ArticleJournal of chemical theory and computation2012
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed.
- Target-Centric Multiplexed Screening of an Herbal Extract Identifies a Novel Dual AACS central science · 2026Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model.ACS sensors · 2019Article
- Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).Biochimica et biophysica acta · 2016Review
- Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.ACS nano · 2016Article
- Magic angle spinning nuclear magnetic resonance characterization of voltage-dependent anion channel gating in two-dimensional lipid crystalline bilayers.Biochemistry · 2015Article
- Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin.The journal of physical chemistry letters · 2014Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.Journal of chemical theory and computation · 2014Article
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.Journal of computational chemistry · 2014Article
- Trivalent cations switch the selectivity in nanopores.Journal of molecular modeling · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Obstructing toxin pathways by targeted pore blockage.Chemical reviews · 2012Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
A theoretical framework is presented to model ion and DNA translocation across a nanopore confinement under an applied electric field. A combined Grand Canonical Monte Carlo Brownian Dynamics (GCMC/BD) algorithm offers a general approach to study ion permeation through wide molecular pores with a direct account of ion-ion and ion-DNA correlations. This work extends previously developed theory by incorporating the recently developed coarse-grain polymer model of DNA by de Pablo and colleagues [Knotts, T. A.; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. J. Chem. Phys. 2007, 126] with explicit ions for simulations of polymer dynamics. Atomistic MD simulations were used to guide model developments. The power of the developed scheme is illustrated with studies of single-stranded DNA (ss-DNA) oligomer translocation in two model cases: a cylindrical pore with a varying radius and a well-studied experimental system, the staphylococcal α-hemolysin channel. The developed model shows good agreement with experimental data for model studies of two homopolymers: ss-poly(dA)(n) and ss-poly(dC)(n). The developed protocol allows for direct evaluation of different factors (charge distribution and pore shape and size) controlling DNA translocation in a variety of nanopores.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.