Molecular Dynamics Simulation and Density Functional Theory Study of Chemisorption of Propranolol Optical Isomers on a Uracil‐modified Carbon Paste Electrode

To reveal the nature of the interaction of the optical isomers of propranolol with the surface of carbon paste electrodes modified by uracil, we performed a combined computational and experimental study. Our study comprised the different modes of complexation between propranolol and uracil molecules covering the carbon paste electrode within two approaches: molecular dynamics simulation (MD ) and quantum mechanics (QM) modeling. A graphene layer was used as a model of the carbon paste electrode. The computations showed that uracil modification of the carbon paste electrode surface enhanced the selectivity toward the D‐isomer of propranolol as compared to the unmodified case. These theoretical results agree with our voltammetric measurements.     

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD‐based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907‐atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.     

Spin-Phonon Coupling and Slow-Magnetic Relaxation in Pristine Ferrocenium

We report the spin dynamic properties of non-substituted ferrocenium complexes. Ferrocenium shows a field-induced single-molecule magnet behaviour in DMF solution while cobaltocene lacks slow spin relaxation neither in powder nor in solution. Multireference quantum mechanical calculations give a non-Aufbau orbital occupation for ferrocenium with small first excitation energy that agrees with the relatively large measured magnetic anisotropy for a transition metal S=1/2 system. The analysis of the spin relaxation shows an important participation of quantum tunnelling, Raman, direct and local-mode mechanisms which depend on temperature and the external field conditions. The calculation of spin-phonon coupling constants for the vibrational modes shows that the first vibrational mode, despite having a low spin-phonon constant, is the most efficient process for the spin relaxation at low temperatures. In such conditions, vibrational modes with higher spin-phonon coupling constants are not populated. Additionally, the vibrational energy of this first mode is in excellent agreement with the experimental fitted value obtained from the local-mode mechanism.     

Surface reduction of freely floating smectic bubbles

Elongated freely floating smectic bubbles are observed during their relaxation to equilibrium sphere shape. Unlike soap bubbles that perform weakly damped oscillations into equilibrium, this relaxation is overdamped in smectics by internal structure reorganisation processes. The bubble area reduction of centimetre-sized freely floating bubbles with few nanometres film thickness is recorded with high-speed optical imaging in microgravity and analysed quantitatively. We find a nearly linear reduction of the film area with time, driven by capillary forces and inhibited by smectic layer reorganisations. Characteristic times are in the milliseconds range, with little correlation to the film thickness and bubble size. Instead, the homogeneity of the films and the number and sizes of islands of excess layers that spontaneously form on the films appear to have crucial influence on the dynamics. The efficiency of this process sets the time scale of the film area shrinkage. We discuss the limitations of a minimalistic model that captures smectic layer reorganisation processes.     

Free energy and states of fractional-order hereditariness

Complex materials, often encountered in recent engineering and material sciences applications, show no complete separations between solid and fluid phases. This aspect is reflected in the continuous relaxation time spectra recorded in cyclic load tests. As a consequence the material free energy cannot be defined in a unique manner yielding a significative lack of knowledge of the maximum recoverable work that can extracted from the material. The non-uniqueness of the free energy function is removed in the paper for power-laws relaxation/creep function by using a recently proposed mechanical analogue to fractional-order hereditariness.     

Impact of side‐chain length on the phase structures of P3ATs and P3AT:PCBM films as revealed by SSNMR and FTIR

It is known that poly(3‐alkylthiophene) (P3AT) side‐chain length notably influences the photovoltaic performances of relating devices. However, comprehensively study on its impact on the structures of P3ATs and their blends with [6, 6]‐phenyl‐C₆₁ butyric acid methyl ester (PCBM) is insufficient. By using solid‐state NMR and FTIR techniques, four P3ATs and their PCBM blends are investigated in this work, focusing on the phase structures as modulated by side‐chain length. Recently, we revealed multiple crystalline main‐chain packings of packing a and b together with a mesophase in poly(3‐butylthiophene) (P3BT) films (DOI: 10.1021/acs.macromol.6b01828). Here, the semicrystalline structures are investigated on poly(3‐hexylthiophene) (P3HT), poly(3‐octylthiophene) (P3OT), and poly(3‐dodecylthiophene) (P3DDT) with traditional form I modification, where packing a and the amorphous phase are probed. Furthermore, crystallized side chain within packing a is detected in both P3OT and P3DDT films, which shows a FTIR absorption at 806 cm⁻¹. Structural studies are also conducted on P3AT:PCBM blends. Compared with the pure P3ATs, the polymer crystallinities of the blends show reduction of about 40% for P3OT and P3DDT, whereas only about 10% for P3HT. Moreover, in P3BT:PCBM and P3HT:PCBM, the crystalline polymers and PCBM are phase separated, while in P3OT:PCBM and P3DDT:PCBM, blend components are mostly miscible. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 751–761     

Opinion dynamics in networks with heterogeneous confidence and influence

We propose a discrete-time model of opinion dynamics. The neighborhood relationship is decided by confidence radius and influence radius of each agent. We investigate the influence of heterogeneity in confidence/influence distribution on the behavior of the network. The simulations suggest that the heterogeneity of single confidence or influence networks can promote the opinions to achieve consensus. It is shown that the heterogeneous influence radius systems converge in fewer time steps and more often in finite time than the heterogeneous confidence radius systems. We find that heterogeneity does not always promote consensus, and there is an optimal heterogeneity so that the relative size of the largest consensus cluster reaches maximum in heterogeneous confidence and influence networks.     

Direct and adjoint global stability analysis of turbulent transonic flows over a NACA0012 profile

In this work, various turbulent solutions of the two‐dimensional (2D) and three‐dimensional compressible Reynolds averaged Navier–Stokes equations are analyzed using global stability theory. This analysis is motivated by the onset of flow unsteadiness (Hopf bifurcation) for transonic buffet conditions where moderately high Reynolds numbers and compressible effects must be considered. The buffet phenomenon involves a complex interaction between the separated flow and a shock wave. The efficient numerical methodology presented in this paper predicts the critical parameters, namely, the angle of attack and Mach and Reynolds numbers beyond which the onset of flow unsteadiness appears. The geometry, a NACA0012 profile, and flow parameters selected reproduce situations of practical interest for aeronautical applications. The numerical computation is performed in three steps. First, a steady baseflow solution is obtained; second, the Jacobian matrix for the RANS equations based on a finite volume discretization is computed; and finally, the generalized eigenvalue problem is derived when the baseflow is linearly perturbed. The methodology is validated predicting the 2D Hopf bifurcation for a circular cylinder under laminar flow condition. This benchmark shows good agreement with the previous published computations and experimental data. In the transonic buffet case, the baseflow is computed using the Spalart–Allmaras turbulence model and represents a mean flow where the high frequency content and length scales of the order of the shear‐layer thickness have been averaged. The lower frequency content is assumed to be decoupled from the high frequencies, thus allowing a stability analysis to be performed on the low frequency range. In addition, results of the corresponding adjoint problem and the sensitivity map are provided for the first time for the buffet problem. Finally, an extruded three‐dimensional geometry of the NACA0012 airfoil, where all velocity components are considered, was also analyzed as a Triglobal stability case, and the outcoming results were compared to the previous 2D limited model, confirming that the buffet onset is well detected. Copyright © 2014 John Wiley & Sons, Ltd.     

Dynamic stability of externally pressurized elastic rings subjected to high rates of loading

Of interest here is the influence of loading rate on the stability of structures where inertia is taken into account, with particular attention to the comparison between static and dynamic buckling. This work shows the importance of studying stability via perturbations of the initial conditions, since a finite velocity governs the propagation of disturbances. The method of modal analysis that determines the fastest growing wavelength, currently used in the literature to analyze dynamic stability problems, is meaningful only for cases where the velocity of the perfect structure is significantly lower than the associated wave propagation speeds.