Evolutionary Algorithms for Applications of Biological Networks: A Review

Liu, Gufeng; Liu, Qunfeng; Ma, Lijia; Shao, Zengyang

doi:10.1007/978-3-030-84522-3_8

Cited by 4 publications

(1 citation statement)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…100 global, SciPy101 global and local and user-defined optimization algorithms can be used. Though not the focus of this study, extensive work has been done to examine the best optimization algorithms for biological-based networks [102][103][104]. The selected optimization method changes the intrinsic rate coefficient values while minimizing a least squares loss function incorporating experimental data.…”

mentioning

confidence: 99%

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Weckel-Dahman,

Carlsen,

Swanson

2024

Preprint

View full text Add to dashboard Cite

Attaining a complete thermodynamic and kinetic characterization for processes involving multiple interconnected rare-event transitions remains a central challenge in molecular biophysics. This challenge is amplified when the process must be understood under a range of reaction conditions. Herein, we present a condition-responsive kinetic modeling framework that can combine the strengths of bottom-up rate quantification from multiscale simulations with top-down solution refinement using experimental data. Although this framework can be applied to any process, we demonstrate its use for electrochemically driven transport through channels and transporters. Using the Cl−/H+antiporter ClC-ec1 as a model system, we show how robust and predictive kinetic solutions can be obtained when the solution space is grounded by thermodynamic constraints, seeded through multiscale rate quantification, and further refined with experimental data, such as electrophysiology assays. Turning to the Shaker K+channel, we demonstrate that robust solutions and biophysical insights can also be obtained with sufficient experimental data. This multi-pathway method proves capable of identifying single-pathway dominant mechanisms but also highlights that competing and off-pathway flux is still essential to replicate experimental findings and to describe concentration-dependent channel rectification.

show abstract

mentioning

confidence: 99%

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Weckel-Dahman,

Carlsen,

Swanson

2024

Preprint

View full text Add to dashboard Cite

show abstract

A protein-protein interaction network aligner study in the multi-objective domain

Menor-Flores,

Vega-Rodríguez

2024

Computer Methods and Programs in Biomedicine

View full text Add to dashboard Cite

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Weckel-Dahman,

Carlsen,

Swanson

2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Attaining a complete thermodynamic and kinetic characterization for processes involving multiple interconnected rare-event transitions remains a central challenge in molecular biophysics. This challenge is amplified when the process must be understood under a range of reaction conditions. Herein, we present a novel condition-responsive kinetic modeling framework that can combine the strengths of bottom-up rate quantification from multiscale simulations with top-down solution refinement using both equilibrium and nonequilibrium experimental data. Although this framework can be applied to any process, we demonstrate its use for electrochemically driven transport through channels and transporters via the development of electrochemically responsive rates. Using the Cl − /H + antiporter ClC-ec1 as a model system, we show how optimal and predictive kinetic solutions can be obtained when the solution space is grounded by thermodynamic constraints, seeded through multiscale rate quantification, and further refined with experimental data, such as electrophysiology assays. Turning to the Shaker K + channel, we demonstrate that optimal solutions and biophysical insights can also be obtained with sufficient experimental data. This multipathway method also proves capable of identifying single-pathway dominant channel mechanisms but reveals that competing and off-pathway flux is still essential to replicate experimental findings and to describe concentration-dependent channel rectification.

show abstract

Evolutionary Algorithms for Applications of Biological Networks: A Review

Cited by 4 publications

References 71 publications

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

A protein-protein interaction network aligner study in the multi-objective domain

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Contact Info

Product

Resources

About