A5063277841- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Research Data Management Practices
- Advanced Electron Microscopy Techniques and Applications
- Advanced X-ray Imaging Techniques
- Electron and X-Ray Spectroscopy Techniques
- Molecular Junctions and Nanostructures
- Machine Learning in Materials Science
- Advanced Database Systems and Queries
- Electrochemical Analysis and Applications
- Gold and Silver Nanoparticles Synthesis and Applications
- Radiomics and Machine Learning in Medical Imaging
- Advanced Data Storage Technologies
- Medical Imaging Techniques and Applications
- Various Chemistry Research Topics
- Advancements in Semiconductor Devices and Circuit Design
- Organic Electronics and Photovoltaics
- Medical Image Segmentation Techniques
- Magnetic Properties and Applications
- Metallic Glasses and Amorphous Alloys
- Nanowire Synthesis and Applications
- Computer Graphics and Visualization Techniques
- Semiconductor materials and devices
- Thermodynamic and Structural Properties of Metals and Alloys
- Fullerene Chemistry and Applications
Brookhaven National Laboratory
2020-2022
Kitware (United States)
2012-2022
National Synchrotron Light Source II
2022
West Virginia University
2022
University of Pittsburgh
2010-2012
University of Sheffield
2005-2008
University of Leeds
2006
University of Birmingham
2006
The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, related areas. It offers flexible, high quality rendering, a powerful plugin architecture. Typical uses include building structures, formatting input files, analyzing output of wide variety chemistry packages. By using the CML file format as its native document type, seeks to enhance semantic...
The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Standards and Source (ODOSOS) chemistry. It aims make it easier carry out chemistry research by promoting interoperability between software, encouraging cooperation developers, developing community resources Standards. This contribution looks back on work carried past 5 years surveys progress remaining challenges areas Standards, We show that has been very successful bringing together researchers...
The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique computationally bottlenecked by alignment reconstruction which runs from hours to days. We demonstrate real-time with dynamic tomographic visualization enable rapid interpretation of specimen structure immediately as data collected on an microscope. Using geometrically complex chiral nanoparticles, we show volumetric can begin less than 10 minutes a...
Abstract
Exposure of thiol-stabilized gold nanoparticles supported on silicon wafers to UV light leads oxidation the thiol molecules and coagulation nanoparticles, forming densified structures that are resistant removal by solvent exposure. Unoxidized particles may, in contrast, readily be removed leaving behind at surface. This process provides a convenient simple route for fabrication with dimensions ranging from micrometers nanometers. The use masks enables micrometer-scale fabricated rapidly....
Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure properties of small to medium sized molecules. Many thousands calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast other disciplines, such as crystallography, or bioinformatics, where standard formats well-known, unified databases exist, this QC data is generally destined remain locally...
The Visualization Toolkit (VTK) is an open source, permissively licensed, cross-platform toolkit for scientific data processing, visualization, and analysis. It over two decades old, originally developed a very different graphics card architecture. Modern cards feature fully programmable, highly parallelized architectures with large core counts. VTK's rendering code was rewritten to take advantage of modern cards, maintaining most the toolkit's programming interfaces. This offers opportunity...
Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists' research increasingly depends on the quality availability upon which their works built. To highlight some these issues share experiences, First Workshop Sustainable Software Science: Practice Experiences (WSSSPE1) was held in November 2013 conjunction with SC13 Conference. The workshop featured keynote presentations large number (54) solicited...
Author(s): Ercius, Peter; Johnson, Ian; Brown, Hamish; Pelz, Philipp; Hsu, Shang-Lin; Draney, Brent; Fong, Erin; Goldschmidt, Azriel; Joseph, John; Lee, Jason; Ciston, Jim; Ophus, Colin; Scott, Mary; Selvarajan, Ashwin; Paul, David; Skinner, Hanwell, Marcus; Harris, Chris; Avery, Patrick; Stezelberger, Thorsten; Tindall, Craig; Ramesh, Ramamoorthy; Minor, Andrew; Denes, Peter
An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The offers an interactive visualization analytics environment functions well on mobile, laptop desktop devices. It pragmatic solutions to ensure large complex sets are more accessible. Existing applications/frameworks were extended integrate with high-performance computing resources, offer command-line tools automate...
Multidisciplinary integrated research requires the ability to couple diverse sets of data obtained from a range complex experiments and computer simulations. Integrating semantically rich information. In this paper an end-to-end use in computational chemistry is demonstrated utilizing Chemical Markup Language (CML) framework. Semantically generated by NWChem software with FoX library utilized Avogadro molecular editor for analysis visualization.The has been modified coupled write CML...
The effects of defects and electrostatics on charge transport in realistic organic field effect transistors were studied using a combination first principles quantum chemistry calculations Monte Carlo simulations with explicit introduction defect sites. results show that electrostatic interactions dramatically affect the carrier concentration dependence devices include significant number traps, as well its “switch-on” characteristics. Our also decreases linearly function neutral conduction...
Abstract Quantum chemistry must evolve if it wants to fully leverage the benefits of internet age, where worldwide web offers a vast tapestry tools that enable users communicate and interact with complex data at speed convenience button press. The Open Chemistry project has developed an open‐source framework end‐to‐end solution for producing, sharing, visualizing quantum chemical interactively on using array modern approaches. These build some best community projects such as Jupyter...
Advances in detectors and computational technologies provide new opportunities for applied research the fundamental sciences. Concurrently, dramatic increases three V's (Volume, Velocity, Variety) of experimental data scale tasks produced demand real-time processing systems at facilities. Recently, this was addressed by Spark-MPI approach connecting Spark data-intensive platform with MPI high-performance framework. In contrast existing management analytics systems, introduced a middleware...
The visualization toolkit (VTK) is a popular cross-platform, open source for scientific and medical data visualization, processing, analysis. It supports wide variety of formats, algorithms, rendering techniques both polygonal volumetric data. In particular, VTK's volume module has long provided comprehensive set features such as plane clipping, color opacity transfer functions, lighting, other controls needed visualization. However, due to legacy OpenGL backend its reliance on deprecated...
Nowadays, 3D visualization is part of our everyday lives and remains an important tool for understanding complex structures, dynamic simulations, research discoveries. In the meantime, complexity often requires specific hardware, including clusters, as well dedicated software tools. Several efforts, such WebGL remote visualization, have been pushing to web browser. However, technical limitations constrained adoption browsers a means rendering datasets. To surpass these limitations,...
Journal Article Repeatable and Transferable Processing for Electron Tomography: An Open Platform Visualization Reconstruction of 3D Materials Get access Robert Hovden, Hovden School Applied & Engineering Physics, Cornell University, Ithaca NY, USA Search other works by this author on: Oxford Academic Google Scholar Marcus D Hanwell, Hanwell Kitware, Inc., Clifton Park, Utkarsh Ayachit, Ayachit Yi Jiang, Jiang Department Ithaca, Maynard, Maynard David A Muller Microscopy Microanalysis, Volume...
Exposure of Langmuir–Blodgett (LB) films a C60 adduct supported on silicon wafers to UV light leads cross-linking the moieties, which are resistant removal by solvent exposure, whereas unexposed moieties readily removed. This process provides convenient and simple route for fabrication highly conjugated surface-attached structures, with dimensions ranging from micrometres (using masks) few tens nanometres using emitted scanning near-field optical microscope (SNOM). The SNOM writing velocity...
Journal Article Advanced Platform for 3D Visualization, Reconstruction, and Segmentation with Electron Tomography Get access Yi Jiang, Jiang Department of Physics, Cornell University, Ithaca, NY, USA Search other works by this author on: Oxford Academic Google Scholar Marcus D Hanwell, Hanwell Kitware, Inc., Clifton Park, Elliot Padgett, Padgett School Applied & Engineering Ithaca Shawn Waldon, Waldon David A Muller, Muller USAKavli Institute at Nanoscale Science, New York Robert Hovden...
Contemporary advancements in low-cost automation and computation, reduced barrier to entry developing artificial intelligence/machine learning (AI/ML), increased ability represent complex materials digital form have led a number of accelerated discovery platforms. However, many these approaches operate with completely rigid vertical integration an isolated feedback loop using limited modalities. In order make substantial impact on discovering new energy materials, AI-driven experiments must...