Evidence map›Paper›PMID 20459161›Full record

ArticleThe Journal of chemical physics2010

Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics.

Abhishek Singharoy, Anastasia M Yesnik, Peter Ortoleva

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Multiscale simulation of microbe structure and dynamics.Progress in biophysics and molecular biology · 2011
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Abhishek SingharoyDepartment of Chemistry, Center for Cell and Virus Theory, Indiana University, Bloomington, Indiana 47405, USA.
Anastasia M Yesnik
Peter Ortoleva

Funding

First-Principles, Computer-Aided Nanosystem Design and AnalysisR21EB008951 · NIBIB · TRUSTEES OF INDIANA UNIVERSITY · PI ORTOLEVA, PETER J. · 2008 to 2009
$413k
NIBIB NIH HHS R21 EB008951
6 · The paper itself

Abstract

Electrostatic effects in nanosystems are understood via a physical picture built on their multiscale character and the distinct behavior of mobile ions versus charge groups fixed to the nanostructure. The Poisson-Boltzmann equation is nondimensionalized to introduce a factor lambda that measures the density of mobile ion charge versus that due to fixed charges; the diffusive smearing and volume exclusion effects of the former tend to diminish its value relative to that from the fixed charges. We introduce the ratio sigma of the average nearest-neighbor atom distance to the characteristic size of the features of the nanostructure of interest (e.g., a viral capsomer). We show that a unified treatment (i.e., lambda proportional to sigma) and a perturbation expansion around sigma=0 yields, through analytic continuation, an approximation to the electrostatic potential of high accuracy and computational efficiency. The approach was analyzed via Padé approximants and demonstrated on viral system electrostatics; it can be generalized to accommodate extended Poisson-Boltzmann models, and has wider applicability to nonequilibrium electrodiffusion and many-particle quantum systems.

Indexed as

Models, MolecularStatic ElectricityAlgorithmsCapsidMolecular ConformationNanostructuresReproducibility of ResultsViruses

Identifiers

PMID20459161
PMCPMC2878355

What OpenQuestion holds

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Registered trials

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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.