The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves ...three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.
Abstract
DrugCentral is a drug information resource (http://drugcentral.org) open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue. Since the 2016 ...release, 103 new approved drugs were updated. The following new data sources have been included: Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS), FDA Orange Book information, L1000 gene perturbation profile distance/similarity matrices and estimated protonation constants. New and existing entries have been updated with the latest information from scientific literature, drug labels and external databases. The web interface has been updated to display and query new data. The full database dump and data files are available for download from the DrugCentral website.
Abstract
DrugCentral is a public resource (http://drugcentral.org) that serves the scientific community by providing up-to-date drug information, as described in previous papers. The current release ...includes 109 newly approved (October 2018 through March 2020) active pharmaceutical ingredients in the US, Europe, Japan and other countries; and two molecular entities (e.g. mefuparib) of interest for COVID19. New additions include a set of pharmacokinetic properties for ∼1000 drugs, and a sex-based separation of side effects, processed from FAERS (FDA Adverse Event Reporting System); as well as a drug repositioning prioritization scheme based on the market availability and intellectual property rights forFDA approved drugs. In the context of the COVID19 pandemic, we also incorporated REDIAL-2020, a machine learning platform that estimates anti-SARS-CoV-2 activities, as well as the ‘drugs in news’ feature offers a brief enumeration of the most interesting drugs at the present moment. The full database dump and data files are available for download from the DrugCentral web portal.
In traditional molecular dynamics (MD) simulations, atoms and coarse-grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital ...role, more complex models are required. In this paper we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. We discuss parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts.
Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging ...from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials.
Program Title: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
CPC Library link to program files:https://doi.org/10.17632/cxbxs9btsv.1
Developer's repository link:https://github.com/lammps/lammps
Licensing provisions: GPLv2
Programming language: C++, Python, C, Fortran
Supplementary material:https://www.lammps.org
Nature of problem: Many science applications in physics, chemistry, materials science, and related fields require parallel, scalable, and efficient generation of long, stable classical particle dynamics trajectories. Within this common problem definition, there lies a great diversity of use cases, distinguished by different particle interaction models, external constraints, as well as timescales and lengthscales ranging from atomic to mesoscale to macroscopic.
Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions 1. The time integration algorithm is based on the Størmer-Verlet symplectic integrator 2, which provides better stability than higher-order non-symplectic methods. In addition, LAMMPS supports a wide range of interatomic potentials, constraints, diagnostics, software interfaces, and pre- and post-processing features.
Additional comments including restrictions and unusual features: This paper serves as the definitive reference for the LAMMPS code.
1S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117 (1995) 1–19.2L. Verlet, Computer experiments on classical fluids: I. Thermodynamical properties of Lennard–Jones molecules, Phys. Rev. 159 (1967) 98–103.
Chemical genomics aims to comprehensively define, and ultimately predict, the effects of small molecule compounds on biological systems. Chemical activity profiling approaches must consider chemical ...effects on all pathways operative in mammalian cells. To enable a strategic and maximally efficient chemical profiling of pathway space, we have created the NCATS BioPlanet, a comprehensive integrated pathway resource that incorporates the universe of 1,658 human pathways sourced from publicly available, manually curated sources, which have been subjected to thorough redundancy and consistency cross-evaluation. BioPlanet supports interactive browsing, retrieval, and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of corresponding bioactivity assay, as well as visualization of pathways on a 3-dimensional globe, in which the distance between any two pathways is proportional to their degree of gene component overlap. Using this resource, we propose a strategy to identify a minimal set of 362 biological assays that can interrogate the universe of human pathways. The NCATS BioPlanet is a public resource, which will be continually expanded and updated, for systems biology, toxicology, and chemical genomics, available at http://tripod.nih.gov/bioplanet/.
We analyze the magnitude of the radiation pressure and electrostrictive stresses exerted by light confined inside GaAs semiconductor WGM optomechanical disk resonators, through analytical and ...numerical means, and find the electrostrictive stress to be of prime importance. We investigate the geometric and photoelastic optomechanical coupling resulting respectively from the deformation of the disk boundary and from the strain-induced refractive index changes in the material, for various mechanical modes of the disks. Photoelastic optomechanical coupling is shown to be a predominant coupling mechanism for certain disk dimensions and mechanical modes, leading to total coupling gom and g(0) reaching respectively 3 THz/nm and 4 MHz. Finally, we point towards ways to maximize the photoelastic coupling in GaAs disk resonators, and we provide some upper bounds for its value in various geometries.
Abstract
In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that ...can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein–protein interactions, protein–disease and protein–phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.
The successful incorporation of active proteins into synthetic polymers could lead to a new class of materials with functions found only in living systems. However, proteins rarely function under the ...conditions suitable for polymer processing. On the basis of an analysis of trends in protein sequences and characteristic chemical patterns on protein surfaces, we designed four-monomer random heteropolymers to mimic intrinsically disordered proteins for protein solubilization and stabilization in non-native environments. The heteropolymers, with optimized composition and statistical monomer distribution, enable cell-free synthesis of membrane proteins with proper protein folding for transport and enzyme-containing plastics for toxin bioremediation. Controlling the statistical monomer distribution in a heteropolymer, rather than the specific monomer sequence, affords a new strategy to interface with biological systems for protein-based biomaterials.
The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly ...available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins. Here, we describe two resources developed by the KMC: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD. We briefly describe the types and sources of data considered by the KMC and then highlight features of the Pharos interface designed to enable intuitive access to the IDG knowledgebase. The aim of Pharos is to encourage 'serendipitous browsing', whereby related, relevant information is made easily discoverable. We conclude by describing two use cases that highlight the utility of Pharos and TCRD.
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