Multiscale modeling of solids at the nanoscale: dynamic approach

2008 ◽  
Vol 86 (2) ◽  
pp. 391-400 ◽  
Author(s):  
B Shiari ◽  
R E Miller ◽  
D D Klug
Keyword(s):  
Computational Cost ◽  
Atomistic Simulations ◽  
Process Variables ◽  
Dynamic Approach ◽  
Multiscale Models ◽  
Major Class ◽  
Dislocation Plasticity ◽  
System Temperature ◽  
Cyclic Indentation ◽  
Insight Into

One major class of multiscale models directly couples a region described with full atomistic detail to a surrounding region modeled using continuum concepts and finite element methods. Here, the development of a new dynamic approach to such coupled atomistic-continuum models is discussed with insight into the key ideas and features, with emphasis on fundamental difficulties involved in dynamic multiscale models. Simulations of nanoindentation in single crystals are performed to demonstrate the power of the developed method in capturing both long-range dislocation plasticity and short-range atomistic phenomena during single or cyclic loading without the computational cost of full atomistic simulations. The effects of several process variables are investigated, including system temperature and rate of indentation. The deformation mechanisms and the surface evaluation that occur during a series of single and cyclic indentation simulations are discussed. PACS Nos.: 81.07.–b or 73.22.–f

Coupled Atomistic/Discrete Dislocation Simulations of Nanoindentation at Finite Temperature

2005 ◽  
Vol 127 (4) ◽  
pp. 358-368 ◽  
Author(s):  
Behrouz Shiari ◽  
Ronald E. Miller ◽  
William A. Curtin
Keyword(s):  
Finite Temperature ◽  
Computational Cost ◽  
Computational Method ◽  
Atomistic Simulations ◽  
Computational Framework ◽  
Reflected Waves ◽  
Indentation Process ◽  
Discrete Dislocation ◽  
Atomistic Region ◽  
System Temperature

Simulations of nanoindentation in single crystals are performed using a finite temperature coupled atomistic/continuum discrete dislocation (CADD) method. This computational method for multiscale modeling of plasticity has the ability of treating dislocations as either atomistic or continuum entities within a single computational framework. The finite-temperature approach here inserts a Nose-Hoover thermostat to control the instantaneous fluctuations of temperature inside the atomistic region during the indentation process. The method of thermostatting the atomistic region has a significant role on mitigating the reflected waves from the atomistic/continuum boundary and preventing the region beneath the indenter from overheating. The method captures, at the same time, the atomistic mechanisms and the long-range dislocation effects without the computational cost of full atomistic simulations. The effects of several process variables are investigated, including system temperature and rate of indentation. Results and the deformation mechanisms that occur during a series of indentation simulations are discussed.

scholarly journals Relating source-receiver interferometry to an inverse-scattering series to derive a new method to estimate internal multiples

Geophysics ◽  
2016 ◽  
Vol 81 (3) ◽  
pp. Q27-Q40 ◽  
Author(s):  
Katrin Löer ◽  
Andrew Curtis ◽  
Giovanni Angelo Meles
Keyword(s):  
Inverse Scattering ◽  
Computational Cost ◽  
Synthetic Data ◽  
Data Set ◽  
Inverse Scattering Series ◽  
Internal Multiples ◽  
Multiple Prediction ◽  
New Formula ◽  
3D Applications ◽  
Insight Into

We have evaluated an explicit relationship between the representations of internal multiples by source-receiver interferometry and an inverse-scattering series. This provides a new insight into the interaction of different terms in each of these internal multiple prediction equations and explains why amplitudes of estimated multiples are typically incorrect. A downside of the existing representations is that their computational cost is extremely high, which can be a precluding factor especially in 3D applications. Using our insight from source-receiver interferometry, we have developed an alternative, computationally more efficient way to predict internal multiples. The new formula is based on crosscorrelation and convolution: two operations that are computationally cheap and routinely used in interferometric methods. We have compared the results of the standard and the alternative formulas qualitatively in terms of the constructed wavefields and quantitatively in terms of the computational cost using examples from a synthetic data set.

A Process Planning Method for Improving the Build Performance in Stereolithography

1999 ◽  
Author(s):  
Aaron P. West ◽  
David W. Rosen
Keyword(s):  
Process Planning ◽  
Planning Method ◽  
Analytical Models ◽  
Multi Objective Optimization ◽  
Process Variables ◽  
Build Time ◽  
Insight Into ◽  
Conflicting Goals ◽  
Selection Of

Abstract A process planning method is presented in this paper to aid stereolithography users in the selection of appropriate values of build process variables in order to achieve specific goals and characteristics that are desirable in the end prototype. To accomplish this, user-defined input in the form of goal preferences and feature tolerances are used to control how the prototype will be built by way of process planning. The user inputs will be used to drive the creation of the process plan so that a prototype is produced, which reflects the intent of the operator. The process planning method is adapted from multi-objective optimization and utilizes empirical data, analytical models, and heuristics to quantitatively relate build process variables to goals of surface finish, accuracy, and build time. The objective is to render decision support by handling tradeoffs among conflicting goals quantitatively and give the user some degree of insight into what quality of prototype may ultimately be produced. The process planning method is demonstrated on a part with non-trivial geometric features.

scholarly journals Magnesium-rich nanoprecipitates in calcite: atomistic mechanisms responsible for toughening in Ophiocoma wendtii

2020 ◽  
Vol 22 (18) ◽  
pp. 10056-10062 ◽  
Author(s):  
Alexander Broad ◽  
Ian J. Ford ◽  
Dorothy M. Duffy ◽  
Robert Darkins
Keyword(s):  
Crack Propagation ◽  
Atomistic Simulations ◽  
Ophiocoma Wendtii ◽  
Insight Into

Atomistic simulations provide insight into an example of the superiority of biogenic crystals, where Mg-rich nanoprecipitates in calcite inhibit crack propagation.

scholarly journals Activity corrections are required for accurate anaerobic digestion modelling

2018 ◽  
Vol 77 (8) ◽  
pp. 2057-2067 ◽  
Author(s):  
Mauricio Patón ◽  
Rebeca González-Cabaleiro ◽  
Jorge Rodríguez
Keyword(s):  
Anaerobic Digestion ◽  
Control Variable ◽  
Computational Cost ◽  
Inorganic Phosphorus ◽  
Process Variables ◽  
Modelling Framework ◽  
Sulfide Inhibition ◽  
Key Variables ◽  
Case Simulation ◽  
The Impact

Abstract The impact on the prediction of key process variables in anaerobic digestion (AD) when activity corrections are neglected (e.g. when ideal solution is assumed) is evaluated in this paper. The magnitude of deviations incurred in key variables was quantified using a generalised physicochemistry modelling framework that incorporates activity corrections. Deviations incurred on the intermediate and partial alkalinity ratio (a key control variable in AD) already reach values over 20% in typical AD scenarios at low ionic strengths. Deviations of moderate importance (∼5%) in free ammonia, hydrogen sulfide inhibition, as well as in the biogas composition, were observed. Those errors become very large for components involving multiple deprotonations, such as inorganic phosphorus, and their magnitude (∼40%) would impede proper precipitation modelling. A dynamic AD case simulation involving a series of overloads showed model underpredictions of the process acidification when activity corrections are neglected. This compromises control actions based on such models. Based on these results, a systematic incorporation of activity corrections in AD models is strongly recommended. This will prevent model overfitting to observations related to inaccurate physicochemistry modelling, at a marginal computational cost. Alternatives for these implementations are also discussed.

scholarly journals On the Hardness of Offline Multi-objective Optimization

2007 ◽  
Vol 15 (4) ◽  
pp. 475-491 ◽  
Author(s):  
Olivier Teytaud
Keyword(s):  
Evolutionary Algorithms ◽  
Convergence Rate ◽  
Random Search ◽  
Computational Cost ◽  
Multiobjective Evolutionary Algorithms ◽  
Multi Objective Optimization ◽  
Multi Objective ◽  
Conflicting Objectives ◽  
Insight Into ◽  
Better Than

It has been empirically established that multiobjective evolutionary algorithms do not scale well with the number of conflicting objectives. This paper shows that the convergence rate of all comparison-based multi-objective algorithms, for the Hausdorff distance, is not much better than the convergence rate of the random search under certain conditions. The number of objectives must be very moderate and the framework should hold the following assumptions: the objectives are conflicting and the computational cost is lower bounded by the number of comparisons is a good model. Our conclusions are: (i) the number of conflicting objectives is relevant (ii) the criteria based on comparisons with random-search for multi-objective optimization is also relevant (iii) having more than 3-objectives optimization is very hard. Furthermore, we provide some insight into cross-over operators.

scholarly journals Molecular photoswitches mediating the strain-driven disassembly of supramolecular tubules

2017 ◽  
Vol 114 (45) ◽  
pp. 11850-11855 ◽  
Author(s):  
Jean W. Fredy ◽  
Alejandro Méndez-Ardoy ◽  
Supaporn Kwangmettatam ◽  
Davide Bochicchio ◽  
Benjamin Matt ◽  
...  
Keyword(s):  
Essential Feature ◽  
Operation Mode ◽  
Building Blocks ◽  
Water Soluble ◽  
Atomistic Simulations ◽  
Supramolecular Architecture ◽  
Mechanical Responses ◽  
Pulling Forces ◽  
Nonlinear Operation ◽  
Insight Into

Chemists have created molecular machines and switches with specific mechanical responses that were typically demonstrated in solution, where mechanically relevant motion is dissipated in the Brownian storm. The next challenge consists of designing specific mechanisms through which the action of individual molecules is transmitted to a supramolecular architecture, with a sense of directionality. Cellular microtubules are capable of meeting such a challenge. While their capacity to generate pushing forces by ratcheting growth is well known, conversely these versatile machines can also pull microscopic objects apart through a burst of their rigid tubular structure. One essential feature of this disassembling mechanism is the accumulation of strain in the tubules, which develops when tubulin dimers change shape, triggered by a hydrolysis event. We envision a strategy toward supramolecular machines generating directional pulling forces by harnessing the mechanically purposeful motion of molecular switches in supramolecular tubules. Here, we report on wholly synthetic, water-soluble, and chiral tubules that incorporate photoswitchable building blocks in their supramolecular architecture. Under illumination, these tubules display a nonlinear operation mode, by which light is transformed into units of strain by the shape changes of individual switches, until a threshold is reached and the tubules unleash the strain energy. The operation of this wholly synthetic and stripped-down system compares to the conformational wave by which cellular microtubules disassemble. Additionally, atomistic simulations provide molecular insight into how strain accumulates to induce destabilization. Our findings pave the way toward supramolecular machines that would photogenerate pulling forces, at the nanoscale and beyond.

An Atomistic View of Interface-Mediated Dislocation Plasticity in Thin Metal Films

2003 ◽  
Vol 795 ◽  
Author(s):  
E. S. Ege ◽  
Y.-L. Shen
Keyword(s):  
Initial Point ◽  
Metal Films ◽  
Thin Metal ◽  
Atomistic Simulations ◽  
Thin Metal Films ◽  
Plastic Yielding ◽  
Modeling Framework ◽  
Interfacial Sliding ◽  
Dislocation Plasticity ◽  
Dimensional Crystal

ABSTRACTAtomistic simulations using molecular statics are carried out to study dislocation plasticity in thin metal films attached to stiff substrates. The analysis utilizes a sample two-dimensional crystal, with an embedded initial point defect used for triggering dislocation activities in a controlled manner. The existence of an interface between the film and the substrate is shown to delay plastic yielding and lead to film strengthening. The capability of atoms to slide along the interface plays a crucial role in determining the macroscopic stress-strain response and the microscopic dislocation activities. Within the modeling framework we examine the quantitative interfacial sliding behavior and the resulting dislocation-interface interactions and their consequences.

scholarly journals Efficient inference of recent and ancestral recombination within bacterial populations

2016 ◽  
Author(s):  
Rafal Mostowy ◽  
Nicholas J. Croucher ◽  
Cheryl P. Andam ◽  
Jukka Corander ◽  
William P. Hanage ◽  
...  
Keyword(s):  
Genetic Material ◽  
Computational Cost ◽  
Bacterial Genomes ◽  
Accurate Identification ◽  
Bacterial Populations ◽  
Recombination Hotspots ◽  
Whole Genomes ◽  
Multiple Species ◽  
Bacterial Genes ◽  
Insight Into

AbstractProkaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In sim-ulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared to state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analysing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/

scholarly journals Molecular determinants and bottlenecks in the unbinding dynamics of biotin-streptavidin

2017 ◽  
Author(s):  
Pratyush Tiwary
Keyword(s):  
Atomistic Simulations ◽  
Enhanced Sampling ◽  
Protein Ligand Interactions ◽  
Direct Benefits ◽  
Molecular Determinants ◽  
Bond Stretching ◽  
Ligand Interactions ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Insight Into

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its extremely long residence times, being one of the strongest known non-covalent interactions in nature, and is heavily used across the biotechnological industry. In this work we gain understanding into the molecular determinants and bottlenecks in the unbinding of the dimeric biotinstreptavidin system in its wild type and with N23A mutation. Using new enhanced sampling methods with full atomistic resolution, we reproduce the variation caused by N23A mutation in experimentally reported residence time. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during unbinding and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the unbinding. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacodynamics. An improved understanding of biotin-streptavidin unbinding dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

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