Simulation of the female pelvic mobility and vesical pressure changes employing fluid-structure interaction method.

Introduction And Hypothesis: This study aims to develop a fluid-structural interaction (FSI) method to pinpoint the effects of pressure changes inside the bladder and their impact on the supporting structure and the urethra mobility.

Methods: A physiological model of the nulliparous female pelvis, including the organs, supportive structures, and urine, was developed based on magnetic resonance images. Soft tissues with nonlinear hyperelastic material characteristics were modeled.

Interaction between the Human OX2 Orexin Receptor and Suvorexant and Some of Its Analogues: SAPT (DFT) Interaction Energy Decomposition Analysis.

In this study, the interaction energy () of suvorexant (as an orexin receptor antagonist) and some of its analogues with the important residues of the human OX2 orexin receptor, determined by molecular docking, is calculated using the symmetry-adapted perturbation theory-density functional theory (SAPT (DFT)) method. Also, the important residues with the dominant interaction with each ligand are determined based on the obtained SAPT (DFT) interaction energies. To analyze the interaction of the receptor with each ligand, the decomposition of to its constituent components including electrostatic (), exchange (), induction (), and exchange-induction (), dispersion (), and exchange-dispersion () is performed.

Decomposition of the interaction energy of several flavonoids with Escherichia coli DNA Gyr using the SAPT (DFT) method: The relation between the interaction energy components, ligand structure, and biological activity.

In this study, the SAPT (DFT) method is used to determine the components of the electronic interaction energies (electrostatic (E), exchange (E), induction (E), exchange-induction (E), dispersion (E), and exchange-dispersion (E)) between the several selected flavonoids and the important residues of the active site of Escherichia coli DNA Gyr determined by molecular docking. A significant linear correlation between the calculated SAPT (DFT) interaction energies of flavonoids and their experimental pIC50 values is found, which is not observed for the free binding energies (ΔG) of flavonoids obtained from molecular docking. The variation of the interaction energy components of flavonoids with their structural differences is investigated to find the relation between the flavonoids structures and their biological activity based on the interaction energy components.

Simulation of high-viscosity-ratio multicomponent fluid flow using a pseudopotential model based on the nonorthogonal central-moments lattice Boltzmann method.

In this research, the development of a pseudopotential multicomponent model with the capability of simulating high-viscosity-ratio flows is discussed and examined. The proposed method is developed based on the non-orthogonal central moments model in the lattice Boltzmann method, and the exact difference model (EDM) is used to apply the intercomponent interaction force. In contrast to the original Shan-Chen model, in which the applying force has the viscosity-dependent error term, the error term of this model does not depend on the viscosity.

Meshless lattice Boltzmann method for the simulation of fluid flows.

A meshless lattice Boltzmann numerical method is proposed. The collision and streaming operators of the lattice Boltzmann equation are separated, as in the usual lattice Boltzmann models. While the purely local collision equation remains the same, we rewrite the streaming equation as a pure advection equation and discretize the resulting partial differential equation using the Lax-Wendroff scheme in time and the meshless local Petrov-Galerkin scheme based on augmented radial basis functions in space.

Molecular dynamics simulation of (13)C NMR powder lineshapes of CO in structure I clathrate hydrate.

Guest molecules in nonspherical cages of inclusion compounds can possess non-uniform spatial distributions and motion. This can lead to anisotropic lineshapes in the solid-state NMR spectra of the guest species. In this work, we use our previously developed molecular dynamics-based methodology to calculate the lineshape anisotropy of guest CO species in cages of the structure I (sI) clathrate hydrate as an example of the above phenomenon.

Molecular dynamics study of congruent melting of the equimolar ionic liquid-benzene inclusion crystal [emim][NTf(2)].C(6)H(6).

We use molecular dynamics simulations to study the structure, dynamics, and details of the mechanism of congruent melting of the equimolar mixture of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl) imide with benzene, [emim][NTf(2)]C(6)H(6). Changes in the molecular arrangement, radial distribution functions, and the dynamic behavior of species are used to detect the solid to liquid transition, show an indication of the formation of polar islands by aggregating of the ions in the liquid phase, and characterize the melting process. The predicted enthalpy of melting DeltaH(m)=38+/-2 kJ mol(-1) for the equimolar inclusion mixture at 290 K is in good agreement with the differential scanning calorimetry experimental results of 42+/-2 kJ mol(-1).

Molecular dynamics simulation of imidazolium-based ionic liquids. II. Transport coefficients.

A systematic molecular dynamics study is performed to determine the dynamics and transport properties of 12 room-temperature ionic liquids family with 1-alkyl-3-methylimidazolium cation, [amim](+) (alkyl = methyl, ethyl, propyl, and butyl), with counterions, PF(6)(-), NO(3)(-), and Cl(-). The goal of the work is to provide molecular level understanding of the transport coefficients of these liquids as guidance to experimentalists on choosing anion and cation pairs to match required properties of ionic liquid solvents. In the earlier paper (Part I), we characterized the dynamics of ionic liquids and provided a detailed comparison of the diffusion coefficients for each ion using the Einstein and Green-Kubo formulas.

Molecular dynamics simulation of imidazolium-based ionic liquids. I. Dynamics and diffusion coefficient.

Molecular dynamics simulations are used to study the dynamics and transport properties of 12 room-temperature ionic liquids of the 1-alkyl-3-methylimidazolium [amim](+) (alkyl = methyl, ethyl, propyl, and butyl) family with PF(6)(-), NO(3)(-), and Cl(-) counterions. The explicit atom transferable force field of Canongia Lopes et al. [J.