Search

We present a non-reactive force field for molecular dynamics simulations of interfaces between passivated amorphous surfaces and their interaction with water. The force field enables large-scale dynamic simulations of dry and lubricated tribological contacts and is tailored to surfaces with hydrogen, hydroxyl and aromatic surface passivation. To favour its compatibility with existing force-field parameterizations for liquids and allow a straightforward extension to other types of surface passivation species, we adopt the commonly used OPLS functional form. The optimisation of the force-field parameters is systematic and follows a protocol that can be reused for other surface-molecule combinations. Reference data are calculated with gradient- and dispersion-corrected density functional theory and include the bonding structure and elastic deformation of bulk and surface structures as well as surface adhesion and water adsorption energy landscapes. The conventions adopted to define the different force-field atom types are based on the hybridisation of carbon orbitals and enable a simple and efficient parameter optimisation strategy based on quantum-mechanical calculations performed only on crystalline reference structures. Transferability tests on amorphous interfaces demonstrate the effectiveness of this approach. After testing the force field, we present two examples of application to tribological problems. Namely, we investigate relationships between dry friction and the corrugation of the contact potential energy surface and the dependency of friction on the thickness of interface water films. We finally discuss the limitations of the force field and propose strategies for its improvement and extension.

We report on time-resolved coherent diffraction imaging of gas-phase silver nanoparticles, strongly heated via their plasmon resonance. The x-ray diffraction images reveal a broad range of phenomena for different excitation strengths, from simple melting over strong cavitation to explosive disintegration. Molecular dynamics simulations fully reproduce this behavior and show that the heating induces rather similar trajectories through the phase diagram in all cases, with the very different outcomes being due only to whether and where the stability limit of the metastable superheated liquid is crossed., Comment: 17 pages, 8 figures (including supplemental material)

The development of epitaxy techniques for localized growth of crystalline silicon nanofilms and nanostructures has been crucial to recent advances in electronics and photonics. A precise definition of the crystal growth location, however, requires elaborate pre-epitaxy processes for substrate patterning. Our molecular dynamics simulations reveal that homoepitaxial silicon nanofilms can be directly deposited by a crystalline silicon tip rubbing against the substrate, thus enabling geometrically controlled crystal growth with no need for substrate pre-patterning. We name this solid-phase epitaxial growth triboepitaxy as it solely relies on shear-induced amorphization and recrystallization that occur even at low temperature at the sliding interface between two silicon crystals. The interplay between the two concomitant, shear-induced processes is responsible for the formation of an amorphous sliding interface with constant nanometric thickness. If the two elastically anisotropic crystals slide along different crystallographic orientations, the amorphous layer can move unidirectionally perpendicular to the sliding plane, causing the crystal with lowest elastic energy per atom to grow at the expenses of the other crystal. As triboepitaxial growth is governed by the shear elastic response of the two crystals along the sliding direction, it can be implemented as a mechanical scanning-probe lithography method in which epitaxial growth is controlled by tuning the crystallographic misorientation between tip and substrate, the tip's size or the normal force. These results suggest a radically new way to conceive nanofabrication techniques that are based on tribologically induced materials transformations., Comment: 35 pages, 13 figures, 1 table

In this paper, the term formula code refers to fragments of source code that implement a mathematical formula. We present empirical studies that analyze the diversity and frequency of formula code in open-source-software projects. In an exploratory study, we investigated what kinds of formulas are implemented in real-world Java projects and derived syntactical patterns and constraints. We refined these patterns for sum and product formulas to automatically detect formula code in software archives and to reconstruct the implemented formula in mathematical notation. In a quantitative study of a large sample of engineered Java projects on GitHub we analyzed the frequency of formula code and estimated that one of 700 lines of code in this sample implements a sum or product formula. For a sample of scientific-computing projects, we found that one of 100 lines of code implements a sum or product formula. To assess the need for tool support, we investigated the helpfulness of comments for program understanding in a sample of formula-code fragments and performed an online survey. Our findings provide first insights into the characteristics of formula code, that can motivate further studies on the role of formula code in software projects and the design of formula-related tools., Comment: 31 pages, 4 figures, 8 tables

We deform representative volume elements of amorphous carbon obtained from melt-quenches in molecular dynamics calculations using bond-order and machine learning interatomic potentials. A Drucker-Prager law with a zero-pressure flow stress of $41.2$~GPa and an internal friction coefficient of $0.39$ describes the deviatoric stress during flow as a function of pressure. We identify the mean coordination number as the order parameter describing this flow surface. However, a description of the dynamical relaxation of the quenched samples towards steady-state flow requires an additional order parameter. We suggest an intrinsic strain of the samples as a possible order parameter and present equations for its evolution. Our results provide insights into rehybridization and pressure dependence of friction between coated surfaces as well as routes towards the description of amorphous carbon in macroscale models of deformation., Comment: 12 pages, 3 figures

Viscosities $\eta$ and diffusion coefficients $D_s$ of linear and branched alkanes at high pressures $P$$<$0.7 GPa and temperatures $T$=500-600 K are calculated by equilibrium molecular dynamics. Combining Stokes-Einstein, free volume and random walk concepts results in an accurate viscosity model $\eta(D_s(P,T))$ for the considered P and T. All model parameters (hydrodynamic radius, random walk step size and attempt frequency) are defined as microscopic ensemble averages and extracted from EMD simulations rendering $\eta(D_s(P,T))$ a parameter-free predictor for lubrication simulations., Comment: 5 pages, 4 figures, supplementary material available on demand

The quantitative evaluation of the carbon hybridization state by X-ray photoelectron spectroscopy (XPS) has been a surface-analysis problem for the last three decades due to the challenges associated with the unambiguous identification of the characteristic binding energy values for sp$^2$ and sp$^3$-bonded carbon. While the sp$^2$ binding energy is well established, there is disagreement for the sp$^3$ value in the literature. Here, we compute the binding energy values for model structures of pure and doped-diamond using density functional theory. The simulation results indicate that the large band-gap of diamond allows defects to pin the Fermi level, which results in large variations of the C(1s) core electron energies for sp$^3$-bonded carbon, in agreement with the broad range of experimental C(1s) binding energy values for sp$^3$ carbon reported in the literature. Fermi level pinning by boron is demonstrated by experimental C(1s) binding energies of highly B-doped ultrananocrystalline diamond that are in good agreement to simulations., Comment: revised version

We analyze how to obtain non-resonant and resonant Raman spectra within the Placzek as well as the Albrecht approximation. Both approximations are derived from the matrix element for light scattering by application of the Kramers, Heisenberg and Dirac formula. It is shown that the Placzek expression results from a semi-classical approximation of the combined electronic and vibrational transition energies. Molecular hydrogen, water and butadiene are studied as test cases. It turns out that the Placzek approximation agrees qualitatively with the more accurate Albrecht formulation even in the resonant regime for the excitations of single vibrational quanta. However, multiple vibrational excitations are absent in Placzek, but can be of similar intensities as single excitations under resonance conditions. The Albrecht approximation takes multiple vibrational excitations into account and the resulting simulated spectra exhibit good agreement with experimental Raman spectra in the resonance region as well., Comment: resubmission

Background: Performance bugs can lead to severe issues regarding computation efficiency, power consumption, and user experience. Locating these bugs is a difficult task because developers have to judge for every costly operation whether runtime is consumed necessarily or unnecessarily. Objective: We wanted to investigate how developers, when locating performance bugs, navigate through the code, understand the program, and communicate the detected issues. Method: We performed a qualitative user study observing twelve developers trying to fix documented performance bugs in two open source projects. The developers worked with a profiling and analysis tool that visually depicts runtime information in a list representation and embedded into the source code view. Results: We identified typical navigation strategies developers used for pinpointing the bug, for instance, following method calls based on runtime consumption. The integration of visualization and code helped developers to understand the bug. Sketches visualizing data structures and algorithms turned out to be valuable for externalizing and communicating the comprehension process for complex bugs. Conclusion: Fixing a performance bug is a code comprehension and navigation problem. Flexible navigation features based on executed methods and a close integration of source code and performance information support the process., Comment: 10 pages, 7 figures, Proceedings of the 2015 ACM/IEEE International Symposium on Empirical Software Engineering and Measurement (ESEM 2015), IEEE, 2015, pp. 225-234

Absolute binding energies of core electrons in molecules and bulk materials can be efficiently calculated by spin paired density-function theory employing a $\Delta$ Kohn-Sham ($\Delta$KS) scheme corrected by offsets that are highly transferable. These offsets depend on core level and atomic species and can be determined by comparing $\Delta$KS energies to experimental molecular X-ray photoelectron spectra. We demonstrate the correct prediction of absolute and relative binding energies on a wide range of molecules, metals and insulators., Comment: Misspelled author name corrected. Contents unchanged