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(a) Lipid bilayer where the C2 atoms are highlighted in red. (b) The thickness of membrane (T) as a function of time. (c) The area per lipid (APL) as a function of time. (d) Lipid order parameters (OP) with respect to C2 and C3 atoms.

(a) Lipid bilayer where the C2 atoms are highlighted in red. (b) The thickn...

in Simulating Membrane Proteins with Constant pH Molecular Dynamics > A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
Published: January 2023
FIG. 5.1 (a) Lipid bilayer where the C2 atoms are highlighted in red. (b) The thickness of membrane (T) as a function of time. (c) The area per lipid (APL) as a function of time. (d) Lipid order parameters (OP) with respect to C2 and C3 atoms. More about this image found in (a) Lipid bilayer where the C2 atoms are highlighted in red. (b) The thickn...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Appendix

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_app1
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... Appendix Packmol input files DMPC_15nm.inp and wt4_box.pkm used in Chap. 3, Secs. 3.1 and 3.4, respectively. Note that the lipid coordinates used to construct both leaflets are identical and correspond to those in the file dmpc.pdb provided in the SIRAH distribution...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Section

Series: AIPP Books, Methods
Published: January 2023
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... Appendix Packmol input files DMPC_15nm.inp and wt4_box.pkm used in Chap. 3, Secs. 3.1 and 3.4, respectively. Note that the lipid coordinates used to construct both leaflets are identical and correspond to those in the file dmpc.pdb provided in the SIRAH distribution...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Section

Series: AIPP Books, Methods
Published: January 2023
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... Appendix Packmol input files DMPC_15nm.inp and wt4_box.pkm used in Chap. 3, Secs. 3.1 and 3.4, respectively. Note that the lipid coordinates used to construct both leaflets are identical and correspond to those in the file dmpc.pdb provided in the SIRAH distribution...
Images
(a) Schematic of the P3HT OECT used to stabilize a bacterial lipid monolayer to study its drug-mediated destabilization. With permission from Pitsalidis et al., Adv. Mater. 30(39), 1803130 (2018). Copyright 2019 Wiley-VCH Verlang GmbH & Co. (b) Schematic of a bioprotonic device comprising bilayer-embedded gramicidin ion channels for proton transport studies. With permission from Hemmatian et al., Nat. Commun. 7(1), 12981 (2016). Copyright 2016 Springer Nature. (c) Schematic of a CNT inserted into an ∼200-nm-diameter patch of lipid bilayer spanning the aperture of a solid-state nanopore. With permission from Tunuguntla et al., Science 357(6353), 792–796 (2017). Copyright 2017 American Association for the Advancement of Science. (d) Schematic of the native membrane on a chip OECT platform for combined optical and electrical ion channel studies. With permission from Pappa et al., ACS Nano 14(10), 12538–12545 (2020). Copyright 2020 American Chemical Society.

(a) Schematic of the P3HT OECT used to stabilize a bacterial lipid monolaye...

in In vitro Bioelectronic Systems > Introduction to BioelectronicsMaterials, Devices, and Applications
Published: November 2022
FIG. 9.6 (a) Schematic of the P3HT OECT used to stabilize a bacterial lipid monolayer to study its drug-mediated destabilization. With permission from Pitsalidis et al., Adv. Mater. 30 (39), 1803130 (2018). Copyright 2019 Wiley-VCH Verlang GmbH & Co. (b) Schematic of a bioprotonic More about this image found in (a) Schematic of the P3HT OECT used to stabilize a bacterial lipid monolaye...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Simulating Membrane Proteins with Constant pH Molecular Dynamics

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_005
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... ). Before lipid equilibration with OpenMM, the input scripts generated by CHARMM-GUI need to execute again offline with CHARMM. Lipids are equilibrated with OpenMM, where the protein is restrained. Finally, the CpHMD simulation that starts from the final frame of the lipid equilibration can be carried out...
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Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_003
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... (AIP Publishing, Melville, New York, 2023), pp. 3-1–3-20. Simulating Membrane Systems Biological membranes constitute enormously complex objects formed of hundreds to thousands of different species of lipids in a crowded mix with a similarly massive variety of proteins, continuously exchanging...
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Main steps for the system setup of the SERCA pump embedded in a DMPC bilayer. (1) Bilayer generation by phospholipid packing, (2) SERCA insertion and orientation by coordinate shifting, (3) removal of lipids in close contact with SERCA, (4) coarse-grain mapping, and (5) system solvation by WT4 packing.

Main steps for the system setup of the SERCA pump embedded in a DMPC bilaye...

in Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER > A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
Published: January 2023
FIG. 3.2 Main steps for the system setup of the SERCA pump embedded in a DMPC bilayer. (1) Bilayer generation by phospholipid packing, (2) SERCA insertion and orientation by coordinate shifting, (3) removal of lipids in close contact with SERCA, (4) coarse-grain mapping, and (5) system solvation More about this image found in Main steps for the system setup of the SERCA pump embedded in a DMPC bilaye...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

References

Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...References References Barrera , E. E. , Frigini , E. N. , Porasso , R. D. , and Pantano , S. , “ Modeling DMPC lipid membranes with SIRAH force-field ,” J. Mol. Model.   23 , 259 ( 2017 ). 10.1007/s00894-017-3426-5 Barrera , E. E. , Machado , M. R...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

References

Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
...References References Abellón-Ruiz , J. , Kaptan , S. S. , Baslé , A. , Claudi , B. , Bumann , D. , Kleinekathöfer , U. , and Van Den Berg , B. , “ Structural basis for maintenance of bacterial outer membrane lipid asymmetry ,” Nat. Microbiol.   2 , 1616 – 1623...
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Book cover for The International Handbook of Physics Education Research: Learning Physics

Student Understanding of Thermal Physics

Series: AIPP Books, Professional
Published: March 2023
10.1063/9780735425477_003
EISBN: 978-0-7354-2547-7
ISBN: 978-0-7354-2544-6
..., the approach to thermal equilibrium of two objects with different initial temperatures, and the process of lipid molecules assembling into a micelle. Students were asked to describe what they saw in the representation of the process. Each of the three processes was accompanied by a diagram showing the reverse...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

References

Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... , A. D. and Pastor , R. W. , “ Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types ,” J. Phys. Chem. B   114 , 7830 – 7843 ( 2010 ). 10.1021/jp101759q Lee , C. , Kang , H. J. , von Ballmoons , C. , Newstead , S. , Uzdavinys , P...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
Open the PDF for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules in another window
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A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_001
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
..., the force field was expanded in a second version, Martini 2, which included new models of not only new and more specialized lipids ( López et al., 2013 ; Melo et al., 2015 ; and Gu et al., 2017 ), but also many other biomolecules such as proteins ( Monticelli et al...
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Book cover for The International Handbook of Physics Education Research: Learning Physics

The International Handbook of Physics Education Research: Learning Physics

Series: AIPP Books, Professional
Published: March 2023
10.1063/9780735425477
EISBN: 978-0-7354-2547-7
ISBN: 978-0-7354-2544-6
Open the PDF for The International Handbook of Physics Education Research: Learning Physics in another window
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A Guide to Titratable Martini Simulations

Series: AIPP Books, Methods
Published: January 2023
10.1063/9780735425279_004
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
.... Introduction The Martini force-field is one of the most popular force-fields for simulating biologically relevant systems at close to atomic resolution. Originally, the Martini force-field has been applied to simulations of lipid bilayers ( Marrink et al., 2004 ) with a second version expanding...
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Images
(a) Modification of an oxide layer in traditional ISFET. (b) Modification of gate or channel surface in EGFET/OECT. (c) Introducing additional cell/lipid layer in the ionic circuit between the gate and the channel.

(a) Modification of an oxide layer in traditional ISFET. (b) Modification o...

in Transistors in Bioelectronics > Introduction to BioelectronicsMaterials, Devices, and Applications
Published: November 2022
FIG. 4.17 (a) Modification of an oxide layer in traditional ISFET. (b) Modification of gate or channel surface in EGFET/OECT. (c) Introducing additional cell/lipid layer in the ionic circuit between the gate and the channel. More about this image found in (a) Modification of an oxide layer in traditional ISFET. (b) Modification o...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

References

Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... , A. H. , and Mark , A. E. , “ Coarse grained model for semiquantitative lipid simulations ,” J. Phys. Chem. B   108 ( 2 ), 750 – 760 ( 2004 ). 10.1021/jp036508g Marrink , S. J. , Risselada , H. J. , Yefimov , S. , Tieleman , D. P. , and de Vries , A. H...
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Book cover for A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

References

Series: AIPP Books, Methods
Published: January 2023
0
EISBN: 978-0-7354-2527-9
ISBN: 978-0-7354-2524-8
... and L.   Brand (Elsevier, 2011 ), Vol. 487, pp. 545 – 574 . Luan , B. , Tien , H. , and Zhou , R. , “ Complete wetting of graphene by biological lipids ,” Nanoscale   8 , 5750 – 5754 ( 2016 ). 10.1039/c6nr00202a Luan , B. , Xu , G. , Feng , M. , Cong , L...
Images
Schematic illustration of the synthesis of the 2D mesoporous PPy nanosheets. (a) Formation of spherical micelles and 2D lipid bilayers derived from the self-assembly of block polymers and aliphatic amine in mixed solvents at room temperature, respectively. (b) Supramolecular sandwich-like structure formed by monolayer arrangement of the spherical blockpolymers micelles on the 2D surfaces of the octadecylamine bilayers. (c) Coassembly of block polymer micelles and pyrrole monomers on the octadecylamine surfaces. (d) Formation of pristine 2D mesoporous PPy nanosheets by synergic template-directed polymerization of pyrrole monomers upon the addition of ammonium persulfate. (e) As-made mesoporous PPy nanosheets after the removal of both octadecylamine and block polymer templates. (f) Nitrogen adsorption–desorption isotherm of the mPPy-1 and 2 nanosheets.

Schematic illustration of the synthesis of the 2D mesoporous PPy nanosheets...

in Analytical Techniques for Pore Size and Specific Surface Area Analysis > Advanced Analytical Techniques for Characterization of 2D Materials
Published: December 2022
FIG. 8.4 Schematic illustration of the synthesis of the 2D mesoporous PPy nanosheets. (a) Formation of spherical micelles and 2D lipid bilayers derived from the self-assembly of block polymers and aliphatic amine in mixed solvents at room temperature, respectively. (b) Supramolecular sandwich More about this image found in Schematic illustration of the synthesis of the 2D mesoporous PPy nanosheets...