From Chirps to Random-FM Excitations in Pulse Compression Ultrasound Systems

Pulse compression is often practiced in ultrasound Non Destructive Testing (NDT) systems using chirps. However, chirps are inadequate for setups where multiple probes need to operate concurrently in Multiple Input Multiple Output (MIMO) arrangements. Conversely, many coded excitation systems designed for MIMO miss some chirp advantages (constant envelope excitation, easiness of bandwidth control, etc.) and may not be easily implemented on hardware originally conceived for chirp excitations. Here, we propose a system based on random-FM excitations, capable of enabling MIMO with minimal changes with respect to a chirp-based setup. Following recent results, we show that random-FM excitations retain many advantages of chirps and provide the ability to frequency-shape the excitations matching the transducers features.Comment: 4 pages, 4 figures. Post-print from conference proceedings. Note that paper in conference proceedings at http://dx.doi.org/10.1109/ULTSYM.2012.0117 has some rendering issue

but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers

A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the α-helical conformer of polyglutamine is very stable, dimers of α-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, β-nanotube, and β-pseudohelix conformers are also too short-lived to initiate aggregation. The β-hairpin- containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which β -hairpin-containing conformers act as templates for fibril formation

Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal

Transferable MARTINI Model of Poly(ethylene Oxide)

Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model featuring a high degree of transferability. The model is parametrized on (a) a set of 8 free energies of transfer of dimethoxyethane (PEO dimer) from water to solvents of varying polarity; (b) the radius of gyration in water at high dilution; and (c) matching angle and dihedral distributions from atomistic simulations. We demonstrate that our model behaves well in five different areas of application: (1) it produces accurate densities and phase behavior or small PEO oligomers and water mixtures; (2) it yields chain dimensions in good agreement with the experiment in three different solvents (water, diglyme, and benzene) over a broad range of molecular weights ( 3c1.2 kg/mol to 21 kg/mol); (3) it reproduces qualitatively the structural features of lipid bilayers containing PEGylated lipids in the brush and mushroom regime; (4) it is able to reproduce the phase behavior of several PEO-based nonionic surfactants in water; and (5) it can be combined with the existing MARTINI PS to model PS-PEO block copolymers. Overall, the new PEO model outperforms previous models and features a high degree of transferability

Unfolding the interaction between microplastics and (trace) elements in water: A critical review

Plastic and microplastic pollution is an environmental and societal concern. The interaction of plastic with organic chemicals in the environment has attracted scientific interest. New evidences have highlighted an unexpectedly high affinity of environmental plastics also for metal ions. The degree and typology of plastic ageing (including from mechanical, UV and biological degradations) appear as a pivotal factor determining such an interaction. These earlier evidences recently opened a new research avenue in the plastic pollution area. This review is the first to organize and critically discuss knowledge developed so far. Results from field and laboratory studies of metal accumulation on plastic are presented and the environmental factors most likely to control such an interaction are discussed. On the light of this knowledge, a generalist conceptual model useful for building hypotheses on the mechanisms at stake and directing future studies was elaborated and presented here. Furthermore, all available data on the thermodynamics of the plastic-metal interaction obtained from laboratory experiments are inventoried and discussed here, highlighting methodological and technical challenges that can potentially affect cross-comparability of data and their relevance for environmental settings. Finally, insights and recommendations on experimental approaches and analytical techniques that can help overtaking current limitations and knowledge gaps are proposed

Two decades of Martini:Better beads, broader scope

The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around for nearly two decades. Originally developed for lipid-based systems by the groups of Marrink and Tieleman, the Martini model has over the years been extended as a community effort to the current level of a general-purpose force field. Apart from the obvious benefit of a reduction in computational cost, the popularity of the model is largely due to the systematic yet intuitive building-block approach that underlies the model, as well as the open nature of the development and its continuous validation. The easy implementation in the widely used Gromacs software suite has also been instrumental. Since its conception in 2002, the Martini model underwent a gradual refinement of the bead interactions and a widening scope of applications. In this review, we look back at this development, culminating with the release of the Martini 3 version in 2021. The power of the model is illustrated with key examples of recent important findings in biological and material sciences enabled with Martini, as well as examples from areas where coarse-grained resolution is essential, namely high-throughput applications, systems with large complexity, and simulations approaching the scale of whole cells. This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Computational Biochemistry and Biophysics

Polyply:A python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle

Selection of the optimal extraction protocol to investigate the interaction between trace elements and environmental plastic

The interaction between environmental plastic and trace elements is an issue of concern. Understanding their interaction mechanisms is key to evaluate the potential threats for the environment. To this regard, consolidating confidence in extraction protocols can help in understanding the amount of different species present on plastic surface, as well as the potential mobility of trace elements present inside the plastic matrix (e.g., additives). Here we tested the efficacy of different reagents to mimic the elemental phases bonded to meso- and microplastic in the environment, in relation to the grade of ageing and the polymer composition. Results showed that a relatively high portion of trace elements is bonded in a weak phase and that other phases abundant in other matrices (e.g., oxides and bonded to organic matter) are only present to a limited degree in the plastic samples. The comparison of different sample types highlighted the important role of plastic ageing in governing interactions with trace elements, while the polymer composition has a limited influence on this process. Finally, the future steps toward a tailored extraction scheme for environmental plastic are proposed.publishedVersio