Tomaž Mohorič

QAL : A query algebra of complex objects

Abstract The main motivation for the development of a query algebra of complex objects QAL is the study of the operations needed to query the structural aspects of object-oriented databases which are due to the advantages of the object-oriented database model over conventional relational and functional database models. The basic operations of the QAL query algebra evolved from relational algebras and the FQL family of functional query languages by refining their operations for the manipulation of objects. In order to support the features specific to object-oriented data models, QAL offers: (i) a set of operations which provide the means for querying conceptual schemata and (ii) an operation which provides a simple and efficient way of querying nested components of complex objects. We show through a case-study consisting of a comprehensive set of examples how these operations can be employed to express a class of queries specific to object-oriented databases

Effects of the translational and rotational degrees of freedom on the hydration of simple solutes

Molecular dynamics simulations with separate thermostats for rotational and translational motion were used to study the effect of these degrees of freedom on the structure of water around model solutes. To describe water molecules we used the SPC/E model. The simplest solute studied here, the hydrophobe, was represented as a Lennard-Jones particle. Since direct interaction between the hydrophobe and water molecules has no angular dependence the influence of the increase of the rotational temperature on the solvation of a hydrophobe is only indirect. In the next step the central solute was assumed to be charged with either a positive or a negative charge to mimic an ion in water. Hence, depending on the charge of the ion, the neighboring water molecules assumed different angular distributions. The principal conclusions of this work are: (i) an increase of the translational temperature always decreases the height of the first peak in the solute-water radial distribution function; (ii) an increase of the rotational temperature yields an increase in the first peak in the solute-water radial distribution function for hydrophobes and cations; (iii) in contrast to this, the solvation peak decreases around ions with sufficiently large negative charge; and (iv) an increase of the rotational temperature affects cations in an opposite way to anions. For this reason complex molecules with a small net charge may not be very sensitive to variation of the rotational temperature.

Fast rotational motion of water molecules increases ordering of hydrophobes in solutions and may cause hydrophobic chains to collapse

Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of waters rotational motion on the interaction among Lennard-Jones solutes. The situation with rotational temperature higher than the translational one (TR > TT) is mimicking the effects of microwaves on model solutions. Molecular dynamics simulations suggest that solutions of Lennard-Jones solutes become increasingly more structured with the rise in TR, while keeping the TT constant. This is evidenced by an increase of the first and the second peak of the solute-solute radial distribution function. In addition, the first peak moves toward slightly larger distances; the effect seems to be caused by the destabilization of water molecules in the first hydration shell around hydrophobic solutes. More evidence of strong effects of the rotationally excited water is provided by the simulations of short hydrophobic polymers, which upon an increase in TR assume more compact conformations. In these simulations, we see the re-distribution of water molecules, which escape from hydrophobic pockets to better solvate the solvent exposed monomers.

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

The application of the integral equation theory to study the hydrophobic interaction

The Wertheims integral equation theory was tested against newly obtained Monte Carlo computer simulations to describe the potential of mean force between two hydrophobic particles. An excellent agreement was obtained between the theoretical and simulation results. Further, the Wertheims integral equation theory with polymer Percus-Yevick closure qualitatively correctly (with respect to the experimental data) describes the solvation structure under conditions where the simulation results are difficult to obtain with good enough accuracy.

Dynamic Assembly of Magnetic Colloidal Vortices

Magnetic colloids in external time-dependent fields are subject to complex induced many-body interactions governing their self-assembly into a variety of equilibrium and out-of-equilibrium structures such as chains, networks, suspended membranes, and colloidal foams. Here, we report experiments, simulations, and theory probing the dynamic assembly of superparamagnetic colloids in precessing external magnetic fields. Within a range of field frequencies, we observe dynamic large-scale structures such as ordered phases composed of precessing chains, ribbons, and rotating fluidic vortices. We show that the structure formation is inherently coupled to the buildup of torque, which originates from internal relaxation of induced dipoles and from transient correlations among the particles as a result of short-lived chain formation. We discuss in detail the physical properties of the vortex phase and demonstrate its potential in particle-coating applications.

Microwave irradiation affects ion pairing in aqueous solutions of alkali halide salts

Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of waters rotational motion on the ion pairing of ionic solutes in aqueous solutions. The situation with rotational temperature higher than the translational one, Trot>Ttrs, is mimicking the non-equilibrium effects of microwaves on model solutions of alkali halide salts. The simulations reveal that an increase in the rotational temperature at constant translational temperature exerts significant changes in the structure of the solution. The latter are reflected in increased pairing of the oppositely charged ions, which can be explained by the weaker ability of rotationally excited water to screen and separate the opposite charges. It seems that Collins law of matching water affinities retains its validity also in the non-equilibrium situation where the rotational temperature exceeds the translational one. On the other hand, the equilibrium effect (i.e., an increase in the solutions overall temperature T≡Trot = Ttrs) favors the formation of small-small (NaCl), while it has a little effect on large-large (CsI) ion pairs. This is in accordance with water becoming less polar solvent upon a temperature increase. Furthermore, we investigated the effects of excited translational motion of water (and ions) on the ion pairing by increasing the translational temperature, while keeping the rotational one unchanged (i.e., Ttrs>Trot). Interestingly, in certain cases the faster translational motion causes an increase in correlations. The temperature variations in the like-ion association constants, Kas++ and Kas--, are also examined. Here the situation is more complex but, in most cases, a decrease in the ion pairing is observed.

Effects of translational and rotational degrees of freedom on properties of the Mercedes–Benz water model

Non–equilibrium Monte Carlo and molecular dynamics simulations are used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes–Benz water model. We establish a non–equilibrium steady state where rotational and translational temperatures can be tuned. We separately show that Monte Carlo simulations can be used to study non-equilibrium properties if sampling is performed correctly. By holding one of the temperatures constant and varying the other one, we investigate the effect of faster motion in the corresponding degrees of freedom on the properties of the simple water model. In particular, the situation where the rotational temperature exceeded the translational one is mimicking the effects of microwaves on the water model. A decrease of rotational temperature leads to the higher structural order while an increase causes the structure to be more Lennard–Jones fluid like.

Database model for design data

A construction database model (CDM) used for the conceptual level modeling of design objects is presented. A primary purpose of the CDM model is the modeling of hierarchically structured objects and construction dependencies among objects. CDM is an attribute-based data model. The CDM model represents various abstractions identified in certain semantic database models by means of attributes. To distinguish between different abstractions, the notion of attribute role is introduced. Special attention is paid to the representation of derived properties of the object. They are described by means of a constructor. The constructor makes possible the description and reevaluation of the design object construction process. The CDM is used as a data model for a storage system designed for storing data in CAD applications.<<ETX>>

Extending database programming language with declarative querying facilities

The query language OVAL which is intended for the integration with the database programming language based on C++ is proposed in this paper. The work addresses the impedance mismatch problem between the syntax and the semantics of the programming and query language. The query language OVAL is based on the functional query language FQL extending it for the manipulation of complex objects. The salient features of the OVAL query language are: (i) functional nature of the query language, which makes the language suitable for the integration with the procedural programming languages and provides modular style of query definition, (ii) the use of schema information for expressing queries and (iii) recursive evaluation of the algebraic operations on set structured complex objects.