Free energy, entropy, and internal energy of hydrophobic interactions: Computer simulations

1993 ◽  
Vol 98 (8) ◽  
pp. 6445-6454 ◽  
Author(s):  
David E. Smith ◽  
A. D. J. Haymet
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Computer Simulations ◽  
Hydrophobic Interactions ◽  
Energy Entropy

THERMAL FLUCTUATIONS IN CASIMIR PISTONS

2012 ◽  
Vol 14 ◽  
pp. 425-434
Author(s):  
M. LOMNITZ ◽  
C. VILLARREAL
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Thermal Fluctuations ◽  
Energy Entropy

We present analytical and simple expressions to determine the free energy, internal energy, entropy, as well as the pressure acting at the interface of a perfectly conducting rectangular Casimir piston. We show that infrared divergencies linear in temperature become cancelled within the piston configuration, and show a continuous behavior consistent with intuitive expectations.

First and second laws of thermodynamics: relationship, “inconsistency”, hidden effects

2020 ◽  
pp. 63-73
Author(s):  
A. M. Savchenko ◽  
Yu. V. Konovalov ◽  
A. V. Laushkin
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Second Law Of Thermodynamics ◽  
Second Law ◽  
Entropy Of Mixing ◽  
Ideal Mixing ◽  
Laws Of Thermodynamics ◽  
Relationship Of ◽  
The Relationship

The relationship of the first and second laws of thermodynamics based on their energy nature is considered. It is noted that the processes described by the second law of thermodynamics often take place hidden within the system, which makes it difficult to detect them. Nevertheless, even with ideal mixing, an increase in the internal energy of the system occurs, numerically equal to an increase in free energy. The largest contribution to the change in the value of free energy is made by the entropy of mixing, which has energy significance. The entropy of mixing can do the job, which is confirmed in particular by osmotic processes.

Studies in the Vulcanization of Rubber. I—Thermochemistry of Vulcanization of Rubber

1930 ◽  
Vol 3 (4) ◽  
pp. 631-639
Author(s):  
John T. Blake
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Chemical Reaction ◽  
Effect Of Temperature ◽  
Heat Of Reaction ◽  
Chemical Affinity ◽  
Direct Measure ◽  
Total Change

Abstract WHEN a chemical reaction takes place, it is usually accompanied by an absorption or evolution of heat. The amount of the heat interchange is not a direct measure of the chemical affinity involved in the reaction, nor is it a measure of the free energy of the reaction. The heat of reaction, however, is a measure of the total change in internal energy and is of importance, therefore, in calculating the effect of temperature on a reaction and in elucidating the mechanism of it.

scholarly journals Standardizing a Protocol for Studying pH-dependent Transient Conformations using Computer Simulations

2020 ◽  
Author(s):  
Ruhar Singh ◽  
Andrew M Lynn
Keyword(s):  
Free Energy ◽  
High Temperature ◽  
Protein Stability ◽  
Computer Simulations ◽  
Energy Landscape ◽  
Alpha Helix ◽  
Free Energy Landscape ◽  
Pka Values ◽  
Constant Ph ◽  
Ph Dependent

1.ABSTRACTUnderstanding pH-dependent protein stability is important in biological - transport, storage, and delivery, in vivo conditions such as aggregation potential in neurodegenerative disease, and in studying the folding/unfolding of proteins. Using computer simulations, we can replace complex experimental determination and provide an atomistic-level interpretation of the cause and effect of pH on protein stability. Here, we standardize a method that provides a framework through which we examined pH-dependent transient conformations during unfolding simulations of proteins. Constant pH simulations utilized in the prediction of pKa values of charged groups of the peptide. The calculated pKa values employed to fix the appropriate protonation state of the amino acid to simulate the effect of pH on the system. Trajectories from multiple high-temperature MD simulations of the protein sample the conformational space during unfolding for a given pH state. The ensemble of conformations is analyzed from its free energy landscape to identify transient and stable conformations both at a given pH and between different pH. As a test system RN80, a protein fragment analog of the C-peptide from bovine pancreatic ribonuclease-A used to measure the accuracy of the predictions from simulations. Experimental measures of the helix content determined as a function of pH display a bell-shaped curve, i.e. RN80 alpha-helix formation is maximum at pH5 with a subsequent loss in helicity at higher and lower pH. The main forces stabilizing the alpha-helix are a salt-bridge formed between Glu-2 and Arg-10 and cation-pi-interaction between Tyr-8 and His-12. Our protocol includes constant pH calculations, optimal high-temperature simulations, and Free Energy landscape analysis exhibited the agreement with the experimental observations.

scholarly journals Free energy versus internal energy potential for heavy quark systems at finite temperature

2014 ◽  
Vol 931 ◽  
pp. 607-611
Author(s):  
Taesoo Song ◽  
Su Houng Lee ◽  
Kenji Morita ◽  
Che Ming Ko
Keyword(s):  
Free Energy ◽  
Heavy Quark ◽  
Internal Energy ◽  
Finite Temperature ◽  
Energy Potential
Sign in / Sign up

Export Citation Format

Share Document