Euler characteristic and related measures for random geometric sets

By an elementary calculation we obtain the exact mean values of Minkowksi functionals for a standard model of percolating sets. In particular, a recurrence theorem for the mean Euler characteristic recently put forward is shown to be incorrect. Related previous mathematical work is mentioned. We also conjecture bounds for the threshold density of continuum percolation, which are associated with the Euler characteristic.     

A note on a result by M. Bognár concerning the Hahn--Mazurkiewicz Theorem

Summary In this note we use Theorem 2.4 in<span lang=EN-US style='font-size:10.0pt;mso-ansi-language:EN-US'>[1]to give a very short proof of a recent result due to M. Bognár (Theorem A in [3]). We also prove that Bognár's result is in fact equivalent to the classical Hahn-Mazurkiewicz Theorem. Finally we give generalizations in the non-compact setting.     

Finite-Dimensional Approximations for Scattering Theory Operators in the Wave-Packet Representation

We consider some types of packet discretization for continuous spectra in quantum scattering problems. As we previously showed, this discretization leads to a convenient finite-dimensional (i.e., matrix) approximation for integral operators in the scattering theory and allows reducing the solution of singular integral equations connected with the scattering theory to some suitable purely algebraic equations on an analytic basis. All singularities are explicitly singled out. Our primary emphasis is on realizing the method practically.     

Analogues of Coherent and Dissipative Structures in Social and Historical Processes

An analogy between social and hydrodynamic processes is developed. The relation of the state system to the passionarity theory suggested by L. N. Gumilev is discussed.     

Lemniscates and inequalities for the logarithmic capacities of continua

It is shown that if P(z) = z ⁿ + ? is a polynomial with connected lemniscate E(P) = {z: ¦P(z)¦ ≤ 1} and m critical points, then, for any n? m+1 points on the lemniscate E(P), there exists a continuum γ ? E(P) of logarithmic capacity cap γ ≤ 2^?1/n which contains these points and all zeros and critical points of the polynomial. As corollaries, estimates for continua of minimum capacity containing given points are obtained.     

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

COSMO-RS: A novel view to physiological solvation and partition questions

Both, dielectric continuum solvation models as well as surface or group based methods using polarity and lipophilicity parameters have been proven to be useful tools for the analysis of solvation and partition questions. For the first time, COSMO-RS provides an integrated theory, which combines the aspects of continuum solvation and surface interactions, and which ends up with chemical potentials of molecules in almost arbitrary solvents and mixtures. Due to its sound theoretical basis, COSMO-RS does not only provide a new quantitative access to solvation and partition properties in well defined solvents, but it also opens a novel view and gives a better understanding of the general problem of solvation. Finally, this allows for a generalisation of COSMO-RS to sophisticatedphysiological partition problems involving as complex phases as blood, brain, or cell membranes. The use of COSMO-RS for drug discovery and design is demonstrated by applications to blood-brain partition coefficients, and water solubility.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Solvent effects on 17O nuclear magnetic shielding: N-methylformamide in polar and apolar solutions

The solvent effect on ¹⁷O isotropic shielding was computed by different methods: the polarizable continuum model and a mixed approach, including a few real solvent molecules treated as the solute. The experimental data show that the behavior of protic and aprotic solvents is markedly different: we found that the continuum approach describes well the observed shielding at various dielectric constants for aprotic solvents, while the mixed procedure is needed when hydrogen bonds to the magnetic centre are present.Contribution to the Jacopo Tomasi Honorary Issue     

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001