scholarly journals Ensemble of DNA Kinks

2019 ◽  
Vol 224 ◽  
pp. 03005 ◽  
Author(s):  
Ludmila V. Yakushevich ◽  
Larisa A. Krasnobaeva
Keyword(s):  
Hydrogen Bonds ◽  
Dynamic Characteristics ◽  
Dynamic Properties ◽  
Double Helix ◽  
Statistical Properties ◽  
Dna Molecule ◽  
Open States

The DNA open states, which are locally unwound regions of the double helix within which hydrogen bonds between complementary nitrous bases are broken, are often modeled as quasiparticles – DNA kinks. Most of the works on the DNA kinks are devoted to the studies of their dynamic properties, as well as their role in the functioning of the molecule. However, if not one but N open states are formed in the DNA molecule it is reasonable to consider the problem of the statistics of the ensemble of N DNA kinks. The statistical properties of such an ensemble are still poorly understood. In the present work, we study these properties applying new data on the dynamic characteristics of DNA kinks.

Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification

2018 ◽  
Vol 16 (01) ◽  
pp. 1840003 ◽  
Author(s):  
Artem Ryasik ◽  
Mikhail Orlov ◽  
Evgenia Zykova ◽  
Timofei Ermak ◽  
Anatoly Sorokin
Keyword(s):  
Physical Properties ◽  
Systematic Approach ◽  
Dynamic Properties ◽  
Sequence Classification ◽  
Promoter Prediction ◽  
Dna Molecule ◽  
Dna Fragment ◽  
Promoter Dna ◽  
Open States ◽  
Selection Of

Predicting promoter activity of DNA fragment is an important task for computational biology. Approaches using physical properties of DNA to predict bacterial promoters have recently gained a lot of attention. To select an adequate set of physical properties for training a classifier, various characteristics of DNA molecule should be taken into consideration. Here, we present a systematic approach that allows us to select less correlated properties for classification by means of both correlation and cophenetic coefficients as well as concordance matrices. To prove this concept, we have developed the first classifier that uses not only sequence and static physical properties of DNA fragment, but also dynamic properties of DNA open states. Therefore, the best performing models with accuracy values up to 90% for all types of sequences were obtained. Furthermore, we have demonstrated that the classifier can serve as a reliable tool enabling promoter DNA fragments to be distinguished from promoter islands despite the similarity of their nucleotide sequences.

Electron microscopic assays of restriction endonuclease cutting, exonuclease digestion, and hybridization

1984 ◽  
Vol 42 ◽  
pp. 686-687
Author(s):  
Mark Hannibal ◽  
Jacob Varkey ◽  
Michael Beer
Keyword(s):  
Electron Microscope ◽  
Low Temperature ◽  
Restriction Endonuclease ◽  
Double Helix ◽  
Test Material ◽  
Electron Microscopic ◽  
Exonuclease Iii ◽  
Dna Molecule ◽  
Linear Molecules ◽  
Exonuclease Digestion

Workman and Langmore have recently proposed a procedure for isolating particular chromatin fragments. The method requires restriction endonuclease cutting of the chromatin and a probe, their digestion with two exonucleases which leave complimentary single strand termini and low temperature hybridization of these. We here report simple electron microscopic monitoring of the four reactions involved.Our test material was ϕX-174 RF DNA which is cut once by restriction endonuclease Xho I. The conversion of circles to linear molecules was followed in Kleinschmidt spreads. Plate I shows a circular and a linear DNA molecule. The rate of cutting is shown in Figure 1.After completion of the endonuclease cutting, one portion of the DNA was treated with exonuclease III, an enzyme known to digest the 3' terminals of double helical DNA. Aliquots when examined in the electron microscope reveal a decreasing length of double helix and increasing bushes at the ends.

The Dynamic Characteristics of Rigid Frame Single-Rib Arch Bridge

2013 ◽  
Vol 368-370 ◽  
pp. 1426-1430
Author(s):  
Li Xiong Gu ◽  
Rong Hui Wang
Keyword(s):  
Dynamic Characteristics ◽  
Bending Strength ◽  
Dynamic Properties ◽  
Structural Parameters ◽  
Bending Stiffness ◽  
Torsional Stiffness ◽  
Lateral Stiffness ◽  
Arch Bridge ◽  
Vertical Stiffness ◽  
Rigid Frame

In this paper, by establishing the finite element model to study the dynamic characteristics of rigid frame single-rib arch bridge. By respectively changing structural parameters of the span ratios, and the compressive stiffness of arch, and the bending stiffness of arch, and the bending stiffness of bridge girder, and the layout of boom to find out the regularity of the structure on lateral stiffness, and vertical stiffness, and torsional stiffness as well as dynamic properties, it come out the results of that lateral stiffness of the structure is weaker, and increasing the span ratios and the compressive strength of arch are conducive to the improvement of the overall stiffness, and improving the bending strength of arch and layout of boom are less effect on the overall stiffness and mode shape.

Dynamic Property Evaluation of a Long-Span Cable-Stayed Bridge (Sutong Bridge) by a Bayesian Method

2018 ◽  
Vol 19 (01) ◽  
pp. 1940010 ◽  
Author(s):  
Yan-Chun Ni ◽  
Qi-Wei Zhang ◽  
Jian-Feng Liu
Keyword(s):  
Natural Frequency ◽  
Dynamic Characteristics ◽  
Structural Damage ◽  
Dynamic Properties ◽  
Modal Identification ◽  
Modal Parameters ◽  
Modal Parameter ◽  
Cable Stayed Bridge ◽  
Long Span ◽  
Sutong Bridge

Modal identification aims at identifying the dynamic properties including natural frequency, damping ratio, and mode shape, which is an important step in further structural damage detection, finite element model updating, and condition assessment. This paper presents the work on the investigation of the dynamic characteristics of a long-span cable-stayed bridge-Sutong Bridge by a Bayesian modal identification method. Sutong Bridge is the second longest cable-stayed bridge in the world, situated on the Yangtze River in Jiangsu Province, China, with a total length of 2 088[Formula: see text]m. A short-term nondestructive on-site vibration test was conducted to collect the structural response and determine the actual dynamic characteristics of the bridge before it was opened to traffic. Due to the limited number of sensors, multiple setups were designed to complete the whole measurement. Based on the data collected in the field tests, modal parameters were identified by a fast Bayesian FFT method. The first three modes in both vertical and transverse directions were identified and studied. In order to obtain modal parameter variation with temperature and vibration levels, long-term tests have also been performed in different seasons. The variation of natural frequency and damping ratios with temperature and vibration level were investigated. The future distribution of the modal parameters was also predicted using these data.

scholarly journals Mathematical Modeling of Open States in Double Stranded DNA Molecule Depending on 2H/1H Ratio

2019 ◽  
Vol 14 (2) ◽  
pp. 612-624 ◽  
Author(s):  
S.S. Dzhimak ◽  
M.I. Drobotenko ◽  
A.A. Basov ◽  
A.A. Svidlov ◽  
M.G. Baryshev
Keyword(s):  
Mathematical Modeling ◽  
Hydrogen Bond ◽  
Deuterium Atom ◽  
Living System ◽  
Dna Molecule ◽  
Dna Base Pair ◽  
A Chain ◽  
Time Required ◽  
Open States ◽  
Bond Disruption

The evaluation results of the possible deuterium atoms effect on the DNA base pair opening are presented in the article. The cause of these processes is the replacement of protium with deuterium atom due to the increase of energy required to break the hydrogen bond. These processes can be studied by method of mathematical modeling, with account of open states between base pairs being the key condition of the adequacy of the mathematical model of the DNA. The experiment data show that the presence of deuterium in a chain of nucleotides can cause - depending on the value of hydrogen bond disruption energy - both increase and decrease in probability of open states occurrence. For example: hydrogen bond disruption energy of 0.358·10-22 n·m, non-zero probability of open states occurrence is observed in case of the absence of deuterium in the molecule, and with hydrogen bond disruption energy of 0.359·10-22 n·m or more such probability equals zero. Also, when one deuterium atom is present in a molecule, non-zero probability is observed even with hydrogen bond disruption energy equal to 0.368·10-22 n·m (i.e. more than 0.358·10-22 n·m). Thus participation of deuterium atoms in the formation of hydrogen bonds of double helixes of a DNA molecule can cause the changes in the time required for transfer of genetic information, which can explain the effect of even minor deviations in deuterium concentration in a medium on metabolic processes in a living system.

DYNAMIC CHARACTERISTICS OF THE KAO PING HSI BRIDGE UNDER SEISMIC LOADING WITH FOCUS ON CABLE SIMULATION

2011 ◽  
Vol 11 (06) ◽  
pp. 1179-1199 ◽  
Author(s):  
MING-YI LIU ◽  
LI-CHIN LIN ◽  
PAO-HSII WANG
Keyword(s):  
Finite Element ◽  
Dynamic Characteristics ◽  
Hybrid Method ◽  
Dynamic Properties ◽  
Seismic Loading ◽  
Cable System ◽  
Initial Shape ◽  
Element Computation ◽  
Southern Taiwan ◽  
Finite Element Computation

The objective of this study is to thoroughly investigate the dynamic characteristics of the Kao Ping Hsi Bridge located in southern Taiwan. A one-element cable system (OECS) and a multi-element cable system (MECS) are presented for simulating the dynamic properties of the cables of the bridge. By a finite element computation procedure, the initial shape, modal, and seismic analyses are conducted for the bridge using either the OECS or MECS model. A hybrid method combining both the two-loop iteration and the catenary function is proposed to determine the initial shapes using the MECS model. Convergent and smooth initial shapes can be obtained using such a method. The results indicate that the OECS model can yield solution in an efficient way, whereas the MECS model should be used if solutions of greater accuracy are desired.

scholarly journals Dynamic Properties of Clean Sand Modified with Granulated Rubber

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Dervis Volkan Okur ◽  
Seyfettin Umut Umu
Keyword(s):  
Shear Modulus ◽  
Dynamic Characteristics ◽  
Dynamic Properties ◽  
Damping Ratio ◽  
Relative Size ◽  
Cyclic Behavior ◽  
Damping Capacity ◽  
Resonant Column ◽  
Strain Dependent

Waste automobile tires are used as additives or replacements instead of traditional materials in civil engineering works. In geotechnical engineering, tires are shredded to certain sizes and mixed with soil, especially used as backfill material behind retaining walls or fill material for roadway embankments. Compared to soil, rubber has high damping capacity and low shear modulus. Therefore, it requires the determination of the dynamic characteristics of rubber/soil mixtures. In this paper, the cyclic behavior of recycled tire rubber and clean sand was studied, considering the effects of the amount and particle size of the rubber and confining stresses. A total of 40 stress-controlled tests were performed on an integrated resonant column and dynamic torsional shear system. The effects of the relative size and proportion of the rubber on the dynamic characteristics of the mixtures are discussed. The dynamic properties, such as the maximum shear modulus, strain-dependent shear modulus, and damping ratio, are examined. For practical purposes, simple empirical relationships were formulated to estimate the maximum shear modulus and the damping ratio. The change in the shear modulus and damping ratio with respect to shear strain with 5% of rubber within the mixture was found to be close to the behavior of clean sand.

Dynamic Characteristics of Balanced Robotic Manipulators with Joint Flexibility

Robotica ◽  
1992 ◽  
Vol 10 (6) ◽  
pp. 485-495 ◽  
Author(s):  
S.B. Lee ◽  
H.S. Cho
Keyword(s):  
Dynamic Characteristics ◽  
High Speed ◽  
Dynamic Properties ◽  
Dynamic Performance ◽  
Robotic Manipulators ◽  
Open Loop ◽  
Joint Flexibility ◽  
Damping Characteristics ◽  
Large Joint ◽  
Joint Deformation

SUMMARYThe mass balancing of robotic manipulators has been shown to have favorable effects on the dynamic characteristics. In actual practice, however, since conventional manipulators have flexibility at their joints, the improved dynamic properties obtainable for rigid manipulators may be influenced by those joint flexibilities. This paper investigates the effects of the joint flexibility on the dynamic properties and the controlled performance of a balanced robotic manipulator. The natural frequency distribution and damping characteristics were investigated through frequency response analyses. To evaluate the dynamic performance a series of simulation studies of the open loop dynamics were made for various trajectories, operating velocities, and joint stiffnesses. These simulations were also carried out for the balanced manipulator with a PD controller built-in inside motor control loop. The results show that, at low speed, the joint flexibility nearly does not influence the performance of the balanced manipulator, but at high speed it tends to render the balanced manipulator susceptible to vibratory motion and yields large joint deformation error.

The Dynamic Characteristics of Neoprene Vulcanizates

1949 ◽  
Vol 22 (2) ◽  
pp. 450-464 ◽  
Author(s):  
N. L. Catton ◽  
E. H. Krismann ◽  
W. N. Keen
Keyword(s):  
Natural Rubber ◽  
Dynamic Characteristics ◽  
Dynamic Properties ◽  
Complete Solution ◽  
Practical Application ◽  
Testing Methods ◽  
Synthetic Rubber ◽  
Engineering Data ◽  
Rubber Part ◽  
Vibration Problems

Abstract The utilization of the elastomeric spring goes back at least to the days of solid rubber carriage tires. The use of such materials to dampen vibration or absorb shock expanded rapidly despite the lack of engineering data and the inadequacy of testing methods for proper evaluation. Within the last twenty years these materials have been used in many dynamic applications, even though no appropriate means existed for the measurement of dynamic properties to determine their suitability for the particular service. Coincident with the practical application of rubber parts to vibration problems, engineers developed considerable data on the use of natural rubber in springs. Marked differences in performance were encountered when engineers were obliged to replace natural rubber with synthetic rubber in spring applications. Some engineers redesigned the rubber part used and obtained workable, although not entirely acceptable, performance. Design alone was not a complete solution to the problem, and it was necessary to call on the rubber technologist to produce vulcanizates having properties especially suitable for dynamic service.

scholarly journals Influence of Environmental Parameters on the Stability of the DNA Molecule

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1446
Author(s):  
Alexander Svidlov ◽  
Mikhail Drobotenko ◽  
Alexander Basov ◽  
Eugeny Gerasimenko ◽  
Anna Elkina ◽  
...  
Keyword(s):  
External Environment ◽  
Environmental Parameters ◽  
High Viscosity ◽  
Rate Of Change ◽  
Dna Molecule ◽  
Twisted State ◽  
Physiological Processes ◽  
Dna Strands ◽  
The Stability ◽  
Open States

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

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