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406 results for “Bilayer”
Experimental data for "Electric field drives Chern transition in Hofstadter bands of twisted double bilayer graphene"
<p>This experimental dataset was used in our study of "Electric field drives Chern transition in Hofstadter bands of twisted double bilayer graphene".</p>
Set simulations small pure bilayers with cholesterol (max 128 lipids) using charmm36 ff in gromacs (DPPC)
<p>Collection simulations of small pure bilayers (max 128 phospholipids) with cholesterol in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <ol> <li>DPPC_128_CHL1_32_310K</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
Simulations POPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of POPC (512 lipids) bilayers in gromacs using the charmm36 force field. The list of systems can be found below where the several parameter are:</p> <ol> <li>POPC_512_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K_tip3p (500ns)</li> <li>POPC_512_NaCl_Dang_150mM_310K (500ns)</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
DPPC bilayer after 100 ns
<p>Equilibrated system of 128 DPPC lipids and 3655 water molecules after 100 ns.</p> <p><strong>Details:</strong> Berger united atom lipids (needs lipid.itp and dppc.itp from Peter Tieleman's web site at <a href="http://moose.bio.ucalgary.ca/">http://moose.bio.ucalgary.ca/</a>). Area per lipid: 0.645 (+/- 0.010) nm<sup>2</sup>.</p> <p>Also available at: <a href="http://www.softsimu.net/downloads.shtml">http://www.softsimu.net/downloads.shtml</a></p> <p><strong>References:</strong></p> <ol> <li><a href="http://dx.doi.org/10.1016/S0006-3495(03)75094-2">Major artifacts due to truncating electrostatic interactions</a>, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen, Biophys. J. 84, 3636-3645 (2003)</li> <li><a href="http://dx.doi.org/10.1021/jp031281a">Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions</a>, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen, J. Phys. Chem. B 108, 4485-4494 (2004).</li> </ol>
Figure data for Dynamical Correlations and Order in Magic-Angle Twisted Bilayer Graphene
<p>This repository contains the data corresponding to all figures in the main text of the 2024 (to appear) Phys. Rev. X article <em>Dynamical Correlations and Order in Magic-Angle Twisted Bilayer Graphene</em>. See README for notes on how to access. </p> <p>The simulation code used to generate this data is available on github.<br>w2dynamics simulations: <a href="https://github.com/lcrippa/w2dynamics-matbg-symmetric">https://github.com/lcrippa/w2dynamics-matbg-symmetric</a><br>TRIQS simulations: <a href="https://github.com/gautamra/TBLG_ordered">https://github.com/gautamra/TBLG_ordered</a></p>
Quantitative results of the analysis of human bioengineered tissues corresponding to the work "Generation of tissue-like models of human bilayered tissues functionalized with olive oil components"
<p>This file contains the raw dataset generated in the work entitled "GENERATION OF NOVEL TISSUE-LIKE MODELS OF HUMAN BILAYERED TISSUES FUNCTIONALIZED WITH BIOACTIVE COMPONENTS OBTAINED FROM OLIVE OIL". These results correspond to the quantification of the histological results obtained in this work.</p>
Transport effects of twist-angle disorder in mesoscopic twisted bilayer graphene
<p>Magic-angle twisted bilayer graphene is a tunable material with remarkably flat energy bands near the Fermi level, leading to fascinating transport properties and correlated states at low temperatures. However, grown pristine samples of this material tend to break up into landscapes of twist-angle domains, strongly influencing the physical properties of each individual sample. This poses a significant problem to the interpretation and comparison between measurements obtained from different samples. In this work, we study numerically the effects of twist-angle disorder on quantum electron transport in mesoscopic samples of magic-angle twisted bilayer graphene. We find a significant property of twist-angle disorder that distinguishes it from onsite-energy disorder: it leads to an asymmetric broadening of the energy-resolved conductance. The magnitude of the twist-angle variation has a strong effect on conductance, while the number of twist-angle domains is of much lesser significance. We further establish a relationship between the asymmetric broadening and the asymmetric density of states of twisted bilayer graphene at angles smaller than the first magic angle. Our results show that the qualitative differences between the types of disorder in the energy-resolved conductance of twisted bilayer graphene samples can be used to characterize them at temperatures above the critical temperatures of the correlated phases, enabling systematic experimental studies of the effects of the different types of disorders also on the other properties such as the competition of the different types of correlated states appearing at lower temperatures.</p> <p>The provided repository contains all data and scripts to reproduce the figures of the manuscript. </p>
All-atom Gromacs Trajectory of POPC/TOCL bilayer mixture
<p>All-atom bilayer mixture of POPC/TOCL 1:1 simulated in an NPT ensemble with Gromacs and the CHARMM36 force field from Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (<a href="https://doi.org/10.1021/acs.molpharmaceut.1c00926">https://doi.org/10.1021/acs.molpharmaceut.1c00926</a>). The trajectory represents 540 ns with frames output every 20 ps. The bilayer has 120 lipids total (60 lipids per leaflet) and is hydrated with 100 waters/lipid and sodium ions to neutralize the system. The simulation was done at 37C (310.15K).</p> <p>POPC is 16:0,18:1 PC; TOCL is tetraoleoyl cardiolipin</p>
All-atom Gromacs Trajectory of POPC/POPE/TOCL bilayer mixture
<p>All-atom bilayer mixture of POPC/POPE//TOCL 50/25/25 mol% simulated in an NPT ensemble with Gromacs and the CHARMM36 force field from Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (<a href="https://doi.org/10.1021/acs.molpharmaceut.1c00926">https://doi.org/10.1021/acs.molpharmaceut.1c00926</a>). The trajectory represents 570 ns with frames output every 20 ps. The bilayer has 120 lipids total (60 lipids per leaflet) and is hydrated with 75 waters/lipid and sodium ions to neutralize the system. The simulation was done at 37C (310.15K).</p> <p>POPC is 16:0,18:1 PC; POPE is 16:0,18:1 PE; TOCL is tetraoleoyl cardiolipin</p>
All-atom Gromacs Trajectory of POPE/TOCL bilayer mixture
<p>All-atom bilayer mixture of POPE/TOCL 1:1 simulated in an NPT ensemble with Gromacs and the CHARMM36 force field from Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (<a href="https://doi.org/10.1021/acs.molpharmaceut.1c00926">https://doi.org/10.1021/acs.molpharmaceut.1c00926</a>). The trajectory represents 530 ns with frames output every 20 ps. The bilayer has 120 lipids total (60 lipids per leaflet) and is hydrated with 100 waters/lipid and sodium ions to neutralize the system. The simulation was done at 37C (310.15K).</p> <p>POPE is 16:0,18:1 PE; TOCL is tetraoleoyl cardiolipin</p>
The effect of the graded bilayer design on the strain depth profiles and microstructure of CuW nano-multilayers
<p>In this document we share:</p> <p>-the XRD in-plane scans acquired on Cu/W multilayers at different incidence angle,</p> <p>-the in-situ stress curvature data acquired during multilayer growth,</p> <p>-the in plane d-spacing derived at different incidence angle, used for the simulation of the strain gradient.</p>
Transport signatures of Van Hove singularities in mesoscopic twisted bilayer graphene
<p>Magic-angle twisted bilayer graphene exhibits quasi-flat low-energy bands with Van Hove singularities close to the Fermi level. These singularities play an important role in the exotic phenomena observed in this material, such as superconductivity and magnetism, by amplifying electronic correlation effects. In this work, we study the correspondence of four-terminal conductance and the Fermi surface topology as a function of the twist angle, pressure, and energy in mesoscopic, ballistic samples of small-angle twisted bilayer graphene. We establish a correspondence between features in the wide-junction conductance and the presence of van Hove singularities in the density of states. Moreover, we identify additional transport features, such as a large, pressure-tunable minimal conductance, conductance peaks coinciding with non-singular band crossings, and unusually large conductance oscillations as a function of the system size. Our results suggest that twisted bilayer graphene close the magic angle is a unique system featuring simultaneously large conductance due to the quasi-flat bands, strong quantum non-linearity due to the Van Hove singularities and high sensitivity to external parameters, which could be utilized in high-frequency device applications and sensitive detectors.</p> <p>The provided repository contains all data and scripts to reproduce the figures of the manuscript. In the new version of the repository we also provide scripts to create finite samples for conductance calculations and to create periodic samples for band structure calculations.</p>
Implementing electronic signatures of graphene and hexagonal boron nitride in twisted bilayer molybdenum disulfide
<p><strong>Abstract</strong></p> <p>Angeli and MacDonald reported a superlattice-imposed Dirac band in twisted bilayer molybdenum disulphide (tBL MoS2) for small twist angles towards the R_h^M (parallel) stacking. Using a hierarchical set of theoretical methods, we show that the superlattices differ for twist angles with respect to metastable R_h^M (0°) and lowest-energy H_h^h (60°) configurations. When approaching R_h^M stacking, identical domains with opposite spatial orientation emerge. They form a honeycomb superlattice, yielding Dirac bands and a lateral spin texture distribution with opposite-spin-occupied K and K’ valleys. Small twist angles towards the H_h^h configuration (60°) generate H_h^h and H_h^X stacking domains of different relative energies and, hence, different spatial extensions. This imposes a symmetry break in the moiré cell, which opens a gap between the two top-valence bands, which become flat already for relatively small moiré cells. The superlattices impose electronic superstructures resembling graphene and hexagonal boron nitride into trivial semiconductor MoS<sub>2</sub>.</p> <p>The data set published in this repository was used to create the preprint published at <strong>https://doi.org/10.26434/chemrxiv-2023-rx2fz</strong>.</p> <p><strong>Content of repository</strong></p> <ul> <li>"ReaxFF_structure_optimization.zip": contains the inputs and outputs for all structure optimizations for ML, BL, and tBL systems using the Reax force field, performed using LAMMPS.</li> <li>" bilayer_verification_ReaxFF_with_DFT.zip": contains the inputs and outputs for verifying the results of the Reax force field by running DFT geometry optimization and total energy calculations in FHI-aims for the high-symmetry bilayer stackings.</li> <li>"QATK_band_structures_and_eff_mass.zip": contains the inputs and outputs of all calculations done via QuantumATK (QATK), including calculations for ML, BL, and tBL systems on DFT and DFTB level of theory.</li> <li>"TB_fit.zip": contains the Python scripts and input data (DFTB band structure) used to fit the TB Hamiltonians as described in the Methods section and shown in the Supplementary Material.</li> <li>"effective_masses_from_bands.zip": contains the extraction of the effective hole masses from the bands calculated at the DFTB level of theory in QATK.</li> </ul>
Reconstitution of phase-separated signaling clusters and actin polymerization on supported lipid bilayers
<p>Liquid–liquid phase separation driven by weak interactions between multivalent molecules contributes to the cellular organization by promoting the formation of biomolecular condensates. At membranes, phase separation can promote the assembly of transmembrane proteins with their cytoplasmic binding partners into micron-sized membrane-associated condensates. For example, phase separation promotes clustering of nephrin, a transmembrane adhesion molecule, resulting in increased Arp2/3 complex-dependent actin polymerization. In vitro reconstitution is a powerful approach to understanding phase separation in biological systems. With a bottom-up approach, we can determine the molecules necessary and sufficient for phase separation, map the phase diagram by quantifying de-mixing over a range of molecular concentrations, assess the material properties of the condensed phase using fluorescence recovery after photobleaching (FRAP), and even determine how phase separation impacts downstream biochemical activity. Here, we describe a detailed protocol to reconstitute nephrin clusters on supported lipid bilayers with purified recombinant protein. We also describe how to measure Arp2/3 complex-dependent actin polymerization on bilayers using fluorescence microscopy. These different protocols can be performed independently or combined as needed. These general techniques can be applied to reconstitute and study phase-separated signaling clusters of many different receptors or to generally understand how actin polymerization is regulated at membranes.</p>
BeMAGIC_Organic/inorganic heterostructured (bilayered) multiferroic films
<p>BeMAGIC ITN (GA861145)_Organic/inorganic heterostructured (bilayered) multiferroic films. Results from ICN2, UAB and UCAM</p>
Lipid membrane simulations with flat-bottom and double-bilayer setups, part 2/2
<p>To cite: Biriukov, D. and Javanainen, M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J. Chem. Theory Comput. 2023, 19 (18), 6332–6341. DOI: <a href="https://doi.org/10.1021/acs.jctc.3c00614">10.1021/acs.jctc.3c00614</a></p> <p>Gromacs molecular dynamics simulations to compare membrane and solvent properties from lipid membrane simulations with flat-bottom and double-bilayer setups. CHARMM36 force field was used except for simulations with peptides, where a prosECCo model was used [Nencini et al., Biophys. J. 121, 157a (2022)]</p> <p>This dataset contains only double-bilayer simulations. The flat-bottom simulations together with all topologies and mdp files can be found in part 1 : DOI: <a href="https://zenodo.org/record/7973838">10.5281/zenodo.7973838</a></p> <p>Abbreviations in the names of simulation files:</p> <ul> <li>"fb" - simulations with a flat-bottom setup</li> <li>"2m" - simulations with two lipid membranes, i.e., a double-bilayer setup</li> <li>"popc" - membrane is modeled as a POPC lipid bilayer</li> <li>"mix" - a realistic membrane with various lipids is modeled, resembling the composition from [Lorent et al., Nat. Methods 16, 644–652 (2020)]</li> <li>"nak" - only sodium and potassium cations, together with chloride anions, are present in the system</li> <li>"ext" - as "nak", but also calcium and magnesium cations are added</li> <li>"r9" - as "nak" but also R9 (nona-arginine) peptides are added on both sides of the membrane</li> <li>"r9k" - as "nak" but also R9 (nona-arginine) peptides are added on the extracellular side of the membrane</li> <li>"one" - ions are present only on one side of a lipid membrane</li> <li>"freecl" - flat-bottom simulations but without restraints on chloride anions</li> <li>"s" - simulations were performed using the scaled-charge prosECCo75 force field based on CHARMM [Nencini et al., Biophys. J. 121, 157a (2022)]</li> <li>"restr" - restraint .gro file with ionic/peptide <em>z</em> coordinates set to zero</li> </ul>
Lipid membrane simulations with flat-bottom and double-bilayer setups, part 1/2
<p>To cite: Biriukov, D. and Javanainen, M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J. Chem. Theory Comput. 2023, 19 (18), 6332–6341. DOI: <a href="https://doi.org/10.1021/acs.jctc.3c00614">10.1021/acs.jctc.3c00614</a></p> <p>Gromacs molecular dynamics simulations to compare membrane and solvent properties from lipid membrane simulations with flat-bottom and double-bilayer setups. CHARMM36 force field was used except for simulations with peptides, where a prosECCo model was used [Nencini et al., Biophys. J. 121, 157a (2022)]</p> <p>This dataset contains all the topologies and flat-bottom simulation files. The double-bilayer simulation files can be found in part 2: DOI: <a href="https://zenodo.org/record/7974633">10.5281/zenodo.7974633</a></p> <p>Abbreviations in the names of simulation files:</p> <ul> <li>"fb" - simulations with a flat-bottom setup</li> <li>"2m" - simulations with two lipid membranes, i.e., a double-bilayer setup</li> <li>"popc" - membrane is modeled as a POPC lipid bilayer</li> <li>"mix" - a realistic membrane with various lipids is modeled, resembling the composition from [Lorent et al., Nat. Methods 16, 644–652 (2020)]</li> <li>"nak" - only sodium and potassium cations, together with chloride anions, are present in the system</li> <li>"ext" - as "nak", but also calcium and magnesium cations are added</li> <li>"r9" - as "nak" but also R9 (nona-arginine) peptides are added on both sides of the membrane</li> <li>"r9k" - as "nak" but also R9 (nona-arginine) peptides are added on the extracellular side of the membrane</li> <li>"one" - ions are present only on one side of a lipid membrane</li> <li>"freecl" - flat-bottom simulations but without restraints on chloride anions</li> <li>"s" - simulations were performed using the scaled-charge prosECCo75 force field based on CHARMM [Nencini et al., Biophys. J. 121, 157a (2022)]</li> <li>"restr" - restraint .gro file with ionic/peptide <em>z</em> coordinates set to zero</li> </ul> <p> </p>
Relaxation effects in twisted bilayer molybdenum disulfide: structure, stability, and electronic properties
<p><strong>Abstract</strong></p> <p>Manipulating the interlayer twist angle is a powerful tool to tailor the properties of layered two-dimensional crystals. The twist angle has a determinant impact on these systems' atomistic structure and electronic properties. This includes the corrugation of individual layers, formation of stacking domains and other structural elements, and electronic structure changes due to the atomic reconstruction and superlattice effects. However, how these properties change with the twist angle, <em>θ</em>, is not yet well understood. Here, we monitor the change of twisted bilayer (tBL) MoS<sub>2</sub> characteristics as a function of <em>θ</em>. We identify distinct structural regimes, each with particular structural and electronic properties. We employ a hierarchical approach ranging from a reactive force field through the density-functional-based tight-binding approach and density-functional theory. To obtain a comprehensive overview, we analyzed a large number of tBLs with twist angles in the range of <span class="math-tex">\(\theta=0.2^\circ\dots59.6^\circ\)</span>. Some systems include up to half a million atoms, making structure optimization and electronic property calculation challenging. For <span class="math-tex">\(13^\circ \lessapprox \theta \lessapprox 47^\circ\)</span>, the structure is well-described by a moiré regime composed of two rigidly twisted monolayers. At small twist angles (<span class="math-tex">\(\theta\leq3^\circ\)</span> and <span class="math-tex">\(57^\circ\leq\theta\)</span>), a domain-soliton regime evolves, where the structure contains large triangular stacking domains, separated by a network of strain solitons and short-ranged high-energy nodes. The corrugation of the layers and the emerging superlattice of solitons and stacking domains affects the electronic structure. Emerging predominant characteristic features are Dirac cones at <em>K</em> and kagome bands. These features flatten for <em>θ</em> approaching 0<sup>∘</sup> and 60<sup>∘</sup>. Our results show at which range of <em>θ</em> the characteristic features of the reconstruction, namely extended stacking domains, the soliton network, and superlattice, emerge and give rise to exciting electronics. We expect our findings also to be relevant for other tBL systems.</p> <p>DOI: 10.1088/2053-1583/aceb75</p> <p><strong>Overview</strong></p> <p>This repository contains calculation files, optimized structures, and visualization movies for studies of twisted-bilayer MoS<sub>2</sub>, focussing on structural properties and electronic structure. Each directory has its own README.md file with additional information, separated by what data is included and the method used.</p> <p><strong>Geometry optimization</strong></p> <ul> <li>Directory `calc_structure_optimization_ReaxFF`: calculation files of the structure optimization of all studied structures, done with ReaxFF.</li> <li>Directory `calc_structure_optimization_DFT`: validation calculation files of the ReaxFF-optimized structures using DFT optimization.</li> </ul> <p><strong>Electronic structure calculations</strong></p> <ul> <li>Directory `calc_electronic_properties_DFT`: calculation files of electronic structure calculations on the DFT level.</li> <li>Directory `calc_electronic_properties_DFTB`: calculation files of electronic structure calculations on the DFTB level</li> </ul> <p><strong>Results</strong></p> <ul> <li>Directory `structures_rigidly_twisted`: structure files in cif format of the rigidly twisted (flat) systems, labeled by their twist angle.</li> <li>Directory `structures_fully_optimized`: structure files in cif format of the fully ReaxFF-optimized systems, labeled by their twist angle.</li> <li>Directory `movies`: visualization of the change of the interlayer distance landscape and the strain fields with the twist angle.</li> <li>Additionally, the script `plot_interlayer_distance.py` is included, which was used to create the individual frames of the movie showing the interlayer distance.</li> </ul>
MD simulation of sphingomyelin (d18:1/18:0) bilayer in water
<p>MD simulations of sphingomyelin (d18:1/18:0) bilayer in water, NPT, 328 K. 128 SM + 5120 TIP3P water molecules, CHARMM36 force field.</p>
Data from: Functional regulation of aquaporin dynamics by lipid bilayer composition
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