Statistical theory of force-induced unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force F_c(T) for unzipping calculated in the constant force ensemble is found to depend on the potential parameter k which measures the stiffness associated with a single strand of DNA and on D, the well depth of the on-site potential representing the strength of hydrogen bonds in a base pair. The dependence on temperature of F_c(T) is found to be (T_D - T)^1/2 (T_D being the thermal denaturation temperature) with F_c(T_D) = 0 and F_c(0) = . We used the constant extension ensemble to calculate the average force F(y) required to stretch a base pair a y distance apart. The value of F(y) needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance for y 1.0 . The force F(y) in both cases is found to have a very large value for y 0.2 compared to the critical force found from the constant force ensemble to which F(y) approaches for large values of y. It is shown that the value of F(y) at the peak depends on the value of k which measures the energy barrier associated with the reduction in DNA strand rigidity as one passes from dsDNA to ssDNA and on the value of the depth of the on-site potential. The effect of defects on the position and height of the peak in the F(y) curve is investigated by replacing some of the base pairs including the one being stretched by defect base pairs. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of an eye when a base pair far from ends is stretched are investigated.     

Influence of isotopic substitution on the diffusion and thermal diffusion coefficient of binary liquids

The mutual mass diffusion coefficient (D) and the thermal diffusion coefficient ( D _T) of the liquids acetone, benzene, benzene-d ₁, benzene-d ₃, benzene-d ₅, benzene-d ₆, benzene- ¹³C₆, n-hexane, toluene, 1, 2, 3, 4-tetrahydronaphtalene, isobutylbenzene, and 1, 6-dibromohexane in protonated and perdeuterated cyclohexane have been measured with a transient holographic grating technique at a temperature of 25 ^°C. The mass diffusion coefficient shows a pronounced concentration dependence. Perdeuteration of cyclohexane only leads to marginal changes of the mass diffusion coefficient. The Stokes-Einstein equation describes the limiting tracer diffusion coefficients well if the solute molecule is smaller than the solvent. It is not capable to describe the small isotope effect of a few percent. On the other hand, the isotope effect, which is independent of concentration, is in agreement with the Enskog theory, that does not provide the absolute value of the mass diffusion coefficient of the liquid mixtures. The thermal diffusion coefficient of all the binary mixtures shows a moderate and almost linear concentration dependence. Its isotope effect, which is the change of D _T upon deuteration of cyclohexane, varies with mole fraction. The thermophoretic force acting on any tracer molecule in cyclohexane changes by the same amount when cyclohexane is perdeuterated, irrespective of the magnitude of the thermophoretic force before deuteration. This change of the thermophoretic force is equal but of opposite sign to the difference between the thermophoretic forces acting on cyclohexane and perdeuterated cyclohexane as tracers in any of the above liquids.     

Note on the interfacial tension of phase-separated polymer solutions

Earlier theoretical calculations of the interfacial tension of phase-separated polymer solutions as a function of the degree of polymerizationN and the temperatureT, based partly on the mean-field approximation, had led toN ^–1/4(1–T/T _c )^3/2 for fixedN1 andT approaching the critical solution temperatureT _c It is here remarked that the scaling procedure of de Gennes then modifies this toN ^–0.37(1–T/T _c )^1.26, which is in close accord with the experimentalN ^–0.44(1–T/T _c )^1.26. The simplest mean-field picture yieldsN ^–1/2(1–T/T _c )^3/2.     

Analysis of positron diffusion data

In this paper we present and discuss experimental methods to determine the positron diffusion coefficient from slow positron beam measurements. We also evaluate the use of the annihilation line Doppler-broadening technique in positron diffusion measurements, as compared on the more commonly used method of positronium fraction. The effects of incomplete positron thermalization and uncertainties of the positron implantation profile at low-positron incident energies to the measured data are discussed. We apply the presented methods to the model case of A1(110) system in the temperature range from 20 to 500 K. This data shows that Doppler-broadening and positronium fraction measurements give consistent results for the positron diffusion coefficient in A1(110), where D₊(300 K) = 1.7(2) cm²/s with the temperature dependence D₊ T ^–0.62(3).     

Kinetic processes of muonium formation by thermalized electrons in the spur model

Diffusion of a thermalized electron in the field of a Coulomb centre is considered. The time dependence of the probability for the electron not to be captured by the Coulomb centre ( ⁺) at the momentt,P _D (t), is obtained. The quantityP _D (t) coincides with the precession amplitude at the muon frequency and is determined by the parameter/l _CT ( is an averaged distance from an electron to a muon att=0 andl _CT =e ²/(2T) is the Onsager length) that reflects the relation between electron potential and kinetic energies at t=0. When/l _CT –1 the precession amplitudeP _D (t) decreases up to 30% during the timel _CT ² /D-(D-is the diffusion coefficient) and then it becomes almost constant. The dependence ofP _D () on/l _CT is presented.     

Contactless density measurement of high-temperature BiFeO<Subscript>3</Subscript> and BaTiO<Subscript>3</Subscript>

The density of liquid and undercooled BiFeO₃ and high-temperature solid, liquid, and undercooled BaTiO₃ was measured with an electrostatic levitation furnace. The density was obtained with an ultraviolet-based imaging technique that allowed excellent sample contrast throughout all phases of processing, including at elevated temperatures. Over the 1250- to 1490-K temperature range, the density of liquid BiFeO₃ can be expressed as _L(T)=6.70×10³–1.31(T-T_m)(kgm^-3) (±2 per cent) with T_m=1423 K, yielding a volume coefficient of thermal expansion _L(T)=1.9×10^-4 K^-1. For BaTiO₃, the density of the solid can be expressed as _S(T)=5.04×10³–0.21(T-T_m) (T_m=1893 K) over the 1220- to 1893-K range, yielding a volume coefficient of thermal expansion _S(T)=4.2×10^-5 K^-1, whereas that of the liquid can be expressed as _L(T)=4.04×10³-0.34(T-T_m) over the 1300- to 2025-K range with _L(T)=8.4×10^-5 K^-1. PACS 77.84.-s; 81.05.Je; 81.20.n     

NMR self-diffusion study of organic glasses: COANP,MBANP, PNP,NPP

A pulsed field gradient proton spin-echo NMR self-diffusion study of organic glasses COANP, MBANP, PNP and NPP in their liquid and weakly supercooled states was performed. The NMR phase diagrams, based on the proton NMR transverse relaxation time (T ₂) temperature hysteresis data of these materials, clearly give evidence of the onset of a glass phase on cooling the isotropic liquids below their respective melting temperatures. The self-diffusion data exhibit in the supercooled glassy state a non-Arrhenius behaviour and can be described in terms of the Vogel-Fulcher modification of the Arrhenius law,D=D exp{–E _a /[k _B (T–T _VF )]}. The activation energiesE _a and Vogel-Fulcher temperaturesT _VF are 83.2 meV and 239 K for COANP, 66 meV and 249 K for MBANP, and 85 meV and 245 K for PNP, respectively. The flow viscosity data obtained for COANP in the same temperature region as well conform to the Vogel-Fulcher behaviour, exp{E _a ⁽⁾ /[k _B (T–T _VF )]}, withE _a ⁽⁾ =80.4 meV andT _VF =239 K. In case of COANPD was found to increase with decreasing diffusion time in the supercooled (glassy) melt just belowT _M whereas no such behaviour was found aboveT _M .     

The Yang-Lee edge singularity in spherical models

The density of Yang-Lee zeros in the thermodynamic limit is discussed for ferromagnetic spherical models of general dimensionalities and arbitrary range of interaction. In all cases the zeros lie on the imaginary axis in the complex magnetic field planeH=H+iH with a density (H) that exhibits a square root singularity(H) (H-H ₀), with=1/2, as the edge of the gap atH=H ₀(T) is approached forT>T _c. WhenTT _c one hasH ₀(T)(TT _c ) with critical exponent=+.Supported by the National Science Foundation in part through the Materials Science Center at Cornell University.     

High-frequency response and wavelength dispersion of the linear electro-optic effect in PZN-PT (88/12) single crystal

We have characterized the wavelength dispersion of the high- and low-frequency values of the linear electro-optic coefficient r _c = r ₃₃–(n _o/n _e)³ r ₁₃ of poled 0.88 Pb(Zn_1/3Nb_2/3)O₃–0.12 PbTiO₃ single crystal. The measurements have been investigated as a function of the laser wavelength from 0.465 to 1.32 m. Clamped r ^S and unclamped r ^T values of the electro-optic coefficient as well as the acoustic contribution r ^a have been established. We obtained a ratio of r ^S/r ^T = 30%, which is independent of the wavelength of the light beam. The value of r ^S _c at the wavelength of 633 nm was found to be equal to 50±5 pm/V, which is a rather high value.This revised version was published online in March 2005. In the previous version, the published online date was missing     

Fractional Moment Estimates for Random Unitary Operators

We consider unitary analogs of d-dimensional Anderson models on l²( $$\mathbb(z)$$^d) defined by the product U=D S where S is a deterministic unitary and D is a diagonal matrix of i.i.d. random phases. The operator S is an absolutely continuous band matrix which depends on parameters controlling the size of its off-diagonal elements. We adapt the method of Aizenman–Molchanov to get exponential estimates on fractional moments of the matrix elements of U(U –z)^–1, provided the distribution of phases is absolutely continuous and the parameters correspond to small off-diagonal elements of S. Such estimates imply almost sure localization for U.     

Phase separation of symmetrical polymer mixtures in thin-film geometry

Monte Carlo simulations of the bond fluctuation model of symmetrical polymer blends confined between two neutral repulsive walls are presented for chain lengthN _A=N _B=32 and a wide range of film thicknessD (fromD=8 toD=48 in units of the lattice spacing). The critical temperaturesT _c (D) of unmixing are located by finite-size scaling methods, and it is shown that , wherev ₃0.63 is the correlation length exponent of the three-dimensional Ising model universality class. Contrary to this result, it is argued that the critical behavior of the films is ruled by two-dimensional exponents, e.g., the coexistence curve (difference in volume fraction of A-rich and A-poor phases) scales as , where ₂ is the critical exponent of the two-dimensional Ising universality class ( ₂=1/8). Since for largeD this asymptotic critical behavior is confined to an extremely narrow vicinity ofT _c (D), one observes in practice effective exponents which gradually cross over from ₂ to ₃ with increasing film thickness. This anomalous flattening of the coexistence curve should be observable experimentally.     

Chemical diffusion in molybdenum disulphide

Ceramic molybdenum disulphide (MoS₂) was equilibrated at an ambient sulphur vapour partial pressure p(S₂), 10 Pa<p(S₂)<1000 Pa. After the step change of p(S₂) to a new value, the equilibration kinetics was monitored by measuring electrical conductivity. The application of the solution of Fick's second law (with the initial condition: no concentration gradient in specimen and the boundary condition: surface concentration constant) to the kinetic data gave the chemical diffusion coefficient. The chemical diffusion coefficient, D_chem, determined at 1273 K, was D_chem=(3.20±0.32)*10⁻⁷ cm² s⁻¹ and was found to be independent of sulphur vapour partial pressure. The usefulness of transient electrical conductivity method for determining real values of diffusion data was discussed in terms of defect structure of the studied material.     

Transient-state method for coupled evaluation of Soret and Fick coefficients,and related tortuosity factors,using free and porous packed thermodiffusion cells: Application to CuSO4 aqueous solution ( 0.25M)

The measurement of Soret coefficients in liquids is not easy and usually not very precise because the resulting concentration gradient is small and moreover can be perturbed by undesired convection currents. In order to suppress, or to drastically reduce these convection currents, the use of a porous medium is sometimes suggested. The question arises as to whether the Soret coefficient is the same in free fluid and in porous medium. This is the aim of this paper. To this end, for a given liquid mixture, the time evolution of the vertical concentration gradient is experimentally measured in the same thermodiffusion cell filled first with the free liquid and next with a porous medium followed by saturation by the liquid mixture. Both the isothermal diffusion (Fick) coefficient and the Soret coefficient can be deduced, providing that a correct working equation is used. The proposed equation results from integration of the general mass conservation equation with realistic boundary conditions (zero mass flux at the boundaries) and some simplifying assumptions rendering this equation more tractable than the one proposed some decades ago by Bierlein (J.A. Bierlein, J. Chem. Phys. 23, 10 (1955)). The method is applied here to an electrolytic solution (CuSO4, 0.25 M) at a mean temperature of 37^°C. The Soret coefficients in free and porous medium (zircon microspheres in the range of 250- 315 ^. 10^-6m) may be considered to be equal ( S_T = 13.2±0.5 ^. 10^-3 K^-1) and the tortuosity factors for the packed medium are the same relative to thermodiffusion and Fick coefficients ( = 1.51±0.02).     

Scaling of the surface tension of phase-separated polymer solutions

The tension of the interface between the equilibrium phases of a phase-separated polymer solution is obtained in the simplest mean-field approximation from the functional equation for the composition profile of the interface. For temperaturesT near the critical solution temperatureT _c, i.e., for Flory parameter near _c, and for high degrees of polymerizationN, the profile and tension scale with=N ^1/2(– _c), just as do the compositions of the coexisting phases in mean-field approximation. The surface tension in the asymptotic limitN, _c at fixedx, is found to be given bya ²/kT _c (2c'/c)^1/2 N ^-5/4(x), wherea is the lattice spacing of an underlying lattice (or, roughly, the length of a monomer),c andc are the vertical and total coordination numbers of the lattice, and(x) is a scaling function, known for allx, with the asymptotic behavior asx0 and asx. The latter implies that becomes independent ofN asN at fixedT nearT _c; the former implies that becomes proportional toN ^–1/2(1–T/T _c)^3/2 asTT _c at fixedN1, as found previously.     

MD simulation of concentrated polymer solutions: Structural relaxation near the glass transition

We examine by molecular dynamics simulations the relaxation of polymer-solvent mixtures close to the glass transition. The simulations employ a coarse-grained model in which polymers are represented by bead-spring chains and solvent particles by monomers. The interaction parameters between polymer and solvent are adjusted such that mixing is favored. We find that the mixtures have one glass transition temperature T _g or critical temperature T _c of mode-coupling theory (MCT). Both T _g and T _c (> T _g decrease with increasing solvent concentration . The decrease is linear for the concentrations studied (up to = 25%. Above T _c we explore the structure and relaxation of the polymer-solvent mixtures on cooling. We find that, if the polymer solution is compared to the pure polymer melt at the same T, local spatial correlations on the length scale of the first peak of the static structure factor S(q) are reduced. This difference between melt and solution is largely removed when comparing the S(q) of both systems at similar distance to the respective T _c. Near T _c we investigate dynamic correlation functions, such as the incoherent intermediate scattering function (t), mean-square displacements of the monomers and solvent particles, two non-Gaussian parameters, and the probability distribution P(ln r;t) of the logarithm of single-particle displacements. In accordance with MCT we find, for instance, that (t) obeys the time-temperature superposition principle and has relaxation times which are compatible with a power law increase close (but not too close) to T _c. In divergence to MCT, however, the increase of depends on the wavelength q, small q values having weaker increase than large ones. This decoupling of local and large-length scale relaxation could be related to the emergence of dynamic heterogeneity at low T. In the time window of the relaxation an analysis of P(ln r;t) reveals a double-peak structure close to T _c. The first peak correponds to “slow” particles (monomer or solvent) which have not moved much farther than 10% of their diameter in time t, whereas the second occurs at distances of the order of the particle diameter. These “fast” particles have succeeded in leaving their nearest-neighbor cage in time t. The simulation thus demonstrates that large fluctuations in particle mobility accompany the final structural relaxation of the cold polymer solution in the vicinity of the extrapolated T _c.     

Magnon contribution to the magnetoresistance of iron nanowires deposited using pulsed electrodeposition

Iron nanowires with a square cross section are grown by pulsed electrodeposition within a newly developed nanochannel template that allows for easy characterization. Measurements of the magnetoresistance as a function of magnetic field and temperature are performed within a large parameter window allowing for the investigation of the magnonic contribution to the magnetoresistance of electrodeposited iron nanowires. Values for the temperature dependent magnon stiffness D (T) are extracted: D (T) = D₀(1 – d₁T²) = 365(1 – 4.4 × 10^–6 · T² · K^–2) meV Ų.

     

Neutron scattering study of the two-dimensional spinS=1/2 square-lattice Heisenberg antiferromagnet Sr2CuO2Cl2

We have carried out a neutron scattering investigation of the static structure factorS(q _2D ) (q _2D is the in-plane wave vector) in the two-dimensional spinS=1/2 square-lattice Heisenberg antiferromagnet Sr₂CuO₂Cl₂. For the spin correlation length we find quantitative agreement with Monte Carlo results over a wide range of temperature. The combined Sr₂CuO₂Cl₂-Monte Carlo data, which cover the length scale from 1 to 200 lattice constants, are predicted without adjustable parameteres by renormalized classical theory for the quantum nonlinear sigma model. For the structure factor peakS(0), on the other hand, we findS(0) ² for the reduced temperature range 0.16<T/2 _s <0.36, whereas current theories predict that at low temperaturesS(0)T ^{2 2}. This discrepancy has important implications for the interpretation of many derivative quantities such as NMR relaxation rates. In the ordered phase, we have measured the temperature dependence of the out-of-plane spin-wave gap. Its low-temperature value of 5.0 meV corresponds to an XY anisotropyJ _XY /J=1.4×10^–4. From measurements of the sublattice mangetization we obtain =0.22±0.01 for the order parameter exponent. This may either reflect tricricality as in La₂CuO₄, or it may indicate finite-size two-dimensional XY behavior as suggested by Bramwell and Holdsworth. As in theS=1 system K₂NiF₄, the gap energy in Sr₂CuO₂Cl₂ scales linearly with the order parameter up to the Néel temperature. We also reanalyze static structure factor data for K₂NiF₄ using the exact low temperature result for the correlation length of Hasenfratz and Niedermayer and including the Ising anisotropy explicitly. Excellent agreement between experiment and theory is obtained for the correlation length, albeit with the spin-stiffness _s reduced by 20% from the spin-wave value. As in Sr₂CuO₂Cl₂ we find thatS(0) ² for the reduced temperature range 0.22<T/2 _s <0.47.     

Thermoelectric power of heavy-fermion compounds

We calculate the diffusion thermopower of the Anderson lattice as a model for heavyfermion compounds in a semi-phenomenological theory. In this theory, the thermopower is expressed by the dynamical susceptibility which describes spin fluctuations and can be measured by neutron scattering. The Kondo effect is taken into account for a singlef-electron spin which is coupled to all other spins and to the conduction electrons. This approach neglects multiple intesite-scattering of the conduction electrons. We obtain a Kondo termS ₍₁₎ ^d (T) (in which the thermopower of non-interacting spins is multiplied by a factor which describes the spin dynamics) and a resonance termS ₍₂₎ ^d (T) of opposite sign which vanishes for vanishing interactions. The superposition of both terms leads to a broad maximum of the thermopower roughly at the Kondo temperatureT _K and to an additional minimum belowT _K . ForT0 the termS ₍₁₎ ^d vanishes asT ² and the termS ₍₂₎ ^d becomes proportional toT. We also show that the Sommerfeld expansion leads to an incorrect result for the low temperature resistivity of the Anderson lattice and that the Gorter-Nordheim relation does not hold at low temperatures.     

Mass-spectroscopic study of the diffusion and solubility of helium in submicrocrystalline palladium

By the method of helium thermal desorption from submicrocrystalline palladium presaturated in the gaseous phase, the diffusion coefficient D _eff and solubility coefficient C _eff of helium are measured in the range P=0–3 MPa and T=293–508 K. The pressure dependence of C _eff flattens at high pressures. At low saturation pressures, the temperature dependences of the diffusion and solubility coefficients may be divided into (1) high-temperature (400–508 K) and (2) low-temperature (293–400 K) ranges described by the exponentials D _{1, 2}=D ₀exp (−E _{1, 2} ^D /kT) and C _{1, 2}=C ₀exp (−E _{1, 2} ^S /kT). The energies of diffusion activation are E ₂ ^D =0.0036±0.0015 eV and E ₁ ^D =0.33±0.03 eV, and the solution energies are E ₂ ^S =−0.025±0.008 eV and E ₁ ^S =0.086±0.008 eV in the low-and high-temperature ranges, respectively. Mechanisms behind the diffusion and solution of helium are discussed.     

Thermodynamic properties of the spin-Peierls transition in CuGeO3

We present an investigation of the spin-Peierls transition atT _SP=14.5 K in polycrystalline CuGeO₃ through specific-heat and thermal-expansion measurements. Clear second-order phase-transition anomalies are found in both properties atT _SP, although only a small entropy of S0.1 Rn2 is released at the transition. Most of the entropy is released atT _SP<T<150 K, where the temperature dependence of the magnetic contribution to the specific heat as well as the thermal expansion exhibit extrema atT ^*40 K. These are caused by one-dimensional antiferromagnetic fluctuations along the Cu chains, possibly accompanied by structural fluctuations. Using Ehrenfest's relation, a hydrostatic pressure coefficient (T _SP/_p)_p0 (0.45±0.06) K/kbar is derived.