Search results for "Biomolecules"
showing 10 items of 549 documents
An approach to evaluation of sheet bending force under successive multiaxial stress condition
2009
A new bending under tension test is presented in this paper. This method tries to evaluate bending forces in sheet under successive multiaxial stress condition. This test is carried out in only one step with a pinned cylinder over a material that has been previously deformed to pure shear condition. Due to that, the bending process is made under higher back tension forces than the ones involved in the common methods previously studied in the literature. This entails high pressure values in the sheet-bending tool contact that affects the corresponding friction process. Material is strongly strengthened as a consequence of the deformation practiced in it, and as a result of that, bending forc…
A Three-State Model for the Photophysics of Adenine
2006
An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine…
Iterative integral equation methods for structural coarse-graining
2021
In this paper, new Newton and Gauss-Newton methods for iterative coarse-graining based on integral equation theory are evaluated and extended. In these methods, the potential update is calculated from the current and target radial distribution function, similar to iterative Boltzmann inversion, but gives a potential update of quality comparable with inverse Monte Carlo. This works well for the coarse-graining of molecules to single beads, which we demonstrate for water. We also extend the methods to systems that include coarse-grained bonded interactions and examine their convergence behavior. Finally, using the Gauss-Newton method with constraints, we derive a model for single bead methano…
Intermolecular structure factors of macromolecules in solution: Integral equation results
1999
The inter-molecular structure of semidilute polymer solutions is studied theoretically. The low density limit of a generalized Ornstein-Zernicke integral equation approach to polymeric liquids is considered. Scaling laws for the dilute-to-semidilute crossover of random phase (RPA) like structure are derived for the inter-molecular structure factor on large distances when inter-molecular excluded volume is incorporated at the microscopic level. This leads to a non-linear equation for the excluded volume interaction parameter. For macromolecular size-mass scaling exponents, $\nu$, above a spatial-dimension dependent value, $\nu_c=2/d$, mean field like density scaling is recovered, but for $\n…
Modeling of the Halloysite Spiral Nanotube
2015
A computational SCC-DFTB investigation dealing with the structure of hydrated and anhydrous halloysite nanotubes with a spiral geometry is reported. The peculiar characteristics of these systems are described in terms of tetrahedral and octahedral distortions, of hydrogen bonds geometries involving water molecules and the surfaces in the hydrated nanotube, and of the interlayer interactions in the anhydrous one. When the properties of the spiral nanotube are compared with those of the kaolinite sheet, a certain degree of intrinsic disorder in the halloysite systems is revealed, due to the intrinsic nature of the spiral folding. This is particularly evident in the hydrogen bonds network occu…
A synchrotron radiation X-ray scattering study of aqueous solutions of native DNA
1999
Synchrotron radiation small-angle X-ray scattering (SAXS) was used to investigate solutions of native DNA at different ionic strengths and temperatures. The mass per unit length, radius of gyration of the cross-section of DNA and apparent second virial coefficient (A2) were obtained from Zimm plots in the rodlike particle approximation. The values of A2 obtained in this way are positive and almost constant indicating that the repulsive interactions still influence the scattering patterns at resolutions as high as 5-8 nm. SAXS measurements in continuous temperature scans indicate that the rod approximation is valid over a wide temperature range during DNA melting and confirm that the rodlike…
Resonant X-ray scattering in biological structure research
2007
The use of anomalous X-ray scattering of light elements like sulfur and phosphorus is of particular interest in biological structure research. These elements serve as native labels in proteins, nucleic acids and membranes. Their medium scattering power is drastically changed at their K absorption edges at wavelengths between 5 and 6 A where X-ray absorption excludes the use of open air diffractometers. The construction of a new diffractometer tunable to wavelengths between 1.2 and 7 A is presented. First results of anomalous scattering from sulfur in bacteriorhodopsin near the K absorption edge have been obtained recently. Their possible impact on crystallography will be considered. A compa…
Effect of opsin on the shape of the potential energy surfaces at the conical intersection of the Rhodopsin chromophore
2008
Abstract In order to disentangle the role of the protein in the control of the photoisomerization of the chromophore of the visual pigment Rhodopsin, we compare the structure of the ground and excited potential energy surfaces of gas-phase and opsin-embedded 11- cis retinal chromophore at the corresponding (lowest energy) conical intersections. It is shown that, along the branching plane, the asymmetric opsin environment destabilizes one of the ground state relaxation channels emerging from the conical intersection. This suggests that opsin promotes the formation of the product (bathorhodopsin) via enhanced decay probability along the all- trans exit channel. In contrast, in the gas-phase n…
"Table 2" of "Measurement of the correlations between the polar angles of leptons from top quark decays in the helicity basis at $\sqrt{s}=7$TeV usin…
2017
The correlation factors for the statistical uncertainties between any two bins of the unfolded distribution.
What is the order of the two-dimensional polymer escape transition?
2007
An end-grafted flexible polymer chain in three-dimensional space between two pistons undergoes an abrupt transition from a confined coil to a flowerlike conformation when the number of monomers in the chain, $N$, reaches a critical value. In two-dimensional (2D) geometry, excluded-volume interactions between monomers of a chain confined inside a strip of finite length $2L$ transform the coil conformation into a linear string of blobs. However, the blob picture raises questions about the nature of this escape transition. To check theoretical predictions based on the blob picture we study 2D single-polymer chains with excluded-volume interactions and with one end grafted in the middle of a st…