scholarly journals Large-scale ab initio simulation of light–matter interaction at the atomic scale in Fugaku

2022 ◽  
pp. 109434202110657
Author(s):  
Yuta Hirokawa ◽  
Atsushi Yamada ◽  
Shunsuke Yamada ◽  
Masashi Noda ◽  
Mitsuharu Uemoto ◽  
...  
Keyword(s):  
Ab Initio ◽  
Large Scale ◽  
Fourier Transforms ◽  
Atomic Scale ◽  
Code Optimization ◽  
Ab Initio Simulation ◽  
Sham Equation ◽  
Matter Interaction ◽  
Light Matter Interaction ◽  
First Time

In the field of optical science, it is becoming increasingly important to observe and manipulate matter at the atomic scale using ultrashort pulsed light. For the first time, we have performed the ab initio simulation solving the Maxwell equation for light electromagnetic fields, the time-dependent Kohn-Sham equation for electrons, and the Newton equation for ions in extended systems. In the simulation, the most time-consuming parts were stencil and nonlocal pseudopotential operations on the electron orbitals as well as fast Fourier transforms for the electron density. Code optimization was thoroughly performed on the Fujitsu A64FX processor to achieve the highest performance. A simulation of amorphous SiO2 thin film composed of more than 10,000 atoms was performed using 27,648 nodes of the Fugaku supercomputer. The simulation achieved excellent time-to-solution with the performance close to the maximum possible value in view of the memory bandwidth bound, as well as excellent weak scalability.

scholarly journals Direct atomistic simulation of brittle-to-ductile transition in silicon single crystals

2010 ◽  
Vol 1272 ◽  
Author(s):  
Dipanjan Sen ◽  
Alan Cohen ◽  
Aidan P. Thompson ◽  
Adri Van Duin ◽  
William A. Goddard III ◽  
...  
Keyword(s):  
Single Crystals ◽  
Atomistic Simulation ◽  
Large Scale ◽  
Elevated Temperatures ◽  
Experimental Studies ◽  
Crack Tip ◽  
Threshold Value ◽  
Atomic Scale ◽  
Brittle To Ductile Transition ◽  
First Time

AbstractSilicon is an important material not only for semiconductor applications, but also for the development of novel bioinspired and biomimicking materials and structures or drug delivery systems in the context of nanomedicine. For these applications, a thorough understanding of the fracture behavior of the material is critical. In this paper we address this issue by investigating a fundamental issue of the mechanical properties of silicon, its behavior under extreme mechanical loading. Earlier experimental work has shown that at low temperatures, silicon is a brittle material that fractures catastrophically like glass once the applied load exceeds a threshold value. At elevated temperatures, however, the behavior of silicon is ductile. This brittle-to-ductile transition (BDT) has been observed in many experimental studies of single crystals of silicon. However, the mechanisms that lead to this change in behavior remain questionable, and the atomic-scale phenomena are unknown. Here we report for the first time the direct atomistic simulation of the nucleation of dislocations from a crack tip in silicon only due to an increase of the temperature, using large-scale atomistic simulation with the first principles based ReaxFF force field. By raising the temperature in a computational experiment with otherwise identical boundary conditions, we show that the material response changes from brittle cracking to emission of a dislocation at the crack tip, representing evidence for a potential mechanisms of dislocation mediated ductility in silicon.

scholarly journals Controlled and Stabilized Light-Matter Interaction in Graphene: Plasmonic Film with Large-Scale 10-nm Lithography

2016 ◽  
Vol 4 (11) ◽  
pp. 1811-1823 ◽  
Author(s):  
Yaowu Hu ◽  
Prashant Kumar ◽  
Yi Xuan ◽  
Biwei Deng ◽  
Minghao Qi ◽  
...  
Keyword(s):  
Large Scale ◽  
Matter Interaction ◽  
Light Matter Interaction

scholarly journals Delta variant with P681R critical mutation revealed by ultra-large atomic-scale ab initio simulation: Implications for the fundamentals of biomolecular interactions

2021 ◽  
Author(s):  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Praveen Rao ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Amino Acid ◽  
Ab Initio ◽  
Infection Rate ◽  
Large Scale ◽  
Atomic Scale ◽  
Spike Protein ◽  
Furin Cleavage ◽  
Double Mutation ◽  
Furin Cleavage Site ◽  
High Infection

ABSTRACTSARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing the virus to invade human cells much faster and with increased efficiency. Particularly, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain including the effect of double mutation and compare the results with the wild type. We have recently developed a method of calculating the amino acid-amino acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant find is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.

scholarly journals Ab Initio Formation of Galaxies, Groups and Large-Scale Structure

2000 ◽  
Vol 174 ◽  
pp. 434-444
Author(s):  
Antonaldo Diaferio
Keyword(s):  
Dark Matter ◽  
Ab Initio ◽  
Structure Formation ◽  
Galaxy Formation ◽  
Large Scale ◽  
Cold Dark Matter ◽  
Global Properties ◽  
Small Scales ◽  
First Time ◽  
The Universe

AbstractFor the first time, the combination of semi-analytic modelling of galaxy formation and N-body simulations of cosmic structure formation enables us to model, at the same time, both the photometric and the clustering properties of galaxies. Two Cold Dark Matter Universes provide a reasonable fit to the observed properties of galaxies, groups and clusters, including luminosities, colours, density and velocity biases. We show how the properties of galaxies and groups on small scales are inextricably connected with the global properties of the Universe.

Scheming

2018 ◽  
Author(s):  
Seán Damer
Keyword(s):  
Social Class ◽  
Housing Policy ◽  
Large Scale ◽  
Class Structure ◽  
Local Council ◽  
Housing Scheme ◽  
Post War ◽  
First Time ◽  
The Voice ◽  
House Building

This book seeks to explain how the Corporation of Glasgow, in its large-scale council house-building programme in the inter- and post-war years, came to reproduce a hierarchical Victorian class structure. The three tiers of housing scheme which it constructed – Ordinary, Intermediate, and Slum-Clearance – effectively signified First, Second and Third Class. This came about because the Corporation uncritically reproduced the offensive and patriarchal attitudes of the Victorian bourgeoisie towards the working-class. The book shows how this worked out on the ground in Glasgow, and describes the attitudes of both authoritarian housing officials, and council tenants. This is the first time the voice of Glasgow’s council tenants has been heard. The conclusion is that local council housing policy was driven by unapologetic considerations of social class.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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