Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls (DW), interpolating between bound and unbound segments of the chain. The free energy of the DWs is calculated to leading order beyond the Gaussian approximation. Thermodynamic instabilities (e.g. DNA unzipping and/or thermal denaturation) can be understood in terms of DW formation.Comment: 4 pages, 5 figures, to appear in Phys. Rev. Let

Punching shear strength of steel fibre reinforced lightweight concrete slabs.

One of the problems in slab-column connections is the punching shear failure at over loads. Such failures are sudden and catastrophic, and are undesirable since they do not allow an overall yield mechanism to develop. Fibre reinforcement restrains cracking, and increases the tensile strength of concrete and bond resistance of steel reinforcement. Therefore, it should be possible to use steel fibres as shear reinforcement. This investigation is a study of the structural behaviour of fibre reinforced lightweight concrete flat slabs in punching shear. Twenty full scale connections were tested simply supported on all four sides and loaded centrally through a column stub. The mix consisted of Lytag, sand and fly ash as partial replacement of cement. The main variables studied were the fibre volume, fibre type, column size, amount of reinforcement and concrete strength. Extensive measurements of deformations were made throughout the tests. Fibre reinforcement reduced all the deformations of the plain concrete slab at all stages of loading. For a given serviceability criterion, the presence of fibres increased the service load of the corresponding plain concrete slab by 15-50%. Fibres also increased the post-yield ductility and energy absorption characteristics of the slabs by. 125-260% and 240-270% respectively. The presence of fibres improved the load at first crack, punching shear strength and the residual resistance after punching by about 35%, 40% and 150-400% respectively. Fibres also produced gradual punching failures and sometimes changed the mode of failure into flexure. Empirical and theoretical equations have been proposed to predict both ultimate flexural and punching shear strength of steel fibre reinforced concrete slab-column connections and they show good agreement with data from other investigations. It is concluded that fly-ash can be successfully used in structural lightweight concrete mixes. The addition of fibres in lightweight concrete connections reduces deformations in general, delays the formation of flexural and inclined shear cracking, and increases the service load, ultimate strength, ductility and energy absorption characteristics

Erratum: "Ab initio calculations on the ground and excited states of BeOH and MgOH" [J. Chem. Phys. 111, 10484 (1999)]

Journal URL: http://jcp.aip.org

Ab initio calculations on the ground and excited states of BeOH and MgOH

Journal URL: http://jcp.aip.org

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

Thermodynamic instabilities in one dimensional particle lattices: a finite-size scaling approach

One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of particles must be demonstrated on a case-by-case basis by examining the (non-) analyticity properties of the corresponding transfer integral (TI) equation. The present note deals with the generic Peyrard-Bishop model of DNA denaturation. In the absence of exact statements about the spectrum of the singular TI equation, I use Gauss-Hermite quadratures to achieve a single-parameter-controlled approach to rounding effects; this allows me to employ finite-size scaling concepts in order to demonstrate that a phase transition occurs and to derive the critical exponents.Comment: 5 pages, 6 figures, subm. to Phys. Rev.

Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Effect of defects on thermal denaturation of DNA Oligomers

The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range repulsion and the flat part without well of the Morse potential. The stacking energy between the two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.Comment: 11 pages including 5 postscript figure; To be appear in Phys. Rev.