scholarly journals The free-energy cost of accurate biochemical oscillations

2015 ◽  
Vol 11 (9) ◽  
pp. 772-778 ◽  
Author(s):  
Yuansheng Cao ◽  
Hongli Wang ◽  
Qi Ouyang ◽  
Yuhai Tu
Keyword(s):  
Free Energy ◽  
Energy Cost ◽  
Biochemical Oscillations

scholarly journals Size dependence of hydrophobic hydration at electrified gold/water interfaces

2021 ◽  
Vol 118 (15) ◽  
pp. e2023867118
Author(s):  
Alessandra Serva ◽  
Mathieu Salanne ◽  
Martina Havenith ◽  
Simone Pezzotti
Keyword(s):  
Free Energy ◽  
Energy Cost ◽  
Correction Term ◽  
Hydrophobic Hydration ◽  
Outer Sphere ◽  
Gold Surface ◽  
Electrochemical Reactions ◽  
Water Interface ◽  
Hydrophobic Solutes ◽  
Small Hydrophobic

Hydrophobic hydration at metal/water interfaces actively contributes to the energetics of electrochemical reactions, e.g. CO2 and N2 reduction, where small hydrophobic molecules are involved. In this work, constant applied potential molecular dynamics is employed to study hydrophobic hydration at a gold/water interface. We propose an adaptation of the Lum–Chandler–Weeks (LCW) theory to describe the free energy of hydrophobic hydration at the interface as a function of solute size and applied voltage. Based on this model we are able to predict the free energy cost of cavity formation at the interface directly from the free energy cost in the bulk plus an interface-dependent correction term. The interfacial water network contributes significantly to the free energy, yielding a preference for outer-sphere adsorption at the gold surface for ideal hydrophobes. We predict an accumulation of small hydrophobic solutes of sizes comparable to CO or N2, while the free energy cost to hydrate larger hydrophobes, above 2.5-Å radius, is shown to be greater at the interface than in the bulk. Interestingly, the transition from the volume dominated to the surface dominated regimes predicted by the LCW theory in the bulk is also found to take place for hydrophobes at the Au/water interface but occurs at smaller cavity radii. By applying the adapted LCW theory to a simple model addition reaction, we illustrate some implications of our findings for electrochemical reactions.

scholarly journals Universal lower bound on the free-energy cost of molecular measurements

2017 ◽  
Vol 95 (6) ◽  
Author(s):  
Suman G. Das ◽  
Madan Rao ◽  
Garud Iyengar
Keyword(s):  
Free Energy ◽  
Lower Bound ◽  
Energy Cost

scholarly journals Activity of Antimicrobial Peptide Aggregates Decreases with Increased Cell Membrane Embedding Free Energy Cost

Biochemistry ◽  
2018 ◽  
Vol 57 (18) ◽  
pp. 2606-2610 ◽  
Author(s):  
Rongfeng Zou ◽  
Xiaomin Zhu ◽  
Yaoquan Tu ◽  
Junchen Wu ◽  
Markita P. Landry
Keyword(s):  
Free Energy ◽  
Cell Membrane ◽  
Antimicrobial Peptide ◽  
Energy Cost

scholarly journals The free-energy cost of interaction between DNA loops

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lifang Huang ◽  
Peijiang Liu ◽  
Zhanjiang Yuan ◽  
Tianshou Zhou ◽  
Jianshe Yu
Keyword(s):  
Free Energy ◽  
Energy Cost ◽  
Dna Loops

scholarly journals Activity of Antimicrobial Peptides Decreases with Increased Cell Membrane Crossing Free Energy Cost

2018 ◽  
Author(s):  
Rongfeng Zou ◽  
Xiaomin Zhu ◽  
Yaoquan Tu ◽  
Junchen Wu ◽  
Markita P. Landry
Keyword(s):  
Free Energy ◽  
Antibacterial Activity ◽  
Cell Membrane ◽  
Antimicrobial Peptides ◽  
Intermolecular Interactions ◽  
Energy Cost ◽  
Bacterial Resistance ◽  
Free Energy Calculations ◽  
Intramolecular Interactions ◽  
Promising Alternative

ABSTRACTAntimicrobial peptides (AMPs) are a promising alternative to mitigating bacterial infections in light of increasing bacterial resistance to antibiotics. However, predicting, understanding, and controlling the antibacterial activity of AMPs remains a significant challenge. While peptide intramolecular interactions are known to modulate AMP antimi-crobial activity, peptide intermolecular interactions remain elusive in their impact on peptide bioactivity. Herein, we test the relationship between AMP intermolecular interactions and antibacterial efficacy by controlling AMP intermolecular hydrophobic and hydrogen bonding interactions. Molecular dynamics simulations and Gibbs free energy calculations in concert with experimental assays show that increasing intermolecular interactions via inter-peptide aggregation increases the energy cost for the peptide to cross the bacterial cell membrane, which in turn decreases the AMP antibacterial activity. Our findings provide a route for predicting and controlling the antibacterial activity of AMPs against Gramnegative bacteria via reductions of intermolecular AMP interactions.

Free energy cost and accuracy in branched selection processes of biosynthesis

1983 ◽  
Vol 16 (4) ◽  
pp. 415-519 ◽  
Author(s):  
Clas Blomberg
Keyword(s):  
Free Energy ◽  
Nucleic Acid ◽  
Mathematical Models ◽  
Error Correction ◽  
Energy Cost ◽  
Acid Synthesis ◽  
Main Aspect ◽  
Selection Processes ◽  
Energy Processes ◽  
Underlying Processes

Selection in biochemical synthesis processes is a very important task: processes as protein or nucleic acid synthesis must be very accurate although the cell abounds with closely related molecules which, intuitively, should be difficult to distinguish. The mechanisms of selection and the underlying processes have been extensively studied in the last years, and the ideas have been developed into mathematical models to visualize the potentials of recognition and error correction. There are several aspects on this, the main aspect of the present work being the important fact that the cell must pay for the increased accuracy in terms of available free energy: processes are driven from equilibrium, and do away with appreciable dissipation.

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