scholarly journals Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

2005 ◽  
Vol 33 (14) ◽  
pp. 4496-4506 ◽  
Author(s):  
E. Lindahl
Keyword(s):  
Normal Mode ◽  
Low Frequency ◽  
Dna Structures ◽  
Mode Amplitude

THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS

2003 ◽  
Vol 13 (04) ◽  
pp. 903-936 ◽  
Author(s):  
T. GLOBUS ◽  
D. WOOLARD ◽  
M. BYKHOVSKAIA ◽  
B. GELMONT ◽  
L. WERBOS ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Low Frequency ◽  
Biological Materials ◽  
Mode Analysis ◽  
Resonance Structure ◽  
Terahertz Frequency ◽  
Dna Molecules ◽  
Phonon Modes

The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.

Source models of great earthquakes from ultra low-frequency normal mode data

2014 ◽  
Vol 233 ◽  
pp. 41-67 ◽  
Author(s):  
K. Lentas ◽  
A.M.G. Ferreira ◽  
E. Clévédé ◽  
J. Roch
Keyword(s):  
Normal Mode ◽  
Low Frequency ◽  
Great Earthquakes ◽  
Source Models

scholarly journals Heart Rate Variability of Children with Mitral Valve Prolapse in Orthostatic Test

2021 ◽  
Vol 6 (3) ◽  
pp. 293-299
Author(s):  
T. M. Krainyk ◽  
◽  
S. H. Starodubtsev ◽  
O. V. Petrenko ◽  
O. V. Dovgan ◽  
...  
Keyword(s):  
Heart Rate ◽  
Nervous System ◽  
Mitral Valve ◽  
Mitral Valve Prolapse ◽  
Sinus Node ◽  
Low Frequency ◽  
Control Group ◽  
Orthostatic Test ◽  
Very Low Frequency ◽  
Mode Amplitude

The purpose of the research was to study the state of autonomic regulation in prepubertal children with mitral valve prolapse during an orthostatic test Materials and methods. The study involved 2 groups: the main – 26 children aged 10-11 years with mitral valve prolapse, and a control group – 22 relatively healthy children. The adaptive mechanisms were monitored by analyzing heart rate variability. All children participated in a cardiorhythmic examination at rest lying down and during an active orthostatic test. Results and discussion. Among the indicators that had significant differences, the indicators of regulatory process adequacy index and mode amplitude should be noted. In the group of children with mitral valve prolapse, an increase of the regulatory process adequacy index indicated the predominance of the functioning of the sinus node over the activity of the sympathetic division of the autonomic nervous system. An increase in the adequacy index and mode amplitude indicates the connection of the central structures of rhythm control (subcortical rhythms) during a change in body position. Stress index also increased. This index of tension of regulatory systems shows the activity of the mechanisms of sympathetic regulation, the state of central regulation. Children in the control group had a well-coordinated response of the sympathetic nervous system to the orthostatic test: the low frequency spectrum and very low frequency indicators increased. While in main group, the value of low frequency spectrum (the work of the sinus node) increased, the value of very low frequency (the reaction of the central structures of the nervous system) decreased. This indicates dysfunction of the most important reactions, which also affects the daily activities of children, increases the risk of mitral valve prolapse complications. Conclusion. In children with mitral valve prolapse, the absence of a pronounced typical reaction to an ortho test is a reflection of an adaptive-regulatory overstrain in conditions of morphological determinacy of connective tissue dysplasia, which are trying to ensure the adequacy of intracardiac hemodynamics. The data obtained will be useful for predicting the reaction of the body of children with mitral valve prolapse to physical activity of varying intensity

scholarly journals Identification of interference normal mode pairs of low frequency sound in shallow water

2019 ◽  
Vol 68 (13) ◽  
pp. 134304
Author(s):  
Rui-Jie Meng ◽  
Shi-Hong Zhou ◽  
Feng-Hua Li ◽  
Yu-Bo Qi
Keyword(s):  
Shallow Water ◽  
Normal Mode ◽  
Low Frequency ◽  
Frequency Sound

Statistics of acoustic normal mode energy for low frequency long range propagation in the ocean: Comparisons between observations and theory.

2010 ◽  
Vol 128 (4) ◽  
pp. 2395-2395
Author(s):  
Tarun K. Chandrayadula ◽  
John A. Colosi ◽  
Peter F. Worcester ◽  
Matthew A. Dzieciuch ◽  
James A. Mercer ◽  
...  
Keyword(s):  
Long Range ◽  
Normal Mode ◽  
Low Frequency ◽  
Mode Energy
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