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

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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.

Introduction.-The \"classical theory of irreversible thermodynamics\"1 may be said to have its origin in the formulation of the \"reciprocity relations\" by Onsager.2 The basis of this theory may be summarized briefly as follows (for a complete discussion see works cited in ref. 1 and 2): in the limit of small excursions from thermodynamic equilibrium, changes in the properties of any system are described by certain formalized force8 and fluxe8. In general, the flux of any property (e.g., matter, heat, electricity, etc.) may be taken as linearly dependent upon all the forces (concentration or temperature gradients, potential differences, etc.). If, in this set of linear equations-called the \"phenomenological equations\"-the forces and fluxes are properly defined, the coefficient Li1 of the jth force in the equation for the ith flux must, according to the \"reciprocity relations,\" equal the coefficient Lit, defined in the same manner. The correct choice of these forces and fluxes is determined by the condition that the time rate of change of the entropy of the system be given by the sum over the products of each force by its corresponding flux. The application of this treatment to processes involving simultaneous gradients of temperature, concentration, chemical potential, or electrical potential has been uniformly successful, provided only that the gradients are sufficiently small, i.e., the system is nearly at equilibrium. Exactly how near the equilibrium state the system must be, however, in order that the postulated linearity will suffice as an adequate approximation is not always made clear; for most purely physical phenomena of this type, as, for example, Thompson and Peltier heats, it appears that the formulation is adequate under nearly all experimental conditions. In diffusion and chemical reaction, on the other hand, the several approximations described above are almost never satisfactory in cases of practical interest, and the deductions of this type of theory become, to a large extent, only academically interesting. It would appear that in these cases, at least, a higher degree of approximation in relating the forces and fluxes of a given system is required. Unfortunately, any attempt in this direction requires that the linear relation between forces and fluxes, and hence the symmetry properties of the matrix of phenomenological coefficients (the Onsager conditions), be given up, and the whole approach becomes impractically cumbersome. An additional problem arises from the fact that, strictly speaking, thermodynamic variables such as entropy which appear in the algebraic formulation are not well defined except at thermodynamic equilibrium, and their precise meaning becomes less clear the further the system deviates from this state. Any attempt to describe a nonequilibrium system in terms of purely thermodynamic variables must suffer from this logical difficulty, and it is not immediately apparent that there exists any way in which this conflict can be resolved within the framework of the classical theory of continuum thermohydrodynamics. On the other hand, there is quite general treatment of irreversible procsses based

Irreversible thermodynamics and rate theory.

Solutions of the simplified time-dependent Nernst-Planck electrodiffusion equations for various membrane models under the influence of a step voltage change are presented. Comparison of the results for a membrane with continuous sites to those for membranes with two, three or five intermediate sites shows little difference either qualitatively or quantitatively in the concentration of the diffusible ion inside the membrane, although some quantitative differences are evident in the calculated currents.

Ion flow through a membrane: concentration and current responses to a step potential change

Consideration has been given to two of the electronic repulsion integrals arising in the quantum‐mechanical energy calculation of the triatomic hydrogen molecular complex when no restrictions are placed on the effective nuclear charges of the composite atomic orbitals. The formulation of the integrals is first developed on a general basis and then restricted to the H3 molecule. The possibility of extension of the mathematical processes to similar electron interaction integrals in more complex molecules is pointed out. The integration formulas are given as rapidly converging series.

Evaluation of Some Electron Repulsion Integrals Needed in Molecular Quantum Mechanics. A Method of Calculation of Two Electron Multi‐Center Repulsion Integrals without the Use of the Neumann Expansion

Physical sciences contribute to biomedical research by introducing new investigative tools, instrumental methods, and physical and chemical techniques. Physical sciences also purvey principles and basic concepts such as thermodynamics, equilibrium theory, and reaction-rate theory. The role of the physical sciences in biomedical research also is to provide appropriate theoretical interpretations which will allow more than em- pirical utilization of the experimental data obtained using the physical methods. Few single events have had a greater mutual impact on the medical and physical sciences than Roentgen's discovery of X-rays. In the medical sciences radiology has achieved a prominent position in clinical diagnosis; in the physical sciences X-rays have disclosed information on the structure of the atom, and X-ray diffraction affords almost direct observation of molecular structure. In general, physical methods functioning as extensions ofhuman sense perception are performing expanding roles in basic and applied research and in diagnosis and treatment of disease. This article treats the physical methods of absorption spectroscopy, fluorescence, and optical rotatory dispersion as applied to the determina- tion of protein conformation. With these instruments, information on protein structure can be obtained and changes in protein conformation can be detected in media approximating that of the physiological state, and most important the means ofobservation does not affect the property under study. Emphasis will be placed on the interpretation ofexperimental

The Role of the Physical Sciences in Biomedical Research

https://www.pnas.org/content/pnas/43/5/421.full.pdf

Henry Eyring

Papers

Irreversible thermodynamics and rate theory.

Ion flow through a membrane: concentration and current responses to a step potential change

Evaluation of Some Electron Repulsion Integrals Needed in Molecular Quantum Mechanics. A Method of Calculation of Two Electron Multi‐Center Repulsion Integrals without the Use of the Neumann Expansion

The Role of the Physical Sciences in Biomedical Research

Strain electrometry and corrosion i. general considerations on interfacial electrical transients.