Journal: Frontiers in Cellular Neuroscience

Article Title: Exploring the impact of the stargazin V143L mutation on the dynamics of the AMPA receptor: stargazin complex

doi: 10.3389/fncel.2024.1505846

Figure Lengend Snippet: Heatmaps of ΔSASA per protein in the WT (A) and V143L (B) AMPAR:STG systems, and ΔΔSASA (ΔSASA V143L − ΔSASA WT ) per protein (C) . The values were expressed in Å 2 .

Article Snippet: AMPAR α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors ATD Amino-terminal domain CACNG2 Calcium voltage-gated channel secondary subunit gamma 2 CTERM C-TERMinal domain CTZ Cyclothiazide ECD ExtraCellular domain ECH ExtraCellular helix elec Electrostatic EPSP Excitatory PostSynaptic potentials ER Endoplasmic reticulum HB Hydrogen bonds LBD Ligand-binding domain LJ Lennard-Jones LTD Long-term depression MD Molecular dynamics MM Molecular mechanics MMPBSA Molecular mechanics Poisson Boltzmann surface area method PME Particle-Mesh Ewald PPI Protein-protein interaction SASA Solvent-accessible surface area SB Salt bridges TARP Transmembrane AMPAR regulatory protein TMD TransMembrane domain vdW van der Waals

Techniques:

Journal: Frontiers in Cellular Neuroscience

Article Title: Exploring the impact of the stargazin V143L mutation on the dynamics of the AMPA receptor: stargazin complex

doi: 10.3389/fncel.2024.1505846

Figure Lengend Snippet: Pore radii of STG WT (A) and V143L (B) GluA2:STG complexes. The orange lines at 1.4 and 2.3 Å help identify between non-conductive and O1 and O2 conductance level for each AMPAR . The values were calculated at intervals of 10 ns and expressed in Å.

Article Snippet: AMPAR α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors ATD Amino-terminal domain CACNG2 Calcium voltage-gated channel secondary subunit gamma 2 CTERM C-TERMinal domain CTZ Cyclothiazide ECD ExtraCellular domain ECH ExtraCellular helix elec Electrostatic EPSP Excitatory PostSynaptic potentials ER Endoplasmic reticulum HB Hydrogen bonds LBD Ligand-binding domain LJ Lennard-Jones LTD Long-term depression MD Molecular dynamics MM Molecular mechanics MMPBSA Molecular mechanics Poisson Boltzmann surface area method PME Particle-Mesh Ewald PPI Protein-protein interaction SASA Solvent-accessible surface area SB Salt bridges TARP Transmembrane AMPAR regulatory protein TMD TransMembrane domain vdW van der Waals

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Structures and atom type notations of ( a ) phenyl propionic acid, Phpr, ( b ) choline chloride, ChCl. Atom color code: (Cyan) carbon, (red) oxygen, (blue) nitrogen, (green) chloride ion, (light gray) hydrogen. Atomic label was used in molecular dynamics simulations. The molecular structures were visualized by the VMD package .

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Coordination number (N C(i−j) ) of Phpr, choline and chloride iones obtained by molecular dynamics simulations.

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Spatial distribution functions of relevant atoms around phenyl propionic acid in DES at ( a ) 298 K, ( b ) 321 K, ( c ) 400 K and 0.1 MPa were calculated using TRAVIS software: yellow, choline cation; green, chloride anion; red, Phpr molecule. The isodensity used for the SDF corresponding to choline cation, Phpr, and chloride anion are 2, 2, and 4 times bulk density.

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques: Software

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Fraction of hydrogen bond percent occupancies for ( a ) Cl – –Phpr (Cl-H4), ( b ) Cl – –choline (Cl–H14), ( c ) Phpr–Phpr (O1–H4), and ( d ) Phpr–choline (O1–H14) in DES at 293, 321, and 400 K and 0.1 MPa. The data were analyzed using the VMD package .

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Interaction energies of Phpr-choline, Phpr–Cl − , choline–Cl − , Phpr–Phpr in DES were calculated using ‘NAMD energy’ plugins of the VMD package at ( a ) 293 K, ( b ) 321 K and ( c ) 400 K.

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: The normalized-distribution of molecular dipole moment vector of Phpr in a pure state; ( a ), in DES system; ( b ), and the normalized-distribution of choline cation in pure choline chloride system; ( c ) and in DES system; ( d ) The data were fitted using Gnuplot 5.2.6 ( http://www.gnuplot.info/ ).

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques: Plasmid Preparation

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: The normalized-distribution of the ( a ) angle of choline on Phpr, ( b ) Phpr on the Phpr, ( c ) choline on the chloride and ( d ) Phpr on the chloride at 293, 321 and 400 K in 0.1 MPa. The data were fitted using Gnuplot 5.2.6 ( http://www.gnuplot.info/ ).

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: The self- diffusion coefficient (Å 2 /ns) of chloride anion, choline cation and phenyl propionic acid molecules (Phpr) obtaine from MD simulations for different size DES system and thermodynamic limit ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{D}}_{\mathrm{i},\mathrm{ self}}^{\infty }$$\end{document} D i , self ∞ ) at 293, 321 and 400 K and 0.1 MPa.

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques: Diffusion-based Assay

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: Correlation between the logarithm and the reciprocal temperature (Arrhenius plot) for the diffusion coefficients of the Cl − (green), choline (orange) and HBD, Phpr, (pink) in investigated DES. Data plots were generated by gnuplot 5.2.6 ( http://www.gnuplot.info/ ).

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques: Diffusion-based Assay, Generated

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: The Arrhenius equation parameters of species of studied DES.

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques:

Journal: Scientific Reports

Article Title: Insights into the interactions and dynamics of a DES formed by phenyl propionic acid and choline chloride

doi: 10.1038/s41598-021-85260-z

Figure Lengend Snippet: The initial configuration of the studied DES containing 402 Phpr; pink color, 198 choline; blue color, and 198 Cl − ; green color was randomly generated using the PACKMOL package .

Article Snippet: Molecular dynamics (MD) simulations for the considered DES were carried out using cubic boxes consisted of 67 mol% phenyl propionic acid molecules (Phpr) and 33 mol% choline chloride (ChCl).

Techniques: Generated

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Phenomena in the lithium electrolysis cell.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Effect of cathode height on electrolysis efficiency.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Effect of anode radius on electrolysis efficiency.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Effect of electrolyte height on electrolysis efficiency.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Effect of ACD on electrolysis efficiency.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Orthogonal design and simulation results for lithium electrolysis cell.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Royal Society Open Science

Article Title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

doi: 10.1098/rsos.191124

Figure Lengend Snippet: Simulation results of lithium electrolysis cell by orthogonal design.

Article Snippet: In this research, a model coupled multiphysical fields for simulating lithium electrolysis cell has been developed by applying COMSOL.

Techniques: Electrolysis

Journal: Data in Brief

Article Title: Dataset of noise signals generated by smart attackers for disrupting state of health and state of charge estimations of battery energy storage systems

doi: 10.1016/j.dib.2024.111200

Figure Lengend Snippet: Current noise signals due to the FDIA analyzed using a signal analyzer tool in MATLAB to show its magnitude in the upper plot, power spectrum in the middle plot and normalized frequency in the bottom plot – Case 1.

Article Snippet: In this additional case, we explore the impact of high-noise adversarial signals on the SoC estimation process using MATLAB 2024b ( https://www.mathworks.com/help/simscape-battery/ug/estimate-soc-of-lithium-iron-phosphate-battery.html ) simulations with Lithium Iron Phosphate (LiFePO4) battery models (see ).

Techniques:

Journal: Data in Brief

Article Title: Dataset of noise signals generated by smart attackers for disrupting state of health and state of charge estimations of battery energy storage systems

doi: 10.1016/j.dib.2024.111200

Figure Lengend Snippet: Voltage noise signals due to the FDIA analyzed using a signal analyzer tool in MATLAB to show its magnitude in the upper plot, power spectrum in the middle plot and normalized frequency in the bottom plot – Case 1.

Article Snippet: In this additional case, we explore the impact of high-noise adversarial signals on the SoC estimation process using MATLAB 2024b ( https://www.mathworks.com/help/simscape-battery/ug/estimate-soc-of-lithium-iron-phosphate-battery.html ) simulations with Lithium Iron Phosphate (LiFePO4) battery models (see ).

Techniques:

Journal: Data in Brief

Article Title: Dataset of noise signals generated by smart attackers for disrupting state of health and state of charge estimations of battery energy storage systems

doi: 10.1016/j.dib.2024.111200

Figure Lengend Snippet: Current noise signals due to the FDIA analyzed using a signal analyzer tool in MATLAB to show its magnitude in the upper plot, power spectrum in the middle plot and normalized frequency in the bottom plot – Case 2.

Article Snippet: In this additional case, we explore the impact of high-noise adversarial signals on the SoC estimation process using MATLAB 2024b ( https://www.mathworks.com/help/simscape-battery/ug/estimate-soc-of-lithium-iron-phosphate-battery.html ) simulations with Lithium Iron Phosphate (LiFePO4) battery models (see ).

Techniques:

Journal: Data in Brief

Article Title: Dataset of noise signals generated by smart attackers for disrupting state of health and state of charge estimations of battery energy storage systems

doi: 10.1016/j.dib.2024.111200

Figure Lengend Snippet: Voltage noise signals due to the FDIA analyzed using a signal analyzer tool in MATLAB to show its magnitude in the upper plot, power spectrum in the middle plot and normalized frequency in the bottom plot – Case 2.

Article Snippet: In this additional case, we explore the impact of high-noise adversarial signals on the SoC estimation process using MATLAB 2024b ( https://www.mathworks.com/help/simscape-battery/ug/estimate-soc-of-lithium-iron-phosphate-battery.html ) simulations with Lithium Iron Phosphate (LiFePO4) battery models (see ).

Techniques:

Journal: Data in Brief

Article Title: Dataset of noise signals generated by smart attackers for disrupting state of health and state of charge estimations of battery energy storage systems

doi: 10.1016/j.dib.2024.111200

Figure Lengend Snippet:

Article Snippet: In this additional case, we explore the impact of high-noise adversarial signals on the SoC estimation process using MATLAB 2024b ( https://www.mathworks.com/help/simscape-battery/ug/estimate-soc-of-lithium-iron-phosphate-battery.html ) simulations with Lithium Iron Phosphate (LiFePO4) battery models (see ).

Techniques: Battery, Biomarker Discovery