Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Influence of elastic anisotropy on structural nanoscale textures

We study the influence of elastic anisotropy on nanoscale precursor textures that exist in some shape-memory alloys and show that tweed occurs in the limit of high elastic anisotropy while a nanocluster phase-separated state occurs for values of anisotropy inhibiting the formation of martensite. These results are consistent with specific heat data, elastic constant measurements, and zero-field cooling or field cooling experiments in nonstoichiometric NiTi alloys.

Equivalent representation form of oscillators with elastic and damping nonlinear terms

In this work we consider the nonlinear equivalent representation form of oscillators that exhibit nonlinearities in both the elastic and the damping terms. The nonlinear damping effects are considered to be described by fractional power velocity terms which provide better predictions of the dissipative effects observed in some physical systems. It is shown that their effects on the system dynamics response are equivalent to a shift in the coefficient of the linear damping term of a Duffing oscillator. Then, its numerical integration predictions, based on its equivalent representation form given by the well-known forced, damped Duffing equation, are compared to the numerical integration values of its original equations of motion. The applicability of the proposed procedure is evaluated by studying the dynamics response of four nonlinear oscillators that arise in some engineering applications such as nanoresonators, microresonators, human wrist movements, structural engineering design, and chain dynamics of polymeric materials at high extensibility, among others

On the Application of Beam on Elastic Foundation Theory to the Analysis of Stiffened Plate Strips

The main objective of this thesis is to show that plate strips subjected to transverse line loads can be analysed by using the beam on elastic foundation (BEF) approach. It is shown that the elastic behaviour of both the centre line section of a semi infinite plate supported along two edges, and the free edge of a cantilever plate strip can be accurately predicted by calculations based on the two parameter BEF theory. The transverse bending stiffness of the plate strip forms the foundation. The foundation modulus is shown, mathematically and physically, to be the zero order term of the fourth order differential equation governing the behaviour of BEF, whereas the torsion rigidity of the plate acts like pre tension in the second order term. Direct equivalence is obtained for harmonic line loading by comparing the differential equations of Levy's method (a simply supported plate) with the BEF method. By equating the second and zero order terms of the semi infinite BEF model for each harmonic component, two parameters are obtained for a simply supported plate of width B: the characteristic length, 1/ λ, and the normalized sum, n, being the effect of axial loading and stiffening resulting from the torsion stiffness, nlin. This procedure gives the following result for the first mode when a uniaxial stress field was assumed (ν = 0): 1/λ = √2B/π and nlin = 1. For constant line loading, which is the superimposition of harmonic components, slightly differing foundation parameters are obtained when the maximum deflection and bending moment values of the theoretical plate, with v = 0, and BEF analysis solutions are equated: 1 /λ= 1.47B/π and nlin. = 0.59 for a simply supported plate; and 1/λ = 0.99B/π and nlin = 0.25 for a fixed plate. The BEF parameters of the plate strip with a free edge are determined based solely on finite element analysis (FEA) results: 1/λ = 1.29B/π and nlin. = 0.65, where B is the double width of the cantilever plate strip. The stress biaxial, v > 0, is shown not to affect the values of the BEF parameters significantly the result of the geometric nonlinearity caused by in plane, axial and biaxial loading is studied theoretically by comparing the differential equations of Levy's method with the BEF approach. The BEF model is generalised to take into account the elastic rotation stiffness of the longitudinal edges. Finally, formulae are presented that take into account the effect of Poisson's ratio, and geometric non linearity, on bending behaviour resulting from axial and transverse inplane loading. It is also shown that the BEF parameters of the semi infinite model are valid for linear elastic analysis of a plate strip of finite length. The BEF model was verified by applying it to the analysis of bending stresses caused by misalignments in a laboratory test panel. In summary, it can be concluded that the advantages of the BEF theory are that it is a simple tool, and that it is accurate enough for specific stress analysis of semi infinite and finite plate bending problems.

Methane combustion kinetic rate constants determination: an ill-posed inverse problem analysis

Methane combustion was studied by the Westbrook and Dryer model. This well-established simplified mechanism is very useful in combustion science, for computational effort can be notably reduced. In the inversion procedure to be studied, rate constants are obtained from [CO] concentration data. However, when inherent experimental errors in chemical concentrations are considered, an ill-conditioned inverse problem must be solved for which appropriate mathematical algorithms are needed. A recurrent neural network was chosen due to its numerical stability and robustness. The proposed methodology was compared against Simplex and Levenberg-Marquardt, the most used methods for optimization problems.

Stability constants and thermodynamic parameters of cadmium complexes with sulfonamides and cephapirin

Stability constant (log beta) and thermodynamic parameters of Cd2+ complexes with sulfonamide and cephapirin were determined by Polarographic technique at pH = 7.30 ± 0.01 and µ = 1.0 M KNO3 at 250°C. The sulfonamides were sulfadiazine, sulfisoxazole, sulfamethaxazole, sulfamethazine, sulfathiazole, sulfacetamide and sulfanilamide used as primary ligands and cephapirin as secondary ligand. Cd2+ formed 1:1:1, 1:2:1 and 1:1:2 complexes. The nature of electrode processes were reversible and diffusion controlled. The stability constants and thermodynamic parameters (deltaG, deltaH and deltaS) were determined. The formation of the metal complexes has been found to be spontaneous, exothermic in nature, and entropically unfavourable at higher temperature.

Determination of Alkalinity and dissociation constants of high salinity waters: use of F5BC titration function

Measurements of parameters expressed in terms of carbonic species such as Alkalinity and Acidity of saline waters do not analyze the influence of external parameters to the titration such as Total free and associated Carbonic Species Concentration, activity coefficient, ion pairing formation and Residual Liquid Junction Potential in pH measurements. This paper shows the development of F5BC titration function based on the titrations developed by Gran (1952) for the carbonate system of natural waters. For practical use, samples of saline waters from Pocinhos reservoir in Paraiba were submitted to titration and linear regression analysis. Results showed that F5BC involves F1x and F2x Gran functions determination, respectively, for Alkalinity and Acidity calculations without knowing "a priori" the endpoint of the titration. F5BC also allows the determination of the First and Second Apparent Dissociation Constant of the carbonate system of saline and high ionic strength waters.

Stereological study of the elastic fiber and smooth muscle cell system in the bovine and buffalo penis

Samples of ten penises of Mediterranean buffaloes and ten penises of Red Sindhi cattle were used. The thickness of the tunica albuginea (TA), distribution of smooth muscle cells (SMC) and volume density (Vv) of elastic system fibers in TA, corpus cavernosum (CC) and corpus spongiosum (CS) were evaluated. The Vv of elastic system fibers in buffalo and bovine penis was respectively 4.07% ±0.88% and 3.36% ±1.21% in TA; 17.32% ±2.21% and 13.14% ±1.27% (CC), 26.58% ±4.31% and 31.36% ±3.67% (CS). The CC of buffalo presented higher Vv of elastic fibers than bovine, while in the CS the Vv of elastic fibers in buffaloes was smaller than in cattle. The TA thickness showed a significant difference among the species studied. The arrangement of SMC in the bovine penises and in the water buffalo suggests that this pattern is common to animals that have fibroelastic penises.

A comparative study of aging of the elastic fiber system of the diaphragm and the rectus abdominis muscles in rats

In the present study the age-related changes of the striated muscle elastic fiber system were investigated in the diaphragm and rectus abdominis muscles of 1-, 4-, 8- and 18-month-old rats. The activation patterns of these muscles differ in that the diaphragm is regularly mobilized tens of times every minute during the entire life of the animal whereas the rectus abdominis, although mobilized in respiration, is much less and more irregularly activated. The elastic fibers were stained by the Verhoeff technique for mature elastic fibers. Weigert stain was used to stain mature and elaunin elastic fibers, and Weigert-oxone to stain mature, elaunin and oxytalan elastic fibers. The density of mature and elaunin elastic fibers showed a progressive increase with age, whereas the amount of oxytalan elastic fibers decreased in both diaphragm and rectus abdominis muscles and their muscular fascias. These age-related quantitative and structural changes of the elastic fiber system may reduce the viscoelastic properties of the diaphragm and rectus abdominis muscles, which may compromise the transmission of tensile muscle strength to the tendons and may affect maximum total strength.

Phonon spectra and thermodynamic properties of rare gas solids based on empirical and semi-empirical (ab initio) two-body potentials : a comparative study /

We study the phonon dispersion, cohesive and thermal properties of raxe gas solids Ne, Ar, Kr, and Xe, using a variety of potentials obtained from different approaches; such as, fitting to crystal properties, purely ab initio calculations for molecules and dimers or ab initio calculations for solid crystalline phase, a combination of ab initio calculations and fitting to either gas phase data or sohd state properties. We explore whether potentials derived with a certain approaxih have any obvious benefit over the others in reproducing the solid state properties. In particular, we study phonon dispersion, isothermal ajid adiabatic bulk moduli, thermal expansion, and elastic (shear) constants as a function of temperatiue. Anharmonic effects on thermal expansion, specific heat, and bulk moduli have been studied using A^ perturbation theory in the high temperature limit using the neaxest-neighbor central force (nncf) model as developed by Shukla and MacDonald [4]. In our study, we find that potentials based on fitting to the crystal properties have some advantage, particularly for Kr and Xe, in terms of reproducing the thermodynamic properties over an extended range of temperatiures, but agreement with the phonon frequencies with the measured values is not guaranteed. For the lighter element Ne, the LJ potential which is based on fitting to the gas phase data produces best results for the thermodynamic properties; however, the Eggenberger potential for Ne, where the potential is based on combining ab initio quantum chemical calculations and molecular dynamics simulations, produces results that have better agreement with the measured dispersion, and elastic (shear) values. For At, the Morse-type potential, which is based on M0ller-Plesset perturbation theory to fourth order (MP4) ab initio calculations, yields the best results for the thermodynamic properties, elastic (shear) constants, and the phonon dispersion curves.

An approximation method for evaluating centrifugal distortion constants in XH2 bent symmetric molecules

University of Cochin

NIR to UV absorption spectra and the optical constants of phthalocyanines in glassy medium

Optical absorption studies of phthalocyanines (Pc-s) in borate glass matrix have been reported for the first time. Measurements have been done corresponding to photon energies between 1.1 and 6.2 eV for free base, manganese, iron, nickel, molybdenum, cobalt and copper phthalocyanines. Several new discrete transitions are observed in the UV–vis region of the spectra in addition to a strong continuum component of absorption in the IR region. Values of some of the important optical constants viz. absorption coefficient (α), molar extinction coefficient (ε), absorption cross-section (σa), band width (Δλ), electric dipole strength (q2) and oscillator strength (f) for the relevant electronic transitions are also presented. All the data reported for Pc-s in the new matrix have been compared with those corresponding to solution, vapor and thin film media.

Shot noise anomalies in elastic nondegenerate diffusive conductors

We present a theoretical investigation of shot-noise properties in nondegenerate elastic diffusive conductors. Both Monte Carlo simulations and analytical approaches are used. Two interesting phenomena are found: (i) the display of enhanced shot noise for given energy dependences of the scattering time, and (ii) the recovery of full shot noise for asymptotic high applied bias. The first phenomenon is associated with the onset of negative differential conductivity in energy space that drives the system towards a dynamical electrical instability in excellent agreement with analytical predictions. The enhancement is found to be strongly amplified when the dimensionality in momentum space is lowered from three to two dimensions. The second phenomenon is due to the suppression of the effects of long-range Coulomb correlations that takes place when the transit time becomes the shortest time scale in the system, and is common to both elastic and inelastic nondegenerate diffusive conductors. These phenomena shed different light in the understanding of the anomalous behavior of shot noise in mesoscopic conductors, which is a signature of correlations among different current pulses.