A5043900157- Computational Drug Discovery Methods
- Photonic and Optical Devices
- Machine Learning in Materials Science
- Nonlinear Optical Materials Research
- Protein Structure and Dynamics
- Plasmonic and Surface Plasmon Research
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Chemical Synthesis and Analysis
- Click Chemistry and Applications
- Molecular Junctions and Nanostructures
- Protein Degradation and Inhibitors
- Force Microscopy Techniques and Applications
- Quantum Dots Synthesis And Properties
- Innovative Microfluidic and Catalytic Techniques Innovation
- Perovskite Materials and Applications
- Spectroscopy and Quantum Chemical Studies
- Microbial Natural Products and Biosynthesis
- Semiconductor Lasers and Optical Devices
- Lanthanide and Transition Metal Complexes
- Mechanical and Optical Resonators
- Advanced Photonic Communication Systems
- Photochemistry and Electron Transfer Studies
- Advanced Data Storage Technologies
- Photonic Crystals and Applications
Scripps Research Institute
2020-2025
Scripps Institution of Oceanography
2020-2023
University of Washington
2010-2021
Scripps (United States)
2020-2021
Oak Ridge National Laboratory
2017-2020
Seattle University
2014
AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other in Suite, it lacks support modeling specific features such as macrocycles or explicit water molecules. Here, we describe implementation this functionality 1.2.0. Additionally, 1.2.0 supports AutoDock4.2 scoring function, simultaneous docking multiple ligands, a batch mode large number ligands. Furthermore, implemented Python bindings facilitate scripting...
QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, some model Hamiltonians. Implemented real space algorithms include variational, diffusion, reptation Carlo. uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable optimizing tens thousands parameters. The orbital auxiliary-field method also implemented, enabling cross...
AutoDock4 is a widely used program for docking small molecules to macromolecular targets. It describes ligand-receptor interactions using physics-inspired scoring function that has been proven useful in variety of drug discovery projects. However, compared more modern and recent software, longer execution times, limiting its applicability large scale dockings. To address this problem, we describe an OpenCL implementation AutoDock4, called AutoDock-GPU, leverages the highly parallel...
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by compound databases into representative protein binding-site conformations, thus taking account the dynamic properties binding sites. also describe preliminary obtained 24 systems involving eight proteins proteome SARS-CoV-2. The involves temperature replica exchange sampling, making massively parallel...
AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other engines in Suite, it lacks features that support modeling specific systems such as macrocycles or water explicitly. Here, we describe implementation these functionality 1.2.0. Additionally, 1.2.0 supports AutoDock4.2 scoring function, simultaneous multiple ligands, a batch mode for large number ligands. Furthermore, implemented Python bindings facilitate scripting...
The near-field effects of plasmonic optical antennas are being explored in applications ranging from biosensors to solar cells. We demonstrate that photoluminescence emission enhancement CdSe quantum dots (QDs) can be obtained the absence any excitation near single silver nanoprisms. spectral dependence radiative and nonradiative decay rate QDs closely follows nanoparticle plasmon scattering spectrum. Using both experiment theory we show that, enhancement, ratio is proportional efficiency....
Chip-scale integration of electronics and photonics is recognized as important to the future information technology, exploitation best properties electronics, photonics, plasmonics achieve this objective. However, significant challenges exist including matching sizes electronic photonic circuits; achieving low-loss transition between plasmonics; developing integrating new materials. This review focuses on a hybrid material approach illustrating importance both chemical engineering concepts....
The performance of highly nonlinear organic electro-optic (EO) materials incorporated into nanoscale slots is examined. It shown that EO coefficients as large 190 pm/V can be obtained in 150 nm wide plasmonic slot waveguides but the decrease for narrower slots. Possible mechanism lead to such a are discussed. Monte-Carlo computer simulations performed, confirming chromophore-surface interactions one important factor influencing coefficient narrow These particular interest applications...
<pre>AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other engines in AutoDock Suite, it lacks features that support modeling specific systems such as macrocycles or water explicitly. Here, we describe implementation these functionality 1.2.0. Additionally, 1.2.0 supports AutoDock4.2 scoring function, simultaneous multiple ligands, a batch mode for large number ligands. Furthermore, implemented Python bindings...
We propose, simulate, and experimentally validate a new mechanical detection method to analyze atomic force microscopy (AFM) cantilever motion that enables noncontact discrimination of transient events with ~100 ns temporal resolution without the need for custom AFM probes, specialized instrumentation, or expensive add-on hardware. As an example application, we use screen thermally annealed poly(3-hexylthiophene):phenyl-C(61)-butyric acid methyl ester photovoltaic devices under realistic...
Time-to-solution for structure-based screening of massive chemical databases COVID-19 drug discovery has been decreased by an order magnitude, and a virtual laboratory deployed at scale on up to 27,612 GPUs the Summit supercomputer, allowing average molecular docking 19,028 compounds per second. Over one billion were docked two SARS-CoV-2 protein structures with full optimization ligand position 20 poses docking, each in under 24 hours. GPU acceleration high-throughput optimizations program...
We measured the electro-optic (EO) coefficients (r33) of thin-film devices made from several monolithic, high number density organic EO chromophores with and without additional charge barrier layers. found that a cross-linkable benzocyclobutene layer was very effective in suppressing unwanted, leakage current, keeping poling voltage nearly identical to applied voltage. This proved be superior titanium dioxide (TiO2) layer. The suppression current combination new chromophore enabled...
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability bind a given protein receptor within drug-discovery campaign. Experimental screening expensive and time consuming, it desirable carry out large scale calculations high-throughput manner narrow the experimental search space. Few of existing computational tools were designed with high performance computing mind. Therefore, optimizations maximize use high-performance resources available at...
Coupled plasmonic/chromophore systems are of interest in applications ranging from fluorescent biosensors to solar photovoltaics and photoelectrochemical cells because near-field coupling metal nanostructures can dramatically alter the optical performance nearby materials. We show that CdSe quantum dots (QDs) near single silver nanoprisms exhibit photoluminescence lifetimes yields depend on excitation wavelength, apparent violation Kasha–Vavilov rule. attribute variation QD lifetime with...
Abstract Recent advances in structural biology have led to the publication of a wealth high‐resolution x‐ray crystallography (XRC) and cryo‐EM macromolecule structures, including many complexes with small molecules interest for drug design. While it is common incorporate information from atomic coordinates these into docking (e.g., pharmacophore models or scaffold hopping), there are limited methods directly leverage underlying density information. This desirable because does not rely on...
Microbiota metabolism generates diverse bile acids that are associated with health and disease, but the molecular targets mechanisms of action for these metabolites have not been fully elucidated. Using acid photoaffinity probes chemoproteomics, we found many protein microbiota-derived secondary in mammalian cells. Of note, discovered deoxycholic (DCA) binds transmembrane domain stimulator interferon genes (STING), promotes its oligomerization agonist stimulation type I signaling ex vivo...
We study the top surface composition of blends conjugated polymer regioregular poly-3-hexylthiophene (P3HT) with fullerene (6,6)-phenyl-C(61)-butyric acid methyl ester (PCBM), an important model system for organic photovoltaics (OPVs), using near-edge X-ray absorption fine structure spectroscopy (NEXAFS). compare ratio P3HT to PCBM near air/film interface that results from preparing blend films on two sets substrates: (1) poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS)...
We present a supercomputer-driven pipeline for
We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type interactions among molecules by representing groups atoms within those in terms ellipsoids (rather than spheres). Our systematically translates arbitrary underlying all-atom (AA) representation a molecular system multisite ellipsoidal potential family Gay–Berne potentials. As method enables levels coarse-graining, or even multiple coarse-graining single simulation, we describe as Level Detail (LoD)...
Organic nonlinear optical (ONLO) chromophores are key components in electro-optic (EO) devices, particularly on chip. They have the potential to footprints compatible with silicon-based devices. Materials based ONLO extremely easy process, being plastics. The development of better requires study how strong EO properties individual and well they can be organized a host material and, ultimately, densely packed neat material. We now assess existing perform as materials compare optimal...
High-performance computing (HPC) increasingly relies on heterogeneous architectures to achieve higher performance.In Oak Ridge Leadership Facility (OLCF), this trend continues as its latest supercomputer, Summit, entered production in early 2019.The combination of IBM POWER 9 CPU and Nvidia V100 GPU, along with a fast NVLink2 interconnect other technologies, pushes system performance new height breakes the exascale barrier by certain measures.Due Summit's powerful GPUs much GPU-CPU ratio,...
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations contribute to passive permeation by encouraging intramolecular H-bonds. AutoDock-GPU Vina model macrocyclic ligands flexibly, without requiring the enumeration conformers before docking. Here, we characterize performance method for handling compounds, which is implemented default behaviour preparation with our pipeline,...