scholarly journals Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5472 ◽  
Author(s):  
Fatima Sajadi ◽  
Christopher N. Rowley
Keyword(s):  
Dielectric Constant ◽  
Force Field ◽  
Lipid Bilayers ◽  
Water Permeability ◽  
Form Factors ◽  
Potential Of Mean Force ◽  
Water Model ◽  
Water Permeation ◽  
Low Viscosity ◽  
Water Models

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification when calculating membrane physical properties. The water permeability predicted by these models is significantly different; the mTIP3P-model diffusion in solution and at the lipid–water interface is anomalously fast due to the spuriously low viscosity of mTIP3P-model water, but the potential of mean force of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials. As a result, the rates of water permeation calculated the FB water models are slower than the experimental value by a factor of 15–17, while simulations with the mTIP3P model only underestimate the water permeability by a factor of 3.

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

2018 ◽  
Author(s):  
Fatima Sajadi ◽  
Christopher Rowley
Keyword(s):  
Dielectric Constant ◽  
Force Field ◽  
Lipid Bilayers ◽  
Form Factors ◽  
Water Model ◽  
Low Viscosity ◽  
Chemical Potentials ◽  
Water Models ◽  
Experimental Values ◽  
High Dielectric

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the TIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of DPPC and POPC bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid--water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials.

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

2018 ◽  
Author(s):  
Fatima Sajadi ◽  
Christopher Rowley
Keyword(s):  
Dielectric Constant ◽  
Force Field ◽  
Lipid Bilayers ◽  
Form Factors ◽  
Water Model ◽  
Low Viscosity ◽  
Chemical Potentials ◽  
Water Models ◽  
Experimental Values ◽  
High Dielectric

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the TIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of DPPC and POPC bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid--water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials.

scholarly journals Water Permeability of Asymmetric Planar Lipid Bilayers

2001 ◽  
Vol 118 (4) ◽  
pp. 333-340 ◽  
Author(s):  
Andrey V. Krylov ◽  
Peter Pohl ◽  
Mark L. Zeidel ◽  
Warren G. Hill
Keyword(s):  
Lipid Bilayers ◽  
Water Permeability ◽  
Plasma Membranes ◽  
Apical Membrane ◽  
Planar Lipid Bilayers ◽  
Osmotic Gradient ◽  
Asymmetric Membrane ◽  
Intact Cells ◽  
Water Permeation ◽  
Outer Leaflet

To understand how plasma membranes may limit water flux, we have modeled the apical membrane of MDCK type 1 cells. Previous experiments demonstrated that liposomes designed to mimic the inner and outer leaflet of this membrane exhibited 18-fold lower water permeation for outer leaflet lipids than inner leaflet lipids (Hill, W.G., and M.L. Zeidel. 2000. J. Biol. Chem. 275:30176–30185), confirming that the outer leaflet is the primary barrier to permeation. If leaflets in a bilayer resist permeation independently, the following equation estimates single leaflet permeabilities: 1/PAB = 1/PA + 1/PB (Eq. l), where PAB is the permeability of a bilayer composed of leaflets A and B, PA is the permeability of leaflet A, and PB is the permeability of leaflet B. Using for the MDCK leaflet–specific liposomes gives an estimated value for the osmotic water permeability (Pf) of 4.6 × 10−4 cm/s (at 25°C) that correlated well with experimentally measured values in intact cells. We have now constructed both symmetric and asymmetric planar lipid bilayers that model the MDCK apical membrane. Water permeability across these bilayers was monitored in the immediate membrane vicinity using a Na+-sensitive scanning microelectrode and an osmotic gradient induced by addition of urea. The near-membrane concentration distribution of solute was used to calculate the velocity of water flow (Pohl, P., S.M. Saparov, and Y.N. Antonenko. 1997. Biophys. J. 72:1711–1718). At 36°C, Pf was 3.44 ± 0.35 × 10−3 cm/s for symmetrical inner leaflet membranes and 3.40 ± 0.34 × 10−4 cm/s for symmetrical exofacial membranes. From , the estimated permeability of an asymmetric membrane is 6.2 × 10−4 cm/s. Water permeability measured for the asymmetric planar bilayer was 6.7 ± 0.7 × 10−4 cm/s, which is within 10% of the calculated value. Direct experimental measurement of Pf for an asymmetric planar membrane confirms that leaflets in a bilayer offer independent and additive resistances to water permeation and validates the use of .

Multiscale Polarizable Coarse-graining Water Models on Cluster-level Electrostatic Dipoles

2021 ◽  
Author(s):  
Min Li ◽  
John Z.H. Zhang
Keyword(s):  
Force Field ◽  
Liquid Water ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Water Model ◽  
Biological Processes ◽  
Water Models ◽  
Cluster Level

The development of coarse-grained (CG) water model is increasingly important in CG studies of biological processes. In this work, we developed a generic CG force field of liquid water on...

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins

2017 ◽  
Vol 19 (10) ◽  
pp. 7410-7419 ◽  
Author(s):  
Min Li ◽  
John Z. H. Zhang
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Water Model ◽  
Water Molecules ◽  
Water Models

(a) Four water molecules contained in the polarizable CG water models in (b) two-bead polarizable water model 1 (TPW1) and (c) two-bead polarizable water model 2 (TPW2).

scholarly journals Modelling Weirs in Two-Dimensional Shallow Water Models

Water ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 2152
Author(s):  
Gonzalo García-Alén ◽  
Olalla García-Fonte ◽  
Luis Cea ◽  
Luís Pena ◽  
Jerónimo Puertas
Keyword(s):  
Experimental Data ◽  
Shallow Water ◽  
Shallow Water Equations ◽  
Water Model ◽  
Two Dimensional ◽  
Shallow Water Model ◽  
Experimental Dataset ◽  
River Hydraulics ◽  
Shallow Water Models ◽  
Water Models

2D models based on the shallow water equations are widely used in river hydraulics. However, these models can present deficiencies in those cases in which their intrinsic hypotheses are not fulfilled. One of these cases is in the presence of weirs. In this work we present an experimental dataset including 194 experiments in nine different weirs. The experimental data are compared to the numerical results obtained with a 2D shallow water model in order to quantify the discrepancies that exist due to the non-fulfillment of the hydrostatic pressure hypotheses. The experimental dataset presented can be used for the validation of other modelling approaches.

Water permeability of apical and basolateral cell membranes of rat inner medullary collecting duct

1990 ◽  
Vol 259 (6) ◽  
pp. F986-F999 ◽  
Author(s):  
B. Flamion ◽  
K. R. Spring
Keyword(s):  
Water Flow ◽  
Water Permeability ◽  
Cell Membranes ◽  
Apical Membrane ◽  
Collecting Duct ◽  
Basolateral Membrane ◽  
Volume Regulatory Decrease ◽  
Water Permeation ◽  
Inner Medullary Collecting Duct ◽  
Medullary Collecting Duct

To quantify the pathways for water permeation through the kidney medulla, knowledge of the water permeability (Posmol) of individual cell membranes in inner medullary collecting duct (IMCD) is required. Therefore IMCD segments from the inner two thirds of inner medulla of Sprague-Dawley rats were perfused in vitro using a setup devised for rapid bath and luminal fluid exchanges (half time, t1/2, of 55 and 41 ms). Differential interference contrast microscopy, coupled to video recording, was used to measure volume and approximate surface areas of single cells. Volume and volume-to-surface area ratio of IMCD cells were strongly correlated with their position along the inner medullary axis. Transmembrane water flow (Jv) was measured in response to a variety of osmotic gradients (delta II) presented on either basolateral or luminal side of the cells. The linear relation between Jv and delta II yielded the cell membrane Posmol, which was then corrected for membrane infoldings. Basolateral membrane Posmol was 126 +/- 3 microns/s. Apical membrane Posmol rose from a basal value of 26 +/- 3 microns/s to 99 +/- 5 microns/s in presence of antidiuretic hormone (ADH). Because of amplification of basolateral membrane, the ADH-stimulated apical membrane remained rate-limiting for transcellular osmotic water flow, and the IMCD cell did not swell significantly. Calculated transcellular Posmol, expressed in terms of smooth luminal surface, was 64 microns/s without ADH and 207 microns/s with ADH. IMCD cells in anisosmotic media displayed almost complete volume regulatory decrease but only partial volume regulatory increase.

Development of the trappe force field for ammonia

2010 ◽  
Vol 75 (5) ◽  
pp. 577-591 ◽  
Author(s):  
Ling Zhang ◽  
J. Ilja Siepmann
Keyword(s):  
Dielectric Constant ◽  
Nitrogen Atom ◽  
Force Field ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Site Model ◽  
Lennard Jones ◽  
Hydrogen Position ◽  
Partial Charges ◽  
Vapor Liquid

The transferable potentials for phase equilibria (TraPPE) force field is extended through the development of a non-polarizable five-site ammonia model. In this model, the electrostatic interactions are represented by three positive partial charges placed at the hydrogen position and a compensating partial charge placed on an M site that is located on the C3 molecular axis and displaced from the nitrogen atom toward the hydrogen atoms. The repulsive and dispersive interactions are represented by placing a single Lennard–Jones site at the position of the nitrogen atom. Starting from the five-site model by Impey and Klein (Chem. Phys. Lett. 1984, 104, 579), this work optimizes the Lennard–Jones parameters and the magnitude of the partial charges for three values of the M site displacement. This parameterization is done by fitting to the vapor–liquid coexistence curve of neat ammonia. The accuracy of the three resulting models (differing in the displacement of the M site) is assessed through computation of the binary vapor–liquid equilibria with methane, the structure and the dielectric constant of liquid ammonia. The five-site model with an intermediate displacement of 0.08 Å for the M site yields a much better value for the dielectric constant, whereas differences in the other properties are quite small.

Comparison of flow behaviour in pressurized gating systems using water models and numerical simulation

2016 ◽  
Vol 14 (3) ◽  
pp. 652-674
Author(s):  
V. Jaiganesh ◽  
K. Prakasan
Keyword(s):  
Flow Visualization ◽  
Flow Behaviour ◽  
Water Model ◽  
Gating System ◽  
Commercial Software ◽  
Content Type ◽  
Filling Pattern ◽  
Flow Through ◽  
Water Models ◽  
Critical Sections

Purpose The purpose of this work is to visualize the flow behaviour in critical sections of a pressurized gating system. Design/methodology/approach The investigation was carried out using water models of gating system that were designed, invoking the principles of similitude. Water was used as the filling medium, and the manner of flow through various sections of the gating system and the cavity was recorded with a high-speed camera capable of capturing images up to 10,000 frames per second. This was followed by an analysis of the results obtained from each phase. Finally, computer simulations of flow were carried out using commercial software. The manner of filling as observed during experiments and that during simulation were compared so as to draw some useful conclusions on the utility of flow visualization using water models and the capability of software to predict the filling pattern during casting process. It was understood that water models are powerful aids for understanding the intricacies of flow through critical sections of the gating systems. Findings It was observed that water models are a reliable indicator of the mould-filling process. Further, substantial differences in the filling pattern were observed between water model experiments and filling simulation using commercial software. Research limitations/implications The findings are limited to horizontal plate-type castings. Also, the influence of surface roughness in the flow through the runner is not considered. Originality/value This work facilitates understanding of the importance of flow visualization on the quality and reliability of castings.

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