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393 results for “Molecular dynamics simulations”
Supplemental Materials for "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene"
<p>Supplemental Materials for the article entiled "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene" authored by M. Hanine et al. at Laboratory for Relativistic Astrophysics, Department of Physics, Guangxi University, 530004 Nanning, China.</p> <p>email: zw@gxu.edu.cn (Zhao Wang)</p> <p>SuppMater1.zip :</p> <p>Atomistic configurations of the formed PAH molecules (in 4.0 ns) at all studied temperatures are available in .xyz format. These .xyz files contain the atomic coordinates of the formed molecules by giving the total number of atoms that will be read on the first line; the comment text on the second; and the atomic number and three atomic Cartesian coordinates in the following lines. The name of the .xyz file consists of four parts separated by ``\_'' including the source molecule type, the temperature, the formation environment (with NP or in gas phase), and the molecular ID (among multiple molecules formed in a simulation). For instance, ``C6H2\_300K\_gas\_2.xyz'' stands for the 2nd molecule formed from C6H at 300K in the gas phase. Please read the 'readme.txt' file before using the data.</p> <p> </p> <p>SuppMater2.pdf:</p> <p>A data file that contains the DFT-calculated optimized structures and their atomic coordinates.</p> <p> </p> <p>SuppMater3.mp4:</p> <p>An animation demonstrating the formation process of PAHs on a carbon NP.</p>
Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation
A mixed system of cytochrome c (Cyt c, a typical hemoprotein) and DNA was constructed and the interaction between Cyt c and DNA were analyzed by experiment and molecular dynamics (MD) simulation methods, respectively. On the one hand, the experimental results showed: 1. The peroxidase activity of the mixed system was significantly enhanced relative to the Cyt c in 50 mM phosphate buffer solution at 25ºC. 2. UV-Vis spectra study found that, compared with the Cyt c solution, the absorbance of the Cyt c-DNA mixed system increased significantly at 280 nm, while the absorbance decreased at 405 nm, indicating that the overall structure of Cyt c in the mixed system became loose, and the structure around heme group became more compact. 3. Circular Dichroism (CD) studies showed that there was a weak interaction between DNA and Cyt c in the mixed system, which had little effects on the secondary structures of Cyt c. On the other hand, MD simulation results showed: 1. DNA and Cyt c were combined by hydrogen bonding and non-bonding interactions in the mixed system. 2. During the simulation process, N-Terminal α-Helix changed, and Lys13-Cys17 opened, exposing the active center (heme structure) of Cyt c, which may increase the binding of the mixed system to the substrate. 3. The bond length of Fe-N (N in His18 and Fe in heme group) became slightly shorter after equilibrium in the presence of DNA. 4. The Cyt c became loose after binding with DNA. 5. The total binding free energy between Cyt c and DNA was calculated to be -141.9 kJ/mol. The Cyt c-DNA system was in a relatively stable state from energy perspective. The results of the research on the structure and function of the Cyt c-DNA mixed system using experimental method and MD simulation method were consistent. The combination of experimental method and simulation method may provide useful research ideas and effective research methods for further studying the interaction mechanism between hemeprotein and DNA.
Dataset for "Strain induced electrochemical behaviours of ionic liquid electrolytes in an electric double layer capacitor: Insights from molecular dynamics simulations"
<p>The datafile contains molecular dynamics simulation results for analysing the electrochemical behaviour of ionic liquid based EDLC under compression and tension.</p>
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
<p>A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.</p>
Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
<p>These are the files needed to carry out the temperature induced infolding of crambin using Gromacs.</p>
Multiscale molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer
<p>The topology (gro) and trajectory (xtc) files for multiscale - coarse-grained (CG) and atomistic (AT) molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer. The coarse grained simulations are 10 microseconds long and the trajectories have 1 frame saved at every 10 ns, while the atomistic simulations are 100 ns long and have 2 frames saved at every nanosecond. </p>
The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations
<p>We investigated to characterize the dynamics of protein-RNA complexes and their interfaces at molecular level by performing a more systematic analysis. To get insights on the dynamics of protein-RNA complexes, all-atom MD simulations were generated for the manuscript "The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations". Nine protein-RNA complexes are studied in this work: 1ASY (an aspartyl-tRNA synthase/tRNA), 1JBS (a ribotoxin restrictocin/SRD RNA), 1MMS (a ribosomal protein L11/23S), 1OOA (a nuclear factor NF-kappaB p105 subunit/RNA aptamer), 1RKJ (a nucleolin/pre-rRNA), 2R8S (a FAB/P4-P6 RNA ribozyme domain), 2VPL (a 50S ribosomal protein/mRNA), 2ZM5 (a tRNA delta(2)-isopentenylpyrophosphate transferase/tRNA), 3IEV (a GTP-binding protein era/3' end of 16S rRNA). </p><p>Each folder for a complex is organised as followed:</p><ul><li>in <strong>complex</strong> there are the dry MD simulations for the complex protein-RNA with the starting structure</li><li>in <strong>protein</strong> there are the dry MD simulations for the unbound protein with the starting structure</li><li>in <strong>rna</strong> there are the dry MD simulations for the unbound RNA with the starting structure</li></ul><p>In each folder, all the trajectory files are named : <strong>md_(times of simulations).xtc</strong> and the starting structure called : <strong>start.gro</strong>.</p>
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations.
<p>In the present study, we describe the results from a computational microscopy perspective (also known as molecular dynamics simulation) at the atomistic resolution for the two gonadotropin hormone receptors, the follicle-stimulant hormone receptor and the luteinizing/chorionic gonadotropin hormone receptor, which are essential for reproduction in humans.</p>
Data from: Molecular dynamics simulation of the interaction between palmitic acid and high pressure CO2
<p>In this study, molecular dynamics simulation was used to explore the interaction characteristics of palmitic acid and CO2, and the effects of temperature and pressure on the solubility of palmitic acid in CO2 were investigated. In the range of 293K-353K and 5MPa-30MPa, the snapshot of palmitic acid distribution in CO2 shows that the molecular chain of palmitic acid in high-density CO2 system is more straight and more dispersed than that in low-density CO2 system. The radial distribution function further clearly shows that the solubility of palmitic acid in CO2 decreases with the increase of temperature and increases with the increase of pressure, which is consistent with the fatty acid solubility data reported in the literature and the setting rules of supercritical CO2 extraction process conditions. As the temperature decreases and the pressure increases, the interaction energy between palmitic acid and CO2 increases, which is conducive to overcoming the intermolecular force of palmitic acid and promoting dissolution. The solubility parameters of palmitic acid and CO2 can better reflect the trend of palmitic acid solubility changing with temperature and pressure, which can play a guiding role in the determination of process conditions and even the development of new processes.</p>
Molecular Dynamics Simulation Dataset for "Hydrophobic Mismatch Drives Self-Organization of Designer Proteins into Synthetic Membranes"
<p>This repository contains molecular dynamics (MD) simulation data from the study on the self-organization of designer proteins in synthetic membranes. The data includes simulations for different single lipid compositions (DOPC, DPPC, DYPC) denoted as [lipid]-PL* where PL stands for the different TMD constructs. Multi component simulation are named accordingly. The repository provides initial (eqi.gro) and final (prod.gro) coordinates for each simulation. The 'cmd' file in each directory outlines the assembly process of each simulation, and the 'mdp' folder contains all input files for the simulations. </p>
tetramethylammonium chloride molecular dynamics simulations
<p>Simulation data used for the publication: "Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics".</p> <p>Gromacs FFMD simulations:</p> <ul> <li>center-bead</li> <li>center-N</li> <li>charmm</li> <li>lowCHdipole</li> <li>neopentane_plumed</li> <li>surface-H</li> </ul> <p>AIMD simulation:</p> <ul> <li>TMA_64H2O_AIMD_revPBED3_production_trajs</li> </ul>
Interaction Fingerprints for Molecular Dynamics Simulation of MC-LR and MC-LF with PPP1 - Data
<p>This data sets contains all data to reproduce the conclusions of the following manuscript to analyse, aggregate and visualise interaction fingerprints of Molecular Dynamics Simulation data. </p> <p>S. Jaeger-Honz, K. Klein, F. Schreiber: Systematic Analysis, Aggregation and Visualisation of Interaction Fingerprints for Molecular Dynamics Simulation Data, Journal of Cheminformatics 16 (28), 2024, https://doi.org/10.1186/s13321-024-00822-3.</p> <p>The scripts and libraries necessary to rerun the analysis are published under the following DOI: 10.5281/zenodo.10424417</p> <p> </p>
Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations, Molecular dynamics trajectory file
<p>Dataset for molecular dynamics simulations of the article: Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations.</p> <p><a href="../api/records/10473570/draft/files/First_600ns_MD.rar/content" target="_blank" rel="noopener noreferrer">First_600ns_MD.rar</a> contains the 600ns molecular dynamics simulation trajectory file of IL4I1-FAD-CIT complex using desmond.</p> <p><a href="../api/records/10473570/draft/files/Second_500ns_MD_ZL35_F963.rar/content" target="_blank" rel="noopener">Second_500ns_MD_ZL35_F963.rar </a>contains the 500ns molecular dynamics simulation trajectory file of IL4I1-FAD-ZL35 complex, which initial conformation of this part of dynamics simulation was obtained by docking the conformation of the 963rd frame from the first dynamics simulation with ZL35 through induced fit.</p> <p>script.rar include scripts and calculation methods for free energy landscape, RMSD matrix, and thermol MM/GBSA.</p>
Molecular dynamics simulation of a pentameric ligand-gated ion channel DeCLIC
<p>Molecular dynamics simulation trajectories, parameter files for a bacterial pentameric ligand-gated ion channel DeCLIC, in the system with 150mM CaCl2 or NaCl2.</p>
Influence of Molecular Hydrogen on Bulk and Interfacial Properties of Three Imidazolium-Based Ionic Liquids by Experiments and Molecular Dynamics Simulations
<p>Original materials including both experimental and simulation data.</p> <p>Pictures (.bmp) of pendant drop method and the surface light scattering signals (.asc).<br>Raw simulation data for the surface tension. The topology files and all the final structure files(.gro) are included for the two systems at all studied temperature and pressures.</p>
Kreysing_et_al_2024_molecular_dynamics_simulation_data
<p>The molecular dynamics simulation data set accompanying Kreysing et al, 2024, containing (i) representative coordinates and measurements described therein, (ii) selected simulation trajectories, and (iii) LAMMPS input files.</p>
Molecular dynamics simulations for "Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time"
<p>This repository contains the molecular dynamics simulation files for the extant and ancestral RuBisCOs, presented in Amritkar2024 et. al.</p> <p>There are two separate folders, one for the regular MD simulations and the other for MD simulations with gas trajectories.</p> <p>Both folders have the simulation trajectory `.dcd` files and the `.pdb` for their corresponding protein structures.</p> <p>The trajectory files are dried, i.e. water molecules have been removed from them.</p> <p>The data encompasses over 7 extant (pdb ids: 1BWV, 3ZXW, 6FTL, 6URA, 7SNV, 8RUC, 9RUB) and 8 ancestral (Anc-I/I', Anc-I', Anc-I, Anc-IAB, Anc-ICD, Anc-IA, Anc-IB, Anc-I-without-RbcS) RuBisCO complexes.</p> <p>This study performed three types of simulations: with water molecules (labeled as exp01), with water + CO2 molecules (labeled as exp02), and with water + O2 molecules (labeled as exp04).</p> <p>There are two replicates for the exp01 simulations and the simulation length for each is 250 ns.</p> <p>The <em>exp02</em> and <em>exp04</em> files are not present for the RbcS-less (Anc-I/I', Anc-I', Anc-I-without_RbcS, 6URA, and 9RUB) RuBisCOs. The simulation length for the gas simulations is 75 ns and one replicate.</p> <p>Each file is named "<em>RuBisCO-system"</em>."<em>simulation-type</em>".md"replicate-number".dry."<em>pdb or dcd</em>".</p> <p>The files are named with respect to each RuBisCO-id in small (No caps). Anc-I/I' is represented as "anciip" and Anc-I' is represented as "ancip".</p>
Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'
<h2>Melike Berksoz, Canan Atilgan* </h2> <h3>Faculty of Engineering and Natural Sciences, Sabanci University </h3> <p><strong>*Correspondance:</strong> Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu</p> <p>Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes <em>in</em> <em>vivo.</em> A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.</p> <p>Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd). </p>
Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations
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Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics
<p>This .zip file contains the code, simulation scripts and settings, and figure generation scripts for our manuscript "Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics." More detailed descriptions are found in the 0README.txt files within the .zip folder.</p> <p> </p> <p>Manuscript link:</p> <p>https://arxiv.org/abs/2102.06298</p> <p> </p> <p>Manuscript abstract:</p> <p>Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a new particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.</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.