On the temperature Dependence of the orientational Order Parameter in the Nematic Phase of Cyanophenyl Behzoates

The orientational order parameters fot two liquid crystal materials, 4-cyanophenyl 4-butylbenzoate and 4-cyanophenyl 4-pentylbenzoate, have been derived by measuring the change in the refractive index as function of temperature. The order parameters are compared with MaierSaupe theory, and the sharpness of the transitions has been shown using the Haller's plot.     

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An integrated finite element method (FEM) is proposed to simulate incompressible two‐phase flows with surface tension effects, and three different surface tension models are applied to the FEM to investigate spurious currents and temporal stability. A Q2Q1 element is adopted to solve the continuity and Navier–Stokes equations and a Q2‐iso‐Q1 to solve the level set equation. The integrated FEM solves pressure and velocity simultaneously in a strongly coupled manner; the level set function is reinitialized by adopting a direct approach using interfacial geometry information instead of solving a conventional hyperbolic‐type equation. In addition, a consistent continuum surface force (consistent CSF) model is utilized by employing the same basis function for both surface tension and pressure variables to damp out spurious currents and to estimate the accurate pressure distribution. The model is further represented as a semi‐implicit manner to improve temporal stability with an increased time step. In order to verify the accuracy and robustness of the code, the present method is applied to a few benchmark problems of the static bubble and rising bubble with large density and viscosity ratios. The Q2Q1‐integrated FEM coupled with the semi‐implicit consistent CSF demonstrates the significantly reduced spurious currents and improved temporal stability. The numerical results are in good qualitative and quantitative agreements with those of the existing studies. Copyright © 2015 John Wiley & Sons, Ltd.     

A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.     

Mechanics of atoms interacting with a carbon nanotorus: optimal configuration and oscillation behaviour

In this paper, we investigate a carbon nanotorus as a caged molecular structure interacting with an atom. Assuming that the atom is located along the central axis perpendicular to the torus, the interaction energy of the system is determined using the continuum approximation together with the Lennard-Jones potential. This approach avoids the intensive computational calculations that are involved in other modelling approaches. Numerical results are presented in terms of dimensionless variables. The results show that the optimal major radius of the torus has a linear relationship with its minor radius when the atom is symmetrically situated along the torus axis. When the atom is offset from this axis, the minimum energy location shifts away from the centre as the ratio of the major and minor radii exceeds the value of 0.90. Finally, the oscillatory behaviour for the carbon atom is investigated. Our findings predict a novel nano-oscillator which can produce frequencies in the gigahertz range.     

Asymptotic expansion homogenization of discrete fine-scale models with rotational degrees of freedom for the simulation of quasi-brittle materials

Discrete fine-scale models, in the form of either particle or lattice models, have been formulated successfully to simulate the behavior of quasi-brittle materials whose mechanical behavior is inherently connected to fracture processes occurring in the internal heterogeneous structure. These models tend to be intensive from the computational point of view as they adopt an “a priori” discretization anchored to the major material heterogeneities (e.g. grains in particulate materials and aggregate pieces in cementitious composites) and this hampers their use in the numerical simulations of large systems. In this work, this problem is addressed by formulating a general multiple scale computational framework based on classical asymptotic analysis and that (1) is applicable to any discrete model with rotational degrees of freedom; and (2) gives rise to an equivalent Cosserat continuum. The developed theory is applied to the upscaling of the Lattice Discrete Particle Model (LDPM), a recently formulated discrete model for concrete and other quasi-brittle materials, and the properties of the homogenized model are analyzed thoroughly in both the elastic and the inelastic regime. The analysis shows that the homogenized micropolar elastic properties are size-dependent, and they are functions of the RVE size and the size of the material heterogeneity. Furthermore, the analysis of the homogenized inelastic behavior highlights issues associated with the homogenization of fine-scale models featuring strain-softening and the related damage localization. Finally, nonlinear simulations of the RVE behavior subject to curvature components causing bending and torsional effects demonstrate, contrarily to typical Cosserat formulations, a significant coupling between the homogenized stress–strain and couple-curvature constitutive equations.     

Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

A continuum description for cholesteric and nematic twist-bend phases based on symmetry considerations

ABSTRACT

The recently discovered twist-bend nematic phase, N_tb, is a non-uniform equilibrium nematic phase that presents a spontaneous bend with a precession of the nematic director, n, on a conical helix with a tilt angle θ and helical pitch P. The stability of the N_tb phase has been recently demonstrated from the elastic point of view by extending the Frank elastic energy density of the nematic phase to include the symmetry element of the helical axis, t. In the present article, we investigate the influence of an external bulk field (magnetic or electric) on the N_tb phase. Using symmetry arguments we derive the expression for the flexoelectric polarisation in twist-bend nematic phases. We show that, besides the standard contribution related to the spatial variation of the nematic director, two new contributions connected with the existence of the helical axis appear. In the ground state, where the nematic deformation is a pure heliconical deformation, the new contribution vanishes identically, and the total flexoelectric polarisation is perpendicular to the nematic director. Furthermore, as an example, we study the role of an external magnetic field applied parallel to the helical axis for a material with positive magnetic susceptibility anisotropy. We show that the field modifies the range of values of the coupling parameter between the director and the helical axis, thus shifting the interval of values for which this coupling results in the N_tb phase.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.