Current mitigation levels for noise transients impinging on marine mammals are specified by rms pressures. The rms measure critically relies upon choosing the size of averaging window for the squared pressures. Derivation of this window is not standardized, which can lead to 2-12 dB differences in rms sound pressure for the same wave forms. rms pressure does not represent the energy of the nois...

The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynami...

In this paper, we propose a pseudo-spectral multiscale method for simulating complex systems with more than one spatial scale. Using a spectral decomposition, we split the displacement into its mean and fluctuation parts. Under the assumption of localized nonlinear fluctuations, we separate the domain into an MD (Molecular Dynamics) subdomain and an MC (MacrosCopic) subdomain. An interfacial co...

The dynamics of alpha-amylase inhibitors has been investigated using molecular dynamics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based on a coarse-grained single-site-per-residue model with a single-parameter harm...

We examine effects on primordial nucleosynthesis from a truly random spatial distribution in the baryon-to-photon ratio (η). We generate stochastic fluctuation spectra characterized by different spectral indices and root-mean-square fluctuation amplitudes. For the first time we explicitly calculate the effects of baryon diffusion on the nucleosynthesis yields of such stochastic fluctuations. We...

A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consist...

We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate minimal RMSD value of two atomic structures by optimal superimposition. not restricted systems with equal number atoms compare or a unique atom mapping between molecules. The can handle any type chemical structure, including transition states and which cannot be explained only va...

Abstract The mechanisms of thermal conductivity enhancement and the factors influencing viscosity are great interest in study nanofluids, while molecular dynamics (MD) simulations considering nanofluids provide more accurate predictions microscopic properties than conventional experimental studies. MD non-equilibrium reversing perturbation methods were used to viscosity, taking into account a v...

The solution structure of the self-complementary DNA hexamer 5'd(GCATGC)2 comprising the specific target site for the restriction endonuclease Sph 1 is investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics. All the nonexchangeable proton resonances are assigned sequentially, and from time-dependent nuclear Overhauser enhancement measurements a set of 15...