Non-Markovian quantum state diffusion for absorption spectra of molecular aggregates

In many molecular systems one encounters the situation where electronic excitations couple to a quasi-continuum of phonon modes. That continuum may be highly structured e.g. due to some weakly damped high frequency modes. To handle such a situation, an approach combining the non-Markovian quantum state diffusion (NMQSD) description of open quantum systems with an efficient but abstract approximation was recently applied to calculate energy transfer and absorption spectra of molecular aggregates [Roden, Eisfeld, Wolff, Strunz, PRL 103 (2009) 058301]. To explore the validity of the used approximation for such complicated systems, in the present work we compare the calculated (approximative) absorption spectra with exact results. These are obtained from the method of pseudomodes, which we show to be capable of determining the exact spectra for small aggregates and a few pseudomodes. It turns out that in the cases considered, the results of the two approaches mostly agree quite well. The advantages and disadvantages of the two approaches are discussed

Inter-species variation in the oligomeric states of the higher plant Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase

In darkened leaves the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a regulatory multi-enzyme complex with the small chloroplast protein CP12. GAPDH also forms a high molecular weight regulatory mono-enzyme complex. Given that there are different reports as to the number and subunit composition of these complexes and that enzyme regulatory mechanisms are known to vary between species, it was reasoned that protein-protein interactions may also vary between species. Here, this variation is investigated. This study shows that two different tetramers of GAPDH (an A2B2 heterotetramer and an A4 homotetramer) have the capacity to form part of the PRK/GAPDH/CP12 complex. The role of the PRK/GAPDH/CP12 complex is not simply to regulate the 'non-regulatory' A4 GAPDH tetramer. This study also demonstrates that the abundance and nature of PRK/GAPDH/CP12 interactions are not equal in all species and that whilst NAD enhances complex formation in some species, this is not sufficient for complex formation in others. Furthermore, it is shown that the GAPDH mono-enzyme complex is more abundant as a 2(A2B2) complex, rather than the larger 4(A2B2) complex. This smaller complex is sensitive to cellular metabolites indicating that it is an important regulatory isoform of GAPDH. This comparative study has highlighted considerable heterogeneity in PRK and GAPDH protein interactions between closely related species and the possible underlying physiological basis for this is discussed. © 2011 The Author(s)

Bunge’s Mathematical Structuralism Is Not a Fiction

In this paper, I explore Bunge’s fictionism in philosophy of mathematics. After an overview of Bunge’s views, in particular his mathematical structuralism, I argue that the comparison between mathematical objects and fictions ultimately fails. I then sketch a different ontology for mathematics, based on Thomasson’s metaphysical work. I conclude that mathematics deserves its own ontology, and that, in the end, much work remains to be done to clarify the various forms of dependence that are involved in mathematical knowledge, in particular its dependence on mental/brain states and material objects

Shake table testing of a tuned mass damper inerter (Tmdi)-equipped structure and nonlinear dynamic modeling under harmonic excitations

This paper presents preliminary experimental results from a novel shaking table testing campaign investigating the dynamic response of a two-degree-of-freedom (2DOF) physical specimen with a grounded inerter under harmonic base excitation and contributes a nonlinear dynamic model capturing the behavior of the test specimen. The latter consists of a primary mass connected to the ground through a high damping rubber isolator (HDRI) and a secondary mass connected to the primary mass through a second HDRI. Further, a flywheel-based rack-and-pinion inerter prototype device is used to connect the secondary mass to the ground. The resulting specimen resembles the tuned mass damper inerter (TMDI) configuration with grounded inerter analytically defined and numerically assessed by the authors in a number of previous publications. Physical specimens with three different inerter coefficients are tested on the shake table under sine-sweep excitation with three different amplitudes. Experimental frequency response functions (FRFs) are derived manifesting a softening nonlinear behavior of the specimens and enhanced vibration suppression with increased inerter coefficient. Further, a 2DOF parametric nonlinear model of the specimen is established accounting for non-ideal inerter device behavior and its potential to characterize experimental response time-histories, FRFs, and force-displacement relationships of the HDRIs and of the inerter is verified

The transformative potential of reflective diaries for elite English cricketers

The sport of cricket has a history of its players suffering from mental health issues. The psychological study of cricket and, in particular, the attendant demands of participating at an elite level has not previously received rigorous academic attention. This study explored ten elite male cricketers’ experiences of keeping a daily reflective diary for one month during the competitive season. The aim was to assess how valuable qualitative diaries are in this field. Participants were interviewed regarding their appraisal of the methodology as a self‐help tool that could assist coping with performance pressures and wider life challenges. Three outcomes were revealed: first, that diary keeping was an effective opportunity to reflect upon the past and enhance one’s self (both as an individual and a performer); second, that diary keeping acted as a form of release that allowed participants to progress; and third, that diary keeping allowed participants to discover personal patterns of success that increased the likeliness of optimum performance

Dynamic relaxation of the elastic properties of hard carbon films

The effect of enhanced atomic mobility on the growth of hard carbon films was examined. Tetrahedrally bonded amorphous carbon films were deposited by condensing energetic carbon ions using an arc-discharge deposition method. The deposition temperature varied between 50 and 400 °C. The dependence of elastic properties on deposition temperature was examined by determining the frequency-dependent propagation velocity of ultrasonic surface acoustic waves induced by a laser. A remarkable decrease in elastic coefficient was revealed above the deposition temperature of 300 °C and complete relaxation was obtained at 400 °C. This observation was analyzed by using a simple model which was in turn supported by molecular dynamics simulations. The relaxation turns out to be a thermally activated, dynamic process with an activation energy of 0.57 eV. Possible relaxation mechanisms associated with the migration of atoms or defects on a growing surface are discussed.Peer reviewe

AI-driven science communication: Leveraging LLMs and knowledge graphs for seamless knowledge exchange

Purpose Scientific knowledge is increasingly captured in structured formats, such as knowledge graphs, yet it remains largely inaccessible to non-technical users. We present EcoToxFred, a prototype conversational AI agent that enables intuitive, natural language access to curated environmental toxicology data. Designed to support users without programming expertise, EcoToxFred facilitates the exploration of complex datasets, such as chemical exposures and species-specific hazard information in European surface waters.Methods EcoToxFred integrates a large language model (LLM) with a Neo4j graph database via a retrieval-augmented generation (RAG) architecture. The system employs a decision-making agent to interpret user queries, invoke appropriate tools, and translate natural language input into formal graph queries. Outputs are validated and returned in multiple formats, like text, tables, and interactive maps, and are grounded in structured, curated monitoring and hazard data.Results The agent bridges the gap between human intent and formal data retrieval, enabling researchers, policy advisors, and stakeholders to pose complex, multi-step queries without prior training in query languages. By grounding LLM outputs in structured data, we demonstrate the system’s ability to respond to diverse question types and deliver transparent, accurate, and context-aware results. EcoToxFred successfully answers broad and highly specific queries, bridging natural language input with formal data retrieval.Conclusion EcoToxFred represents a scalable and transferable framework for human-AI interaction in domain-specific contexts, combining natural language interfaces with structured data. By lowering access barriers to scientific knowledge, the system supports evidence-based decision-making and fosters responsible, human-centered AI use in environmental science and beyond

Airborne observations of the Eyjafjalla volcano ash cloud over Europe during air space closure in April and May 2010

© Author(s) 2011. This work is distributed under the Creative Commons Attribution 3.0 LicenseAirborne lidar and in-situ measurements of aerosols and trace gases were performed in volcanic ash plumes over Europe between Southern Germany and Iceland with the Falcon aircraft during the eruption period of the Eyjafjalla1 volcano between 19 April and 18 May 2010. Flight planning and measurement analyses were supported by a refined Meteosat ash product and trajectory model analysis. The volcanic ash plume was observed with lidar directly over the volcano and up to a distance of 2700 km downwind, and up to 120 h plume ages. Aged ash layers were between a few 100 m to 3 km deep, occurred between 1 and 7 km altitude, and were typically 100 to 300 km wide. Particles collected by impactors had diameters up to 20 μm diameter, with size and age dependent composition. Ash mass concentrations were derived from optical particle spectrometers for a particle density of 2.6 g cm-3 and various values of the refractive index (RI, real part: 1.59; 3 values for the imaginary part: 0, 0.004 and 0.008). The mass concentrations, effective diameters and related optical properties were compared with ground-based lidar observations. Theoretical considerations of particle sedimentation constrain the particle diameters to those obtained for the lower RI values. The ash mass concentration results have an uncertainty of a factor of two. The maximum ash mass concentration encountered during the 17 flights with 34 ash plume penetrations was below 1 mg m-3. The Falcon flew in ash clouds up to about 0.8 mg m-3 for a few minutes and in an ash cloud with approximately 0.2 mg -3 mean-concentration for about one hour without engine damage. The ash plumes were rather dry and correlated with considerable CO and SO2 increases and O3 decreases. To first order, ash concentration and SO2 mixing ratio in the plumes decreased by a factor of two within less than a day. In fresh plumes, the SO2 and CO concentration increases were correlated with the ash mass concentration. The ash plumes were often visible slantwise as faint dark layers, even for concentrations below 0.1 mg m-3. The large abundance of volatile Aitken mode particles suggests previous nucleation of sulfuric acid droplets. The effective diameters range between 0.2 and 3 μm with considerable surface and volume contributions from the Aitken and coarse mode aerosol, respectively. The distal ash mass flux on 2 May was of the order of 500 (240-1600) kgs -1. The volcano induced about 10 (2.5-50) Tg of distal ash mass and about 3 (0.6-23) Tg of SO2 during the whole eruption period. The results of the Falcon flights were used to support the responsible agencies in their decisions concerning air traffic in the presence of volcanic ash.Peer reviewe

Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells

Spinorial Field and Lyra Geometry

The Dirac field is studied in a Lyra space-time background by means of the classical Schwinger Variational Principle. We obtain the equations of motion, establish the conservation laws, and get a scale relation relating the energy-momentum and spin tensors. Such scale relation is an intrinsic property for matter fields in Lyra background.Comment: 10 pages. Some misprints correcte