Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.     

In memory of Professor Ali H. Nayfeh

Nonlinear Dynamics - In this paper, we propose and numerically study a nonlinear, asymmetric, passive metamaterial that achieves giant non-reciprocity with (i) broadband frequency operation and...     

Meccanica

Instructions for Authors

Meccanica     

Experimental details of the Stopped Beam RISING campaign

The RISING (Rare ISotope INvestigations at GSI) project constitutes a major pan-european initiative to study nuclear structure in exotic nuclei. A brief outline of the technical details specific to studies of isomeric decays following relativistic projectile fragmentation reactions is presented.     

Two-to-one resonant multi-modal dynamics of horizontal/inclined cables. Part II: Internal resonance activation,reduced-order models and nonlinear normal modes

Resonant multi-modal dynamics due to planar 2:1 internal resonances in the non-linear, finite-amplitude, free vibrations of horizontal/inclined cables are parametrically investigated based on the second-order multiple scales solution in Part I [1] (in press). The already validated kinematically non-condensed cable model accounts for the effects of both non-linear dynamic extensibility and system asymmetry due to inclined sagged configurations. Actual activation of 2:1 resonances is discussed, enlightening on a remarkable qualitative difference of horizontal/inclined cables as regards non-linear orthogonality properties of normal modes. Based on the analysis of modal contribution and solution convergence of various resonant cables, hints are obtained on proper reduced-order model selections from the asymptotic solution accounting for higher-order effects of quadratic nonlinearities. The dependence of resonant dynamics on coupled vibration amplitudes, and the significant effects of cable sag, inclination and extensibility on system non-linear behavior are highlighted, along with meaningful contributions of longitudinal dynamics. The spatio-temporal variation of non-linear dynamic configurations and dynamic tensions associated with 2:1 resonant non-linear normal modes is illustrated. Overall, the analytical predictions are validated by finite difference-based numerical investigations of the original partial-differential equations of motion.     

Nonlinear curvature-based model and resonant finite-amplitude vibrations of symmetric cross-ply laminates

Moving from a general plate theory, a modified general classical laminated plate theory (MGCLPT) exhibiting nonlinear curvatures but still allowing for some worth features of linear curvature models (von Karman) is formulated. Starting from MGCLPT partial differential equations, a minimal discretized model suitable for the analysis of resonant finite-amplitude vibrations of symmetric cross-ply laminates, with immovable or movable supports, is obtained via the Galerkin procedure. Periodic responses of a single-mode model and of a 3:1 internally resonant two-mode model excited at primary resonance are obtained via the multiple time scale method. The influence of various system parameters (thickness ratio, plate aspect, number of laminae, kind of material, mode number) is addressed, and the comparison of nonlinear vibration results as obtained with the MGCLPT and the von Karman models for different boundary conditions shows some interesting differences.     

Crystallization and crystal structure of poly(ester amide)s derived from L‐tartaric acid

The crystal structure and crystallization behavior of a series of poly(ester amide)s derived from L ‐tartaric acid, 1,6‐hexanediamine, and 6‐amino‐1‐hexanol were examined. The study included aregic polymers containing 5, 10, and 20% of ester groups in addition to the syndioregic polymer containing equal amounts of amide and ester groups. X‐ray diffraction data revealed that all the aregic poly(ester amide)s adopt the same crystal structure as the parent polyamide made of L ‐tartaric acid, and 1,6‐hexanediamine. In this structure, chains are slightly compressed and arranged as in the α‐form of nylon 66. Solid‐state nuclear magnetic resonance (NMR) revealed that ester groups are excluded from the crystal phase except for the case of the syndioregic polymer. Isothermal crystallization kinetics was analyzed according to the Avrami theory. Crystallization rates were found to decrease regularly with increasing contents in ester groups and with increasing crystallization temperature. Avrami exponent values close to 2 were found whereas spherulitic morphologies were observed by optical microscopy. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 116–125, 2007