There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.

https://science.sciencemag.org/content/sci/220/4598/671.full.pdf

Optimization by Simulated Annealing

The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

http://dns2.asia.edu.tw/~ysho/YSHO-English/1000%20WC/PDF/J%20Che%20Phy132,%20154104.pdf

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

http://webpages.icav.up.pt/PTDC/BIA-BEC/104097/2008/23.pdf

MRBAYES: Bayesian inference of phylogenetic trees

From the Publisher:
This is the first comprehensive treatment of feed-forward neural networks from the perspective of statistical pattern recognition. After introducing the basic concepts, the book examines techniques for modelling probability density functions and the properties and merits of the multi-layer perceptron and radial basis function network models. Also covered are various forms of error functions, principal algorithms for error function minimalization, learning and generalization in neural networks, and Bayesian techniques and their applications. Designed as a text, with over 100 exercises, this fully up-to-date work will benefit anyone involved in the fields of neural computation and pattern recognition.

/pdf/neural-networks-for-pattern-recognition-34puigiau1.pdf

Neural networks for pattern recognition

We make an analogy between images and statistical mechanics systems. Pixel gray levels and the presence and orientation of edges are viewed as states of atoms or molecules in a lattice-like physical system. The assignment of an energy function in the physical system determines its Gibbs distribution. Because of the Gibbs distribution, Markov random field (MRF) equivalence, this assignment also determines an MRF image model. The energy function is a more convenient and natural mechanism for embodying picture attributes than are the local characteristics of the MRF. For a range of degradation mechanisms, including blurring, nonlinear deformations, and multiplicative or additive noise, the posterior distribution is an MRF with a structure akin to the image model. By the analogy, the posterior distribution defines another (imaginary) physical system. Gradual temperature reduction in the physical system isolates low energy states (``annealing''), or what is the same thing, the most probable states under the Gibbs distribution. The analogous operation under the posterior distribution yields the maximum a posteriori (MAP) estimate of the image given the degraded observations. The result is a highly parallel ``relaxation'' algorithm for MAP estimation. We establish convergence properties of the algorithm and we experiment with some simple pictures, for which good restorations are obtained at low signal-to-noise ratios.

/pdf/stochastic-relaxation-gibbs-distributions-and-the-bayesian-4c0mbkv82j.pdf

Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images

A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two‐dimensional rigid‐sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four‐term virial coefficient expansion.

/pdf/equation-of-state-calculations-by-fast-computing-machines-3uajhlns3j.pdf

Equation of state calculations by fast computing machines

Adsorption of Gases in Multimolecular Layers

On a Theory of the van der Waals Adsorption of Gases

In a previous paper (Jahn and Teller 1937) the following theorem was established: A configuration of a polyatomic molecule for an electronic state having orbital degeneracy cannot be stable with respect to all displacements of the nuclei unless in the original configuration the nuclei all lie on a straight line. The proof given of this theorem took no account of the electronic spin, and in the present paper the justification of this is investigated. An extension of the theorem to cover additional degeneracy arising from the spin is established, which shows that if the total electronic state of orbital and spin motion is degenerate, then a non-linear configuration of the molecule will be unstable unless the degeneracy is the special twofold one (discussed by Kramers 1930) which can occur only when the molecule contains an odd number of electrons. The additional instability caused by the spin degeneracy alone, however, is shown to be very small and its effect for all practical purposes negligible. The possibility of spin forces stabilizing a non-linear configuration which is unstable owing to orbital degeneracy is also investigated, and it is shown that this is not possible except perhaps for molecules containing heavy atoms for which the spin forces are large. Thus whilst a symmetrical nuclear configuration in a degenerate orbital state might under exceptional circumstances be rendered stable by spin forces, it is not possible for the spin-orbit interaction to cause instability of an orbitally stable state. 1—General theorem for molecules with spin Just as before we must see how the symmetry of the molecular framework determines whether the energy of a degenerate electronic state with spin depends linearly upon nuclear displacements. This is again determined by the existence of non-vanishing perturbation matrix elements which are linear in the nuclear displacements. These matrix elements are integrals involving the electronic wave functions with spin and the nuclear dis­placements, and we deduce as before from their transformation properties whether for a given molecular symmetry they can be different from zero.

Edward Teller

Papers

Equation of state calculations by fast computing machines

Adsorption of Gases in Multimolecular Layers

On a Theory of the van der Waals Adsorption of Gases

Stability of Polyatomic Molecules in Degenerate Electronic States. I. Orbital Degeneracy

Interaction of the van der Waals Type Between Three Atoms