A conformational search method for organic molecules and bimolecular complexes is presented. The method, termed Tork, uses normal-mode analysis in bond-angle-torsion coordinates and focuses on a key subset of torsional coordinates to identify natural molecular motions that lead the initial conformation to new energy minima. New conformations are generated via distortion along these modes and th...

We have performed laser-Doppler vibrometry measurements of the vibration of a double-paddle oscillator. Seven modes with principally out-of-plane motion have been identified. Their resonance frequencies and mode shapes are in excellent agreement with three-dimensional finite element simulations. We have found that the second antisymmetric torsional mode has exceptionally good vibration isolatio...

Molecular dynamics simulations using ab initio force fields and signal processing techniques are combined to analyze the dynamic properties of a minimum unit of a field programmable random molecular array also called nanocell. We analyze stretching, angular, and torsional internal modes at several temperatures of operation and their correlations as well as the possibility of signal modulation a...

Low-frequency Raman spectra of the porous structure formed on C-implanted silicon were examined using the 514.5 and 488 nm lines of Ar laser. The sharp low-frequency Raman peaks were observed with narrow linewidth and large intensity. According to usual vibration theory of the elastic body and related symmetry analysis, they are identified as the localized acoustic phonon torsional modes result...

The HET-s prion fibril, which is found in the filamentous fungus Podospora anserina, exhibits conformational changes due to variations in pH. Here, we explain the effects of changing pH on the conformational changes of fibrils through the fundamental eigenmodes of the fibrils, in particular the torsional and bending modes, using a parameter free elastic networkmodel. In particular, themotion re...

A wave optics numerical analysis of the force and torque on a semicylindrical optical wing is presented. Comparisons with a recently reported ray optics analysis indicate good agreement when the radius is large compared with the wavelength of light, as expected. Surprisingly, we find that the dominant rotationally stable angle of attack at α≈-15° is relatively invariant to changes in radius and...

A computational approach is used to predict the mode of organization of lipid molecules. The calculated aggregate states are fully compatible with the lipid phase preference: bilayers for dipalmitoylphosphatidylcholine, micelles for palmitoyllysophosphatidylcholine, and inverted structures for protonated dioleoylphosphatidic acid. The minimal conformational energy of the isolated molecule is ca...

The low frequency vibrations of the ethylamino backbone of six conformers of tryptamine have been studied in the ground and excited states using dispersed fluorescence spectroscopy, rotationally resolved laser induced fluorescence, and ab initio calculations. Four low frequency vibrational modes of the backbone, which involve torsional and librational motions of the ethylamino group, have been ...

A method is derived to detect and localize linear damage in a structure using the measured modal vibration parameters. This method is applicable when the vibration strain energy is stored in the axial or torsional modes, which differentiates it from previously derived strain-energy-based methods. The new method is compared to the previously derived flexibility-change method for comparison. Both...

Torsional Alfven waves are likely excited with bursts in rotating magnetars. These waves are probably propagated through corotating atmospheres toward a vacuum exterior. We have studied the physical effects of the azimuthal wave number and the characteristic height of the plasma medium on wave transmission. In this work, explicit calculations were carried out based on the three-layered cylindri...