaly. Based on our results for the susceptibility and the recently improved understanding of the He scattering mechanism we argue that the larger anomalous dip is due to a direct interaction of the He atoms with electron-hole excitations at the Fermi level.Comment: RevTeX, 32 pages, 17 figures, submitted to Phys. Rev.

Study of Strain and Temperature Dependence of Metal Epitaxy

Metallic films are important in catalysis, magneto-optic storage media, and interconnects in microelectronics, and it is crucial to predict and control their morphologies. The evolution of a growing crystal is determined by the behavior of each individual atom, but technologically relevant structures have to be described on a time scale of the order of (at least) tenths of a second and on a length scale of nanometers. An adequate theory of growth should describe the atomistic level on very short time scales (femtoseconds), the formation of small islands (microseconds), as well as the evolution of mesoscopic and macroscopic structures (tenths of seconds). The development of efficient algorithms combined with the availability of cheaper and faster computers has turned density functional theory (DFT) into a reliable and feasible tool to study the microscopic aspects of growth phenomena (and many other complex processes in materials science, condensed matter physics, and chemistry). In this paper some DFT results for diffusion properties on metallic surfaces are presented. Particularly, we will discuss the current understanding of the influences of strain on the diffusion (energy barrier and prefactor) of a single adatom on a substrate. A DFT total energy calculation by its nature is primarily a static calculation. An accurate way to describe the spatial and temporal development of a growing crystal is given by kinetic Monte Carlo (KMC). We will describe the method and its combination with microscopic parameters obtained from ab initio calculations. It is shown that realistic ab initio kinetic Monte Carlo simulations are able to predict an evolving mesoscopic structure on the basis of microscopic details.Comment: 25 pages, 6 figures, In: ``Morphological Organisation during Epitaxial Growth and Removal'', Eds. Z. Zhang, M. Lagally. World Scientific, Singapore 1998. other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Anomalies in He atom scattering spectra of the H-covered Mo(110) and W(110) surfaces

Helium atom scattering (HAS) studies of the H-covered Mo(110) and W(110) surfaces reveal a twofold anomaly in the respective dispersion curves. In order to explain this unusual behavior we performed density-functional theory calculations of the atomic and electronic structure, the vibrational properties, and the electronic susceptibility of those surfaces. Our work provides evidence for hydrogen adsorption induced Fermi-{}surface nesting. The respective nesting vectors are in excellent agreement with the HAS data and recent angle resolved photoemission experiments of the H-covered alloy system Mo_0.95Re_0.05(110). Also, we investigated the electron-phonon coupling and discovered that the Rayleigh phonon frequency is lowered for those critical wave vectors compared to the clean surfaces. Moreover, the smaller indentation in the HAS spectra can be clearly identified as a Kohn anomaly. Based on our results for the susceptibility and the recently improved understanding of the He scattering mechanism we argue that the larger anomalous dip is due to electron-hole excitations by the He scattering.Comment: 7 pages, RevTeX, 7 figure

Density Functional Theory of Epitaxial Growth of Metals

This chapter starts with a summary of the atomistic processes that occur during epitaxy. We then introduce density functional theory (DFT) and describe its implementation into state-of-the-art computations of complex processes in condensed matter physics and materials science. In particular we discuss how DFT can be used to calculate parameters of microscopic processes such as adsorption and surface diffusion, and how they can be used to study the macroscopic time and length scales of realistic growth conditions. This meso- and macroscopic regime is described by the ab initio kinetic Monte Carlo approach. We discuss several specific theoretical studies that highlight the importance of the different diffusion mechanisms at step edges, the role of surfactants, and the influence of surface stress. The presented results are for specific materials (namely silver and aluminum), but they are explained in simple physical pictures suggesting that they also hold for other systems.Comment: 55 pages, 20 figures, to be published "Growth of Ultrathin Epitaxial Layers", The Chemical Physics of Soild Surfaces, Vol. 8, Eds D. A. King and D. P. Woodruff (Elsevier Science, Amsterdam, 1997

Enhanced electron-phonon coupling at the Mo and W(110) surfaces induced by adsorbed hydrogen

The possible occurrence of either a charge-density-wave or a Kohn anomaly is governed by the presence of Fermi-surface nesting and the subtle interaction of electrons and phonons. Recent experimental and theoretical investigations suggest such an effect for the hydrogen covered Mo and W(110) surfaces. Using density-functional theory we examine the electronic structure and the electron-phonon coupling of these systems. Besides good agreement with the experimental phonon frequencies our study provides a characterization and quantitative analysis of an unusual scenario determining the electronic, vibrational, and structural properties of these surfaces.Comment: 4 Pages, RevTe

Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors

Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-generation antibiotics. To date, however, only one inhibitor has been cocrystallized with AcrB. Thus, in silico struc- ture-based analysis is essential for elucidating the interaction between other inhibitors and the efflux pumps. In this work, we used computer docking and molecular dynamics simulations to study the interaction between AcrB and the compound MBX2319, a novel pyranopyridine efflux pump inhibitor with potent activity against RND efflux pumps of Enterobacteriaceae species, as well as other known inhibitors (D13-9001, 1-[1-naphthylmethyl]-piperazine, and phenylalanylarginine-ß-naphthyl-amide) and the binding of doxorubicin to the efflux-defective F610A variant of AcrB. We also analyzed the binding of a sub- strate, minocycline, for comparison. Our results show that MBX2319 binds very tightly to the lower part of the distal pocket in the B protomer of AcrB, strongly interacting with the phenylalanines lining the hydrophobic trap, where the hydrophobic por- tion of D13-9001 was found to bind by X-ray crystallography. Additionally, MBX2319 binds to AcrB in a manner that is similar to the way in which doxorubicin binds to the F610A variant of AcrB. In contrast, 1-(1-naphthylmethyl)-piperazine and phenylalanylarginine-ß-naphthylamide appear to bind to somewhat different areas of the distal pocket in the B protomer of AcrB than does MBX2319. However, all inhibitors (except D13-9001) appear to distort the structure of the distal pocket, impairing the proper binding of substrates

The deceptive mirror: the dressed body beyond reflection.

This paper explores the role of the mirror in the act of getting dressed. It argues that in daily practices of dress/ing the predominance of the sense of sight in defining the experience of both dress and our self is materialized and enhanced by the omnipresence of an object: the mirror. Despite being mostly ignored in analyses of dressed body, the mirror performs a crucial role in defining both dress and the self in visual terms. By considering how the mirror is implicated in processes of subjectification, we analyze how this affects the relationship people have with clothes as signifiers of their selves. We maintain that in order to escape the gaze and its solidifying effect, we need to look away from the mirror and think of the body not as a subject, but as a fluid composition of forces. By drawing insights from phenomenology and then adhering to the Spinozian philosophy of Deleuze and Guattari, we interrogate the body as something that affectively transforms in the encounter with clothes to then explore it as a site of becoming with and through clothes. It is our aim to offer an experimentation in thinking that might lead to different ways of experiencing our clothes in the everyday as well as of theorizing about their relationship with the human body and the wearers' (supposed) identity

Living through the pandemic in post-Brexit Britain: emotional damage and resilience among middle-aged European citizens.

This study examines the effects of the Coronavirus epidemic and Brexit on the emotional wellbeing of middle aged European citizens who have transnational caring responsibilities in the UK and in Europe. This qualitative research aims to produce an in-depth understanding of the participants' emotional landscape and to explore how their sense of belonging in the UK has been eroded by this combination of factors. The disconnect engendered by Brexit and the forced estrangement from family in Europe have prompted many EU nationals to return home causing a loss of workforce for the UK economy at this crucial time of recovery. This research will explore their experience to identify their needs and to highlight the resources they are using to adapt to the changes. The results will allow government at national and devolved levels to devise a strategy to retain their contribution by rebuilding a sense of home in Britain

Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa

Pseudomonas aeruginosa infections are becoming increasingly difficult to treat due to intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse resistance mechanisms. Hyperexpression of efflux pumps of the Resistance-Nodulation-Cell Division (RND)-type multidrug efflux pumps (e.g., MexAB-OprM), chromosomally encoded by mexAB-oprM, mexCD-oprJ, mexEF-oprN, and mexXY (-oprA) is often detected in clinical isolates and contributes to worrying multi-drug resistance phenotypes. Not all antibiotics are affected to the same extent by the aforementioned RND efflux pumps. The impact of efflux on antibiotic activity varies not only between different classes of antibiotics but also between members of the same family of antibiotics. Subtle differences in physicochemical features of compound-pump and compound-solvent interactions largely determine how compounds are affected by efflux activity. The combination of different high-resolution techniques helps to gain insight into the functioning of these molecular machineries. This review discusses substrate recognition patterns based on experimental evidence and computer simulations with a focus on MexB, the pump subunit of the main RND transporter in P. aeruginosa