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Arieh Ben-Naim

Publications and source records attributed to Arieh Ben-Naim.

6 recordsLinked to original sources
arXiv2018

The lock and key model for Molecular Recognition. Is it time for a paradigm shift?

We review the standard lock and key (LK) model for binding small ligands to larger adsorbent molecule. We discuss three levels of the traditional LK model for binding. Within this model the binding constant or the Gibbs energy of the binding process is related to the total interaction energy between the ligand and the binding site of the adsorbent molecules. When solvent molecules are present, which is the case in all binding processes in biochemistry, we find that a major part of the Gibbs energy of binding could be due to interactions mediated through the solvent molecules. This finding could have major consequences to the applicability of the LK model in drug design, and perhaps require a shift in the prevailing paradigm in this field of research. Keywords: Lock and key model, Binding constant, solvent effect on binding, hydrophilic effect, molecular recognition.

physics.bio-ph↗
arXiv2018

On the Validity of the Assumption of Local Equilibrium in Non-Equilibrium Thermodynamics

The extension of equilibrium thermodynamics to non-equilibrium systems is based on the assumption of "local equilibrium," followed by the assumption that an entropy-density function may be defined, and that this entropy-density would have the same functional dependence on the local densities, (u,v,n), as the total entropy S on the variables (U,V,N). In this article we question the validity of all the assumptions made in the theory of non-equilibrium thermodynamics. We find that the assumption of "local equilibrium" is ill-founded, that it is not clear how to define an entropy-density function, and it is far from clear that such a function, if it exists at all could be integrated to obtain the so-called "entropy production" of the entire system. These findings shed serious doubt on the validity of applying thermodynamic theory to systems far from equilibrium systems.

physics.chem-ph↗
arXiv2017

Can entropy be defined for and the Second Law applied to the entire universe?

This article provides answers to the two questions posed in the title. It is argued that, contrary to many statements made in the literature, neither entropy, nor the Second Law may be used for the entire universe. The origin of this misuse of entropy and the second law may be traced back to Clausius himself. More resent (erroneous) justification is also discussed.

physics.chem-ph↗
arXiv2017

Is Entropy Associated with Time's Arrow?

We start with reviewing the origin of the idea that entropy and the Second Law are associated with the Arrow of Time. We then introduced a new definition of entropy based on Shannons Measure of Information, SMI. The SMI may be defined on any probability distribution, and therefore it is a very general concept. On the other hand entropy is defined on a very special set of probability distributions. More specifically the entropy of a thermodynamic system is related the probability distribution of locations and velocities or momenta of all the particles, which maximized the Shannon Measure of Information. As such, entropy is not a function of time. We also show that the H function, as defined by Boltzmann is an SMI but not entropy. Therefore, while the H-function, as an SMI may change with time, Entropy, as a limit of the SMI does not change with time.

physics.pop-ph↗