scholarly journals Study of Solar Pumped Laser for Fossil-fuel-free Energy Cycle Using Magnesium

2008 ◽  
Vol 36 (APLS) ◽  
pp. 1153-1156 ◽  
Author(s):  
Takayuki FUNATSU ◽  
Takashi YABE ◽  
Tomomasa OHKUBO ◽  
Sigeaki UCHIDA ◽  
Kunio YOSHIDA ◽  
...  
Keyword(s):  
Free Energy ◽  
Fossil Fuel ◽  
Energy Cycle

Demonstrated fossil-fuel-free energy cycle using magnesium and laser

2006 ◽  
Vol 89 (26) ◽  
pp. 261107 ◽  
Author(s):  
T. Yabe ◽  
S. Uchida ◽  
K. Ikuta ◽  
K. Yoshida ◽  
C. Baasandash ◽  
...  
Keyword(s):  
Free Energy ◽  
Fossil Fuel ◽  
Energy Cycle

scholarly journals Evaluation of potential fossil fuel free energy system: Scenarios for optimization of a regional integrated system

2017 ◽  
Vol 142 ◽  
pp. 964-970 ◽  
Author(s):  
Mahsa Daraei ◽  
Eva Thorin ◽  
Anders Avelin ◽  
Erik Dotzauer
Keyword(s):  
Free Energy ◽  
Fossil Fuel ◽  
Energy System ◽  
Integrated System

scholarly journals Structure for Energy Cycle: A unique status of Second Law of Thermodynamics for living systems

2018 ◽  
Author(s):  
Shu-Nong Bai ◽  
Hao Ge ◽  
Hong Qian
Keyword(s):  
Free Energy ◽  
Second Law Of Thermodynamics ◽  
Chemical Kinetic ◽  
Chemical Processes ◽  
Spontaneous Formation ◽  
Energy Cycle ◽  
Molecular Force ◽  
Living Organisms ◽  
Dynamic Formation ◽  
Unique Status

AbstractDistinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schrödinger’sneg-entropyand I. Prigogine’sdissipative structure, we propose a chemical kinetic view that the earliest “live” process is essentially a special interaction between a pair of specific components under a corresponding, particular environmental conditions. The interaction exists as an inter-molecular-force-bond complex (IMFBC) that couples two separate chemical processes: One is the spontaneous formation of an IMFBC driven by the decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two processes that are coupled by the IMFBC were originated independently and considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: This forms the first landmark on the path from things to a being. The dynamic formation and dissemblance of the IMFBCs, as composite individuals, follows a principle designated as “… structure for energy for structure for energy…”, the cycle continues, shortly “structure for energy cycle”. With additional features derived from an IMFBC, such as multiple intermediates, autocatalytic ability of one individual upon the formation of another, aqueous medium, and mutual beneficial relationship between formation of polypeptides and nucleic acids, etc., the IMFBC-centered “live” process spontaneously evolved into more complex living organisms with the characteristics one currently knows.

Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Conformational Sampling ◽  
Atomic Charges ◽  
Loop Region ◽  
Energy Cycle ◽  
Dynamics Simulations ◽  
Aspartate Residue

Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br>

scholarly journals pKa Calculations of Asp26 in Thioredoxin with Alchemical Free Energy Simulations and Hirshfeld-I Atomic Charges

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Atomic Charges ◽  
Energy Cycle ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Aspartate Residue ◽  
Experimental Reference

Thioredoxin is a protein that has been used as model system by various computational methods to predict the pK<sub>a</sub> of aspartate residue Asp26 which is 3.5 units higher than the solvent exposed Asp20. Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between the two aspartic acid residues is calculated with the Amber99sb force field in alchemical transformation. The varying polarization of Asp20/26 in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 positions and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of polarization of both aspartate residues in the free energy cycle by the HI atomic charges improve the results from the nonpolarizable force field and reproduces the experimental reference delta pK<sub>a</sub> value.

Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Conformational Sampling ◽  
Atomic Charges ◽  
Loop Region ◽  
Energy Cycle ◽  
Dynamics Simulations ◽  
Aspartate Residue

Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br>

Encultured minds, not error reduction minds

2020 ◽  
Vol 43 ◽  
Author(s):  
Robert Mirski ◽  
Mark H. Bickhard ◽  
David Eck ◽  
Arkadiusz Gut
Keyword(s):  
Free Energy ◽  
Error Reduction ◽  
Energy Principle ◽  
Free Energy Principle ◽  
Current Article

Abstract There are serious theoretical problems with the free-energy principle model, which are shown in the current article. We discuss the proposed model's inability to account for culturally emergent normativities, and point out the foundational issues that we claim this inability stems from.

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