Abstract: The autoregressive neural networks are emerging as a powerful computational tool to solve relevant problems in classical and quantum mechanics. One of their appealing functionalities is that, after they have learned a probability distribution from a dataset, they allow exact and efficient sampling of typical system configurations. Here we employ a neural autoregressive distribution estimator (NADE) to boost Markov chain Monte Carlo (MCMC) simulations of a paradigmatic classical model of spin-glass theory, namely, the two-dimensional Edwards-Anderson Hamiltonian. We show that a NADE can be trained to accurately mimic the Boltzmann distribution using unsupervised learning from system configurations generated using standard MCMC algorithms. The trained NADE is then employed as smart proposal distribution for the Metropolis-Hastings algorithm. This allows us to perform efficient MCMC simulations, which provide unbiased results even if the expectation value corresponding to the probability distribution learned by the NADE is not exact. Notably, we implement a sequential tempering procedure, whereby a NADE trained at a higher temperature is iteratively employed as proposal distribution in a MCMC simulation run at a slightly lower temperature. This allows one to efficiently simulate the spin-glass model even in the low-temperature regime, avoiding the divergent correlation times that plague MCMC simulations driven by local-update algorithms. Furthermore, we show that the NADE-driven simulations quickly sample ground-state configurations, paving the way to their future utilization to tackle binary optimization problems.

Abstract: Due to the potential application of DNA for biophysics and optoelectronics, the electronic energy states and transitions of this genetic material have attracted a great deal of attention recently. However, the fluorescence and corresponding physical process of DNA under optical excitation with photon energies below ultraviolet are still not fully clear. In this work, we experimentally investigate the photoluminescence (PL) properties of single-stranded DNA (ssDNA) samples under near-ultraviolet (NUV) and visible excitations (270 similar to 440 nm). Based on the dependence of the PL peak wavelength (lem) upon the excitation wavelength (lex), the PL behaviors of ssDNA can be approximately classified into two categories. In the relatively short excitation wavelength regime, lem is nearly constant due to exciton-like transitions associated with delocalized excitonic states and excimer states. In the relatively long excitation wavelength range, a linear relation of lem = Alex + B with A 0 or A < 0 can be observed, which comes from electronic transitions related to coupled vibrational-electronic levels. Moreover, the transition channels in different excitation wavelength regimes and the effects of strand length and base type can be analyzed on the basis of these results. These important findings not only can give a general description of the electronic energy states and transitional behaviors of ssDNA samples under NUV and visible excitations, but also can be the basis for the application of DNA in nanoelectronics and optoelectronics.

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: 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: Molecular dynamics simulations are used to study the effects of different cations on the permeation of charged polymers through flat capillaries with heights below 2 nm. Interestingly, we found that, despite being monovalent, Li+ , Na+ , and K+ cations have different effects on polymer permeation, which consequently affects their transmission speed throughout those capillaries. We attribute this phenomenon to the interplay of the cations' hydration free energies and the hydrodynamic drag in front of the polymer when it enters the capillary. Different alkali cations exhibit different surface versus bulk preferences in small clusters of water under the influence of an external electric field. This paper presents a tool to control the speed of charged polymers in confined spaces using cations.

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: For column structures, such as fee-based alloys viewed along the cube direction, the concept of electron channelling through the atom columns is more and more used to interpret the corresponding HREM images. In the case of(partially) disordered columns, the projected potential approach which is used in the channelling description must be questioned since the arrangement of the atoms along the beam direction might affect the exit wave of the electrons. In this paper, we critically inspect this top-bottom effect using multi-slice calculations. A modified channelling theory is introduced which turns out to be very appropriate for the interpretation of these results. For substitutionally disordered column structures, it is also discussed how to link the chemical composition of the material to statistical data of the HREM image. This results in a convenient tool to discern images taken at different thicknesses and focus values.

Abstract: The Zn-carboxylate-based porous coordination polymer MOF-5 [Zn4O(bdc)3] and the metal oxide loaded materials ZnO@MOF-5 and TiO2@MOF-5 were loaded in a second step with the precursor [ClAuCO] to yield intermediate materials denoted as [ClAuCO]@MOF-5, [ClAuCO]/ZnO@MOF-5 and [ClAuCO]/TiO2@MOF-5. These composites were decomposed to Au@MOF-5, Au/ZnO@MOF-5 and Au/TiO2@MOF-5 under hydrogen at 100 °C. The nanoparticle-loaded hybrid materials were characterised by powder X-ray diffraction (PXRD), IR spectroscopy, X-ray photoelectron spectroscopy (XPS) and N2 sorption measurements, which reveal an intact MOF-5 structure that maintains a high specific surface area. For Au@MOF-5, crystalline Au nanoparticles were distributed over the MOF matrix in a homogeneous fashion with a size of ca. 13 nm, evidenced by high resolution transmission electron microscopy. In the case of Au/ZnO@MOF-5, the Au and metal oxide particles of a few nm in size were coexistent in a given volume of the MOF-5 matrix and were not separated in different crystalline MOF particles. For the TiO2 loaded materials the oxide is preferentially located near the outer surface of the MOF particles, leading to an increase of larger exterior Au particles in comparison to very small interior Au particles as observed for the other materials. Au@MOF-5, Au/ZnO@MOF-5 and Au/TiO2@MOF-5 were tested in liquid-phase oxidation of alcohols. Preliminary results show a high activity for the Au loaded materials in this reaction. This observation is attributed to the microstructure of the composites with very small Au particles distributed homogeneously over the MOF matrix.

Abstract: Metalorganic frameworks (MOFs) as well as porous coordination polymers (PCPs) are porous, organicinorganic hybrid solids with zeolite-like structures and properties. Due to their extraordinarily high surface area and well defined pore structure MOFs can be used for the stabilization of metal nanoparticles with adjustable size. The embedded metal nanoparticles are still accessible for other reagents due to the high porosity of the MOF systems. This fact makes metal@MOF systems especially interesting for heterogeneous catalysis, gas storage and chemical sensing. This review compiles the cases of metal nanoparticles supported by or embedded into MOFs reported so far and the main aspects and problems associated with these novel nanocomposite systems. The determination of the dispersion and the location of the particles at the MOF support, the control of the loading degree and its effect on the catalytic activity of the system are discussed as well as the partial degradation of the MOF structure upon particle formation. Examples of the introduction of stabilizing groups into the MOF network that direct the loading and can influence the size and shape of the embedded particles are still rare and point into the possible direction of future investigations. Finally, the formation of bimetallic nanoparticles, which are stabilized and supported by a MOF network, will also be reviewed.

Abstract: Zeolitic growth is often absent or occurs in separate phases when synthetic strategies based on the combination of zeolite templates and mesopore templating agents are applied. In this work, zeolitic growth and mesopore formation have been investigated at different temperatures by applying a one-pot templating approach, based on a TS-1 zeolite synthesis whereby part of the microtemplate (tetrapropylammonium hydroxide, TPAOH) is replaced by a mesotemplate (hexadecyltrimethylammonium bromide, CTMABr). Moreover, the synthesis duration and the molar ratio of the microtemplate/mesotemplate have also been studied. The different syntheses clearly show the inherent competitive mechanism between zeolitic growth and mesopore formation. These insights have led to the conclusion that by following a one-pot templating strategy with standard, nonexotic commercial templates, i.e. CTMABr and TPAOH, it is not possible to develop a true hierarchical mesoporous zeolite, meaning a mesoporous siliceous material with highly crystalline zeolitic walls. The resultant materials are instead combined zeolitic/mesoporous composite structures with, however, highly tuneable and controllable porosity characteristics.