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We employed an empirical molecular mechanical model and non-equilibrium molecular dynamics simulations to investigate the structure of aqueous solutions of some prototypical polar compounds upon microwave heating. Microwave irradiation has been taken into account implicitly by performing simulations at a rotational temperature exceeding the translational one (Tr> Tt). We studied aqueous solutions of 5 polar compounds (acetone, acetaldehyde, dimethylether, methanol, and acetonitrile), which have been recently classified as hydroneutral or hydrophilic, depending on their hydration number determined experimentally via dielectric spectroscopy. We have shown that the two groups of polar compounds could indeed be distinguished also based on the changes in their hydration upon a Tr increase. Moreover, we have clearly demonstrated the crucial effects of mass and charge distribution in a solute molecule on its hydration properties under the studied non-equilibrium microwave conditions.

The utility of the Adverse Outcome Pathway (AOP) concept has been largely recognized by scientists, however, the AOP generation is still mainly done manually by screening through evidence and extracting probable associations. To accelerate this process and increase the reliability, we have developed an semi-automated workflow for AOP hypothesis generation. In brief, association mining methods were applied to high-throughput screening, gene expression, in vivo and disease data present in ToxCast and Comparative Toxicogenomics Database. This was supplemented by pathway mapping using Reactome to fill in gaps and identify events occurring at the cellular/tissue levels. Furthermore, in vivo data from TG-Gates was integrated to finally derive a gene, pathway, biochemical, histopathological and disease network from which specific disease sub-networks can be queried. To test the workflow, non-genotoxic-induced hepatocellular carcinoma (HCC) was selected as a case study. The implementation resulted in the identification of several non-genotoxic-specific HCC-connected genes belonging to cell proliferation, endoplasmic reticulum stress and early apoptosis. Biochemical findings revealed non-genotoxic-specific alkaline phosphatase increase. The explored non-genotoxic-specific histopathology was associated with early stages of hepatic steatosis, transforming into cirrhosis. This work illustrates the utility of computationally predicted constructs in supporting development by using pre-existing knowledge in a fast and unbiased manner.

We study active microrheology in two-dimensional (2D) magnetic networks. To this end, we use Langevin dynamics computer simulations where single non-magnetic or magnetic tracer particles are pulled through the network structures via a constant force f. Structural changes in the network around the pulled tracer particle are characterized in terms of pair correlation functions. These functions indicate that the non-magnetic tracer particles tend to strongly affect the network structure leading to the formation of channels at sufficiently high forces, while the magnetic tracer particles modify the network structure only slightly. At zero pulling force, f = 0, both non-magnetic and magnetic tracer particles are localized, i.e. they do not show diffusive behavior in the long-time limit. Nevertheless, the friction coefficient, as obtained from the steady-state velocity of the tracer particles, seems to indicate a linear-response regime at small values of f. Beyond the latter linear response regime, the diffusion dynamics of the tracer particles are anisotropic with superdiffusive behavior in force direction. This transport anomaly is investigated via van Hove correlation functions and residence time distributions.

We employed non-equilibrium molecular dynamics simulations to investigate the hydrogen-bond dynamics in bulk water upon microwave heating. Microwave irradiation has been taken into account implicitly by performing simulations at a rotational temperature exceeding the translational one (Tr > Tt). We have shown that the effect of an increased Tr results in a modified geometry of the average path for hydrogen-bond switch and in decreased characteristic decay times for the reorientation of a water molecule. We also confirmed the validity of the extended jump model to describe hydrogen-bond dynamics under the studied non-equilibrium conditions.

Complex rheological properties of soft disordered solids, such as colloidal gels or glasses, inspire a range of novel applications. However, the microscopic mechanisms of their response to mechanical loading are not well understood. Here, we elucidate some aspects of these mechanisms by studying a versatile model system, i.e. two-dimensional superparamagnetic colloids in a precessing magnetic field, whose structure can be tuned from a hexagonal crystal to a disordered gel network by varying the external field opening angle θ. We perform Langevin dynamics simulations subjecting these structures to a constant shear rate and observe three qualitatively different types of material response. In hexagonal crystals (θ = 0°), at a sufficiently low shear rate, plastic flow occurs via successive stress drops at which the stress releases due to the formation of dislocation defects. The gel network at θ = 48°, on the contrary, via bond rearrangement and transient shear banding evolves into a homogeneously stretched network at large strains. The latter structure remains metastable after switching off of the shear. At θ = 50°, the external shear makes the system unstable against phase separation and causes a failure of the network structure leading to the formation of hexagonal close packed clusters interconnected by particle chains. At a microcopic level, our simulations provide insight into some of the mechanisms by which strain localization as well as material failure occur in a simple gel-like network. Furthermore, we demonstrate that new stretched network structures can be generated by the application of shear.

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.

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.

Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's 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.

Molecular dynamics simulations with separate thermostats for rotational and translational motions were used to study the effects of these degrees of freedom on the structure of water at a fixed density. To describe water molecules, we used the SPC/E model. The results indicate that an increase of the rotational temperature, $T_\textrm{R}$, causes a significant breaking of the hydrogen bonds. This is not the case, at least not to such an extent, when the translational temperature, $T_\textrm{T}$, is raised. The probability of finding an empty spherical cavity (no water molecule present) of a given size, strongly decreases with an increase of $T_\textrm{R}$, but this only marginally affects the free energy of the hydrophobe insertion. The excess internal energy increases proportionally with an increase of $T_\textrm{R}$, while an increase of $T_\textrm{T}$ yields a much smaller effect at high temperatures. The diffusion coefficient of water exhibits a non-monotonous behaviour with an increase of the rotational temperature., Comment: 9 pages, 9 figures

The Wertheim's 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 Wertheim's 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.

The accuracy of the activity coefficient expression (Hansen-Vieillefosse-Belloni (HVB) equation), valid within the hypernetted-chain (HNC) approximation, was tested in a wide concentration range against newly obtained grand canonical Monte Carlo data for the size and charge asymmetric primitive model electrolytes. In some cases, uncharged hard sphere component was also present. The HVB expression enables a direct calculation of the excess chemical potential, without invoking the time consuming calculation via the Gibbs-Duhem relation. We found the Ornstein-Zernike (OZ)/HNC results for the mean activity coefficient, as well as for the reduced excess internal energy and osmotic coefficient, to be in good agreement with the machine calculations performed for the same model. The accuracy of the results was found to be dependent on the packing fraction of the solutions. The mean spherical approximation calculations were also used to describe the thermodynamics of these systems and compared with the OZ/HNC and simulation results.

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.

Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water’s 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 in...

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.

The database model CDM intended for modelling design objects is presented. All properties of the design object are modeled by means of functions. For modelling dynamic dependencies among objects we introduce the notion of dynamic function . The dynamic function comprises capabilities for the description of the object static structure and algorithmic dependencies among objects. Some constraints and practical problems in using dynamic functions in the domain of geometric modelling are identified.

The paper presents a Construction Database Model used for conceptual level modelling and manipulation of design objects. A primary intention of the CDM model is modelling hierarchically structured objects and generic dependencies between objects in design or in engineering applications. The CDM is an attribute based data model, therefore, all object properties are described by attributes. The leading idea of the CDM model is the representation of various abstractions identified in the semantic database models GSM, IFO, SAM* and FDM with attributes. To distinguish between different abstractions, the notion of attribute role is introduced. Attribute role divides attributes into different categories on the basis of the attribute meaning. Attributes can be of ordinary, structural, derived and implicit role, representing ordinary object properties, hierarchical structure, generic properties and properties defined implicitly with a specific abstraction.Special attention is paid to the representation of generic object properties, which are described by means of a derived attribute or constructor. The constructor enables the description and reevaluation of design object construction process.

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.