Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics.

In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra

Molecular line shape parameters for exoplanetary atmospheric applications

We describe the recent updates to the ExoMol database regarding the molecular spectral line shapes. ExoMol provides comprehensive molecular line lists with a special emphasis on the applications involving characterization of hot atmospheres such as those found in exoplanets and cool stars. Among important requirements of such applications are (i) the broadening parameters for hydrogen and helium dominating atmospheres and (ii) very broad ranges of temperature and pressures. The current status of the available line shape data in the literature, demands from the exoplanetary community and their specific needs are discussed

PocketGraph : graph representation of binding site volumes

The representation of small molecules as molecular graphs is a common technique in various fields of cheminformatics. This approach employs abstract descriptions of topology and properties for rapid analyses and comparison. Receptor-based methods in contrast mostly depend on more complex representations impeding simplified analysis and limiting the possibilities of property assignment. In this study we demonstrate that ligand-based methods can be applied to receptor-derived binding site analysis. We introduce the new method PocketGraph that translates representations of binding site volumes into linear graphs and enables the application of graph-based methods to the world of protein pockets. The method uses the PocketPicker algorithm for characterization of binding site volumes and employs a Growing Neural Gas procedure to derive graph representations of pocket topologies. Self-organizing map (SOM) projections revealed a limited number of pocket topologies. We argue that there is only a small set of pocket shapes realized in the known ligand-receptor complexes

Zeolite crystal layers coupled to piezoelectric sensors

Microporous zeolite crystals were successfully coupled onto the gold electrodes of quartz crystal microbalances (QCM). A self-assembled monolayer of thiol-alkoxysilane coupling agent on the gold surface was used as the interfacial layer to promote adhesion of the zeolite crystals to the QCM. The resulting, densely packed single layers of zeolite crystals were stable to at least 625 K. Transient sorption behavior of organic vapor pulses, dynamic vapor sorption isotherms and nitrogen sorption isotherms at liquid nitrogen temperature were examined to characterize the zeolite-coated QCMs. Depending on the type of zeolite coating, the resonance frequency response to vapor pulses could be increased up to 500-fold compared to the bare QCM. The regular micropores (0.3-0.8 nm) of the QCM-attached zeolite crystals were found to control molecular access into the extensive intrazeolite volume. Selectivity of the frequency response in excess of 100:1 toward molecules of different size and/or shape could be demonstrated. An additional recognition mechanism based upon intrazeolite diffusion rates was also established

Shape mode analysis exposes movement patterns in biology: flagella and flatworms as case studies

We illustrate shape mode analysis as a simple, yet powerful technique to concisely describe complex biological shapes and their dynamics. We characterize undulatory bending waves of beating flagella and reconstruct a limit cycle of flagellar oscillations, paying particular attention to the periodicity of angular data. As a second example, we analyze non-convex boundary outlines of gliding flatworms, which allows us to expose stereotypic body postures that can be related to two different locomotion mechanisms. Further, shape mode analysis based on principal component analysis allows to discriminate different flatworm species, despite large motion-associated shape variability. Thus, complex shape dynamics is characterized by a small number of shape scores that change in time. We present this method using descriptive examples, explaining abstract mathematics in a graphic way.Comment: 20 pages, 6 figures, accepted for publication in PLoS On

Topological characterization of neutron star crusts

Neutron star crusts are studied using a classical molecular dynamics model developed for heavy ion reactions. After the model is shown to produce a plethora of the so-called "pasta" shapes, a series of techniques borrowed from nuclear physics, condensed matter physics and topology are used to craft a method that can be used to characterize the shape of the pasta structures in an unequivocal way

Phenomenological characterization of sequential dual-curing of off-stoichiometric "thiol-epoxy" systems: Towards applicability

An extensive characterization of a sequential dual-curing system based on off-stoichiometric “thiol-epoxy” mixtures was carried out using thiol compounds of different functionality. The intermediate and final materials obtained after each curing stages at different thiol-epoxy ratios were studied by means of thermomechanical and rheological experiments. The storage and loss modulus and the loss factor tan d were monitored during the curing process to analyse gelation and network structure build-up. The critical ratio for gelation was determined making use of the ideal Flory-Stockmayer theory and compared with experimental results. Intermediate materials obtained in the vicinity of the theoretical critical ratio did not have the mechanical consistency expected for partially crosslinked materials, did not retain their shape and even experienced undesired flow upon heating to activate the second curing reaction. The rheological results showed that the critical ratio is higher than the predicted value and that a softening during the second curing stage affects the shape-retention at this ratio. From the thermomechanical results, a wide range of intermediate and final materials with different properties and applicability can be obtained by properly choosing the thiol-epoxy ratio: from liquid-like to highly deformable intermediate materials and from moderately crosslinked (deformable) to highly crosslinked (brittle) final materials.Postprint (author's final draft

Microbiology and atmospheric processes: Biological, physical and chemical characterization of aerosol particles

The interest in bioaerosols has traditionally been linked to health hazards for humans, animals and plants. However, several components of bioaerosols exhibit physical properties of great significance for cloud processes, such as ice nucleation and cloud condensation. To gain a better understanding of their influence on climate, it is therefore important to determine the composition, concentration, seasonal fluctuation, regional diversity and evolution of bioaerosols. In this paper, we will review briefly the existing techniques for detection, quantification, physical and chemical analysis of biological particles, attempting to bridge physical, chemical and biological methods for analysis of biological particles and integrate them with aerosol sampling techniques. We will also explore some emerging spectroscopy techniques for bulk and single-particle analysis that have potential for in-situ physical and chemical analysis. Lastly, we will outline open questions and further desired capabilities (e. g., in-situ, sensitive, both broad and selective, on-line, time-resolved, rapid, versatile, cost-effective techniques) required prior to comprehensive understanding of chemical and physical characterization of bioaerosols