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Alice in Quantum Land — Quantum Mechanics and its influence in (pop) culture

In this seminar we will discuss Quantum Mechanics (QM) not so much from the traditional point of view of Physics, but to assess the inevitable “reverberations” that this discipline has had, and still has, in popular culture. Indeed, one of the aspects known even to the layman is the strangeness of the laws that govern the subatomic world, where totally counterintuitive things happen. Those who are used to doing science in the traditional way, resting their research on solid epistemological foundations, when confronted with QM must “suspend judgment” and very often use it – very pragmatically – as a simple tool (which Physicists have shown they can do very well). The seminar will focus on the bewilderment that the forerunners of this discipline already had to overcome to accept the “rules” it imposed, and we will see that among them even eminent minds made an enormous effort to accept these rules, when not even going so far as to reject this “new Physics” altogether. The seminar will then briefly explore the more “pop” side, which is how, from the point of view of popularizing science, QM offers excellent tools to intrigue a lay audience.

Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning

With the development of advanced predictive modelling techniques, we are witnessing a steep increase in model development initiatives in genomics that employ high-end machine learning methodologies. Of particular interest are models that predict certain genomic or biological characteristics based solely on DNA sequence information. These models, however, treat the DNA sequence as a mere collection of four, A, T, G and C, letters, thus dismissing the past physico-chemical advancements in science that can enable the use of more intricate information about nucleic acid sequences. Here, we provide a comprehensive database of quantum mechanical and geometric features for all the permutations of 7-meric DNA in their representative B, A and Z conformations. The database is generated by employing the applicable high-cost and time-consuming quantum mechanical methodologies. This can thus make it seamless to associate a wealth of novel molecular features to any DNA sequence, by scanning it with a matching k-meric window and pulling the pre-computed values from our database for further use in modelling. We demonstrate the usefulness of our deposited features through their exclusive use in developing a model for A to C mutation rate constants. The DNA k-mer quantum mechanical parameters can also be found <a href="https://github.com/SahakyanLab/DNAkmerQM" target="_blank" rel="noopener">https://github.com/SahakyanLab/DNAkmerQM</a>, the corresponding research and development code from <a href="https://github.com/SahakyanLab/NucleicAcidsQM" target="_blank" rel="noopener">https://github.com/SahakyanLab/NucleicAcidsQM</a>, and the associated pre-print from <a href="https://doi.org/10.1101/2023.01.25.525597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.01.25.525597</a>.

The Neural Mechanism Underlying The Effect of Musical Training on Phonological Awareness of preschoolers : A Meta-Analysis

Open the record for dataset details and reuse information.

opencc-zeroMar 2024View details →

DNA-silica nanolattices as mechanical metamaterials

Mechanical metamaterials consist of intricate periodic structures made using additive manufacturing techniques. Yet, nanoscale (<10 nm) features cannot be directly printed using these fabrication techniques, although this is the size regime in which enhanced material properties appear. In addition, current additive manufacturing techniques cannot easily combine disparate materials (e.g., soft, biological polymers with hard ceramics) into structural motifs. Here, we show that DNA origami can be used to construct octahedral-based isotropic and anisotropic nanolattices. When coated with a thin silica layer, these nanolattices obtain strength and energy absorption competitive with the best additively manufactured nanolattices. The DNA nanolattices have strut 6 nm diameters and ~50 nm unit cells, which are two orders of magnitude smaller than lithography-based lattices. The silica coating is as thin as ~1.65 nm, which results in enhanced strength. Atom probe tomography confirms the nanoscale distribution of DNA and silica in the octahedral lattice geometry. Finite element modeling (FEM) reveals two dominant failure modes: buckling at lower coating thicknesses and tensile fracture at higher thicknesses. Molecular dynamics (MD) simulations reveal that the DNA delays failure by suppressing buckling within the lattice struts, while the nanoscale silica undergoes a surface buckling mode which contributes to increased strength at large strains.

Results of the mechanical characterization by tensile tests and the in vitro cell-biomaterial interaction analyses by WST-1 and Live/Dead of 3D-printed scaffolds generated by PLA, PCL, FF, FD and GelMA

Dataset containing the quantitative results of the mechanical characterization, and the in vitro cell-biomaterial interaction analyses with neural cells after 72 hours and 7 days of cell culture of the following 3D printed scaffolds: <ul> <li>Polylactic acid (PLA)</li> <li>Polycaprolactone (PCL)</li> <li>Conductive Filaflex (FF)</li> <li>Flexdym (FD)</li> <li>GelMA (G)</li> </ul> The Live/Dead results were quantified using ImageJ software to determine area fractions corresponding to live (green) and dead (red) cells.

Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve

Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (Fragum sueziense) and a closely related non-symbiotic species (Trigoniocardia granifera) under different light conditions to detect potential molecular pathways involved in mollusk photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared to those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologs in T. granifera transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as mollusks and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in driving host-symbiont adaptations in diverse organisms.

opencc-by-4.0Dec 2022View details →

Mechanism for SO2 poisoning of Cu-CHA during low temperature NH3-SCR

Dataset related to the article with the same title and authors: <a href="https://www.sciencedirect.com/science/article/pii/S0021951722005255">Mechanism for SO2 poisoning of Cu-CHA during low temperature NH3-SCR</a>   The zip file contain selected structures and a README.txt file with additional information.

opencc-by-4.0Apr 2024View details →

The proteolytic cleavage of TLR8 Z-loop by furin protease - molecular recognition, reaction mechanism and role of water molecules DATASET_v2

The dataset comprises: i) AlphaFold-Multimer predictions for TLR8LRR-furin complex ii) The optimised structures of QM cluster models for reactant (RE), intermediate1-3 (INT1-INT3), and product (PROD) iii) The optimised structures of QM/MM model for RE, INT1-INT3, PROD iv) Input structures used in MD simulations and parameterization files for non-standard residues for RE, INT1-INT3, PROD v) PyMOL sessions from AQUA-DUCT calculations for RE, INT1-INT3, PROD

opencc-zeroDec 2023View details →

Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs

Background: Sesarmid crabs dominate mangrove habitat as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory is not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove forest ecosystems. Although endogenous cellulases expressions were reported in crab species, it remains unknown if the endogenous enzymes alone can complete the whole lignocellulolytic pathway, or they also depend on the contribution from their intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach. Results: Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab species gut microbiome have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation in mangrove crabs and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. The herbivorous and detritivorous crabs showed highly similar CAZyme composition compared to dissimilarities observed in taxonomic profiles observed in both groups, suggesting a stronger selection force to gut microbiota by its functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of the gut microbiota in supplementing nitrogen that is deficient in plant diet. Conclusions: Endosymbiotic cellulolytic microbes play an important role in lignocellulose degradation in most crab species but their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity for digestion of mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in mangrove crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrate species.

opencc-by-4.0Apr 2024View details →

Hellenistic-Roman bioarchaeological mechanical stress data - MetaMobility project

This database covers the bioarchaeological data we could extract on Hellenistic-Roman period skeletal markers of mechanical stress in the Central and Eastern Mediterranean and Middle East. Specifically, it covers degenerative joint disease (osteoarthritis) in the major appendicular joints of the skeleton, intervertebral disc disease (spinal arthritis on the vertebral bodies and apophyseal joints), Schmorl's nodes and entheseal changes. The database was created as part of the MetaMobility project (EXCELLENCE/0421/0376), which is implemented under the programme of social cohesion “THALIA 2021-2027” cofunded by the European Union, through the Research and Innovation Foundation.

Dataset for publication Reaction Mechanism and Performance of Innovative 2D Germanane-Silicane Alloys SixGe1−xH Electrodes in Lithium-Ion Batteries

A dataset for publication Datase for publication Reaction Mechanism and Performance of Innovative 2D Germanane-Silicane Alloys SixGe1−xH Electrodes in Lithium-Ion Batteries including all relevant data used in the manuscript. Information on how to use the dataset are included in the readme file.

Azole resistance mechanisms and population structure of Aspergillus fumigatus on retail plant products

Aspergillus fumigatus is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant A. fumigatus was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant A. fumigatus across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant A. fumigatus is prevalent in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. Resistant isolates had the TR34/L98H, TR46/Y121F/T289A, G448S, and H147Y cyp51A alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A-mechanisms contribute to pan-azole resistance in some isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components (DAPC) identified three primary clusters. This is consistent with previous studies detecting three clades of A. fumigatus and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates the risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.

opencc-by-4.0Dec 2023View details →

Supplemental Material to Doctoral Thesis "Engineering approach for predicting tunneling crack initiation in trailing-edge adhesive joints of wind turbine blades under mechanical fatigue and thermal residual stresses"

This set supplements the figure data to the doctoral thesis "Engineering approach for predicting tunneling crack initiation in trailing-edge adhesive joints of wind turbine blades under mechanical fatigue and thermal residual stresses", DOI: <a href="https://doi.org/10.14279/depositonce-19144">10.14279/depositonce-19144</a>

The puncture mechanics: an example from the bed bug Cimex lectularius showing traumatic insemination using the paramere

Cimicidae are well-known for traumatic insemination, and males pierce females with their parameres and transfer sperm through them. The shape of parameres is relatively stable in the family, but in some genera the paramere is elongated, appearing less resistant against lateral deflection. To understand the mechanical limitations of the paramere, we studied its penetration mechanics of the common bed bug, Cimex lectularius. We examined the postabdominal morphology, paramere geometry, and material properties and conducted breaking stress experiments on the paramere under wet and dry conditions. Mechanical property gradients are present with the paramere tip as the stiffest region and the base as the most flexible one. These mechanical properties relate to the presence of Ca, Zn, and Si. The basal wing-shaped structure is flexible, enabling it to interlock with the anal region during mating. The paramere is slightly twisted; the tip region is circular in cross-section, and the geometry of the rest is rather complex. In the mechanical test, wet parameres mainly buckled, while dried parameres broke off. The level of structural failures depended on the directions from which the compression forces were applied. Structural, material, and mechanical strengthening mechanisms preventing the paramere from mechanical failure are discussed.

Mentalising mechanisms underly strategic coordination in Guinea baboons (Papio papio)

It remains controversial whether the ability to mentalise is confined to humans. To address this question, Guinea baboons living in a social colony freely came to play a 2-players coordination game with any other baboon, or alone (social vs solo conditions). In fact, in both conditions, they interacted with an identical Artificial Agent. Their choice behaviour depended on the social context and their relative dominance hierarchy. A mentalising computational model accounted for baboons' behaviour better than simpler models without mentalizing components in the social condition while the same baboons used a simpler strategy when they played alone. Together, these findings indicate that computations required for mentalising and used for coordination learning may have evolved in the common ancestor of the Old-World monkey and apes.

opencc-by-sa-4.0Aug 2023View details →

Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism

Code and data for our paper: <a href="doi.org/10.3389/fninf.2024.1323203">Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism</a> Marvin Kaster, Fabian Czappa, Markus Butz-Ostendorf, Felix Wolf

opencc-by-4.0Jan 2024View details →

Data supporting "Transition between mechanical and geometric controls in glacier crevassing processes".

The folders: <ul> <li>results_Geometrical_Regime</li> <li>results_Mechanical_Regime</li> <li>results_3D</li> <li>results_varyingLengthSlope</li> <li>results_varyingVelocity</li> </ul> contain the data for spacing and depth of the crevasses in the different simulations. Each simulation folder is named after the ice thickness H and cohesion c. For example, H300c2 means an ice thickness of 300m and a cohesion of 2MPa. The simulation files contain data measured every 10 frames. Empty files imply two possibilities: -the crevasse(s) are away from the window measurement (the window is approximately 1500m wide around the obstacle). -No crevasses are observed or at least no distinguishable enough. ** The python code readDataMeasuredInSimulations.py use the readDataPP class to plot the measures from the previous folders. All the figures from the paper can be reproduced using this code. ** The full simulation results cannot be transfered as a supplementary material as it is too large (20Go for each simulation). However we provide two full result files: H300_c0_4.abc and  H100_c2.abc. We provide an example of the init.lua file used to launch a simulation with given parameters and configurations. The configurations used in the simulations are all provided in the geometry.zip file. A version of the MPM numerical model can be found in a previous publication at https://www.nature.com/articles/s43247-021-00179-7.

Mechanism of DNA unwinding by MCM8-9 in complex with HROB

HROB promotes the MCM8-9 helicase in DNA damage response. To understand how HROB activates MCM8-9, we defined their interaction interface. We showed that HROB makes important yet transient contacts with both MCM8 and MCM9, and binds the MCM8-9 heterodimer with the highest affinity. MCM8-9-HROB prefer branched DNA structures, and display low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexamer that assembles from dimers on DNA in the presence of ATP. The hexamer involves two repeating protein-protein interfaces between the alternating MCM8 and MCM9 subunits. One of these interfaces is quite stable and forms an obligate heterodimer across which HROB binds. The other interface is labile and mediates hexamer assembly, independently of HROB. The ATPase site formed at the labile interface contributes disproportionally more to DNA unwinding than that at the stable interface. Here, we show that HROB promotes DNA unwinding downstream of MCM8-9 loading and ring formation on ssDNA.

Data from: Physical mechanisms of deep convective boundary layer leading to dust emission in the Taklimakan desert

Deserts play an important role in the climate system, which is closely associated with the emission and transport of dust aerosols. Based on the intensive observation experiment in the Taklimakan Desert, the potential physical processes between the deep convective boundary layer (CBL) and dust emission are revealed in this study. Deep CBL enables the formation of clouds in the late afternoon, leading to significant cooling of surface. Large-scale buoyant coherent structures thereby transform into the mechanical coherent structures confined near the surface. The responses promote the earlier occurrence of low-level jet (LLJ) than in cloudless conditions, which allows the downward transport of LLJ momentum and substantially increases surface wind. Therefore, dust emission is initiated by strong wind at dusk and lasts for several hours. The results are useful to predict dust emissions and improve our understanding of distinctive boundary-layer processes in desert regions.

The respiratory system influences flight mechanics in soaring birds

The subpectoral diverticulum (SPD) is an extension of the respiratory system in birds that dives between the primary muscles responsible for flapping the wing. Surveying the pulmonary apparatus in 68 species showed that the SPD was present in virtually all soaring taxa investigated yet absent in non-soarers. We find that this structure independently evolved with soaring flight at least seven times, indicating that the diverticulum may have a functional and adaptive relationship with this flight style. Using the soaring hawks Buteo jamaicensis and B. swainsoni as models, we show that the SPD is not integral for ventilation, that an inflated SPD can increase the moment arm of cranial parts of the pectoralis, and that pectoralis muscle fascicles are significantly shorter in soaring hawks than in non-soaring birds. This coupling of an SPD-mediated increase in pectoralis leverage with force-specialised muscle architecture produces a pneumatic system adapted for the isometric contractile conditions expected in soaring flight. The discovery of a mechanical role for the respiratory system in avian locomotion underscores the functional complexity and heterogeneity of this organ system and suggests that pulmonary diverticula likely have other undiscovered secondary functions. These data provide a mechanistic explanation for the repeated appearance of the SPD in soaring lineages, demonstrating that the respiratory system can be co-opted to provide novel biomechanical solutions to the challenges of flight and thereby influence the evolution of avian volancy.