Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

We present Swarm-CG, a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal in combination with popular CG force fields such as MARTINI. By coupling fuzzy self-tuning particle swarm optimization to Boltzmann inversion, Swarm-CG performs accurate bottom-up parametrization of bonded terms in CG models composed of up to 200 pseudo atoms within 4-24 h on standard desktop machines, using default settings. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of complex molecular systems interesting for bio- and nanotechnology. Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity, and size. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Demonstration data are available at: www.github.com/GMPavanLab/SwarmCG

Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures

Supramolecular block copolymerzation with optically or electronically complementary monomers provides an attractive bottom-up approach for the non-covalent synthesis of nascent axial organic heterostructures, which promises to deliver useful applications in energy conversion, optoelectronics, and catalysis. However, the synthesis of supramolecular block copolymers (BCPs) constitutes a significant challenge due to the exchange dynamics of non-covalently bound monomers and hence requires fine microstructure control. Furthermore, temporal stability of the segmented microstructure is a prerequisite to explore the applications of functional supramolecular BCPs. Herein, we report the cooperative supramolecular block copolymerization of fluorescent monomers in solution under thermodynamic control for the synthesis of axial organic heterostructures with light-harvesting properties. The fluorescent nature of the core-substituted naphthalene diimide (cNDI) monomers enables a detailed spectroscopic probing during the supramolecular block copolymerization process to unravel a nucleation-growth mechanism, similar to that of chain copolymerization for covalent block copolymers. Structured illumination microscopy (SIM) imaging of BCP chains characterizes the segmented microstructure and also allows size distribution analysis to reveal the narrow polydispersity (polydispersity index (PDI) ≈ 1.1) for the individual block segments. Spectrally resolved fluorescence microscopy on single block copolymerized organic heterostructures shows energy migration and light-harvesting across the interfaces of linearly connected segments. Molecular dynamics and metadynamics simulations provide useful mechanistic insights into the free energy of interaction between the monomers as well as into monomer exchange mechanisms and dynamics, which have a crucial impact on determining the copolymer microstructure. Our comprehensive spectroscopic, microscopic, and computational analyses provide an unambiguous structural, dynamic, and functional characterization of the supramolecular BCPs. The strategy presented here is expected to pave the way for the synthesis of multi-component organic heterostructures for various functions

Novel conopeptides of largely unexplored Indo Pacific <i>Conus</i> sp.

Cone snails are predatory creatures using venom as a weapon for prey capture and defense. Since this venom is neurotoxic, the venom gland is considered as an enormous collection of pharmacologically interesting compounds having a broad spectrum of targets. As such, cone snail peptides represent an interesting treasure for drug development. Here, we report five novel peptides isolated from the venom of Conus longurionis, Conus asiaticus and Conus australis. Lo6/7a and Lo6/7b were retrieved from C. longurionis and have a cysteine framework VI/VII. Lo6/7b has an exceptional amino acid sequence because no similar conopeptide has been described to date (similarity percentage C. asiaticus, has a typical framework III Cys arrangement, classifying the peptide in the M-superfamily. Asi14a, another peptide of C. asiaticus, belongs to framework XIV peptides and has a unique amino acid sequence. Finally, AusB is a novel conopeptide from C. australis. The peptide has only one disulfide bond, but is structurally very different as compared to other disulfide-poor peptides. The peptides were screened on nAChRs, NaV and KV channels depending on their cysteine framework and proposed classification. No targets could be attributed to the peptides, pointing to novel functionalities. Moreover, in the quest of identifying novel pharmacological targets, the peptides were tested for antagonistic activity against a broad panel of Gram-negative and Gram-positive bacteria, as well as two yeast strains

Overcoming the barriers to implementing urban road user charging schemes

Urban road user charging offers the potential to achieve significant improvements in urban transport, but is notoriously difficult to implement. Cities need guidance on the range of factors to be considered in planning and implementing such schemes. This paper summarises the results of a 3 year programme which has collated evidence on the issues of most concern to cities. A state of the art report has provided evidence on 14 themes, ranging from objectives and design to implementation and evaluation. A set of 16 case studies has reviewed experience in design and implementation across Europe. The paper summarises their findings, provides references to more detailed information, presents the resulting policy recommendations to European, national and local government, and outlines the areas in which further research is needed

PILOT: a balloon-borne experiment to measure the polarized FIR emission of dust grains in the interstellar medium

Future cosmology space missions will concentrate on measuring the polarization of the Cosmic Microwave Background, which potentially carries invaluable information about the earliest phases of the evolution of our universe. Such ambitious projects will ultimately be limited by the sensitivity of the instrument and by the accuracy at which polarized foreground emission from our own Galaxy can be subtracted out. We present the PILOT balloon project which will aim at characterizing one of these foreground sources, the polarization of the dust continuum emission in the diffuse interstellar medium. The PILOT experiment will also constitute a test-bed for using multiplexed bolometer arrays for polarization measurements. We present the results of ground tests obtained just before the first flight of the instrument.Comment: 17 pages, 13 figures. Presented at SPIE, Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy VII. To be published in Proc. SPIE volume 915

Electroreduction of CO2/CO to C2 products: process modeling, downstream separation, system integration, and economic analysis.

Direct electrochemical reduction of CO2 to C2 products such as ethylene is more efficient in alkaline media, but it suffers from parasitic loss of reactants due to (bi)carbonate formation. A two-step process where the CO2 is first electrochemically reduced to CO and subsequently converted to desired C2 products has the potential to overcome the limitations posed by direct CO2 electroreduction. In this study, we investigated the technical and economic feasibility of the direct and indirect CO2 conversion routes to C2 products. For the indirect route, CO2 to CO conversion in a high temperature solid oxide electrolysis cell (SOEC) or a low temperature electrolyzer has been considered. The product distribution, conversion, selectivities, current densities, and cell potentials are different for both CO2 conversion routes, which affects the downstream processing and the economics. A detailed process design and techno-economic analysis of both CO2 conversion pathways are presented, which includes CO2 capture, CO2 (and CO) conversion, CO2 (and CO) recycling, and product separation. Our economic analysis shows that both conversion routes are not profitable under the base case scenario, but the economics can be improved significantly by reducing the cell voltage, the capital cost of the electrolyzers, and the electricity price. For both routes, a cell voltage of 2.5 V, a capital cost of $10,000/m2, and an electricity price of <$20/MWh will yield a positive net present value and payback times of less than 15 years. Overall, the high temperature (SOEC-based) two-step conversion process has a greater potential for scale-up than the direct electrochemical conversion route. Strategies for integrating the electrochemical CO2/CO conversion process into the existing gas and oil infrastructure are outlined. Current barriers for industrialization of CO2 electrolyzers and possible solutions are discussed as well

The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster

The regulatory protein NsrR, a member of the Rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (NO) in a variety of pathogenic and non-pathogenic bacteria. It has been proposed that NO directly modulates NsrR activity by interacting with a predicted [Fe-S] cluster in the NsrR protein, but no experimental evidence has been published to support this hypothesis. Here we report the purification of NsrR from the obligate aerobe Streptomyces coelicolor. We demonstrate using UV-visible, near UV CD and EPR spectroscopy that the protein contains an NO-sensitive [2Fe-2S] cluster when purified from E. coli. Upon exposure of NsrR to NO, the cluster is nitrosylated, which results in the loss of DNA binding activity as detected by bandshift assays. Removal of the [2Fe-2S] cluster to generate apo-NsrR also resulted in loss of DNA binding activity. This is the first demonstration that NsrR contains an NO-sensitive [2Fe-2S] cluster that is required for DNA binding activity

Entanglement in nuclear quadrupole resonance

Entangled quantum states are an important element of quantum information techniques. We determine the requirements for states of quadrupolar nuclei with spins >1/2 to be entangled. It was shown that entanglement is achieved at low temperature by applying a magnetic field to a quadrupolar nuclei possess quadrupole moments, which interacts with the electricfield gradient produced by the charge distribution in their surroundings.Comment: 9 pages, 5 figure