A5001274809- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Scientific Computing and Data Management
- Cloud Computing and Resource Management
- Parallel Computing and Optimization Techniques
- Machine Learning in Materials Science
- Computational Drug Discovery Methods
- Advanced Data Storage Technologies
- Catalysis and Oxidation Reactions
- Photochemistry and Electron Transfer Studies
- Quantum Computing Algorithms and Architecture
- Software System Performance and Reliability
- Interconnection Networks and Systems
- Research Data Management Practices
- Molecular Junctions and Nanostructures
- Protein Structure and Dynamics
- Cell Image Analysis Techniques
- Distributed systems and fault tolerance
- Anomaly Detection Techniques and Applications
- Quantum Dots Synthesis And Properties
- Zeolite Catalysis and Synthesis
- Molecular spectroscopy and chirality
- Advanced NMR Techniques and Applications
- Spectroscopy and Laser Applications
- Gene Regulatory Network Analysis
Brookhaven National Laboratory
2016-2024
NanoTechLabs (United States)
2021
Environmental Molecular Sciences Laboratory
2010-2015
John Wiley & Sons (United States)
2010-2015
Pacific Northwest National Laboratory
2010-2015
Battelle
2011-2013
Science and Technology Facilities Council
2007-2008
Daresbury Laboratory
1999-2007
Humboldt-Universität zu Berlin
1999-2001
Utrecht University
1996-1999
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support guide experimental efforts for prediction atomistic electronic properties. In this regard, structure played a special role using first-principle-driven methodologies model complex processes. Over past few decades, rapid development computing technologies tremendous increase in power offered unique chance study transformations sophisticated...
Abstract A description of the ab initio quantum chemistry package GAMESS-UK is presented. The offers a wide range mechanical wavefunctions, capable treating systems ranging from closed-shell molecules through to species involved in complex reaction mechanisms. availability variety correlation methods provides necessary functionality tackle number chemically important tasks, geometry optimization and transition-state location treatment solvation effects prediction excited state spectra. With...
We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu Al impurity centres. Atomic electronic structures as well defect energies been obtained for the main oxidation states of all using our embedded cluster hybrid quantum mechanical/molecular mechanical approach treatment localised ionic solids. With these calculations we were able explain nature a number experimentally observed phenomena. show that zinc excess materials energetics interstitial are very similar...
Despite the recent availability of vaccines against acute respiratory syndrome coronavirus 2 (SARS-CoV-2), search for inhibitory therapeutic agents has assumed importance especially in context emerging new viral variants. In this paper, we describe discovery a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits SARS-Cov-2 main protease (Mpro) by employing scalable high-throughput virtual screening (HTVS) framework targeted compound library over 6.5...
Abstract Heme has a critical role in the chemical framework of cell as an essential protein cofactor and signaling molecule that controls diverse processes molecular interactions. Using phylogenomics-based approach complementary structural techniques, we identify family dimeric hemoproteins comprising domain unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together...
Parallel hardware has become readily available to the computational chemistry research community. This perspective will review current state of parallel software utilizing high-performance computing platforms. Hardware and trends their effect on quantum methodologies, algorithms, development also be discussed.
Chimbuko is the first in situ, scalable, workflow-level performance analysis tool for trace-level and visualization of application performance. This was developed by Co-design Center Online Data Analysis Reduction funded U.S. Department Energy’s Exascale Computing Project. We provide a detailed description Chimbuko’s architecture illustrate our online offline with multiple use cases. also present results deployment scalability as applied to high-energy physics workflow running at large scale...
Abstract We describe the procedure to start an SCF calculation of general type from a sum atomic electron densities, as implemented in GAMESS‐UK. Although is well known for closed‐shell calculations and was already suggested when Direct proposed, less obvious. For instance, there no need converge corresponding Hartree–Fock dealing with open‐shell species. various choices illustrate them test calculations, showing that easier, on average better, than starting converged minimal basis much...
A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The based on Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate Stokes shifts a range organic dye molecules using diverse set exchange-correlation functionals (traditional functionals, global hybrids, range-separated hybrids) followed simulations one-photon absorption resonance Raman scattering...
A novel parallel algorithm for noniterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [Bhaskaran-Nair, K.; Brabec, J.; Aprà, E.; van Dam, H. J. Pittner, Kowalski, K. Chem. Phys.2012, 137, 094112] with the possibility of accelerating numerical calculations using graphics processing units (GPUs) is presented. We discuss performance this approach applied to MRCCSD(T) method (iterative singles and doubles perturbative...
We have investigated the description of excited state relaxation in naked and hydrated TiO2 nanoparticles using Time-Dependent Density Functional Theory (TD-DFT) with three common hybrid exchange-correlation (XC) potentials: B3LYP, CAM-B3LYP BHLYP. Use TD-CAM-B3LYP TD-BHLYP yields qualitatively similar results for all structures, which are also consistent predictions coupled-cluster theory small particles. TD-B3LYP, contrast, is found to make rather different predictions; including apparent...
The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2–3 billion to deliver one new drug. This is both too expensive slow, especially emergencies like COVID-19 pandemic. In silico methodologies need be improved select better lead compounds, so as improve efficiency of later stages protocol, identify those compounds more quickly. No known methodological approach can this combination higher quality speed. Here, we describe an...
Despite the recent availability of vaccines against acute respiratory syndrome coronavirus 2 (SARS-CoV-2), search for inhibitory therapeutic agents has assumed importance especially in context emerging new viral variants. In this paper, we describe discovery a novel non-covalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits SARS-Cov-2 main protease (M pro ) by employing scalable high throughput virtual screening (HTVS) framework targeted compound library over 6.5...
Density Functional Theory calculations are reported on cage structured BN, AlN, GaN and InN sub- low nanosize stoichiometric clusters, including two octahedral families of Td Th symmetry. The structures energetics determined, we observe that BN clusters in particular show high stability with respect to the bulk phase. cluster formation energy is demonstrated include a constant term attribute curvature six tetragonal defects. (BN)60 onion double-bubble structure was found be particularly...
Abstract NWChem is a general‐purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the focuses molecular dynamics, Hartree–Fock theory, and density functional theory methods for both plane‐wave basis sets as well Gaussian sets, tensor contraction engine‐based coupled cluster capabilities, combined quantum mechanics/molecular mechanics descriptions. It was realized from beginning that scalable implementations...
The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment large experimentally relevant systems in molecular chemistry and materials science relies primarily on existence efficient software implementations which are capable leveraging latest advances modern high-performance computing (HPC). With recent trends HPC leading toward increasing reliance heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases...
We report a series of computations on the active site in Ti-substituted zeolites, specifically TS-1. Hybrid QM/MM methods based density functional calculations using BB1K and valence force field are used to study processes hydrolysis Ti–O–Si linkages inversion TiO4 tetrahedra. The structural features resulting tetra- tripodal Ti moieties good agreement with data from EXAFS studies. suggestion is made that species will dominate hydrous conditions, this likely be chemically form. have...
For many computational chemistry packages, being able to efficiently and effectively scale across an exascale cluster is a heroic feat. Collective experience from the Department of Energy's Exascale Computing Project suggests that achieving performance requires far more planning, design, optimization than scaling petascale. In cases, entire rewrites software are necessary address fundamental algorithmic bottlenecks. This in turn tremendous amount resources development time, cannot reasonably...
A novel algorithm for implementing a general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski-Monkhorst exponential ansatz [Jeziorski, B.; Monkhorst, H. J. Phys. Rev. A1981, 24, 1668] is introduced. The proposed utilizes processor groups to calculate equations MRCC amplitudes. In basic formulation, each group constructs related specific subset references. By flexible choice and reference-specific sufficiency conditions designated given group, one can ensure optimum...
Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI for designing scalable applications. At the same time, remains ubiquitous communication subsystem due its standardization, high performance, and availability on leading platforms. In this paper, we explore suitability of using PGAS subsystem. We focus Remote Memory Access (RMA) in which typically includes get, put, atomic memory operations. perform an in-depth exploration design alternatives based...
Faults are commonplace in large scale systems. These systems experience a variety of faults such as transient, permanent and intermittent. Multi-bit typically not corrected by the hardware resulting an error. This paper attempts to answer important question: Given multi-bit fault main memory, will it result application error - hence recovery algorithm should be invoked or can safely ignored? We propose modeling methodology this question. signature (a set attributes comprising system state),...
Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new counter novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome 2 (SARS-CoV-2). One promising approach is train machine learning (ML) and artificial intelligence (AI) tools screen large numbers of small molecules. As a contribution that effort, we aggregating numerous molecules from variety sources, using high-performance computing (HPC) computer diverse properties those...