A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claim...A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claims that all stable conformations are (local or global) minimizers of CGF. These are enough to give a unified explanations and mechanisms to many aspects of protein dynamics such as protein folding;allostery;denaturation;and intrinsically disordered proteins. Formulas of CGF in water environment had been derived via quantum statistics. Applications of them to soluble proteins are: docking Gibbs free energy difference formula and a practical way to search better docking site;single molecule binding affinity;predicting and explaining why structures of a monomeric globular protein looks like a globule and is tightly packed with a hydrophobic core;a representation of the hydrophobic effect;and a wholistic view to structures of water soluble proteins.展开更多
In this paper, the super spectral viscosity （SSV） method is developed by introducing a spectrally small amount of high order regularization which is only activated on high frequencies. The resulting SSV approximatio...In this paper, the super spectral viscosity （SSV） method is developed by introducing a spectrally small amount of high order regularization which is only activated on high frequencies. The resulting SSV approximation is stable and convergent to the exact entropy solution. A Gegenbauer-Chebyshev post-processing for the SSV solution is proposed to remove the spurious oscillations at the disconti-nuities and recover accuracy from the spectral approximation. The ssv method is applied to the scahr periodic Burgers equation and the one-dimensional system of Euler equations of gas dynamics. The numerical results exhibit high accuracy and resolution to the exact entropy solution,展开更多
The evidence here provided shows that the thermodynamics of the second law, as currently understood, originated in a correction of the flaws affecting Clausius original work on this matter. The body of knowledge emerg...The evidence here provided shows that the thermodynamics of the second law, as currently understood, originated in a correction of the flaws affecting Clausius original work on this matter. The body of knowledge emerging from this correction has been here called post-Clausius’ thermodynamics. The said corrections, carried on with the intended goal of preserving the validity of Clausius’ main result, namely the law of increasing entropy, made use of a number of counterintuitive or logically at fault notions. A joint revision of Clausius’ and post-Clausius’ work on the second law, carried on retaining some of Clausius original notions, and disregarding others introduced by post-Clausius thermodynamics, led this author to results in direct contradiction to the law of increasing entropy. Among the key results coming out of this work we find the one stating that the total-entropy change for spontaneous thermodynamic processes is the result of the summation of the opposite-sign contributions coming from the entropic (energy degrading) and negentropic (energy upgrading) changes subsumed by any such process. These results also show, via the total-entropy change for a non-reversible heat engine, that negentropic thermodynamics subsumes post-Clausius thermodynamics as a special case.展开更多
文摘A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claims that all stable conformations are (local or global) minimizers of CGF. These are enough to give a unified explanations and mechanisms to many aspects of protein dynamics such as protein folding;allostery;denaturation;and intrinsically disordered proteins. Formulas of CGF in water environment had been derived via quantum statistics. Applications of them to soluble proteins are: docking Gibbs free energy difference formula and a practical way to search better docking site;single molecule binding affinity;predicting and explaining why structures of a monomeric globular protein looks like a globule and is tightly packed with a hydrophobic core;a representation of the hydrophobic effect;and a wholistic view to structures of water soluble proteins.
文摘In this paper, the super spectral viscosity （SSV） method is developed by introducing a spectrally small amount of high order regularization which is only activated on high frequencies. The resulting SSV approximation is stable and convergent to the exact entropy solution. A Gegenbauer-Chebyshev post-processing for the SSV solution is proposed to remove the spurious oscillations at the disconti-nuities and recover accuracy from the spectral approximation. The ssv method is applied to the scahr periodic Burgers equation and the one-dimensional system of Euler equations of gas dynamics. The numerical results exhibit high accuracy and resolution to the exact entropy solution,
文摘The evidence here provided shows that the thermodynamics of the second law, as currently understood, originated in a correction of the flaws affecting Clausius original work on this matter. The body of knowledge emerging from this correction has been here called post-Clausius’ thermodynamics. The said corrections, carried on with the intended goal of preserving the validity of Clausius’ main result, namely the law of increasing entropy, made use of a number of counterintuitive or logically at fault notions. A joint revision of Clausius’ and post-Clausius’ work on the second law, carried on retaining some of Clausius original notions, and disregarding others introduced by post-Clausius thermodynamics, led this author to results in direct contradiction to the law of increasing entropy. Among the key results coming out of this work we find the one stating that the total-entropy change for spontaneous thermodynamic processes is the result of the summation of the opposite-sign contributions coming from the entropic (energy degrading) and negentropic (energy upgrading) changes subsumed by any such process. These results also show, via the total-entropy change for a non-reversible heat engine, that negentropic thermodynamics subsumes post-Clausius thermodynamics as a special case.
