Acceleration of Biomolecular Simulations using FPGA-based Reconfigurable Computing

A paradigm shift is occurring in the way compute-intensive scientific applications are developed. Thanks to advancements in commercially viable hybrid architectures for High-Performance Computing (HPC), the focus has shifted from improving performance by merely scaling algorithms on von Neumann computing nodes to fully exploiting additional computational capabilities provided by accelerators such as FPGAs (Field Programmable Gate Arrays) and GPGPUs (General Purpose Graphical Processing Units). Computational chemists use Molecular Dynamics (MD) simulations like LAMMPS (Large Scale Atomic Molecular Massively Parallel Systems) and NAMD (NAnoscale Molecular Dynamics) to simulate biomolecular behaviour such as protein folding and small molecule docking to proteins. MD simulations are computationally complex n-body problems, which are time consuming to simulate in biologically relevant scales. Executing such simulations in best available HPC environments is critical for scientific advancements in the field. Thus, as HPC technology evolves, there is a need to update classical biomolecular simulation applications like LAMMPS to better suit the architecture. In this work, we modify LAMMPS (a classical molecular dynamics simulation program developed for CPU-only clusters) to execute on a reconfigurable computer system, SRC-7 H MAP. The SRC-7 H MAP consists of two Altera FPGA logic chips interfaced to a dual-core Intel Xeon processor. Users can benefit by offloading most compute-intensive tasks of the application to the FPGA logic. This work explores the challenges involved in effectively adapting a production level application code optimized for von Neumann architecture, to an FPGA-based hybrid architecture. We have successfully accelerated the non-bonded force computations, the most compute-intensive module in LAMMPS for biomolecular simulations, by 5.0x over a single 3.0 GHz Xeon processor. This performance includes the data transfer overheads and function calling overheads. Further, using the accelerated non-bonded force computations function, we achieve an overall application speed-up of 2.0x to 2.4

Effect of rhizome extract of Acorus calamus on depressive condition induced by forced swimming in mice

The present study evaluated the anti-depressant properties of A. calamus rhizome in a forced swimming test (FST) of mice model. Three doses of methanol extract of rhizome (200,400 and 600 mg extract/kg b.wt) and imipramine (15 mg/kg b.wt), a positive control, were orally administered once a day for the consecutive period of 14 days in Balb/c mice. The effect of extract on immobility period was measured using forced swimming test. The levels of cortisol monoamine oxidase and neurotransmitters were analyzed using standard methods. The anti-depressant effect was observed maximum at the dose of 200 mg/kg. b.wt that caused 23.82% reduction in immobility period. The extract also significantly attenuated the FST-induced elevation of plasma cortisol, monoamine oxidase activity and returned the altered levels of neurotransmitters near to the normal levels in brain. These results of the present study suggest that the extract of A. calamus rhizome  has  antidepressant-like activity which is mediated by modulating the central neurochemical as well as HPA (hypothalamic-pituitary-adrenal) axis in response to stress induced by FST. Therefore, A.calamus rhizome may be used as a valuable herbal supplement for the treatment of depression related conditions

Effect of rhizome extract of Acorus calamus on depressive condition induced by forced swimming in mice

The present study evaluated the anti-depressant properties of A. calamus rhizome in a forced swimming test (FST) of mice model. Three doses of methanol extract of rhizome (200,400 and 600 mg extract/kg b.wt) and imipramine (15 mg/kg b.wt), a positive control, were orally administered once a day for the consecutive period of 14 days in Balb/c mice. The effect of extract on immobility period was measured using forced swimming test. The levels of cortisol monoamine oxidase and neurotransmitters were analyzed using standard methods. The anti-depressant effect was observed maximum at the dose of 200 mg/kg. b.wt that caused 23.82% reduction in immobility period. The extract also significantly attenuated the FST-induced elevation of plasma cortisol, monoamine oxidase activity and returned the altered levels of neurotransmitters near to the normal levels in brain. These results of the present study suggest that the extract of A. calamus rhizome  has  antidepressant-like activity which is mediated by modulating the central neurochemical as well as HPA (hypothalamic-pituitary-adrenal) axis in response to stress induced by FST. Therefore, A.calamus rhizome may be used as a valuable herbal supplement for the treatment of depression related conditions

Chicxulub impact spherules in the North Atlantic and Caribbean: age constraints and Cretaceous-Tertiary boundary hiatus

The Chicxulub impact is commonly believed to have caused the Cretaceous-Tertiary boundary mass extinction and a thin impact spherule layer in the North Atlantic and Caribbean is frequently cited as proof. We evaluated this claim in the seven best North Atlantic and Caribbean Cretaceous-Tertiary boundary sequences based on high-resolution biostratigraphy, quantitative faunal analyses and stable isotopes. Results reveal a major Cretaceous-Tertiary boundary unconformity spanning most of Danian subzone P1a(1) and Maastrichtian zones CF1-CF2 (~400 ka) in the NW Atlantic Bass River core, ODP Sites 1049A, 1049C and 1050C. In the Caribbean ODP Sites 999B and 1001B the unconformity spans from the early Danian zone P1a(1) through to zones CF1-CF4 (~3 Ma). Only in the Demerara Rise ODP Site 1259B is erosion relatively minor and restricted to the earliest Danian zone P0 and most of subzone P1a(1) (~150 ka). In all sites examined, Chicxulub impact spherules are reworked into the early Danian subzone P1a(1) about 150-200 ka after the mass extinction. A similar pattern of erosion and redeposition of impact spherules in Danian sediments has previously been documented from Cuba, Haiti, Belize, Guatemala, south and central Mexico. This pattern can be explained by intensified Gulf stream circulation at times of climate cooling and sea level changes. The age of the Chicxulub impact cannot be determined from these reworked impact spherule layers, but can be evaluated based on the stratigraphically oldest spherule layer in NE Mexico and Texas, which indicates that this impact predates the Cretaceous-Tertiary boundary by about 130-150 k

Polylactic acid coated SBA-15 functionalized with 3-aminopropyl triethoxysilane

In the present study, a pH responsive polylactic acid coated SBA-15 functionalized with 3-aminopropyl triethoxysilane is reported. PLA has been coated on the functionalized SBA-15 by formation of amide linkage between amine functionalized SBA-15 and PLA. The amide linkage is confirmed by FTIR spectroscopic data. The materials are well characterized by FTIR, SEM, EDAX and XRD data. Using the PLA coated functionalized SBA-15 the controlled release of the drug ibuprofen has been studied. The successful delivery of ibuprofen has been achieved on the basis of its pH response

Age of the Earliest Transgressive Event in the Krishna-Godavari Basin, India: Evidence from Dinoflagellate Cysts and Planktonic Foraminifera Biostratigraphy

A combined biostratigraphic study of dinoflagellate cysts and foraminifera was carried out on Early Cretaceous subsurface well cutting sediments from well A (DNG) (2800–2746 m depth) from the Krishna-Godavari Basin, India. The last appearance datum of marker species of dinoflagellate cysts and planktonic foraminifera was considered for the construction of the biostratigraphic framework. The study shows dominance of Early Cretaceous marker dinoflagellate cysts Cassiculosphaeridia magna, Cribroperidinium perforans, Hystrichodinium voigtii, Kleithriasphaeridium eoinodes, and planktonic foraminifera Hedbergella aptiana, Hedbergella mitra, Hedbergella praelippa, Hedbergella tardita, Microhedbergella miniglobularis and Hedbergella mitra species. In addition to this, the dinoflagellate cyst data were compared with the dinoflagellate biozones of Austral and Tethyan provinces. Based on earlier micropalaeontological records from the Krishna-Godavari Basin and the present study, a latest Barremian-early Aptian age has been determined for the earliest marine transgression in the Krishna-Godavari Basin. The early marine incursion during late Barremian-earliest Aptian in the Krishna-Godavari Basin compared to Albian age in Cauvery Basin suggests the opening of east coast from north to south. Citation Statements: 1 0 0 0 Making Science Reliable 1 0 0 0 Citing Publications Supporting Mentioning Contrasting View Citations See all citations for this article at scite.ai scite is a platform that combines deep learning with expert analysis to automatically classify citations as supporting, contrasting or mentioning

Giant Inflammatory Polyposis of the Rectum as a Complication of Ulcerative Colitis

Inflammatory bowel disease is an emerging gastrointestinal disease in Malaysia. One of its rare complications includes giant inflammatory polyposis (GIP). A 39-year-old woman presented with worsening per rectal mucous discharge, associated with blood, colicky abdominal pain, and weight loss. A series of endoscopies at another hospital did not provide an inconclusive diagnosis. Another repeat colonoscopy showed a left-sided colitis with marked erythema and friability with islands of polyps; this was concluded to be an ulcerative colitis based on histopathology; thus, medical treatment was commenced. However, 2 months later, the patient presented with constipation, which required laxatives, as well as a worsened lower abdominal pain. Subsequent colonoscopy revealed obstruction-caused GIP at the mid rectum extending to the lower rectum, which was confirmed by imaging modalities. She was diagnosed with obstructing GIP coupled with ulcerative colitis, and panproctocolectomy and ileal pouch anal anastomosis were planned