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11,506 results for “Dynamics”
Molecular dynamics trajectories obtained from simulations of mechanically-controlled break-junctions and associated zero-bias conductance.
<p>This data set contains structural information and the associated zero-bias conductance of mechanically-controlled break-junction experiments. It contains:</p> <ul> <li>Six (multi) xyz files (trajectory_0X.xyz), which contain different trajectories produced by molecular dynamic simulations (using <a href="https://www.lammps.org/">LAMMPS</a> and <a href="https://docs.lammps.org/Packages_details.html#pkg-reaxff">reactive force fields</a>) of a mechanically-controlled break-junction. These simulations start from a gold wire with attached molecules. One side of the wire is slowly pulled away, until the gold wire is broken apart and a molecular junction is formed. The outermost six layers of the goldwire are frozen in the simulation. The temperature of the simulation was set to 300K.</li> <li>Six files (transmission_0X.dat) with the calculated zero-bias conductance (G/G<sub>0</sub>). Each entry corresponds to the zero-bias conductance of the corresponding structure from the xyz files. The zero-bias conductance was calculated using non-scc DFTB+, as, e.g., described <a href="https://dftbplus-recipes.readthedocs.io/en/latest/transport/carbon2d-trans.html">here</a>.</li> </ul> <p>For more information see dx.doi.org/XXXXXXX.</p>
"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.
<p><strong>Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data</strong><br> 3D ED data sets of 5 compounds and JANA refinement files of 12 compounds</p> <p><strong>Relevant tools</strong><strong>:</strong></p> <ul> <li>PETS2: data reduction and analysis of electron diffraction patterns <ul> <li>Download program and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Palatinus, L. <em>et al.</em> Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. <em>Acta Cryst. B</em><strong>75</strong>, 512–522 (2019). <a href="https://doi.org/10.1107/S2052520619007534">DOI: 10.1107/S2052520619007534</a></li> </ul> </li> <li>JANA2006: crystal structure model refinement program <ul> <li>Download program from <a href="http://jana.fzu.cz/">http://jana.fzu.cz/</a> and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Results here were obtained with JANA2006. We recommend using JANA2020.</li> <li>Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. <em>Z. Kristallogr.</em> <strong>229</strong>, 345–352 (2014). <a href="https://doi.org/10.1515/zkri-2014-1737">DOI: 10.1515/zkri-2014-1737</a></li> </ul> </li> <li>DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives <ul> <li>Program automatically included in JANA2006/JANA2020</li> <li>Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. <em>Acta Cryst. A</em><strong>71</strong>, 235–244 (2015). <a href="https://doi.org/10.1107/S2053273315001266">DOI: 10.1107/S2053273315001266</a></li> </ul> </li> </ul> <p><strong>3D ED data sets:</strong></p> <p>STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a>.</p> <ul> <li>α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)</li> <li>abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)</li> <li>STW_HPM-1, continuous-rotation (1 data set, room temperature)</li> <li>STW_HPM-1, continuous-rotation (1 data set, <em>T</em> = 100 K, cryotransfer)</li> </ul> <p><strong>JANA refinement and CIF files:</strong></p> <p>CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details.</p> <p>JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included.</p> <ul> <li>α-quartz</li> <li>albite</li> <li>mordenite</li> <li>natrolite</li> <li>STW_HPM-1</li> <li>cobalt aluminophosphate (CAP)</li> <li>CAU-36</li> <li>α-glycine</li> <li>carbamazepine</li> <li>(+)-limaspermidine</li> <li>abiraterone acetate</li> <li>MBBF4</li> </ul> <p>For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files.</p> <p>Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.</p>
data sets of "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland"
<p>data sets from "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland"</p> <p>Monthly means ozone profiles data sets of MCH homogenized Dobson D051 and of Brewer B040 used in the article entitled: "Dynamic Linear Modeling estimates of long-term ozone trends from homogenized Dobson Umkehr profiles at Arosa, Switzerland" by Eliane Maillard Barras, Alexander Haefele, René Stübi, Achille Jouberton, Herbert Schill, Irina Petropavlovskikh, Koji Miyagawa, Martin Stanek, and Lucien Froidevaux.</p> <p><a href="https://doi.org/10.5194/acp-2022-344">https://doi.org/10.5194/acp-2022-344</a></p>
Data from: Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs
<p>Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, i.e. resistance, resilience and elasticity, using a tritrophic ---and thus more realistic---plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift towards a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and potentially elasticity as functional diversity declines.</p>
Effect of iron content on thermal conductivity of ferropericlase: implications for planetary mantle dynamics
<p>Dataset for the article "Effect of iron content on thermal conductivity of ferropericlase: implications for planetary mantle dynamics".</p> <p>by Youyue Zhang, Takashi Yoshino, Masahiro Osako, submitted to Journal of Geophysical Research: Solid Earth.</p>
Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations
<p># *"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"*</p> <p>The input files and data used for the paper *"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"* are separated in the different folders depending stage they belong to.</p> <p>## Folders</p> <p> 1. **01_inputs:** The MD trajectory of DhaA used (only protein atoms present)<br> 2. **02_sliced_trajectory:** The CAVER3 results for the sliced trajectory (eight parts)<br> 3. **03_sliced_filtered:** Filtered CAVER3 results and results from the divide-and-conquer approach<br> 4. **04_full_trajectory:** The CAVER3 results for the full trajectory analysis<br> 5. **05_guided_example:** Guided example for the divide-and-conquer approach<br> </p>
Occurrences and R code for: Dynamic distribution modeling of the Swamp Tigertail dragonfly Synthemis eustalacta (Odonata: Anisoptera: Synthemistidae) over a 20-year bushfire regime
<p>Intensity and severity of bushfires in Australia have increased over the past few decades due to climate change, threatening habitat loss for numerous species. Although the impact of bushfires on vertebrates is well-documented, the corresponding effects on insect taxa are rarely examined, although they are responsible for key ecosystem functions and services. Understanding the effects of bushfire seasons on insect distributions could elucidate long-term impacts and patterns of ecosystem recovery. Here, we investigated the effects of recent bushfires, land-cover change, and climatic variables on the distribution of a common and endemic dragonfly, the swamp tigertail (<em>Synthemis</em> <em>eustalacta</em> (Burmeister, 1839)), which inhabits forests that have recently undergone severe burning. We used a temporally dynamic species distribution modeling approach that incorporated 20 years of community-science data on dragonfly occurrence and predictors based on fire, land cover, and climate to make yearly predictions of suitability. We also compared this to an approach that combines multiple temporally static models that use annual data. We found that for both approaches, fire-specific variables had negligible importance for the models, while percent of tree and non-vegetative cover were the most important. We also found that the dynamic model outperformed the static ones when evaluated with cross-validation. Model predictions indicated temporal variation in area and spatial arrangement of suitable habitat but no patterns of habitat expansion, contraction, or shifting. These results highlight not only the efficacy of dynamic modeling to capture spatiotemporal variables, such as vegetation cover for an endemic insect species, but also provide a novel approach to mapping species distributions with sparse locality records.</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 1df
<p>smTIRF-FRET Data for Fig 1, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Research data supporting "Platinum Nanocatalyst Amplification: Redefining the Gold Standard for Lateral Flow Immunoassays with Ultra-Broad Dynamic Range"
<p>Research data supporting the publication: Loynachan C. N., et al., 2017, ACS Nano, DOI: http://dx.doi.org/10.1021/acsnano.7b06229.</p>
Figure 2: Dynamic curve of TSPP tissue concentration within the tumor
<p>TSPP is intravenously injected at 2 mg/kg over a period of ¯ve minutes,<br> and it attains a high saturation level from 24 to 36 hours<br> dC1/dt=k0/v - k C<sub>1</sub><br> after injection. The 12 hour period between the 24 th and 36th hour is<br> called the treatment window, and at some time within this period a physician<br> focuses a 630nm light on the targeted area. Di®erent tissues absorb and expel<br> substances from the blood at di®erent rates, and hence the concentration of<br> TSPP varies from tissue to tissue. Results show that maximum tumor TSPP<br> concentration levels were achieved at approximately 24 hours after administra-<br> tion. We model C1 with the following ¯rst order, linear di®erential equation:<br> C1 =k0/vk [1 - e<sup>kt</sup>]<br> Where:<br> ² C1 is the plasma concentration during injection;<br> ² k is the rate of elimination</p>
Figure 7: Cultural equipment dynamics modeling-MODELING SELF-ORGANIZING SYSTEMS WITH SOCIAL INSECTS ALGORITHMS
<p>The multi-template modelling can be used to model cultural equipment<br> dynamics as described in figure 7. On this figure, we associate a queen to each<br> cultural center (cinema, theatre, ...). Each queen will emit many pheromon<br> templates, each template is associated to a specific criterium (according to age,<br> sex, ...). Initially, we put the material in the residential place. Each material<br> has some characteristics, corresponding to the people living in this residential<br> area. The simulation shows the self-organization processus as the result of the<br> set of the attractive effect of all the centers and all the templates.</p>
Figure 11. Comparison of MultiNet and MST representations-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>In the sentence (7) there are two clauses describing two hypothetical situations. These two<br> situations are connected by the relation COND in MultiNet representation (Figure 11).</p>
Figure 10. Comparison of MultiNet and MST representations.-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>Helbig [18, p. 507] defines the expression (s MCONT c) as “a specification of the<br> informational or mental content c of a mental or informational process s… By default, the second<br> argument c is assumed to be a hypothetical object or situation.”<br> MCONT relation properties are roughly equivalent to those of subject-verb complexes<br> (SVSBs) of MST. MCONT relation can generally be treated as capturing the idea behind what<br> philosophers call propositional attitudes in representational theories of mind [12] or opaque<br> contexts [10] in semantics. For example, consider the sentence in (3) rewritten below as (6) and<br> semantic representation of which is given in Figure 10.</p>
Figure 8. Comparison of MultiNet and MST representations-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>Figure 8 shows the representation of the<br> first reading of the sentence (5) in MWR. The MultiNet is shown at top of the figure, and the corresponding mental space representation is shown at the bottom side. Blue circles mark<br> hypothetical or nonreal objects and situations and red circles mark real objects and situations.<br> Facticity value for John is real, for unicorn it is nonreal, and for the process of riding, marked with<br> blue broken circle, it is non-real as well.</p>
Figure 7. The mental spaces set up by the sentence If John buys the car, he will drive to Berlin.-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>In the sentence (4) there are three proper names which constitute elements of the base space<br> or reality space (R). The CNSB if sets up the hypothetical space (H) with elements identical to those<br> of reality space (Figure 7). Every space’s internal structure is presented in the boxes next to them.<br> In the next part, we will see how MultiNet’s built-in meaning representation mechanisms are<br> capable of representing the basic principles of mental space building outlined above.</p>
Figure 6. The mental spaces set up by the sentence Mary thinks that John smokes.-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>The proper nouns Mary and John setup a base space (B). By the help of background<br> knowledge and activated frames we know that they are names of female and male humans. Not<br> having access to the previous discourse, we also consider their existence presupposed. The SVSB<br> Mary thinks that sets up a belief space (L) relative to space B (Figure 6). The identity connector<br> maintains the referential link between elements a and a ׳ both referring to the same person.</p>
Figure 9. Comparison of MultiNet and MST representations-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>Second interpretation of the sentence (5) can be represented with changing John’s Facticity<br> attribute-value from [FACT = real] to [FACT = nonreal] making the whole situation and its<br> elements non-real (Figure 9).</p>
Figure 5. The mental spaces set up by the second interpretation of the sentence in the film, John is riding a unicorn.-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>Second interpretation: The proper name John exists only in film space without having a<br> counterpart in base space. Therefore, the second interpretation of the sentence is: John is a<br> film character who is riding a unicorn in the film (Figure 5).</p>
Figure 4. The mental spaces set up by the first interpretation of the sentence in the film, John is riding a unicorn-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>First interpretation: The reality space (let’s call it R) contains an element a associated with<br> the proper name John. The noun phrase a unicorn introduces an element b ׳ to the film space<br> (call it F). I is the connector linking a in the space B to a ׳ in the space F (Figure 4). Since the<br> elements of both mental spaces are co-referential, this connector is an identity connector.<br> The rectangles represent the internal structure of the spaces next to them. The dashed line<br> indicates that the space F is set up in relation to R and that it is subordinate to R in<br> discourse.</p>
Figure 1. The upper ontology of sorts in MultiNet (after Helbig [17])-Representing Mental Spaces and Dynamics of Natural Language Semantics
<p>One of the distinguishing features of MultiNet is its commitment to the Cognitive Adequacy<br> requirement. According this requirement [9], semantic representations and knowledge<br> representations should be centered around concepts. Concepts2 are represented by nodes in the<br> graphical representation of the network. Every node belongs to a specific sort defined by the<br> MultiNet’s ontology of sorts (Figure 2).</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.