Evidence map›Paper›PMID 34146585›Full record

ArticleMathematical biosciences2021

Quantitative analysis of mitochondrial ATP synthesis.

E Benjamin Randall, Marcus Hock, Rachel Lopez, Bahador Marzban, Collin Marshall, Daniel A Beard

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Mathematical biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Article
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  4. Article
  5. Review
  6. 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

6 authors.

E Benjamin RandallDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA.
Marcus HockDepartment of Bioengineering, University of California at San Diego, San Diego, 92093, CA, USA.
Rachel LopezDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA.
Bahador MarzbanDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA.
Collin MarshallDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA.
Daniel A BeardDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA. Electronic address: beardda@umich.edu.

Funding

University of Michigan Postbaccalaureate Research Education Program (UM PREP)R25GM086262 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALLEN, BENJAMIN · 2009 to 2024
$6.1M
Training in Multi-Scale Analysis of Biological Structure and FunctionT32EB009380 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Andrew D. McCulloch, Padmini Rangamani · 2009 to 2026
$4.8M
Computational systems analysis of cardiac mechanical-energetic coupling in heart diseaseR01HL144657 · NHLBI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BEARD, DANIEL A · 2019 to 2022
$1.8M
NHLBI NIH HHS R01 HL144657NIBIB NIH HHS T32 EB009380NIGMS NIH HHS R25 GM086262
6 · The paper itself

Abstract

We present a computational framework for analyzing and simulating mitochondrial ATP synthesis using basic thermodynamic and kinetic principles. The framework invokes detailed descriptions of the thermodynamic driving forces associated with the processes of the electron transport chain, mitochondrial ATP synthetase, and phosphate and adenine nucleotide transporters. Assembling models of these discrete processes into an integrated model of mitochondrial ATP synthesis, we illustrate how to analyze and simulate in vitro respirometry experiments and how models identified from in vitro experimental data effectively explain cardiac respiratory control in vivo. Computer codes for these analyses are embedded as Python scripts in a Jupyter Book to facilitate easy adoption and modification of the concepts developed here. This accessible framework may also prove useful in supporting educational applications. All source codes are available on at https://beards-lab.github.io/QAMAS_book/.

Indexed as

Adenosine TriphosphateMitochondriaModels, BiologicalComputer SimulationKineticsThermodynamicsAdenosine TriphosphateBiochemical thermodynamicsBioenergeticsComputational modelingMetabolic pathwaysRespiratory

Identifiers

PMID34146585
PMCPMC8434986

What OpenQuestion holds

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Registered trials

None linked

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.