Influence of Environmental Parameters on the Stability of the DNA Molecule

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.

Polar in-plane surface orientation of a ferroelectric nematic liquid crystal: Polar monodomains and twisted state electro-optics

We show that surface interactions can vectorially structure the three-dimensional polarization field of a ferroelectric fluid. The contact between a ferroelectric nematic liquid crystal and a surface with in-plane polarity generates a preferred in-plane orientation of the polarization field at that interface. This is a route to the formation of fluid or glassy monodomains of high polarization without the need for electric field poling. For example, unidirectional buffing of polyimide films on planar surfaces to give quadrupolar in-plane anisotropy also induces macroscopic in-plane polar order at the surfaces, enabling the formation of a variety of azimuthal polar director structures in the cell interior, including uniform and twisted states. In a π-twist cell, obtained with antiparallel, unidirectional buffing on opposing surfaces, we demonstrate three distinct modes of ferroelectric nematic electro-optic response: intrinsic, viscosity-limited, field-induced molecular reorientation; field-induced motion of domain walls separating twisted states of opposite chirality; and propagation of polarization reorientation solitons from the cell plates to the cell center upon field reversal. Chirally doped ferroelectric nematics in antiparallel-rubbed cells produce Grandjean textures of helical twist that can be unwound via field-induced polar surface reorientation transitions. Fields required are in the 3-V/mm range, indicating an in-plane polar anchoring energy of wP ∼3 × 10−3 J/m2.

Fluorescent properties anionic derivative of thioflavin T

We have investigated the spectral properties of a new benzothiazole dye – a thioflavin T derivative – 3-sulfopropyl-5-methoxy-2-[3-(3,5-diethyl-2-benzothiazolidene)-1-propienyl]-benzothiazolium (Th-C11). Based on quantum-chemical calculations, it is shown that the molecule in the ground state has a flat structure. In an excited state, the minimum energy corresponds to a twisted conformation, in which the aromatic fragments are arranged orthogonally. Since the twisted state is non-fluorescent, the transition to this state (torsion relaxation) is a quenching process. Th-C11 dye exhibits the properties of a fluorescent molecular rotor. As a result of experimental studies, it was found that torsion relaxation of molecular fragments is the main process that determines the strong dependence of the quantum yield and the duration of fluorescence decay on the viscosity of the solvent. A characteristic feature of this dye is the sensitivity of the fluorescence parameters – the quantum yield, the decay duration and the position of the spectrum not only to the viscosity, but also to the polarity of the medium. The paper also explains the dependence of the position of the absorption and fluorescence spectra on the polarity and viscosity of the solvent as a result of the manifestation of the processes of torsion and solvation relaxation of the chromophore and solvent molecules.

Quasi-one-dimensional metallic conduction channels in exotic ferroelectric topological defects

Ferroelectric topological objects provide a fertile ground for exploring emerging physical properties that could potentially be utilized in future nanoelectronic devices. Here, we demonstrate quasi-one-dimensional metallic high conduction channels associated with the topological cores of quadrant vortex domain and center domain (monopole-like) states confined in high quality BiFeO3 nanoislands, abbreviated as the vortex core and the center core. We unveil via the phase-field simulation that the superfine metallic conduction channels along the center cores arise from the screening charge carriers confined at the core region, whereas the high conductance of vortex cores results from a field-induced twisted state. These conducting channels can be reversibly created and deleted by manipulating the two topological states via electric field, leading to an apparent electroresistance effect with an on/off ratio higher than 103. These results open up the possibility of utilizing these functional one-dimensional topological objects in high-density nanoelectronic devices, e.g. nonvolatile memory.

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

<div><div><div><p>We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer, and a twisted state with a structure that appears to reflect a ~55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin’s B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its sidechain packing. The MSM kinetics predict that these configurations exchange on a 14 μs timescale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure, and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.</p></div></div></div>

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

<div><div><div><p>We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer, and a twisted state with a structure that appears to reflect a ~55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin’s B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its sidechain packing. The MSM kinetics predict that these configurations exchange on a 14 μs timescale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure, and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.</p></div></div></div>

Finite Element Analysis of the Effect of Twist on Chain Fatigue Performance

Mooring chains may be installed with twist or become twisted during service. This paper describes an investigation of the effect of a range of twist angles on the fatigue life of studless chain through the use of detailed finite element analysis. The analysis includes the local contact patch deformation and residual stress state that results from plasticity during the proof testing of the chain. The effect of high in-service tension resulting from storms that produces additional plasticity when the chain is loaded in the twisted state is also included. The change in fatigue life at the crown, inner bend and around the contact patch are assessed. Local to the contact patch the fatigue life calculation includes an assessment of the multiaxial stress state. For small angles of twist the calculated fatigue life at the crown and around the contact increases and that at the inner bend sees a marginal reduction. At twist angles above 12 to 14 degrees per link the calculated inner bend and contact patch fatigue lives reduce markedly with increasing twist, but the crown fatigue life continues to increase.

Rotations of 4nπ Research and no Twisted Mechanism Example Analysis Based on the Theory of Braid Group

The Cable or Pipe between the Two Relatively Rotating Platforms Exists the Twisted Problem. from Viewpoint of Braid Group Theory, Rope’s Twisted State is Researched on. Based on the Characteristics of a Special Garside Braids Δn and Δnk , the Equivalence of Two Rotation Modes is Revealed. also, that the Determination of Rotation Mode’s Minimum Rotate Range is 4∏ while Using Braid Theory is Proposed. the Theory of Braid Group can Not only be Used as a Criterion for Determine Whether the Cable is Twisted, Finally, but also can be Used as Avoid Cable Twisted during Mechanism Design.

The dynamics of excited state structural relaxation of 4-dimethylaminobenzonitrile (DMABN) and related compounds

The excited state structural relaxation of4-dimethylaminobenzenes with variouspara-acceptor substituents having double-band emission, local excited (LE) and charge transfer (CT), has been investigated. Fluorescence measurements at different temperatures and in different solvents have confirmed the existence of viscosity-dependent, temperature, and polarity-activated relaxation. The kinetics analysis has shown that the radiative deactivation rate constants of the individual LE and CT states differ by7–112-fold. The dipole moment changes at the excitation for CT states are significantly larger than those for LE states. The spectral-kinetics behavior of compounds studied agrees with the modelsA→A∗→B∗orA→A∗↔B∗, whereA∗is the local excited planar andB∗is the relaxed twisted state of the molecule. The rate constants of the twisted state formation have been calculated in the temperature range293–77K. The activation energies of forward process for compounds studied have been estimated.