In this article, we systematically apply a novel implicit-solvent model, the variational implicit-solvent model (VISM) together with the Coulomb-Field Approximation (CFA), to calculate the hydration free energy of a large set of small organic molecules. Because these molecules have been studied in detail by molecular dynamics simulations and other implicit-solvent models, they provide a good be...

Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in th...

A longstanding challenge in using computational methods for protein structure prediction is the refinement of low-resolution structural models derived from comparative modeling methods into highly accurate atomistic models useful for detailed structural studies. Previously, we have developed and demonstrated the utility of the internal coordinate molecular dynamics (MD) technique, generalized N...

We perform a numerical study of the fluctuations of the rescaled hydrodynamic transverse velocity field during the cooling state of a homogeneous granular gas. We are interested in the role of Molecular Chaos for the amplitude of the hydrodynamic noise and its relaxation in time. For this purpose we compare the results of Molecular Dynamics (MD, deterministic dynamics) with those from Direct Si...

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein-protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers...

Ab initio QMCF-MD simulations of aqueous 18-crown-6 (18C6) and strontium(II)-18-crown-6 (18C6-Sr) were performed to gather insight into their hydration properties. Strongly different characteristics were found for the two solutes in terms of structure and dynamics such as H-bonding. They, however, have in common that their backbone shows high flexibility in aqueous medium, adopting structures s...

In radar signature analysis, the root mean square (RMS) surface slope is utilized to assess the relative contribution of multiple scattering effects. For an exponentially correlated surface, an effective RMS slope can be determined by truncating the high frequency tail of the roughness spectrum. The choice of the cutoff frequency and the effect on surface scattering simulations are discussed.

This paper reports the development of a quantitative target approximation (qTA) model for generating F(0) contours of speech. The qTA model simulates the production of tone and intonation as a process of syllable-synchronized sequential target approximation [Xu, Y. (2005). "Speech melody as articulatorily implemented communicative functions," Speech Commun. 46, 220-251]. It adopts a set of biom...

We introduce a method, known as one-dimensional sonomyography (1-D SMG), that uses A-mode ultrasound signals to detect dynamic thickness changes in skeletal muscle during contraction. We custom-designed a 1-D SMG system to collect synchronized A-mode ultrasound, joint angle, and surface electromyography (EMG) signals of forearm muscles during wrist extension. We extracted the 1-D SMG signal fro...

Standing people are exposed to whole-body vibration in many environments. This paper investigates the effects of horizontal whole-body vibration and standing posture on task performance. Sixteen participants were exposed to random vibration (up to 4 Hz) whilst performing a timed pegboard task in two standing postures. Objective and subjective indicators of performance were used. Time taken to c...