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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.

In this paper, the effect of dissipative energy arising from bulk-viscosity on the collapse of a self-gravitating viscoelastic medium permeated with a nonuniform magnetic field and rotation is analyzed using the standard Jeans mechanism. A local solution of the system of nondimensional linearized perturbation equations, having variable coefficients, is obtained using the normal modes analysis method. The Jeans instability criteria are derived from the characteristic equation (valid under the kinetic and hydrodynamic limits) for parallel and perpendicular wave propagation, modified due to bulk viscosity and Alfvén wave velocity. From the calculated critical values of Jeans wavenumber, it is found that the bulk-viscosity and magnetic field have stabilizing influence on the onset of gravitational instability for each mode of wave propagation. It is observed that the nonuniform rotation does not affect the instability criterion, however, the rotation strongly suppresses the growth rate of the Jeans instability in both the hydrodynamic and kinetic limits. Also, a comparison of the impact of various rotational and magnetic field orientations on the growth rate in viscoelastic fluid is also presented. From the analysis, it is also observed that the presence of dissipative energy reduces the growth rate, in both modes of wave propagation.

The paper presents the analytical solutions for a generalized thermoelastic medium consisting of microtemperatures and voids subjected to a laser pulse loading the medium thermally. The 0.02 ps pulse duration of the non-Gaussian laser beam is apt for heating a homogenous isotropic elastic half-space. A method called the normal mode analysis is employed to evaluate numerically the effects of various variables such as the micro-temperature vector, variation in the fraction field of the volume, first heat flux moment tensor, temperature distribution on the stresses and displacement components of the medium. In addition, the graphical illustration of the physical response of the medium has been presented in the presence and absence of void parameters, as well as in the presence of laser pulse with two different acting periods.

The present paper deals with the problem of thermoelastic interactions in a homogeneous, isotropic three-dimensional medium whose surface suffers a time dependent thermal loading. The problem is treated on the basis of three-phase-lag model and dual-phase-lag model with two temperatures. The medium is assumed to be unstressed initially and has uniform temperature. Normal mode analysis technique is employed onto the non-dimensional field equations to derive the exact expressions for displacement component, conductive temperature, thermodynamic temperature, stress and strain. The problem is illustrated by computing the numerical values of the field variables for a copper material. Finally, all the physical fields are represented graphically to analyze the difference between the two models. The effect of the two temperature parameter is also discussed.

In ["Theory of fractional order generalized thermoelasticity," Journal of Heat Transfer132, 2010] Youssef has proposed a model in generalized thermoelasticity based on the fractional order time derivatives. The current manuscript is concerned with a two-dimensional generalized thermoelastic coupled problem for a homogeneous isotropic and thermally conducting thermoelastic rotating medium in the context of the above fractional order generalized thermoelasticity with two relaxation time parameters. The normal mode analysis technique is used to solve the resulting non-dimensional coupled governing equations of the problem. The resulting solution is then applied to two concrete problems. The effect of the fractional parameter and the time instant on the variations of different field quantities inside the elastic medium are analyzed graphically in the presence of rotation.

The present work is concerned with an electro-magneto-thermoelastic coupled problem for a homogeneous, isotropic, thermally and electrically conducting semi-infinite solid medium in two-dimensional space where an initial magnetic field with constant intensity acts parallel to the plane boundary of the half-space. The surface of the half-space taking as traction free which is subjected to a thermal shock. The modified Ohm's law including the temperature gradient and charge density effect to the governing equations of the generalized thermoelasticity under the temperature rate dependent thermoelasticity (TRDTE) proposed by Green and Lindsay (GL model) has been introduced. Normal mode analysis together with eigenvalue approach technique is used to obtain the general solutions for the physical quantities. Numerical results for the physical quantities are illustrated graphically and analyzed. The graphical results indicate that the effect of the coefficient connecting the temperature gradient and the electric current density of the modified Ohm's law on the plane waves is very pronounced. Comparison are made with the results obtained in the absence of the above coefficient.

An electromagneto-thermoelastic coupled problem for a homogeneous, isotropic, thermally and electrically conducting half-space solid whose surface is subjected to a thermal shock is considered in two-dimensional space. The equations of the theory of generalized electromagneto-thermoelasticity with fractional derivative heat transfer allowing the second sound effects are considered. An initial magnetic field acts parallel to the plane boundary of the half-space. The normal mode analysis and the eigenvalue approach techniques are used to solve the resulting nondimensional coupled field equations for the three theories. Numerical results for the temperature, displacements and thermal stresses distributions are presented graphically and discussed. A comparison is made with the results obtained in the presence and absence of the magnetic field.

The thermoelastic problem of clamped axisymmetric infinite hollow cylinders under thermal shock with variable thermal conductivity is presented. The outer surface of infinite hollow cylinder is considered to be thermally insulated while inner surface is subjected to an initial heating source. In addition, the cylinder is considered to be clamped at its inner and outer radii. Generalized thermoelasticity theories are used to deal with the field quantities. All generalized thermoelasticity theories such as Green and Lindsay, Lord and Shulman, and coupled thermoelasticity (CTE) are considered as special cases of the present theory. Effects of variable thermal conductivity and time parameters on radial displacement, temperature, and stresses of the hollow cylinders are investigated.

A newly identified family of NAD-dependent D-2-hydroxyacid dehydrogenases (D-2-HydDHs) catalyzes the stereo-specific reduction of branched-chain 2-keto acids with bulky hydrophobic side chains to 2-hydroxyacids. They are promising targets for industrial/practical applications, particularly in the stereo-specific synthesis of C3-branched D-hydroxyacids. Comparative modeling and docking studies have been performed to build models of the enzyme-cofactor-substrate complexes and identify key residues for cofactor and substrate recognition. To explore large conformational transitions (domain motions), a normal mode analysis was employed using a simple potential and the protein models. Our analysis suggests that the new D-2-HydDH family members possess the N-terminal NAD(H) binding Rossmann-fold domain and the α-helical C-terminal substrate binding domain. A hinge bending motion between the N- and C-terminal domains was predicted, which would trigger the switch of the conserved essential Lys to form a key hydrogen bond with the C2 ketone of the 2-keto acid substrates. Our findings will be useful for site-directed mutagenesis studies and protein engineering.

Even though its structure is known to atomic resolution, the ways in which the ribosome accomplishes its tasks in synthesizing proteins are still unknown. The key to an understanding of its dynamics might be found in cryo-electron microscopy of trapped states, and an interpretation of the resultant density maps by “molding” the X-ray structures into them. First results, obtained by application of real-space refinement techniques to cryo-EM maps of complexes in different conformations, indicate a complicated internal reorganization. The question arises as to whether the observed conformational changes accompanying ribosomal function might be predictable based on the architecture of the macromolecular complex. It has indeed been possible to derive one of the principal motions (the ratchet motion) by normal mode analysis of the ribosome represented as a simplified mechanical system.

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.