free energy

Free energy simulations
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Monte Carlo or molecular dynamics simulations involve the numerical determinations of the statistical thermodynamics and related structural, energetics and (in the case of MD) dynamical properties of an atomic or molecular assembly on a high speed digital computer

Autoencoders, minimum description length and Helmholtz free energy
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An autoencoder network uses a set of recognition weights to convert an input vector into a code vector. It then uses a set of generative weights to convert the code vector into an approximate reconstruction of the input vector. We derive an objective function for training

Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
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Abstract The Weighted Histogram Analysis Method (WHAM) of Ku et al.(J. Comput. Chem. 13 (1992) 1011), is used to combine free energy perturbations with umbrella sampling calculations. The formulation is general and allows optimal calculation of the free This book examines a system of parabolic-elliptic partial differential equations proposed in mathematical biology, statistical mechanics, and chemical kinetics. In the context of biology, this system of equations describes the chemotactic feature of cellular slime molds and also

Free - energy determinants of alpha-helix insertion into lipid bilayers
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A detailed treatment is provided of the various free - energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving

Free - energy calculations
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Techniques to compute absolute free energies of classical many-body systems are discussed with special emphasis on those techniques that can be used to map the phase diagram of solids and liquids. Recent technical advances in the study of multi-component

The free energy of thiol ester hydrolysis
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Thiol esters, such as aeetyl coenzyme A, the principal biological carrier of activated acetyl groups, have generally been supposed to be energy -rich compounds; ie to have a free energy of hydrolysis at pH 7.0 in the range of-7000 to-1 000 calories per mole. The

Stable fixed points of loopy belief propagation are local minima of the bethe free energy
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We extend recent work on the connection between loopy belief propagation and the Bethe free energy . Constrained minimization of the Bethe free energy can be turned into an unconstrained saddle-point problem. Both converging double-loop algorithms and standard

The generalized distributive law and free energy minimization
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Page 1. The Generalized Distributive Law and Free Energy Minimization Srinivas M. Aji Robert J. McEliece Rainfinity, Inc. Caltech 1 2 3 4 5 6 1 4 2 5 3 6 1 2 3 4 5 6 Claude E. Shannon Symposium Dedication University of California San Diego October 1 2001

A chemical equilibrium algorithm for highly non-ideal multiphase systems: free energy minimization
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A method is presented for calculating equilibrium phase assemblages in very nonideal systems. It be applied to any system for which a thermodynamically consistent model of the free energy which satisfies the usual Maxwell relations and convexity criterion is

Surface free energy determination by contact angle measurements a comparison of various approaches
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One of the parameters characterizing the surfaces of materials is the surface free energy . The most common way to determine its value is to measure the surface tension by the sessile drop method. In this case a contact angle between the surface and the edge of

A generalised diffusion equation for phase separation of a multi-component mixture with interfacial free energy
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A nonlinear multicomponent diffusion equation incorporating uphill diffusion and capillarity effects is studied. In the binary case the problem is the Cahn-Hilliard equation for a regular solution free energy . Global existence is proved. It is shown that the deep quench limit is a

Undergraduate students understandings of entropy and Gibbs free energy
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For many students, the study of thermodynamics presents problems; it is seen as consisting almost entirely of equations which are not understood and which have to be learned by rote in order to do calculations and to pass examinations. This paper describes part of a study

Measurement of structural and free energy changes in hemoglobin by hydrogen exchange methods
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When you can measure something and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory sort. It be the beginning of knowledge, but you have Protein engineering is being used increasingly to study the fine details of the structure and activity of enzymes. How can small effects of mutation on activity be reliably quantified and systematized, and artefacts be recognized A traditional means of doing this in organic Understanding the static and even more the dynamical behavior of complex physical systems is one of the most challenging problems of current research in physics, chemistry and biology. Paradigmatic examples of condensed matter physics are spin glasses and

Rate of shrinkage of tendon collagen heat, entropy and free energy of activation of the shrinkage of untreated tendon. Effect of acid salt, pickle, and tannage
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The shrinkage of leather and collagen, when heated in an aqueous medium, has been the subject of extensive investigations. The history of such studies is outlined adequately by: Mc- Laughlin and Thois 1 and Hobbs . The measurement of shrinkage temperatures

Heat and free energy of formation of carbon dioxide, and of the transition between graphite and diamond
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There are reviewed the existing data on the entropies of oxygen, carbon dioxide, graphite, and diamond, and those on the heats of combustion of natural and artificial graphite and of diamond, includin § the results recently obtained in a joint investigation by the National Perturbation theory is one of the oldest and most useful, general techniques in applied mathematics. Its initial applications to physics were in celestial mechanics, and its goal was to explain how the presence of bodies other than the sun perturbed the elliptical orbits of