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Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets
- Source :
- Nature Communications, Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
- Publication Year :
- 2020
- Publisher :
- Nature Publishing Group UK, 2020.
-
Abstract
- A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations.<br />Measuring interaction energies from experimentally measured single-molecular interactions is challenging. Here, the authors report a gamma work distribution applied to single molecule pulling events for estimating peptide absorption free energy.
- Subjects :
- Work (thermodynamics)
Science
Binding energy
General Physics and Astronomy
02 engineering and technology
010402 general chemistry
01 natural sciences
General Biochemistry, Genetics and Molecular Biology
Article
Molecular dynamics
symbols.namesake
Jarzynski equality
Single-molecule biophysics
Computational models
Statistical physics
Absorption (electromagnetic radiation)
lcsh:Science
Physics
Quantitative Biology::Biomolecules
Multidisciplinary
Nanoscale biophysics
Estimator
Observable
General Chemistry
021001 nanoscience & nanotechnology
0104 chemical sciences
Gibbs free energy
Computational biology and bioinformatics
symbols
lcsh:Q
Protein design
0210 nano-technology
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....951b809c044e3b8b9520a542e332df9d