Adhesive wear with a coarse-grained discrete element model

The use of molecular dynamics (MD) simulations has led to promising results to unravel the atomistic origins of adhesive wear, and in particular for the onset of wear at nanoscale surface asperities. However, MD simulations come with a high computational cost and offer access to only a narrow window of time and length scales. We propose here to resort to the discrete element method (DEM) to mitigate the computational cost. Using DEM particles with contact and cohesive forces, we reproduce the key mechanisms observed with MD, while having particle diameters and system sizes an order of magnitude higher than with MD. The pairwise forces are tuned to obtain a solid with reasonably approximated elastic and fracture properties. The simulations of single asperity wear performed with MD are successfully reproduced with DEM using a range of particle sizes, validating the coarse-graining procedure. More complex simulations should allow the study of wear particles and the evolution of worn surfaces in an adhesive wear context, while reaching scales inaccessible to MD. (c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Large Eddy Simulation of Particle Dynamics Inside a Differentially Heated Cavity

Christoph Bosshard

In nuclear safety, most severe accident scenarios lead to the presence of fission products in aerosol form in the closed containment atmosphere. It is important to understand the particle depletion process to estimate the risk of a release of radioactivity to the environment should a containment break occur. As a model for the containment, we use the three-dimensional differentially heated cavity (DHC) problem. DHC is a cubical box with a hot wall and a cold wall on vertical opposite sides. On the other walls of the cube we have adiabatic boundary conditions. For the velocity field the no-slip boundary condition is valid. The flow of the air in the cavity is described by the Boussinesq equations. Complex flow patterns develop and the flow characteristics depend on the non-dimensional Rayleigh and Prandtl numbers. The predominant flow type in the DHC is a turbulent natural convection flow. This work aims at reaching Rayleigh numbers and turbulent levels as high as possible given the available computational resources. The method used to simulate the turbulent flow is the large eddy simulation (LES) where the dynamics of the large eddies is resolved by the computational grid and the small eddies are modelled by the introduction of subgrid scale quantities using a filter function. Numerically, the LES equations are discretized by the spectral element method. Particle trajectories are computed using the Lagrangian particle tracking method, including the relevant forces (drag, gravity, thermophoresis). Four different particle sets with each set containing one million particles and diameters of 10 μm, 15 μm, 25 μm and 35 μm are simulated. The complexity and the size of the large three-dimensional problem requires the use of massively parallel supercomputers. Spectral element methods are naturally suitable for parallelisation by distributing the elements among the processors. For the Lagrangian particle tracking we use a method where equal numbers of particles are assigned to every processor. The flow field is broadcast and every particle processor tracks the assigned particles, a procedure which leads to a perfect load balancing. Simulation results for the flow field and particle sizes from 15 μm to 35 μm at a Rayleigh number of 109 are compared to previous results from a direct numerical simulation. First order statistics of the LES flow fields are in very good agreement with the direct numerical simulation while the agreement of second order moments is fair. Also the turbulent structures associated to the maximum of turbulent kinetic energy production are correctly reproduced. Particle statistics in the LES and the direct numerical simulation were similar and the settling rates practically identical. Contrary to previous particle simulations in LES, it was found that no model was necessary for the influence of the unresolved flow scales on the particle motions. This can be explained, because the important settling mechanism is through gravity and particle deposition at the walls by turbophoresis is negligible.

EPFL2012

Capacitive detection method evaluation physical parameter extraction from finite element for silicon accelerometer by simulations

Philippe Renaud

A capacitance evaluation method based on the extraction of physical parameters from finite element (FE) analysis is presented. Mechanical simulations and this capacitance evaluation method were applied to a new, highly symmetrical, silicon accelerometer in view of globaly modeling the sensor system. The commercial hardware description language HDL-A(TM) is used to develop a compact behavioral macromodels for SPICE simulators.

1997

On the structural stability of the free and metal-loaded c-terminal domain of the prion protein

Maria Carola Colombo

A misfolded conformer of the cellular prion protein, denoted as scrapie prion protein, is considered responsible for a variety of fatal neurodegenerative diseases. Both, the function of the protein in its native conformation as well as the factors that trigger the protein misfolding and its mechanism remain as yet open issues. The aim of this thesis is to give a contribution to answering these questions by means of a variety of tools currently available in the computational (bio)chemistry community. The capability of the cellular prion protein isoform to bind metal is supported by controversial evidences and atomistic details of putative binding sites are missing. Based on the NMR structure of the C-terminal part of the cellular isoform, we performed a hybrid quantum/classical (QM/MM) Car-Parrinello molecular dynamics study to identify likely Cu(II) binding sites. By means of a bioinformatics approach, we localized the protein regions with the highest propensity for copper ion binding. The identified candidate structures were subsequently refined via QM/MM simulations and then probed by computing their EPR characteristics. Overall best agreement with the experimental EPR data was observed for a binding site involving H187. The previously characterized prion protein Cu(II)-binding sites were substituted for Mn(II) and Zn(II) and subsequently refined by means of the QM/MM Car-Parrinello approach. As a general conclusion, all the Cu-binding sites lead to stable arrangements upon Mn and Zn substitution with relative minor structural changes even within the ps time scale. The validity of the binding motifs obtained was assessed by means of comparison with a pool of known Mn and Zn binding proteins and common features were found and described. The Zn binding site in proximity of H177 was speculated to act as a protein interface zinc site with a possible direct involvement in the aggregation process. The EPR parameters of the Mn-containing binding sites were also computed. The influence of some environmental factors that can possibly trigger the misfolding event were investigated via classical molecular dynamics simulations. Specifically, protein solution containing a monovalent salt (NaCl) in four different concentrations (0.0, 0.05, 0.1, 0.2 M) were simulated at three different pH (pH 2, 4, 7) in order to highlight structural changes and local weaknesses in the protein native structural motifs. The effects of the ionic strength and pH on the secondary structural elements of the protein were identified and characterized whereas the main topological framework was preserved in all simulations. The energy landscape of the cellular to scrapie isoform misfolding pathway is currently under investigation by means of a parallel tempering (replica exchange) enhanced sampling technique in combination with classical molecular dynamics. The screening of the data collected led to the identification of a pool of prion protein scrapie candidates. A set of new folding motifs were characterized. Preliminary results and plans for future investigations are presented. With the goal of providing a structural model for the minimal misfolded aggregate based on the most likely prion protein scrapie candidates, a protein-protein docking approach was used to generate protofibril models and their structural stability and transformations investigated by means of classical molecular dynamics simulations.