The Second Law, Gibbs Free Energy, Geometry, and Protein Folding

2014 ◽  
Vol 3 (3) ◽  
pp. 278-285
Author(s):  
Yi Fang

The fundamental physical law of protein folding is the second law of thermodynamics. The key to solve proteinfolding problem is to derive an analytic formula of the Gibbs free energy. It has been overdue for too long. Let U be a monomeric globular protein whose M atoms 1 M a are classified into hydrophobicity classes H H , ,H 1H 2.

Author(s):  
A. M. Savchenko ◽  
Yu. V. Konovalov ◽  
A. V. Laushkin

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.


Author(s):  
Claudio Giorgi ◽  
Angelo Morro

AbstractThe purpose of the paper is to establish vector-valued rate-type models for the hysteretic properties in deformable ferroelectrics within the framework of continuum thermodynamics. Unlike electroelasticity and piezoelectricity, in ferroelectricity both the polarization and the electric field are simultaneously independent variables so that the constitutive functions depend on both. This viewpoint is naturally related to the fact that an hysteresis loop is a closed curve in the polarization–electric field plane. For the sake of generality, the deformation of the material and the dependence on the temperature are allowed to occur. The constitutive functions are required to be consistent with the principle of objectivity and the second law of thermodynamics. Objectivity implies that the constitutive equations are form invariant within the set of Euclidean frames. Among other results, the second law requires a general property on the relation between the polarization and the electric field via a differential equation. This equation shows a dependence fully characterized by two quantities: the free energy and a function which is related to the dissipative character of the hysteresis. As a consequence, different hysteresis models may have the same free energy. Models compatible with thermodynamics are then determined by appropriate selections of the free energy and of the dissipative part. Correspondingly, major and minor hysteretic loops are plotted.


Entropy ◽  
2022 ◽  
Vol 24 (1) ◽  
pp. 94
Author(s):  
Mohammad Razavi ◽  
Seyed Majid Saberi Fathi ◽  
Jack Adam Tuszynski

The underlying mechanism determining the size of a particular cell is one of the fundamental unknowns in cell biology. Here, using a new approach that could be used for most of unicellular species, we show that the protein synthesis and cell size are interconnected biophysically and that protein synthesis may be the chief mechanism in establishing size limitations of unicellular organisms. This result is obtained based on the free energy balance equation of protein synthesis and the second law of thermodynamics. Our calculations show that protein synthesis involves a considerable amount of entropy reduction due to polymerization of amino acids depending on the cytoplasmic volume of the cell. The amount of entropy reduction will increase with cell growth and eventually makes the free energy variations of the protein synthesis positive (that is, forbidden thermodynamically). Within the limits of the second law of thermodynamics we propose a framework to estimate the optimal cell size at division.


2017 ◽  
Vol 16 (04) ◽  
pp. 1771001 ◽  
Author(s):  
Kyle M. Sundqvist ◽  
David K. Ferry ◽  
Laszlo B. Kish

In his seminal paper, Chua presented a fundamental physical claim by introducing the memristor, “The missing circuit element”. The memristor equations were originally supposed to represent a passive circuit element because, with active circuitry, arbitrary elements can be realized without limitations. Therefore, if the memristor equations do not guarantee that the circuit element can be realized by a passive system, the fundamental physics claims about the memristor as “missing circuit element” loses all its weight. The question of passivity/activity belongs to physics thus we incorporate thermodynamics into the study of this problem. We show that the memristor equations are physically incomplete regarding the problem of passivity/activity. As a consequence, the claim that the present memristor functions describe a passive device lead to unphysical results, such as violating the Second Law of thermodynamics, in infinitely large number of cases. The seminal memristor equations cannot introduce a new physical circuit element without making the model more physical such as providing the Fluctuation–Dissipation Theory of memristors.


2021 ◽  
Vol 22 (17) ◽  
pp. 9653
Author(s):  
Jiacheng Li ◽  
Chengyu Hou ◽  
Xiaoliang Ma ◽  
Shuai Guo ◽  
Hongchi Zhang ◽  
...  

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.


2010 ◽  
Vol 24 (10) ◽  
pp. 1333-1359 ◽  
Author(s):  
GERHARD GERLICH ◽  
RALF D. TSCHEUSCHNER

It is shown that the notorious claim by Halpern et al. recently repeated in their comment that the method, logic, and conclusions of our "Falsification Of The CO2 Greenhouse Effects Within The Frame Of Physics" would be in error has no foundation. Since Halpern et al. communicate our arguments incorrectly, their comment is scientifically vacuous. In particular, it is not true that we are "trying to apply the Clausius statement of the Second Law of Thermodynamics to only one side of a heat transfer process rather than the entire process" and that we are "systematically ignoring most non-radiative heat flows applicable to Earth's surface and atmosphere". Rather, our falsification paper discusses the violation of fundamental physical and mathematical principles in 14 examples of common pseudo-derivations of fictitious greenhouse effects that are all based on simplistic pictures of radiative transfer and their obscure relation to thermodynamics, including but not limited to those descriptions (a) that define a "Perpetuum Mobile Of The 2nd Kind", (b) that rely on incorrectly calculated averages of global temperatures, (c) that refer to incorrectly normalized spectra of electromagnetic radiation. Halpern et al. completely missed an exceptional chance to formulate a scientifically well-founded antithesis. They do not even define a greenhouse effect that they wish to defend. We take the opportunity to clarify some misunderstandings, which are communicated in the current discussion on the non-measurable, i.e., physically non-existing influence of the trace gas CO2 on the climates of the Earth.


Sign in / Sign up

Export Citation Format

Share Document