Hertz Contact at the Nanoscale with a 3D Multiscale Model

2016 ◽  
Vol 846 ◽  
pp. 306-311 ◽  
Author(s):  
Jie Zhang ◽  
Guillaume Michal ◽  
Ahn Kiet Tieu ◽  
Hong Tao Zhu ◽  
Guan Yu Deng
Keyword(s):  
Computational Cost ◽  
Three Dimensional ◽  
Computation Time ◽  
Multiscale Model ◽  
Md Simulations ◽  
Normal Displacement ◽  
Contact Radius ◽  
Asperity Contact ◽  
Fem Model ◽  
Low Computational Cost

This paper presents a three-dimensional multiscale computational model, which is proposed to combine the simplicity of FEM model and the atomistic interactions between two solids. A significant advantage of the model is that atoms are populated in the contact regions, which saves significant computation time compared to fully MD simulations. The model is used in the case of asperity contact. The normal displacement, contact radius and pressure distribution are compared with those from Hertz’s solution and atomistic simulations in the literature. Some important features of nanoscale contacts obtained by MD simulations can be caught by the model with acceptable accuracy and low computational cost.

Molecular Dynamics and Multiscale Simulations of Nanoindentation and Nanoscratch

2010 ◽  
Author(s):  
Peng-zhe Zhu ◽  
Hui Wang ◽  
Yuan-zhong Hu
Keyword(s):  
Molecular Dynamics ◽  
Computational Cost ◽  
Three Dimensional ◽  
Multiscale Model ◽  
Md Simulations ◽  
System Size ◽  
Multiscale Simulations ◽  
First Case ◽  
Chip Volume ◽  
Indenter Shape

Three-dimensional molecular dynamics (MD) simulations have been performed to investigate behaviors of nanoindentation and nano-scratch. The first case concerns the effects of material defect on the nanoindentation of nickel thin film. The defect is modeled by a spherical void embedded in the substrate and located under the surface of indentation. The simulation results reveal that compared to the case without defect, the presence of the void softens the material and allows for larger indentation depth at a given load. MD simulations are then performed for nano-scratch of single crystal copper, with emphasis on the effect of indenter shape (sharp and blunt) on the substrate deformation. The results show that the blunt indenter causes larger deformation region and much more dislocations at both the indentation and scratch stages. It is also found that during the scratching stage the blunt indenter results in larger chip volume in front of the indenter and gives rise to more friction than the sharp indenter. The scope of the simulations has been extended by introducing a multiscale model which couples MD simulations with Finite Element Method (FEM), and multiscale simulations are performed for two-dimensional nanoindentation of copper. The model has been validated by well-consistent load-depth curves obtained from both multiscale and full MD simulations, and by good continuity of deformation observed in the handshake region. The simulations also reveal that indenter radius and indentation velocity significantly affect the nanoindentation behavior. By use of multiscale method, the system size to be explored can be greatly expanded without increasing much computational cost.

Real Gas Effects in Turbomachinery Flows: A Computational Fluid Dynamics Model for Fast Computations

2004 ◽  
Vol 126 (2) ◽  
pp. 268-276 ◽  
Author(s):  
Paolo Boncinelli ◽  
Filippo Rubechini ◽  
Andrea Arnone ◽  
Massimiliano Cecconi ◽  
Carlo Cortese
Keyword(s):  
Fluid Dynamic ◽  
Computational Cost ◽  
Three Dimensional ◽  
Industrial Applications ◽  
Design Tool ◽  
Navier Stokes ◽  
Computational Time ◽  
Real Gas ◽  
Real Gas Effects ◽  
Low Computational Cost

A numerical model was included in a three-dimensional viscous solver to account for real gas effects in the compressible Reynolds averaged Navier-Stokes (RANS) equations. The behavior of real gases is reproduced by using gas property tables. The method consists of a local fitting of gas data to provide the thermodynamic property required by the solver in each solution step. This approach presents several characteristics which make it attractive as a design tool for industrial applications. First of all, the implementation of the method in the solver is simple and straightforward, since it does not require relevant changes in the solver structure. Moreover, it is based on a low-computational-cost algorithm, which prevents a considerable increase in the overall computational time. Finally, the approach is completely general, since it allows one to handle any type of gas, gas mixture or steam over a wide operative range. In this work a detailed description of the model is provided. In addition, some examples are presented in which the model is applied to the thermo-fluid-dynamic analysis of industrial turbomachines.

scholarly journals Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.

2019 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Dynamical Behavior ◽  
Computational Cost ◽  
Three Dimensional ◽  
Md Simulations ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Biomolecular Systems ◽  
Conformational Ensembles ◽  
Independent Experimental Data

<div><div><div><p>SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated in MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a metainference-based hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of multiple-replica simulations with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin multi-domain protein, showing that inclusion of SAXS-restraints is effective in generating reliable and heterogenous conformational ensemble, also improving the agreement with independent experimental data.</p></div></div></div>

Three-Dimensional Vibration of Fluid-Conveying Laminated Composite Cylindrical Shells with Piezoelectric Layers

2019 ◽  
Vol 19 (03) ◽  
pp. 1950026
Author(s):  
Seyed Mohammad Miramini ◽  
Abdolreza Ohadi
Keyword(s):  
Cylindrical Shells ◽  
Computational Cost ◽  
Three Dimensional ◽  
Laminated Composite ◽  
Theory Of Elasticity ◽  
Flowing Fluid ◽  
Piezoelectric Layers ◽  
Elastic Layers ◽  
First Time ◽  
Low Computational Cost

Cylindrical shells containing flowing fluid have wide applications in various industries. They can be enhanced as smart structures through inclusion of piezoelectric layers, of which the dynamic behavior, however, has not been fully understood. In this paper, the vibration and dynamic analysis of a laminated composite hollow cylinder with piezoelectric layers, subjected to an internal incompressible fluid flow is investigated. It is assumed that the shell is simply supported and the fluid is inviscid and irrotational. The differential equations of the elastic layers, piezoelectric layers, and flowing fluid are derived by the three-dimensional (3D) theory of elasticity, theory of piezoelectricity, and potential flow theory, respectively. A well-known recursive method is applied and extended for the first time to solve the fluid-conveying pipes using 3D theory. This approach makes it possible for the solutions to converge to the exact ones with reasonable computational cost. After validating the results against those available in the literature, the vibrational behavior of the system is examined for various cases with the effect of each parameter investigated. Also, the influence of fluid on the vibration and stability of the shell has been analyzed. The present method can be used to analyze and design hybrid shells conveying fluid with high accuracy and low computational cost.

Computational Cost and Accuracy in Calculating Three-Dimensional Radiative Transfer: Results for New Implementations of Monte Carlo and SHDOM

2009 ◽  
Vol 66 (10) ◽  
pp. 3131-3146 ◽  
Author(s):  
Robert Pincus ◽  
K. Franklin Evans
Keyword(s):  
Monte Carlo ◽  
Radiative Transfer ◽  
Variance Reduction ◽  
Parallel Implementation ◽  
Monte Carlo Model ◽  
Computational Cost ◽  
Three Dimensional ◽  
Computation Time ◽  
Flux Divergence ◽  
Pixel Intensity

Abstract This paper examines the tradeoffs between computational cost and accuracy for two new state-of-the-art codes for computing three-dimensional radiative transfer: a community Monte Carlo model and a parallel implementation of the Spherical Harmonics Discrete Ordinate Method (SHDOM). Both codes are described and algorithmic choices are elaborated. Two prototype problems are considered: a domain filled with stratocumulus clouds and another containing scattered shallow cumulus, absorbing aerosols, and molecular scatterers. Calculations are performed for a range of resolutions and the relationships between accuracy and computational cost, measured by memory use and time to solution, are compared. Monte Carlo accuracy depends primarily on the number of trajectories used in the integration. Monte Carlo estimates of intensity are computationally expensive and may be subject to large sampling noise from highly peaked phase functions. This noise can be decreased using a range of variance reduction techniques, but these techniques can compromise the excellent agreement between the true error and estimates obtained from unbiased calculations. SHDOM accuracy is controlled by both spatial and angular resolution; different output fields are sensitive to different aspects of this resolution, so the optimum accuracy parameters depend on which quantities are desired as well as on the characteristics of the problem being solved. The accuracy of SHDOM must be assessed through convergence tests and all results from unconverged solutions may be biased. SHDOM is more efficient (i.e., has lower error for a given computational cost) than Monte Carlo when computing pixel-by-pixel upwelling fluxes in the cumulus scene, whereas Monte Carlo is more efficient in computing flux divergence and downwelling flux in the stratocumulus scene, especially at higher accuracies. The two models are comparable for downwelling flux and flux divergence in cumulus and upwelling flux in stratocumulus. SHDOM is substantially more efficient when computing pixel-by-pixel intensity in multiple directions; the models are comparable when computing domain-average intensities. In some cases memory use, rather than computation time, may limit the resolution of SHDOM calculations.

scholarly journals Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.

2019 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Dynamical Behavior ◽  
Computational Cost ◽  
Three Dimensional ◽  
Md Simulations ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Biomolecular Systems ◽  
Conformational Ensembles ◽  
Independent Experimental Data

<div><div><div><p>SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of metainference with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin, showing that the inclusion of SAXS-restraints is effective in generating a reliable conformational ensemble, improving the agreement with independent experimental data.</p></div></div></div>

scholarly journals RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

2018 ◽  
Author(s):  
Bernat Anton ◽  
Mireia Besalú ◽  
Oriol Fornes ◽  
Jaume Bonet ◽  
Gemma De las Cuevas ◽  
...  
Keyword(s):  
Computational Cost ◽  
Three Dimensional ◽  
Computation Time ◽  
Direct Coupling ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Coupling Analysis ◽  
Direct Information ◽  
Large Proteins ◽  
Direct Coupling Analysis

AbstractMotivationDirect-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. Current algorithms for DCA, although efficient, have a high computational cost of determining Direct Information (DI) values for large proteins or domains. In this paper, we present RADI (Reduced Alphabet Direct Information), a variation of the original DCA algorithm that simplifies the computation of DI values by grouping physicochemically equivalent residues.ResultsWe have compared the first top ranking 40 pairs of DI values and their closest paired contact in 3D. The ranking is also compared with results obtained using a similar but faster approach based on Mutual Information (MI). When we simplify the number of symbols used to describe a protein sequence to 9, RADI achieves similar results as the original DCA (i.e. with the classical alphabet of 21 symbols), while reducing the computation time around 30-fold on large proteins (with length around 1000 residues) and with higher accuracy than predictions based on MI. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure, having a relevant and useful predictive value, while the computation time is reduced between 100 and 2500-fold.AvailabilityRADI is available at https://github.com/structuralbioinformatics/[email protected] informationSupplementary data is available in the git repository.

scholarly journals Force Field Development of β-lactam Class Antibiotics

2020 ◽  
Vol 5 (Spring 2020) ◽  
Author(s):  
Trevor Heinzmann
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Molecular System ◽  
Equations Of Motion ◽  
Computational Cost ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Low Computational Cost

Molecular dynamics (MD) simulation is a computational chemistry technique used to observe how a molecular system behaves as time passes. MD is based on solving Newton’s equations of motion. This requires the use of force fields to describe the potential energy function of each different molecule type in molecular system. In order to develop a force field, charges, bonds, angles, and dihedrals must be parameterized to fit quantum mechanics (QM) data. By basing the force field on QM data, MD simulations have higher accuracy while still using the low computational cost of molecular mechanics. This project focuses on developing well-fit force fields for β-lactam class antibiotics for future MD simulations. Full antibiotics are too large of a molecule to parameterize from scratch, so instead we broke them down into fragments. Smaller molecule fragments allow less terms to be optimized which greatly simplifies force field development. By the transferable nature of parameters in CHARMM force fields, the fragment parameters can be transferred to connecting molecules. Due to this, we can build up larger organic molecule force fields piece by piece.In this work, we developed CHARMM force fields for cephalothin, cefotaxime, ceftazidime, and aztreonam.

scholarly journals Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.

2019 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Dynamical Behavior ◽  
Computational Cost ◽  
Three Dimensional ◽  
Md Simulations ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Biomolecular Systems ◽  
Conformational Ensembles ◽  
Independent Experimental Data

<div><div><div><p>SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of metainference with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin, showing that the inclusion of SAXS-restraints is effective in generating a reliable conformational ensemble, improving the agreement with independent experimental data.</p></div></div></div>

Real Gas Effects in Turbomachinery Flows: A CFD Model for Fast Computations

2003 ◽  
Author(s):  
Paolo Boncinelli ◽  
Filippo Rubechini ◽  
Andrea Arnone ◽  
Massimiliano Cecconi ◽  
Carlo Cortese
Keyword(s):  
Fluid Dynamic ◽  
Computational Cost ◽  
Three Dimensional ◽  
Industrial Applications ◽  
Design Tool ◽  
Navier Stokes ◽  
Computational Time ◽  
Real Gas ◽  
Real Gas Effects ◽  
Low Computational Cost

A numerical model was included in a three-dimensional viscous solver to account for real gas effects in the compressible Reynolds Averaged Navier-Stokes (RANS) equations. The behavior of real gases is reproduced by using gas property tables. The method consists of a local fitting of gas data to provide the thermodynamic property required by the solver in each solution step. This approach presents several characteristics which make it attractive as a design tool for industrial applications. First of all, the implementation of the method in the solver is simple and straightforward, since it does not require relevant changes in the solver structure. Moreover, it is based on a low-computational-cost algorithm, which prevents a considerable increase in the overall computational time. Finally, the approach is completely general, since it allows one to handle any type of gas, gas mixture or steam over a wide operative range. In this work a detailed description of the model is provided. In addition, some examples are presented in which the model is applied to the thermo-fluid-dynamic analysis of industrial turbomachines.

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