Projection of a quantum state on eigenstates of average Hamiltonian.

A scheme for projecting an arbitrary quantum state on eigenstates of average Hamiltonian is described. As an experimental example, projection on entangled Bell states, which are eigenstates of specially constructed average Hamiltonian, is demonstrated for a system of two dipolar-coupled nuclear spins. The results of a direct and time-reversed evolution are added to average out the coherences between different eigenstates and accomplish the projection.

Ab initio study of ionic liquids by KS-DFT/3D-RISM-KH theory.

Properties of molecules solvated in ionic liquids (ILs) are strongly affected by solvent environment. For this reason, to give reliable results, ab initio calculations on solutes in ILs, including ions constituting ionic liquid itself, have to self-consistently account for the change of both electronic and classical solvation structure in ILs. Here, we study the electronic structure of the methyl-methylimidazolium ion in the bulk liquid of [mmim][Cl] by using the self-consistent field coupling of Kohn-Sham density functional theory and three-dimensional molecular theory of solvation (aka 3D-RISM) with the closure approximation of Kovalenko and Hirata. The KS-DFT/3D-RISM-KH method yields the 3D distribution of the IL solvent species around the [mmim] solute, underlying the most important peculiarities of this kind of systems such as the stacking interaction between neighboring cations, and reproduces the enhancement of the dipole moment resulting from the polarization of the cation by the solvent in a very good agreement with the results of an ab initio MD calculation. The KS-DFT/3D-RISM-KH method offers an accurate and computationally efficient procedure to perform ab initio calculations on species solvated in ionic liquids.

Structural information content of networks: graph entropy based on local vertex functionals.

In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties.

Transient finite element analysis of electric double layer using Nernst-Planck-Poisson equations with a modified Stern layer.

A finite element implementation of the transient nonlinear Nernst-Planck-Poisson (NPP) and Nernst-Planck-Poisson-modified Stern (NPPMS) models is presented. The NPPMS model uses multipoint constraints to account for finite ion size, resulting in realistic ion concentrations even at high surface potential. The Poisson-Boltzmann equation is used to provide a limited check of the transient models for low surface potential and dilute bulk solutions. The effects of the surface potential and bulk molarity on the electric potential and ion concentrations as functions of space and time are studied. The ability of the models to predict realistic energy storage capacity is investigated. The predicted energy is much more sensitive to surface potential than to bulk solution molarity.

A multivariate test for similarity of two dissolution profiles.

A multivariate test of size a for assessing the similarity of two dissolution profiles is proposed. The inferential procedure is developed by using the approach for the common mean problem in a multivariate setup due to Halperin (1961). The performance of the proposed method is compared with Intersection Union Test as well as f2 criterion recommended by the FDA through a simulation study. All the methods are illustrated with real examples.

QSPR calculation of normal boiling points of organic molecules based on the use of correlation weighting of atomic orbitals with extended connectivity of zero- and first-order graphs of atomic orbitals.

We report the results of a calculation of the normal boiling points of a representative set of 200 organic molecules through the application of QSPR theory. For this purpose we have used a particular set of flexible molecular descriptors, the so called Correlation Weighting of Atomic Orbitals with Extended Connectivity of Zero- and First-Order Graphs of Atomic Orbitals. Although in general the results show suitable behavior to predict this physical chemistry property, the existence of some deviant behaviors points to a need to complement this index with some other sort of molecular descriptors. Some possible extensions of this study are discussed.

A QSAR toxicity study of a series of alkaloids with the lycoctonine skeleton.

A QSAR toxicity analysis has been performed for a series of 19 alkaloids with the lycoctonine skeleton. GA-MLRA (Genetic Algorithm combined with Multiple Linear Regression Analysis) technique was applied for the generation of two types of QSARs: first, models containing exclusively 3D-descriptors and second, models consisting of physicochemical descriptors. As expected, 3D-descriptor QSARs have better statistical fits. Physicochemical-descriptor containing models, that are in a good agreement with the mode of toxic action exerted by the alkaloids studied, have also been identified and discussed. In particular, TPSA (Topological Polar Surface Area) and nC=O (number of -C(O)- fragments) parameters give the best statistically significant mono- and bidescriptor models (when combined with lipophilicity, MlogP) confirming the importance of H-bonding capability of the alkaloids for binding at the receptor site.

Arithmetic inside the universal genetic code.

The first information system emerged on the earth as primordial version of the genetic code and genetic texts. The natural appearance of arithmetic power in such a linguistic milieu is theoretically possible and practical for producing information systems of extremely high efficiency. In this case, the arithmetic symbols should be incorporated into an alphabet, i.e. the genetic code. A number is the fundamental arithmetic symbol produced by the system of numeration. If the system of numeration were detected inside the genetic code, it would be natural to expect that its purpose is arithmetic calculation e.g., for the sake of control, safety, and precise alteration of the genetic texts. The nucleons of amino acids and the bases of nucleic acids seem most suitable for embodiments of digits. These assumptions were used for the analyzing the genetic code. The compressed, life-size, and split representation of the Escherichia coli and Euplotes octocarinatus code versions were considered simultaneously. An exact equilibration of the nucleon sums of the amino acid standard blocks and/or side chains was found repeatedly within specified sets of the genetic code. Moreover, the digital notations of the balanced sums acquired, in decimal representation, the unique form 111, 222...., 999. This form is a consequence of the criterion of divisibility by 037. The criterion could simplify some computing mechanism of a cell if any and facilitate its computational procedure. The cooperative symmetry of the genetic code demonstrates that possibly a zero was invented and used by this mechanism. Such organization of the genetic code could be explained by activities of some hypothetical molecular organelles working as natural biocomputers of digital genetic texts. It is well known that if mutation replaces an amino acid, the change of hydrophobicity is generally weak, while that of size is strong. The antisymmetrical correlation between the amino acid size and the degeneracy number is known as well. It is shown that these and some other familiar properties may be a physicochemical effect of arithmetic inside the genetic code. The "frozen accident" model, giving unlimited freedom to the mapping function, could optimally support the appearance of both arithmetic symbols and physicochemical protection inside the genetic code.

Multiple grid methods for classical molecular dynamics.

Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.

PCSB--a program collection for structural biology and biophysical chemistry.

We present the first package of Java classes specifically aimed at the handling of structural and biophysical problems. To enable object-oriented programming a basis of fundamental Java classes is required which deals with basic operations of vectors, matrices, amino acid sequences, crystal symmetries and PDB files. Five classes, which carry out these basic operations, were constructed and bundled together with several utility functions in the PCSB package. Furthermore, to demonstrate their applicability and to obtain programs handling common tasks in structural laboratories, we present the first six applications of PCSB. All applications are portable to different platforms and require only the Java Runtime Environment to be installed on the system. available as PDF file.

An analysis of protein folding type prediction by seed-propagated sampling and jackknife test.

In the development of methodology for statistical prediction of protein folding types, how to test the predicted results is a crucial problem. In addition to the resubstitution test in which the folding type of each protein from a training set is predicted based on the rules derived from the same set, cross-validation tests are needed. Among them, the single-test-set method seems to be least reliable due to the arbitrariness in selecting the test set. Although the leaving-one-out (or jackknife) test is more objective and hence more reliable, it may cause a severe information loss by leaving a protein in turn out of the training set when its size is not large enough. In order to overcome the above drawback, a seed-propagated sampling approach is proposed that can be used to generate any number of simulated proteins with a desired type based on a given training set database. There is no need to make any predetermined assumption about the statistical distribution function of the amino acid frequencies. Combined with the existing cross-validation methods, the new technique may provide a more objective estimation for various protein-folding-type prediction methods.