Theoretical study of solvent-mediated Ising-like systems: One-dimensional version

Amano, Ken-ichi

doi:10.1016/j.physa.2012.05.059

Cited by 2 publications

(2 citation statements)

References 36 publications

(64 reference statements)

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“…The tests are conducted in both hard sphere fluid and LJ fluid with hard core potential. The tests of the transform methods are done by using liquid theories [22][23][24], three-dimensional Ornstein-Zernike equation coupled with a hypernetted-chain closure (3D-OZ-HNC) [15]. The grid spacings x, y, and z are set at 0.1d S , 0.1d S , and 0.02d S , respectively.…”

Section: Computational Verification Of the Transform Methodsmentioning

confidence: 99%

Simple transform methods of a force curve obtained by surface force apparatus to the density distribution of a liquid near a surface

Amano

Takahashi

2015

Physica A: Statistical Mechanics and its Applications

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h i g h l i g h t s• Measurement theory for SFA (Surface Force Apparatus) is proposed.• Solvation structure can be obtained experimentally by using the theory proposed here. • Verification tests of the theory are conducted. a b s t r a c tWe propose two simple methods that transform a force curve obtained by a surface force apparatus (SFA) into a density distribution of a liquid near a surface of the SFA probe. The transform methods are derived based on the statistical mechanics of simple liquids, where the liquid is an ensemble of small spheres. The solvent species is limited to only one component and two-body potential between the solvent spheres is arbitrary. However, twobody potential between the SFA probe and the solvent is restricted to rigid potential (i.e., the transform methods are derived within the restriction of the rigid potential). In addition, Kirkwood and linear superposition approximations are applied in order to derive the transform methods. The transform methods are simply tested in both hard-sphere fluid and Lennard-Jones (LJ) fluid with hard core potential. The tests are computationally practiced using a three-dimensional integral equation theory. It is found that the transform method with Kirkwood superposition approximation (transform method 1) generally reproduces the more precise solvation structure than that with linear superposition approximation (transform method 2). In the test of the hard sphere solvent, it is found that the reproducibility becomes better as the number density of the solvent is lower. Furthermore, it is found in the test of the LJ fluid that the reproducibility becomes better as the two-body potential between the SFA probe and the solvent approaches rigid potential. This is because, the transform methods are derived within the model of the rigid potential. It is verified that the transform methods are useful for obtaining of a rough image of the solvation structure. (However, if evaporation or solidification, a phase transition in a local space sandwiched between the two surfaces, occurs while the experiment, the transform methods should not be used.)

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Section: Computational Verification Of the Transform Methodsmentioning

confidence: 99%

Simple transform methods of a force curve obtained by surface force apparatus to the density distribution of a liquid near a surface

Amano

Takahashi

2015

Physica A: Statistical Mechanics and its Applications

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“…The 3D‐Reference Interaction Site Model 18,19,44–48 is a statistical mechanical theory based on the Ornstein‐Zernike integral equation 49 of liquids which estimates the 3D distribution function of the solvent molecules around a given protein. The 3D‐RISM equation is obtained by averaging the six‐dimensional Ornstein‐Zernike equation over the solvent orientations while retaining the orientational coordinates of the solute molecule.…”

Section: Methodsmentioning

confidence: 99%

Aggregation propensities of proteins with varying degrees of disorder

Dey

Biswas

2022

J Comput Chem

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The hydration thermodynamics of a globular protein (AcP), three intrinsically disordered protein regions (1CD3, 1MVF, 1F0R) and a fully disordered protein (α‐synuclein) is studied by an approach that combines an all‐atom explicit water molecular dynamics simulations and three‐dimensional reference interaction site model (3D‐RISM) theory. The variation in hydration free energy with percentage disorder of the selected proteins is investigated through its nonelectrostatic and electrostatic components. A decrease in hydration free energy is observed with an increase in percentage disorder, indicating favorable interactions of the disordered proteins with the solvent. This confirms the role of percentage disorder in determining the aggregation propensity of proteins which is measured in terms of the hydration free energy in addition to their respective mean net charge and mean hydrophobicity. The hydration free energy is decoupled into energetic and entropic terms. A residue‐wise decomposition analysis of the hydration free energy for the selected proteins is evaluated. The decomposition shows that the disordered regions contribute more than the ordered ones for the intrinsically disordered protein regions. The dominant role of electrostatic interactions is confirmed from the residue‐wise decomposition of the hydration free energy. The results depict that the negatively charged residues contribute more to the total hydration free energy for the proteins with negative mean net charge, while the positively charged residues contribute more for proteins with positive mean net charge.

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Theoretical study of solvent-mediated Ising-like systems: One-dimensional version

Cited by 2 publications

References 36 publications

Simple transform methods of a force curve obtained by surface force apparatus to the density distribution of a liquid near a surface

Simple transform methods of a force curve obtained by surface force apparatus to the density distribution of a liquid near a surface

Aggregation propensities of proteins with varying degrees of disorder

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