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.
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.
•Increased translational temperature impacts characteristic times of H-bond switch.•Increased rotational temperature impacts geometry of H-bond switch.•Extended jump model of H-bond dynamics under non-equilibrium conditions confirmed.
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.
•Effect of microwave irradiation on aqueous solutions was modelled as a rotational temperature exceeding the translational one.•Aqueous solutions of 5 prototypical polar compounds were modelled using non-equilibrium molecular dynamics.•Hydrophilic and hydroneutral compounds could be distinguished based on changes in hydration upon rotational excitation.•Mass and charge distribution within a solute crucially affect its hydration properties under non-equilibrium conditions.
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.
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 study active microrheology in 2D with Langevin simulations of tracer particles pulled through magnetic networks by a constant force. While non-magnetic tracers strongly deform the network in order to be able to move through, the magnetic tracers can do so by deforming the structure only slightly.
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.
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 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.
•To support Adverse Outcome Pathway development, we have created a semi-automated workflow for AOP hypothesis generation.•The tool is using high-throughput screening, gene expression, histopathology, biochemical, in vivo and disease data.•The implementation of the workflow is demonstrated via a use case for non-genotoxic-induced hepatocellular carcinoma.•Cell proliferation, endoplasmic reticulum stress and apoptosis are identified as major players in the disease development.•This work illustrates the utility of computationally predicted constructs in supporting AOP development.
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.
We employed molecular dynamics simulations with separate thermostats for translational and rotational temperatures in order to study the effects of these degrees of freedom on the hydration of ions. ...In this work we examine how water models, differing in charge distribution, respond to the rise of rotational temperature. The study shows that, with respect to the distribution of negative charge, popular water models lead to different responses upon an increase of the rotational temperature. The differences arise in hydration of cations, as the negative charge distribution on the model solvent represents the determining factor in such cases. The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Because all the water models examined here have similar distributions of positive charge, they all exhibit similar trends in solvation of anions. In contrast to above, the effect of translational temperature variation is similar for all water-solute pairs; any increase in translational temperature decreases the solute-water correlations.
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