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opencc-zeroFeb 2023View details →

GPS data from cellphones for Mechanical Analog

Motivated by the increasing need to develop a quantitative, science-based, predictive understanding of the dynamics and response of cities when subjected to hazards, in this paper we apply concepts from statistical mechanics and microrheology to develop mechanical analogs for cities with predictive capabilities. We envision a city to be a matrix where people (cell-phone users) are driven by the city's economy and other associated incentives while using the collection of its infrastructure networks in a similar way that thermally driven Brownian probe particles are moving within a complex viscoelastic material. Mean-square displacements (ensemble averages) of thousands of cell-phone users are computed from GPS location data to establish the creep compliance and the resulting impulse response function of a city. The derivation of these time-response functions allows the synthesis of simple mechanical analogs that model satisfactorily the city's behavior under normal conditions. Our study concentrates on predicting the response of cities to acute shocks (natural hazards that stress the entire urban area) that are approximated with a rectangular pulse with finite duration, and we show that the solid-like mechanical analogs for cities that we derived predict that cities revert immediately to their pre-event response suggesting that they are inherently resilient. Our findings are in remarkably good agreement with the recorded response of the Dallas metroplex following the February 2021 North American winter storm, which happened at a time for which we have dependable GPS location data.

Supporting files for manuscript: Effect of the coordination environment on the ability of iron to bind/activate N2: relevance to the nitrogenase mechanism

Supporting files for manuscript 'Effect of the coordination environment on the ability of iron to bind/activate N2: relevance to the nitrogenase mechanism':  input files, optimized structures, checkpoint files usable for molecular orbital diagrams.

dataset for "Corner-bridge flow as pore-scale flow mechanism controlling capillary pressure curve at low saturations"

dataset for "Corner-bridge flow as pore-scale flow mechanism controlling capillary pressure curve at low saturations", including raw images from drainage experiments

Machine-guided path sampling to discover mechanisms of molecular self-organization (Training and validation data)

Training and validation data for the Nature Computational Science manuscript "Machine-guided path sampling to discover mechanisms of molecular self-organization"

Videos: The crystallization mechanism of gel-derived SiO2-TiO2 amorphous nanobeads elucidated by high-temperature in-situ experiments

Supplementary materials detailing high-temperature in-situ TEM experiments. Main article available at:  <a href="https://doi.org/10.1021/acs.cgd.3c00300">https://doi.org/10.1021/acs.cgd.3c00300</a>

Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination

This repository includes the following source datasets: 1. FluorescenceAnisotropyIII.zip This contains following files: <ol> <li>The raw fluorescence anisotropy file (Excel file) showing the values for Polarization, Anisotropy, Total Intensity, Intensity (parallel) and Intensity (perpendicular) for all the samples included in the paper as separate sheets.</li> <li>The analysis files generated in the Graphpad prism.</li> <li>The details of the files.</li> </ol>   2. FT-IR.zip: This contains the normalized values for the FT-IR spectroscopy of the WT RecF, WT RecR, RecF A170W and RecR A147W.   3. Glycerol gradient.zip: This contains the raw gel files for the three sets of independent experiments, standard protein ruler with the respective WT RecF, WT RecO and WT RecR and details regarding the loading of samples on gels.   4. Pull-downII.zip: This contains details of all the pull-down experiments and the raw gel files used for <ol> <li>Quantification</li> <li>The major samples for all the experiments done in triplicate</li> <li>Figure preparation for paper</li> </ol>

Mechanisms of the reaction of elemental sulfur and polysulfides with cyanide and phosphines

Gaussian 16 output files for all computed structures for "Mechanisms of the reaction of elemental sulfur and polysulfides with cyanide and phosphines". Chemistry - A European Journal, 2023, e202203906. DOI: 10.1002/chem.202203906

Datasets for Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17ß13

Datasets used in the publication ' Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17ß13'

Ice Mechanics for 1-D Lake Models

These files are in support of a submission to Geophysical Research Letters by M. MacKay entitled "Ice Concentration Scaling Laws for Freshwater Lakes in Numerical Weather and Climate Prediction"

opencc-by-4.0Feb 2023View details →

Frequency-dependent mechanical properties of the Greenland upper mantle calculated using the Very Broadband Rheology calculator

Frequency-dependent mechanical properties of the Greenland upper mantle calculated using the VBRc Frequency-dependent mechanical properties of the upper mantle beneath Greenland inferred using three-dimensional Bayesian inference of mantle thermodynamic state using the Very Broadband Rheology calculator (VBRc). Mechanical properties include the complex modulus, apparent viscosity, maxwell time, and apparent lithosphere thickness. They have been calculated for two constitutive models of anelastic behaviour - master curve fit with pre-melting scaling and extended Burgers with pseudoperiod scaling. These results are described in: Paxman, G.J.G., Lau, H.C.P., Austermann, J., Holtzman, B.K., Havlin. C., (2023), Inference of the Timescale‐Dependent Apparent Viscosity Structure in the Upper Mantle Beneath Greenland, AGU Advances 4(2), doi: 10.1029/2022AV000751. All variables are contained within a single NetCDF file.

opencc-zeroMar 2023View details →

Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modelling framework, which determines the time-dependency of DNA variant-age-at-onset associations, without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the sign of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages, and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age-dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modelling of large-scale biobank data.

Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility

Snapshots from MD simulations (with umbrella sampling and metadynamics) of respiratory complex I. Only subunits ND1, NDUFS2 and NDUFS7 (with the membrane spanning N-terminus truncated) and rotenone are shown in binding mode (see Fig. 2 of main paper):  1) ROT1:        configurations/rot1.pdb 2) pre-redox:   configurations/rot1.5.pdb 3) ROT2:        configurations/rot2.pdb Force-field and topology files in GROMACS format: 4) Bonded parameters:           parameters/rotenoids_ffBonded.itp 5) Rotenone:                    parameters/rot.itp 6) Dehydrated derivative:       parameters/dehyd_rot.itp

Stress-induced anisotropic poroelasticity in Westerly granite: Mechanical and Ultrasonic data

Data obtained from triaxial loading experiments conducted on thermally cracked Westerly granite which was initially dry and later saturated with water. Text files (.txt) are raw, unprocessed time series of mechanical data including load, shortening and radial and axial strain gauge measurements. Except noted, units are in Volts. Strain gauge voltages can be converted into strain using gauge factor of 2.11 and amplification factor of 40. External shortening can be converted to sample shortening using a machine stiffness of 480 kN/mm. Raw ultrasonic data are combined in folder named BSF*. Data format is binary, and can be read using ASC ltd. software "Insite". Files "sensors.txt" contain ultrasonic sensor positions and time offset corrections. Mechanical and Ultrasonic data are provided for when the sample was dry. Only mechanical data are provided for saturated conditions.

opencc-zeroDec 2022View details →

Data from: Internal injuries in marine fishes caught in beam trawls using electrical versus mechanical stimulations

To improve the ecological and economic sustainability in the Dutch beam trawl fishery, tickler chains were replaced by electrical pulse stimulation to drive sole (Solea solea) out of the seabed. Because electrical stimulation may cause internal injuries, we quantified this risk by sampling fish species from commercial beam trawlers and recording spinal injuries and haemorrhages from X-radiographs and autopsy. To distinguish mechanically and electrical-pulse-induced injuries, we compared injuries in ten species sampled from pulse (PUL) and tickler-chain (TCK) trawlers and four species sampled from PUL trawlers with the stimulus switched on or off. Co-occurrence of a major spinal injury and major haemorrhage at the same location was only observed in PUL samples, and were frequently (40%) observed in cod (Gadus morhua) and in low numbers (0–2%) in whiting (Merlangius merlangus), grey gurnard (Eutrigla gurnardus), and greater sandeel (Hyperoplus lanceolatus), but not in flatfishes and other species. In cod, injury occurrence correlated with fish length, with lower probabilities for small fish. Major spinal injury or major haemorrhage occurrence in PUL (range: <1–16%) was lower than in TCK (range: <1–42%) in eight of the ten species studied. Population-level consequences of pulse-induced injuries are considered negligible.

opencc-zeroApr 2023View details →

Acceleration of Diels-Alder reactions by mechanical distortion

Challenges in quantifying how force affects bond formation have hindered the widespread adoption of mechanochemistry. Here, parallel tip-based methods are used to determine reaction rates, activation energies, and activation volumes of force-accelerated [4+2] Diels-Alder cycloadditions between surface-immobilized anthracene and four dienophiles that differ in electronic and steric demand. The rate dependences on pressure are unexpectedly strong, and significant differences are observed between the dienophiles. Multiscale modeling demonstrates that, in proximity to a surface, mechanochemical trajectories ensue that are distinct from those observed solvothermally or under hydrostatic pressure. These results provide a framework for anticipating how experimental geometry, molecular confinement, and directed force contribute to mechanochemical kinetics.

Data for the manuscript "Ion-mediated condensation controls the mechanics of mitotic chromosomes"

Data accompanying the manuscript "Ion-mediated condensation controls the mechanics of mitotic chromosomes". Each folder contians data to one set of experiments together with scripts to analyse the data and produce plots.

Dataset: Scatter of mechanical properties of 2D biaxial and triaxial braided reinforced composites and their correlation with visual features

The data represents tensile tests of 2D braided biaxial and triaxial composite laminates. Braids were produced on a Herzog radial braiding machine RF 1-176-100 with carbon fiber yarns (Toho Tenax F13 HTS40 12K 800 tex). Test laminates are infused with a VARI process with the 2-component epoxy resin system Hexion RIM235/RIMH237. The infusion is performed at vacuum pressure leves of 20-30 mbar and the resin is cured at room temperature for 24 hours at a pressure level of 250 mbar. A subsequent post-cure step maximizes matrix properties at 70°C for 10 hours. The braid setups have been chosen to achieve four different braids with a fiber angle of 45° on braid mandrels with a diameter of 120 mm, two biaxial ones and two triaxial ones. By using different sizes of braiding ring diameters and yarn forces, homogeneous and inhomogeneous fiber architectures are generated. Braiding setups 1 (biaxial) and 2 (triaxial)  with 130 mm braiding ring diameter and 350 g yarn force result in braids with homogeneous fiber architecture. 3 (biaxial, 400 mm braiding ring, 600 g yarn force) and 4 (triaxial, 250 mm braiding ring, 600 g yarn force) in braids with inhomogeneous scattering of visual characteristics. Single layers are braided on mandrels with a length of 1500 mm and laminates with 6 layers of biaxial and 4 layers of triaxial braids are subsequently infused. Tensile tests are performed on a Schenck-Trebel RM250 universal testing machine according to AITM 1-0007. For each specimen, the individual fiber orientation in each layer is measured prior to infusion by image analysis performed on scans of the braided layers. The results show a strong dependence of the individual fiber orientation of single test specimens on their mechanical properties in case of the presented tensile tests

Dataset for the paper "The Relationship Between Different Python Argument-Passing Mechanisms and Fixes: An Empirical Study"

This is the replication package of the article The Relationship Between Different Python Argument-Passing Mechanisms and Fixes: An Empirical Study   Abstract: Modern programming languages (such as Python, but not only) have introduced a variety of constructs and syntactical elements to make software development more efficient and concise. Examples include lambda functions, comprehension collections, of mechanisms to facilitate the passing of arguments to a function. While many of such constructs may, in principle, be beneficial for developers, recent studies have shown that certain programming constructs introduce atoms of confusion, and may therefore affect program understanding. Moreover, recent work has shown that changes to some constructs, namely functional constructs of Python, induce more fixes than other changes. This paper studies the effect of different Python argument-passing mechanisms to investigate their relationship with code proneness to be fixed. Specifically, we study the fix-proneness for what concerns the function definition, as well as its invocation. This is done by analyzing the evolutionary history of 200 Python projects, for a total of about 3M functions and 12M call sites. While there are varying effects for what concerns parameter declaration mechanisms, we found evidence that keyword-based argument passing is less defect prone than positional argument passing, and this is not affected by size-related confounding factors.

Evaluation of the pKa's of Quinazoline Derivatives : Usage of Quantum Mechanical Based Descriptors

In this study, several quantum mechanical-based computational approaches have been used in order to propose accurate protocols for predicting the pKa’s of quinazoline derivatives, which constitute a very important class of natural and synthetic compounds in organic, pharmaceutical, agricultural and medicinal chemistry areas. Linear relationships between the experimental pKa’s and nine different DFT descriptors (atomic charge on nitrogen atoms (Q(N), ionization energy (I), electron affinity (A), chemical potential (m), hardness (h), electrophilicity index (w), fukui functions (f +, f -), condensed dual descriptor (Df) and local hypersoftness (s(2))) were considered. Several DFT methods (a combination of five DFT functionals and two basis sets) in conjunction with two different implicit solvent models were tested, and among them, M06L/6-311++G(d,p) level of theory employing the CPCM solvation model was found to give the strongest correlations between the DFT descriptors and the experimental pKa’s of the quinazoline derivatives. The calculated atomic charge on N1 atom (Q(N1)) was shown to be the best descriptor to reproduce the experimental pKa’s (R2=0.927), whereas strong correlations were also derived for A, w, m,  and Δf. In the last part, the applicability of isodesmic reaction scheme to the pKa prediction of quinazoline derivatives was tested, and the calculated A was shown to be a well-established method for the classification of molecules, and thus, for the identification of a suitable reference molecule for the calculations. The QM-based protocols presented in this study will enable fast and accurate high-throughput pKa predictions of quinazoline derivatives and the relationships derived can be effectively used in data generation for successful machine learning models for pKa predictions.