A modification of the nudged elastic band method for finding minimum energy paths is presented. One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#

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A climbing image nudged elastic band method for finding saddle points and minimum energy paths

The phenomenon of growth, decline and death—aging—has been the source of considerable speculation (1, 8, 10). This cycle seems to be a more or less direct function of the metabolic rate and this in turn depends on the species (animal or plant) on which are superimposed the factors of heredity and the effects of the stresses and strains of life—which alter the metabolic activity. The universality of this phenomenon suggests that the reactions which cause it are basically the same in all living things. Viewing this process in the light of present day free radical and radiation chemistry and of radiobiology, it seems possible that one factor in aging may be related to deleterious side attacks of free radicals (which are normally produced in the course of cellular metabolism) on cell constituents.* Irradiation of living things induces mutation, cancer, and aging (9). Inasmuch as these also arise spontaneously in nature, it is natural to inquire if the processes might not be similar. It is believed that one mechanism of irradiation effect is through liberation of OH and HO 2 radicals (12). There is evidence, although indirect, that these two highly active free radicals are produced normally in living systems. In the first place, free radicals are present in living cells; this was recently demonstrated in vivo by a paramagnetic resonance absorption method (3). Further, it was shown that the concentration of free radicals increased with increasing metabolic activity in conformity with the postulates set forth some years ago that free radicals were involved in biologic oxidation-reduction reactions (11, 13). Are some of these free radicals OH and/or HO2, or radicals of a similar high order of reactivity, and where might they arise in the cell? The most likely source of OH and HO2 radicals, at least in the animal cell, would be the interaction of the respiratory enzymes involved

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Aging: A Theory Based on Free Radical and Radiation Chemistry

/pdf/brownian-motion-in-a-field-of-force-and-the-diffusion-model-2nbbzrdubb.pdf

Brownian motion in a field of force and the diffusion model of chemical reactions

Stanford Moore, William Stein, and Anfinsen were awarded the Nobel Prize in Chemistry in 1972 for \"their contribution\n to the understanding of the connection between chemical structure and catalytic activity of the active center of the ribonuclease\n molecule.\" In his Nobel Lecture, Anfinsen provided a sketch of the rich history of research that provided the foundation\n for his work on protein folding and the \"Thermodynamic Hypothesis,\" and outlined potential avenues of current and\n future scientific exploration.

https://web.iitd.ac.in/~amittal/1973_Anfinsen_Science.pdf

Principles that Govern the Folding of Protein Chains

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

The significant structure theory of liquids is tested by evaluating the radial distribution function. The calculations are based on face-centered cubic quasi-lattice structure, and the fluctuation in volume is used to describe the thermal displacements of molecules. It is shown that the local structure of liquids has inhomogeneous distributions. The correlation at long ranges becomes negligible because of the fluidized vacancies in our model. The calculations are performed for liquid argon, and the results are in good agreement with experiments.

https://www.pnas.org/content/pnas/78/11/6588.full.pdf

Radial distribution function of liquid argon according to significant structure theory

Rheology. Theory and Applications.

A theory of liquids designed to account for rate as well as thermodynamic properties is given. By considering the molecules of the liquid to be distributed at random among solid‐like and gas‐like equilibrium positions, where the introduction of a new equilibrium position requires a volume increase of about ⅛ the molecular volume, it is possible to derive an explicit partition function for liquids. The model embodies the features previously used in the theory of viscosity and diffusion. The thermodynamic properties of argon, nitrogen and benzene are calculated and compared with experiment.

A Partition Function for Normal Liquids

The historical development of the rate theory of viscosity is briefly reviewed. The Ree‐Eyring equation of generalized viscosity, η= ∑ n=1m(xnβn/αn)(sinh−1βnṡ/βnṡ) is applied successfully in a variety of cases. (For the definitions of the symbols in this equation, reference is made to the text.) We develop here a new method for determining the parameters xn/αn and βn in Eq. (A). According to the method, these parameters are uniquely determined. When we used the parameters determined by the new method, the viscosities for solutions of poly‐γ‐benzyl‐l‐glutamate were calculated from Eq. (A). It is found that Eq. (A) is much superior to other frequently applied viscosity equations.Upon calculating the Newtonian viscosities ηs for fairly concentrated solutions of polyacrylonitrile and of nitrated pine pulp, the following empirical formula is found: ηs≃KC2Mβp12. Here K is a characteristic constant for a solution; C the concentration; M the molecular weight; and βp is the ``principal'' relaxation time. In dilute...

Theory of Non‐Newtonian Flow. III. A Method for Analyzing Non‐Newtonian Flow Curves

By ALVA BENNETT, HELEN JUPNIK, HAROLD OSTERBERG, and OSCAR W. RICHARDS, all with American Optical Company. This new book combines the work of four scientists who have made outstanding contributions to the theory, instrumentation, and application of the phase microscope. It describes phase microscopy fully, including principles, operation, adjustments, use, and various applications. 1951. 320 pages. $7.50.

Henry Eyring

Papers

Radial distribution function of liquid argon according to significant structure theory

Rheology. Theory and Applications.

A Partition Function for Normal Liquids

Theory of Non‐Newtonian Flow. III. A Method for Analyzing Non‐Newtonian Flow Curves

Fundamental principles of polymerization