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The atomic simulation environment—a Python library for working with atoms

Ask Hjorth Larsen, Jens Jørgen Mortensen, Jakob Blomqvist, Ivano E Castelli, Rune Christensen, Marcin Dułak, Jesper Friis, Michael N Groves, Bjørk Hammer, Cory Hargus, Eric D Hermes, Paul C Jennings (+22 others)
2017 Journal of Physics: Condensed Matter  
The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.  ...  For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction.  ...  Acknowledgements The authors acknowledge funding from: The European Union's Horizon 2020 research and innovation program under grant agreement no. 676580 with The Novel Materials Discovery (NOMAD) Laboratory  ... 
doi:10.1088/1361-648x/aa680e pmid:28323250 fatcat:ogp333nznbgcrgwaewi2s7hize

Low-cost Wireless Condition Monitoring for an Ultracold Atom Machine [article]

Matthew Chilcott, Niels Kjærgaard
2020 arXiv   pre-print
We give a specific demonstration for a so-called ultracold atom machine, which is the workhorse of many emerging quantum technologies and marries a broad spectrum of equipment and instrumentation into  ...  As a distinctive feature, our monitoring system taps into physical parameters of the ultracold atom machine both via customized sensor modules that directly perform measurements, and via modules that recruit  ...  ACKNOWLEDGMENT The authors would like to thank Susanne Otto and Ryan Thomas for their testing and feedback on this system.  ... 
arXiv:1909.12589v4 fatcat:dz7se52zwja5xapqxhvmkjco2q

Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

Bruno P. Klaholz
2019 Acta Crystallographica Section D: Structural Biology  
Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis.  ...  Several new tools, some coming from external developments, are integrated or interfaced with Phenix, for example phenix.dock_in_map, CryoFit and ISOLDE for flexible fitting, and Pathwalker to trace the  ...  However, for disordered regions it can be difficult to build a reliable atomic model, in which case the presence of flexible structures needs to be addressed, e.g. by ensemble refinement (Burnley et al  ... 
doi:10.1107/s2059798319013391 pmid:31588919 pmcid:PMC6778849 fatcat:ewjtgsqfjbe5xhtizlshx3akei

buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters

Hubert Santuz, Amélie Bacle, Pierre Poulain, Patrick Fuchs
2021 Journal of Open Source Software  
Acknowledgements The authors thank the community of NMRlipids for useful discussions, especially Samuli Ollila. References  ...  ., 2015) to build Hs, but it is not initially intended for that since its main purpose is to build a topology.  ...  Here, we propose the buildH software to meet this need. buildH is very light and usable in the Unix command line or as a Python module, making it a tool of choice to integrate in analysis pipelines or  ... 
doi:10.21105/joss.03521 fatcat:scxxgkyqorcwlkqv5rfose3cay

atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS

Michael Holmboe
2020 Clays and clay minerals  
The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis.  ...  This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems  ...  at High Performance Computing Center North (HPC2N), Umeå University.  ... 
doi:10.1007/s42860-019-00043-y fatcat:tnqljteemfahjp3qfvlb4epi5q

Virtual atomic and molecular data centre

M.L. Dubernet, V. Boudon, J.L. Culhane, M.S. Dimitrijevic, A.Z. Fazliev, C. Joblin, F. Kupka, G. Leto, P. Le Sidaner, P.A. Loboda, H.E. Mason, N.J. Mason (+20 others)
2010 Journal of Quantitative Spectroscopy and Radiative Transfer  
evaluation, and use of atomic and molecular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data.  ...  It will also provide a forum for training potential users and dissemination of expertise worldwide.  ...  evaluation, and use of atomic and molecular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data.  ... 
doi:10.1016/j.jqsrt.2010.05.004 fatcat:sbdxdlpihjeclbqqwrzhyn46e4

In Touch with Atoms [chapter]

G. Binnig, H. Rohrer
1999 More Things in Heaven and Earth  
Still awaited is a general nanoscopic chemical-analysis method.  ...  It was the first of a growing family of local probes for imaging and measuring, which can serve at the same time as tools.  ... 
doi:10.1007/978-1-4612-1512-7_35 fatcat:gkjnbgjm3ff3nkhbr5254dzypa

In touch with atoms

G. Binnig, H. Rohrer
1999 Reviews of Modern Physics  
Still awaited is a general nanoscopic chemical-analysis method.  ...  It was the first of a growing family of local probes for imaging and measuring, which can serve at the same time as tools.  ... 
doi:10.1103/revmodphys.71.s324 fatcat:ea3ci6ybovhrppydk4bxcxesea

A Science Gateway for Atomic and Molecular Physics [article]

Barry I.Schneider, Klaus Bartschat, Oleg Zatsarinny, Igor Bray, Armin Scrinzi, Fernando Martin, Markus Klinker, Jonathan Tennyson, Jimena D. Gorfinkiel, Sudhakar Pamidighantam
2020 arXiv   pre-print
We describe the creation of a new Atomic and Molecular Physics science gateway (AMPGateway).  ...  Here we outline our efforts to build this AMP gateway and future directions.  ...  The program computes transition-matrix elements for electron collisions with atoms and ions as well as photoionization processes.  ... 
arXiv:2001.02286v1 fatcat:g22fe4vmpnbefcrdtuyltvo2ja

Atomic Simulation Recipes – A Python framework and library for automated workflows

Morten Gjerding, Thorbjørn Skovhus, Asbjørn Rasmussen, Fabian Bertoldo, Ask Hjorth Larsen, Jens Jørgen Mortensen, Kristian Sommer Thygesen
2021 Computational materials science  
A B S T R A C T The Atomic Simulation Recipes (ASR) is an open source Python framework for working with atomistic materials simulations in an efficient and sustainable way that is ideally suited for high-throughput  ...  The ASR leverages the functionality of the Atomic Simulation Environment (ASE) to interface with external simulation codes and attain a high abstraction level.  ...  Acknowledgments We acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program Grant No. 773122 (LIMA) and Grant agreement No. 951786  ... 
doi:10.1016/j.commatsci.2021.110731 fatcat:qkm75gxlkvghpch7byc7csydlu

Modeling protein structure at near atomic resolutions with Gorgon

Matthew L. Baker, Sasakthi S. Abeysinghe, Stephen Schuh, Ross A. Coleman, Austin Abrams, Michael P. Marsh, Corey F. Hryc, Troy Ruths, Wah Chiu, Tao Ju
2011 Journal of Structural Biology  
Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes.  ...  Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details.  ...  MM was supported by a training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-01).  ... 
doi:10.1016/j.jsb.2011.01.015 pmid:21296162 pmcid:PMC3078171 fatcat:sznwv5jhtnef5dac7l5zw2dxay

The benefits of atomic resolution

Zbigniew Dauter, Victor S Lamzin, Keith S Wilson
1997 Current Opinion in Structural Biology  
After a long gestation, the elucidation of the crystal structures of proteins at atomic resolution is now maturing. The use of such data for both refinement and structure solution is advancing apace.  ...  Acknowledgements We thank the European Community for partial support of this work through the BIOTECHNOLOGY programme contracts CT92-0524 and CT96-0189.  ...  We also acknowledge Christoph Hermes and Roelof v Silfhout from the EMBL Hamburg instrumentation group for their continuous efforts in developing and maintaining the beam lines that have allowed collection  ... 
doi:10.1016/s0959-440x(97)80078-4 pmid:9345627 fatcat:2fbnyr26b5b6vbf7xi2panjjje

Building a better atomic clock

2013 Physics today  
., Physics) Building a Better Atomic Clock Thesis directed by Prof.  ...  This revolution in accuracy and precision opens the door for new experiments utilizing the clock as a probe of quantum many-body physics.  ...  But even if the programming and the construction of the hardware is easy, to be a useful tool there must be a graphical user interface (GUI).  ... 
doi:10.1063/pt.5.027159 fatcat:h6o3wzuimfa7tp4rcgqivrvznu

Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures [article]

Aleksandra Badaczewska-Dawid, Alisa Khramushin, Andrzej Kolinski, Ora Schueler-Furman, Sebastian Kmiecik
2019 bioRxiv   pre-print
The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.  ...  In this work, we describe a workflow that generates accurate structural models of peptide-protein complexes starting from protein-peptide models in C-alpha representation generated using CABS-dock molecular  ...  This is also the case for the CABS-dock method [2, 3] a well-established tool for protein-peptide docking.  ... 
doi:10.1101/692160 fatcat:ammzx2jcrbcwhgscya6aknes4q

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus

Lindsey J. Organtini, Hyunwook Lee, Sho Iketani, Kai Huang, Robert E. Ashley, Alexander M. Makhov, James F. Conway, Colin R. Parrish, Susan Hafenstein, G. McFadden
2016 Journal of Virology  
This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best  ...  The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient  ...  A cross-validation test was performed to assess for possible overfitting.  ... 
doi:10.1128/jvi.01112-16 pmid:27535057 pmcid:PMC5068525 fatcat:eghmpkv7pvezpc5pufcknvg4li
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