On-the-Fly Monte Carlo Dominance Ratio Calculation Using the Noise Propagation Matrix

Sutton, Thomas M.; Romano, Paul K.; Nease, Brian R.

doi:10.15669/pnst.2.749

Cited by 7 publications

(3 citation statements)

References 8 publications

(10 reference statements)

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“…Energy minimization, molecular docking and binding energy calculations were performed to validate the potential drug-target interactions. For this, the crystal structures of the protein targets were obtained from RCSB Protein Data Bank (PDB) (www.rcsb.org) (Berman et al, 2000). The proteins for which no crystal structure is available in PDB was modeled using…”

Section: Drug-target Interaction Validation and Visualisationmentioning

confidence: 99%

Identification of multi-targeting and synergistic neuromodulators of epilepsy associated protein-targets in Ayurvedic herbs using network pharmacological approach

Choudhary

Singh

2018

Preprint

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Epilepsy comprises a wide spectrum of neuronal disorders and accounts for about one percent of global disease burden affecting people of all age groups. In the traditional medicinal system of Indian antiquity, commonly known as Ayurveda, epilepsy is recognised as apasmara and a plenty of information is documented regarding the effectiveness of various herbs against it. Towards exploring the complex regulatory mechanisms of Ayurvedic herbs at molecular levels, in this study, a network pharmacological framework is developed for thoroughly examining the anti-epileptic potential of 349 drug-like phytochemicals (DPCs) found in 63Ayurvedic herbs. Interaction networks of phytochemicals in anti-epileptic herbs, their protein targets and associated human pathways are designed at various scales and DPCs are mapped on these networks to uncover complex interrelationships. Neuromodulatory prospects of anti-epileptic herbs are probed and, as a special case study, DPCs that can regulate metabotrophic glutamate receptors (mGluRs) are inspected. An account of novel regulatory phytochemicals against epilepsy is reported by systematically analysing the screened DPCs against DrugBank compounds. A repertoire of DPCs having polypharmacological similarity with anti-epileptic drugs available in DrugBank and those under clinical trials is also reported. Further, a high-confidence PPI network specific to the protein targets of epilepsy was developed and the potential of DPCs to regulate its functional modules was investigated. The study concludes by highlighting a couple of herbs as potential sources of epileptogenic regulators. We believe that the presented schema can open-up the exhaustive explorations of indigenous herbs towards meticulous identification of DPCs against various diseases and disorders.

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Section: Drug-target Interaction Validation and Visualisationmentioning

confidence: 99%

Identification of multi-targeting and synergistic neuromodulators of epilepsy associated protein-targets in Ayurvedic herbs using network pharmacological approach

Choudhary

Singh

2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Two additional features available in MC21 are the use of the Shannon entropy diagnostic (Ueki and Brown, 2005) to help ascertain source convergence, and the ability to estimate the dominance ratio using the Noise Propagation Matrix method (Sutton et al, 2011), which is based on and shares many properties with the Course-Mesh Projection Method (Nease and Ueki, 2007). (Horelik et al, 2013).…”

Section: Variance Reductionmentioning

confidence: 99%

MC21 v.6.0 – A continuous-energy Monte Carlo particle transport code with integrated reactor feedback capabilities

Griesheimer

Gill

Nease

et al. 2015

Annals of Nuclear Energy

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“…Two additional features available in MC21 are the use of the Shannon entropy diagnostic (35) to help ascertain source convergence, and the ability to estimate the dominance ratio using the Noise Propagation Matrix method, (36) which is based on and shares many properties with the Course-Mesh Projection Method. (37)…”

Section: Variance Reductionmentioning

confidence: 99%

MC21 v.6.0 – A Continuous-Energy Monte Carlo Particle Transport Code with Integrated Reactor Feedback Capabilities

Griesheimer

Gill

Nease

et al. 2014

SNA + MC 2013 - Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo

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MC21 is a continuous-energy Monte Carlo radiation transport code for the calculation of the steady-state spatial distributions of reaction rates in three-dimensional models. The code supports neutron and photon transport in fixed source problems, as well as iterated-fission-source (eigenvalue) neutron transport problems. MC21 has been designed and optimized to support large-scale problems in reactor physics, shielding, and criticality analysis applications. The code also supports many in-line reactor feedback effects, including depletion, thermal feedback, xenon feedback, eigenvalue search, and neutron and photon heating. MC21 uses continuous-energy neutron/nucleus interaction physics over the range from 10 −5 eV to 20 MeV. The code treats all common neutron scattering mechanisms, including fast-range elastic and non-elastic scattering, and thermal-and epithermal-range scattering from molecules and crystalline materials. For photon transport, MC21 uses continuous-energy interaction physics over the energy range from 1 keV to 100 GeV. The code treats all common photon interaction mechanisms, including Compton scattering, pair production, and photoelectric interactions. All of the nuclear data required by MC21 is provided by the NDEX system of codes, which extracts and processes data from EPDL-, ENDF-, and ACE-formatted source files. For geometry representation, MC21 employs a flexible constructive solid geometry system that allows users to create spatial cells from first-and second-order surfaces. The system also allows models to be built up as hierarchical collections of previously defined spatial cells, with interior detail provided by grids and template overlays. Results are collected by a generalized tally capability which allows users to edit integral flux and reaction rate information. Results can be collected over the entire problem or within specific regions of interest through the use of phase filters that control which particles are allowed to score each tally. The tally system has been optimized to maintain a high level of efficiency, even as the number of edit regions becomes very large.

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On-the-Fly Monte Carlo Dominance Ratio Calculation Using the Noise Propagation Matrix

Cited by 7 publications

References 8 publications

Identification of multi-targeting and synergistic neuromodulators of epilepsy associated protein-targets in Ayurvedic herbs using network pharmacological approach

Identification of multi-targeting and synergistic neuromodulators of epilepsy associated protein-targets in Ayurvedic herbs using network pharmacological approach

MC21 v.6.0 – A continuous-energy Monte Carlo particle transport code with integrated reactor feedback capabilities

MC21 v.6.0 – A Continuous-Energy Monte Carlo Particle Transport Code with Integrated Reactor Feedback Capabilities

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