Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.     

Dipole,quadrupole, octupole,and dipole–octupole polarizabilities at real and imaginary frequencies for H,HE, and H2 and the dispersion-energy coefficients for interactions between them

We have calculated certain dynamic polarizabilities (for both real and imaginary frequencies) for H, He, and H₂ and the dispersion-energy coefficients for long-range interactions between them. We have done so in a sum-over-states formalism with explicitly electron-correlated wave functions to describe the states. To be precise, we have determined the dipole (α₁), quadrupole (α₂), and octupole (α₃) polarizabilities of H and He for real frequencies (ω) in a range between zero and the first electronic-transition frequency and for imaginary frequencies (iω) on a 32-point Gauss-Legendre grid running from zero to ?ω = 20 E_h, and for H₂, we have found the dipole (α), quadrupole (C), and dipole–octupole (E) polarizability tensors for the same real and imaginary frequencies. The dispersion-energy coefficients, obtained by combining the sum-over-states for-malism for the polarizabilities with analytic integration over ω, gave values of C₆, C₈, and C₁₀ for the atom–atom systems; C, C, C, C, and C for the atom–diatom systems; and C₆, C and C for the H₂? H₂ system. Nearly all the results are considered to be more reliable than those hitherto published and some have been obtained for the first time, e.g., C(iω), E(ω), and E(iω) for H₂ and C, C, and C for the H? H₂ system. © 1993 John Wiley & Sons, Inc.     

Gravitational redshift and the equivalence principle

Two problems have long been confused with each other: the gravitational redshift as discussed by the equivalence principle; and the Doppler shift observed by a detector which moves with constant proper acceleration away from a stationary source. We here distinguish these two problems and give for the first time a solution of the former which is exact within the context of the equivalence principle in a sense discussed in the paper. The equivalence principle leads to transformations between flat spacetimes. These are analyzed, and a generalized Lorentz transformation is proposed which covers transformations from inertial to uniformly accelerated frames of reference.     

Synthesis and characterization of novel elastomeric poly(D,L-lactide urethane) maleate composites for bone tissue engineering

Here, we report the synthesis and characterization of a novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its composites with nano-hydroxyapatite (nHA) as potential weight-bearing composite. The 4PLAUMA/nHA ratios of the composites were 1:3, 2:5, 1:2 and 1:1. FTIR and NMR characterization showed urethane and maleate units integrated into the PLA matrix. Energy dispersion and Auger electron spectroscopy confirmed homogeneous distribution of nHA in the polymer matrix. Maximum moduli and strength of the composites of 4PLAUMA/nHA, respectively, are 1973.31 ± 298.53 MPa and 78.10 ± 3.82 MPa for compression, 3630.46 ± 528.32 MPa and 6.23 ± 1.44 MPa for tension, 1810.42 ± 86.10 MPa and 13.00 ± 0.72 for bending, and 282.46 ± 24.91 MPa and 5.20 ± 0.85 MPa for torsion. The maximum tensile strains of the polymer and composites are in the range of 5–93%, and their maximum torsional strains vary from 0.26 to 0.90. The composites exhibited very slow degradation rates in aqueous solution, from approximately 50% mass remaining for the pure polymer to 75% mass remaining for composites with high nHA contents, after a period of 8 weeks. Increase in ceramic content increased mechanical properties, but decreased maximum strain, degradation rate, and swelling of the composites. Human bone marrow stem cells and human endothelial cells adhered and proliferated on 4PLAUMA films and degradation products of the composites showed little-to-no toxicity. These results demonstrate that novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its nHA composites may have potential applications in regenerative medicine.     

Controlling domain orientation of liquid crystalline block copolymer in thin films through tuning mesogenic chemical structures

Controlling the macroscopic orientation of nanoscale periodic structures of amphiphilic liquid crystalline block copolymers (LC BCPs) is important to a variety of technical applications (e.g., lithium conducting polymer electrolytes). To study LC BCP domain orientation, a series of LC BCPs containing a poly(ethylene oxide) (PEO) block as a conventional hydrophilic coil block and LC blocks containing azobenzene mesogens is designed and synthesized. LC ordering in thin films of the BCP leads to the formation of highly ordered, microphase‐separated nanostructures, with hexagonally arranged PEO cylinders. Substitution on the tail of the azobenzene mesogen is shown to control the orientation of the PEO cylinders. When the substitution on the mesogenic tails is an alkyl chain, the PEO cylinders have a perpendicular orientation to the substrate surface, provided the thin film is above a critical thickness value. In contrast, when the substitution on the mesogenic tails has an ether group the PEO cylinders assemble parallel to the substrate surface regardless of the film thickness value. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 532–541     

Numerical approaches to time evolution of complex quantum systems

We examine several numerical techniques for the calculation of the dynamics of quantum systems. In particular, we single out an iterative method which is based on expanding the time evolution operator into a finite series of Chebyshev polynomials. The Chebyshev approach benefits from two advantages over the standard time-integration Crank-Nicholson scheme: speedup and efficiency. Potential competitors are semiclassical methods such as the Wigner-Moyal or quantum tomographic approaches. We outline the basic concepts of these techniques and benchmark their performance against the Chebyshev approach by monitoring the time evolution of a Gaussian wave packet in restricted one-dimensional (1D) geometries. Thereby the focus is on tunnelling processes and the motion in anharmonic potentials. Finally we apply the prominent Chebyshev technique to two highly non-trivial problems of current interest: (i) the injection of a particle in a disordered 2D graphene nanoribbon and (ii) the spatiotemporal evolution of polaron states in finite quantum systems. Here, depending on the disorder/electron-phonon coupling strength and the device dimensions, we observe transmission or localisation of the matter wave.     

Conformational dynamics of photoexcited conjugated molecules

Time-dependent photoexcitation and optical spectroscopy of pi-conjugated molecules is described using a new method for the simulation of excited state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. Applications are made to poly(p-phenylene vinylene) oligomers. Our analysis shows self-trapping of excitations on about six repeat units in the course of photoexcitation relaxation, identifies specific slow (torsion) and fast (bond-stretch) nuclear motions strongly coupled to the electronic degrees of freedom, and predicts spectroscopic signatures of molecular conformations.