Atomistic Simulation of Nuclear Fuels

2012 ◽  
Vol 1383 ◽  
Author(s):  
Matthias Krack
Keyword(s):  
High Performance ◽  
Program Package ◽  
Quality Level ◽  
Nuclear Fuels ◽  
Elastic Band ◽  
Defect Migration ◽  
Simulation Techniques ◽  
Band Method ◽  
Dynamics Simulations ◽  
Computational Resources

ABSTRACTThe experimental investigation of actinide materials like nuclear fuels is difficult and usually very costly. Therefore a reliable multi-scale modeling of these often hazardous materials starting at the atomistic level is inevitable to gain further insight into this type of materials. The development of new, more advanced simulation methods accompanied by the rapid growth of the available computational resources provided by high-performance computing facilities, allows the modeling of such materials at a new quality level. Also the recent development of the CP2K program package (http://www.cp2k.org) has been partially focused on enabling state-of-the-art simulations of actinide materials using classical potential as well as electronic structure methods. The long-term goal is to perform reliable molecular dynamics simulations for actinide materials including advanced simulation techniques like nudged elastic band or metadynamics simulations. In this work, the CP2K program package and its application to the simulation of defect migration in uranium dioxide (UO2) using the nudged elastic band method is presented.

Vacancy Migration Barrier Energetics and Pathways in Silica

1998 ◽  
Vol 538 ◽  
Author(s):  
L. R. Corrales ◽  
R.M. Van Ginhoven ◽  
J. Song ◽  
H. Jónsson
Keyword(s):  
Point Defect ◽  
Defect Formation ◽  
Vacancy Defect ◽  
Elastic Band ◽  
Simulation Methodology ◽  
Defect Migration ◽  
Migration Pathway ◽  
Empirical Potentials ◽  
Band Method ◽  
Migration Pathways

AbstractA study of vacancy defect migration pathways and energetics in a-quartz is carried out using an empirical simulation methodology that is coupled with the nudged elastic band method. Results from this study indicate that the migration pathway for migration is between adjacent sites. We anticipate the results will guide modifications to empirical potentials for use in the study of point defect formation of more complex systems.

scholarly journals Xenon Diffusion Mechanism and Xenon Bubble Nucleation and Growth Behaviors in Molybdenum via Molecular Dynamics Simulations

Materials ◽  
2019 ◽  
Vol 12 (15) ◽  
pp. 2354 ◽  
Author(s):  
Zhang ◽  
Yun ◽  
Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Diffusion Mechanism ◽  
Nucleation And Growth ◽  
Bubble Nucleation ◽  
Migration Energy ◽  
Elastic Band ◽  
Molecular Statics ◽  
Band Method ◽  
Dynamics Simulations

The behaviors of xenon in molybdenum were studied using molecular statics andmolecular dynamics simulations. The diffusion mechanism of xenon atoms was studied combiningmolecular dynamics, nudged elastic band, and temperature-accelerated dynamics methods. Thevacancy-assisted diffusion mechanism was analyzed and the corresponding energy barriers werecalculated. The clustering process of scattered xenon atoms was studied at an elevated temperature.Xenon bubbles were observed to form when the concentration of xenon atoms exceeded a thresholdconcentration value. Meanwhile, the interaction of xenon bubble and vacancies was investigated viathe nudged elastic band method. The results showed that there exists a region around the xenonbubble where the migration energy of vacancy is significantly influenced. This work provides usefulinsights towards a better understanding of the behaviors of xenon in molybdenum.

scholarly journals Ab Initio Investigation of Helium Mobility in La2Zr2O7 Pyrochlore

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 667
Author(s):  
Yanxia Lu ◽  
Qing Peng ◽  
Chenguang Liu
Keyword(s):  
Nuclear Waste ◽  
Density Functional ◽  
Minimum Energy ◽  
Elastic Band ◽  
Waste Forms ◽  
Band Method ◽  
And Migration ◽  
High Level ◽  
Migration Pathways ◽  
Nuclear Waste Forms

The α-decay of incorporated actinides continuously produces helium, resulting in helium accumulation and causing security concerns for nuclear waste forms. The helium mobility is a key issue affecting the accumulation and kinetics of helium. The energy barriers and migration pathways of helium in a potential high-level nuclear waste forms, La2Zr2O7 pyrochlore, have been investigated in this work using the climbing image nudged elastic band method with density functional theory. The minimum energy pathway for helium to migrate in La2Zr2O7 is identified as via La–La interstitial sites with a barrier of 0.46 eV. This work may offer a theoretical foundation for further prospective studies of nuclear waste forms.

Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following

2021 ◽  
Author(s):  
Vilhjálmur Ásgeirsson ◽  
Benedikt Orri Birgisson ◽  
Ragnar Bjornsson ◽  
Ute Becker ◽  
Frank Neese ◽  
...  
Keyword(s):  
Elastic Band ◽  
Band Method ◽  
Molecular Reactions

scholarly journals CH4 dissociation on the Pd/Cu(111) surface alloy: A DFT study

Open Physics ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 790-798
Author(s):  
Aykan Akça
Keyword(s):  
Catalytic Activity ◽  
Adsorption Energy ◽  
Lower Cost ◽  
Relative Energy ◽  
Catalyst Design ◽  
Elastic Band ◽  
Efficient Catalyst ◽  
Energy Diagram ◽  
Band Method ◽  
Pure Cu

AbstractThe periodic four-layered model of the pure Cu(111) surface has been considered, and the effect of doping with palladium on CH4 dissociation has been investigated. The most stable adsorption geometries of CHx species (x = 1–4) and H atom on the PdCu(111) and pure Cu(111) surfaces have been obtained. Their computed adsorption energy results on the pure Cu(111) surface have been compared with the previously reported studies. Then, transition state geometries of CH4 dehydrogenation steps on both surfaces were calculated by the climbing image nudged elastic band method. Finally, the relative energy diagram for CH4 complete dehydrogenation has been represented. The results show that the PdCu(111) surface is more favorable than the Cu(111) surface in terms of the activation energies. The addition of Pd atoms to the Cu(111) surface significantly improves the catalytic activity. This knowledge can enable an efficient catalyst design at a lower cost using different strategies.

scholarly journals A Comprehensive Review of Cholinesterase Modeling and Simulation

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 580
Author(s):  
Danna De Boer ◽  
Nguyet Nguyen ◽  
Jia Mao ◽  
Jessica Moore ◽  
Eric J. Sorin
Keyword(s):  
Modeling And Simulation ◽  
Binding Site ◽  
Catalytic Efficiency ◽  
Site Location ◽  
Simulation Techniques ◽  
Therapeutic Value ◽  
Docking Calculations ◽  
Computer Based ◽  
Dynamics Simulations ◽  
And Function

The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.

scholarly journals The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: molecular dynamics simulations.

2000 ◽  
Vol 47 (1) ◽  
pp. 47-57 ◽  
Author(s):  
J Mazerski ◽  
I Antonini ◽  
S Martelli
Keyword(s):  
Molecular Dynamics ◽  
Rational Design ◽  
Md Simulations ◽  
Ring System ◽  
Side Chain ◽  
Side Chains ◽  
Intercalation Complex ◽  
Highly Active ◽  
Simulation Techniques ◽  
Dynamics Simulations

Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.

Searching for Saddle Points by Using the Nudged Elastic Band Method:  An Implementation for Gas-Phase Systems

2006 ◽  
Vol 2 (4) ◽  
pp. 895-904 ◽  
Author(s):  
Núria González-García ◽  
Jingzhi Pu ◽  
Àngels González-Lafont ◽  
José M. Lluch ◽  
Donald G. Truhlar
Keyword(s):  
Gas Phase ◽  
Saddle Points ◽  
Elastic Band ◽  
Band Method ◽  
Phase Systems

scholarly journals New Python-based methods for data processing

2013 ◽  
Vol 69 (7) ◽  
pp. 1274-1282 ◽  
Author(s):  
Nicholas K. Sauter ◽  
Johan Hattne ◽  
Ralf W. Grosse-Kunstleve ◽  
Nathaniel Echols
Keyword(s):  
Data Reduction ◽  
Graphics Processing Units ◽  
High Performance ◽  
Array Detectors ◽  
Data Rates ◽  
Python Scripting ◽  
Linac Coherent Light Source ◽  
Future Data ◽  
Scripting Language ◽  
Computational Resources

Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h−1) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units.

Increasing organisational attractiveness

2018 ◽  
Vol 5 (2) ◽  
pp. 124-141 ◽  
Author(s):  
André de Waal
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Performance Level ◽  
Quality Level ◽  
Content Type ◽  
High Performing ◽  
Customer Complaints ◽  
Positive Feeling ◽  
Study Results ◽  
High Performance Level

Purpose Happiness at work (HAW) is receiving much attention in the literature, as HAW seems to have a positive effect on organisational performance, such as in increase of productivity, lower turnover of employees and less customer complaints. There is however no research into the relation between HAW and the attractiveness of an organisation. It stands to reason that people who are happier at work are also happier about their organisation and express this to their family and friends. Having an attractive organisation is becoming increasingly important as the world is currently experiencing an economic boom creating shortages of qualified personnel. The paper aims to discuss this issue. Design/methodology/approach A possible way of creating an attractive organisation is by transforming the workplace into a high-performing organisation (HPO). The study described in this paper is looking in this respect at three hypotheses: H1. Higher HAW will increase the attractiveness of the organisation; H2. Becoming an HPO will increase HAW; and H3. Becoming an HPO will increase the attractiveness of the organisation. A large-scale survey of Dutch managers and employees was undertaken in which the respondents were asked their opinion of the high-performance level and attractiveness of their organisation, and their happiness with their job and organisation. Findings The study results show that the three hypotheses are basically confirmed. Increasing the happiness of work of employees, in general, raises the feeling of how attractive the organisation is to the employees themselves and to the external world. However, this positive feeling is mainly true for the work itself but not so much for how committed employees feel to the organisation. Practical implications Organisations now have knowledge at their disposal about ways to promote happiness in their employees, thus raising their attractiveness to current and future employees. Originality/value The study results indicate that senior management has to make more effort to raise the quality level of the organisation, preferably towards the high performance level, in order for employees to start feeling more committed to their organisation. This is because the study results show that transforming an organisation into a high-performance entity increases happiness of employees at work significantly, especially about their work and in a lesser degree with the commitment they feel towards the organisation itself. This result has not been found before, so this research provides managers for the first time with a validated way to help their staff to become happier and more productive.

Sign in / Sign up

Export Citation Format

Share Document