Abstract: Single-file diffusion (SFD) of an infinite one-dimensional chain of interacting particles has a long-time mean-square displacement ∝t1/2, independent of the type of interparticle repulsive interaction. This behavior is also observed in finite-size chains, although only for certain intervals of time t depending on the chain length L, followed by the ∝t for t→∞, as we demonstrate for a closed circular chain of diffusing interacting particles. Here, we show that spatial correlation of noise slows down SFD and can result, depending on the amount of correlated noise, in either subdiffusive behavior ∝tα, where 0<α<1/2, or even in a total suppression of diffusion (in the limit N→∞). Spatial correlation can explain the subdiffusive behavior in recent SFD experiments in circular channels.

Abstract: The influence of an ellipsoid on the angular order of two-dimensional classical clusters is investigated through Brownian dynamics simulations. We found the following: (1) The presence of an ellipsoid does not influence the start of the angular melting, but reduces the rate at which the inner rings can rotate with respect to each other. (2) Even a small eccentricity of the ellipsoid leads to a stabilization of the angular order of the system. (3) Depending on the position of the ellipsoid in the cluster, a reentrant behavior in the angular order is observed before full radial melting of the cluster sets in. (4) The ellipsoid can lead to a two-step angular melting process: First, the rotation of the inner rings with respect to each other is hindered by the ellipsoid, but on further increasing the kinetic energy of the system, the ellipsoid just starts to behave as a spherical particle with different mobility. The effect of an ellipsoid on the molten system does not depend crucially on the interparticle interaction, but a softer parabolic confinement reduces the angular stabilization.

Abstract: The diffusion of charged particles interacting through a repulsive Yukawa potential, exp(-r/lambda)/r, confined by a parabolic potential in the y direction and subjected to a periodic substrate potential in the x direction is investigated. Langevin dynamic simulations are used to investigate the effect of the particle density, the amplitude of the periodic substrate, and the range of the interparticle interaction potential on the diffusive behavior of the particles. We found that in general the diffusion is suppressed with increasing the amplitude of the periodic potential, but for specific values of the strength of the substrate potential a remarkable increase of the diffusion is found with increasing the periodic potential amplitude. In addition, we found a strong dependence of the diffusion on the specific arrangement of the particles, e. g., single-chain versus multichain configuration. For certain particle configurations, a reentrant behavior of the diffusion is found as a function of the substrate strength due to structural transitions in the ordering of the particles.

Abstract: Diffusive properties of a monodisperse system of interacting particles confined to a quasi-one-dimensional channel are studied using molecular dynamics simulations. We calculate numerically the mean-squared displacement (MSD) and investigate the influence of the width of the channel (or the strength of the confinement potential) on diffusion in finite-size channels of different shapes (i.e., straight and circular). The transition from single-file diffusion to the two-dimensional diffusion regime is investigated. This transition [ regarding the calculation of the scaling exponent (alpha) of the MSD <Delta x(2)(t)> proportional to t(alpha)] as a function of the width of the channel is shown to change depending on the channel's confinement profile. In particular, the transition can be either smooth (i.e., for a parabolic confinement potential) or rather sharp (i.e., for a hard-wall potential), as distinct from infinite channels where this transition is abrupt. This result can be explained by qualitatively different distributions of the particle density for the different confinement potentials.

Abstract: The diffusion of a system of ferromagnetic dipoles confined in a quasi-one-dimensional parabolic trap is studied using Brownian dynamics simulations. We show that the dynamics of the system is tunable by an in-plane external homogeneous magnetic field. For a strong applied magnetic field, we find that the mobility of the system, the exponent of diffusion, and the crossover time among different diffusion regimes can be tuned by the orientation of the magnetic field. For weak magnetic fields, the exponent of diffusion in the subdiffusive regime is independent of the orientation of the external field. DOI: 10.1103/PhysRevE.87.012307

Abstract: We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013)]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their behavior is similar to that of interacting particles in porous materials. Different expressions for the particle jump rates are derived from transition-state theory. Which expression should be used depends on the strength of the interparticle interactions. Analytical expressions for the self-and transport diffusion are derived when correlations, caused by memory effects in the environment, are neglected. The diffusive behavior is studied numerically with kinetic Monte Carlo (kMC) simulations, which reproduces the diffusion including correlations. The effect of correlations is studied by comparing the analytical expressions with the kMC simulations. It is found that the Maxwell-Stefan diffusion can exceed the self-diffusion. To our knowledge, this is the first time this is observed. The diffusive behavior in one-dimensional and higher-dimensional systems is qualitatively the same, with the effect of correlations decreasing for increasing dimension. The length dependence of both the self-and transport diffusion is studied for one-dimensional systems. For long lengths the self-diffusion shows a 1/L dependence. Finally, we discuss when agreement with experiments and simulations can be expected. The assumption that particles in different cavities do not interact is expected to hold quantitatively at low and medium particle concentrations if the particles are not strongly interacting.

Abstract: We analyze the combined effect of three ingredients of an aggregation model-surface tension, particle flow and particle source-representing typical characteristics of many aggregation growth processes in nature. Through extensive numerical experiments and for different underlying lattice structures we demonstrate that the location of incoming particles and their preferential direction of flow can significantly affect the resulting general shape of the aggregate, while the surface tension controls the surface roughness. Combining all three ingredients increases the aggregate shape plasticity, yielding a wider spectrum of shapes as compared to earlier works that analyzed these ingredients separately. Our results indicate that the considered combination of effects is fundamental for modeling the polymorphic growth of a wide variety of structures in confined geometries and/or in the presence of external fields, such as rocks, crystals, corals, and biominerals.

Abstract: Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. Here, we consider a two-dimensional model of Janus disks consisting of a hydrophobic semicircle and an electro-negatively charged one. Placed in a solution, the hydrophobic sides will attract each other while the charged sides will give rise to a repulsive force. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment using a one dimensional harmonic confinement potential. The interest to this system is first of all due to the fact that it could serve as a simple model for membrane formation. Indeed, the recently synthesized new class of artificial amphiphiles, known as Janus dendrimers, were shown to self-assemble in bilayer structures mimicking biological membranes. In turn, Janus particles that combine the amphiphilicity and colloidal rigidity serve as a good model for Janus dendrimers. A variety of ordered membrane-like morphologies are found consisting of single and multiple chain configurations with different orientations of the particles with respect to each other that we summarize in a phase diagram.

Abstract: Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.

Abstract: This paper outlines two different numerical simulation approaches, carried out by our group, used for describing hydrocarbon plasmas in their applications for either nanoparticle formation in the plasma or the growth of nanostructured thin films, such as nanocrystalline diamond (NCD). A plasma model based on the fluid approach is utilized to study the initial mechanisms giving rise to nanoparticle formation in an acetylene plasma. The growth of NCD is investigated by molecular dynamics simulations, describing the interaction of the hydrocarbon species with a substrate.

Abstract: In this study we performed microscopic characterization of mineral particles that were collected in the thorium-rich Fen Complex in Norway and identified and isolated based on autoradiography in function of their radioactivity. For this we combined information obtained with X-ray absorption mu-CT, mu-XRF and mu-XRD, both in bi- and in three-dimensional (tomographic) mode. We demonstrate that radionuclides and metals are heterogeneously distributed both within soil samples and within individual Th-enriched aggregates, which are characterised as low-density mineral bulk particles with high density material inclusions, where Th as well as several metals are highly concentrated. For these sites, it is important to take into account how these inhomogeneous distributions could affect the overall environmental behaviour of Th and progeny upon weathering due to human or environmental factors. Moreover, the estimated size of the Th-containing inclusions as determined in this work represents information of importance for the characterization of radionuclides and toxic metals exposure, as well as for assessing the viability of mining for Th and rare-earth metals in the Fen Complex and the associated environmental impact.

Abstract: Purple non-sulphur bacteria (PNSB) are an emerging group of microbes attractive for applied microbiology applications such as wastewater treatment, plant biostimulants, microbial protein, polyhydroxyalkanoates and H-2 production. These photoorganoheterotrophic microbes have the unique ability to grow selectively on organic carbon in anaerobic photobioreactors. This so-called selectivity implies that the microbial community will have a low diversity and a high abundance of a particular PNSB species. Recently, it has been shown that certain PNSB strains can produce antimicrobials, yet it remains unclear whether these contribute to competitive inhibition. This research aimed to understand which type of antimicrobial PNSB produce and identify whether these compounds contribute to their selective growth. Mining 166 publicly-available PNSB genomes using the computational tool BAGEL showed that 59% contained antimicrobial encoding regions, more specifically biosynthetic clusters of bacteriocins and non-ribosomal peptide synthetases. Inter- and intra-species inhibition was observed in agar spot assays for Rhodobacter blasticus EBR2 and Rhodopseudomonas palustris EBE1 with inhibition zones of, respectively, 5.1 and 1.5-5.7 mm. Peptidomic analysis detected a peptide fragment in the supernatant (SVLQLLR) that had a 100% percentage identity match with a known non-ribosomal peptide synthetase with antimicrobial activity.

Abstract: Background Cell transplantation is likely to become an important therapeutic tool for the treatment of various traumatic and ischemic injuries to the central nervous system (CNS). However, in many pre-clinical cell therapy studies, reporter gene-assisted imaging of cellular implants in the CNS and potential reporter gene and/or cell-based immunogenicity, still remain challenging research topics. Results In this study, we performed cell implantation experiments in the CNS of immunocompetent mice using autologous (syngeneic) luciferase-expressing bone marrow-derived stromal cells (BMSC-Luc) cultured from ROSA26-L-S-L-Luciferase transgenic mice, and BMSC-Luc genetically modified using a lentivirus encoding the enhanced green fluorescence protein (eGFP) and the puromycin resistance gene (Pac) (BMSC-Luc/eGFP/Pac). Both reporter gene-modified BMSC populations displayed high engraftment capacity in the CNS of immunocompetent mice, despite potential immunogenicity of introduced reporter proteins, as demonstrated by real-time bioluminescence imaging (BLI) and histological analysis at different time-points post-implantation. In contrast, both BMSC-Luc and BMSC-Luc/eGFP/Pac did not survive upon intramuscular cell implantation, as demonstrated by real-time BLI at different time-points post-implantation. In addition, ELISPOT analysis demonstrated the induction of IFN-ã-producing CD8+ T-cells upon intramuscular cell implantation, but not upon intracerebral cell implantation, indicating that BMSC-Luc and BMSC-Luc/eGFP/Pac are immune-tolerated in the CNS. However, in our experimental transplantation model, results also indicated that reporter gene-specific immune-reactive T-cell responses were not the main contributors to the immunological rejection of BMSC-Luc or BMSC-Luc/eGFP/Pac upon intramuscular cell implantation. Conclusion We here demonstrate that reporter gene-modified BMSC derived from ROSA26-L-S-L-Luciferase transgenic mice are immune-tolerated upon implantation in the CNS of syngeneic immunocompetent mice, providing a research model for studying survival and localisation of autologous BMSC implants in the CNS by real-time BLI and/or histological analysis in the absence of immunosuppressive therapy.

Abstract: The chromium-based metal organic framework MIL-101(Cr) served as a host for the in situ synthesis of Fe3O4 nano particles. This hybrid nanomaterial was tested as an adsorbent for arsenite and arsenate species in groundwater and surface water and showed excellent affinity towards As-III and As-V species. The adsorption capacities of 121.5 and 80.0 mg g(-1) for arsenite and arsenate species, respectively, are unprecedented. The presence of Ca2+, Mg2+, and phosphate ions and natural organic matter does not affect the removal efficiency or the selectivity. The structural integrity of the hybrid nanomaterial was maintained during the adsorption process and even after desorption through phosphate elution. Additionally, no significant leaching of Cr or Fe species was observed.

Abstract: Co-containing fluoride-phosphates are of interest in sense of delivering high electrode potentials and attractive specific energy values as positive electrode materials for rechargeable batteries. In this paper we report on a new Co-based fluoride-phosphate, LiNaCoPO4F, with a layered structure (2D), which was Rietveld-refined based on X-ray powder diffraction data [P2(1)/c, a = 6.83881(4) angstrom, b = 11.23323(5) angstrom, c = 5.07654(2) angstrom, beta = 90.3517(5) degrees, V = 389.982(3) angstrom(3)] and validated by electron diffraction and high-resolution scanning transmission electron microscopy. The differential scanning calorimetry measurements revealed that 2D-LiNaCoPO4F forms in a narrow temperature range of 520-530 degrees C and irreversibly converts to the known 3D-LiNaCoPO4F modification (Pnma) above 530 degrees C. The non-carbon-coated 2D-LiNaCoPO4F shows reversible electrochemical activity in Li-ion cell in the potential range of 3.0-4.9 V vs. Li/Li+ with an average potential of approximate to 4.5 V and in Na-ion cell in the range of 3.0-4.5 V vs. Na/Na+ exhibiting a plateau profile centered around 4.2 V, in agreement with the calculated potentials by density functional theory. The energy barriers for both Li+ and Na+ migration in 2D-LiNaCoPO4F amount to 0.15 eV along the [001] direction rendering 2D-LiNaCoPO4F as a viable electrode material for high-power Li- and Na-ion rechargeable batteries. The discovery and stabilization of the 2D-LiNaCoPO4F polymorph indicates that temperature influence on the synthesis of A(2)MPO(4)F fluoride-phosphates needs more careful examination with perspective to unveil new structures.