Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the $\phi$X174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.Comment: 5 pages, 4 figures, to appear in Phys. Rev.

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

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

Sociology of Enterprise. Department for Business Innovation & Skills Research Rport

There are more than five million small businesses in the UK. These businesses employ 12.1 million people and account for 33% of the total private sector turnover (BIS, 2014). Although a buoyant small business sector is vital to the success of the UK economy, it is well established that most small businesses never grow or, at best, achieve only modest growth. Accordingly, understanding the factors that drive and shape small business performance is a key concern for both academics and policymakers. By increasing our understanding of these factors, this innovative project can make a major contribution to entrepreneurship research and to the evidence base underpinning enterprise policy

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.

Optimisation of the Explosive Compaction Process for Powder-In- Tube MgB 2 Superconductors Using Numerical Simulations

High quality, ex-situ powder-in-tube (PIT) Introduction Nowadays, superconductivity has a significant impact on many technological sectors, for example in the production of electric motors and magnetic sensors as well as in the energy transmission and storage technology. Superconducting wires and tapes are the key product for the adoption of this high technology, but the selection of a suitable superconducting material is not an easy task. MgB 2 is in general a low cost superconductor compared to other ceramic high T c materials, with a transition temperature near the liquid hydrogen boiling point. It has been estimated that approximately 15% of the generated electricity is dissipated during power transportation. In that respect, MgB 2 can be used for the construction of zero loss superconducting transmission lines, where liquid hydrogen may serve as refrigeration medium. The production of wires, coils and tapes requires forming at very high pressures due to the poor formability of the extremely hard ceramic superconductors. For this reason, the powder-in-tube (PIT) explosive compaction technique is considered to be a very promising powder metallurgy forming process for the fabrication of near full density MgB 2 superconductors as given in The present work is concerned with the optimization of the explosive compaction process, incorporating MgB 2 powders. The optimization is performed on an LS-DYNA numerical simulation model of the explosive compaction, where the external diameter of the tube and the dimensions (length and diameter) of the explosive surrounding of the PIT are used as input parameters. The peak pressure, peak maximum principal stress, porosity, uniformity of the tube radius, and mass of the explosive, are the corresponding simulation outputs, with the porosity being the most important parameter to optimize, since it is directly related to the interparticle bonding of the compact which affects the critical current density of the superconductor. Numerical Simulation of Explosively Densified PIT MgB Powders The shock consolidation process of the superconducting powders is numerically simulated using the LSDYNA finite element code. Since the PIT sample deformation during explosive loading is considered to be axisymmetric, a quarter 3D explicit finite element model is developed which is sufficient to accurately simulate the compaction procedure reducing this way the computational time. The finite element model mesh together with the corresponding experimental setup are demonstrated i

Kinetic and Transport Equations for Localized Excitations in Sine-Gordon Model

We analyze the kinetic behavior of localized excitations - solitons, breathers and phonons - in Sine-Gordon model. Collision integrals for all type of localized excitation collision processes are constructed, and the kinetic equations are derived. We analyze the kinetic behavior of localized excitations - solitons, breathers and phonons - in Sine-Gordon model. Collision integrals for all type of localized excitation collision processes are constructed, and the kinetic equations are derived. We prove that the entropy production in the system of localized excitations takes place only in the case of inhomogeneous distribution of these excitations in real and phase spaces. We derive transport equations for soliton and breather densities, temperatures and mean velocities i.e. show that collisions of localized excitations lead to creation of diffusion, thermoconductivity and intrinsic friction processes. The diffusion coefficients for solitons and breathers, describing the diffusion processes in real and phase spaces, are calculated. It is shown that diffusion processes in real space are much faster than the diffusion processes in phase space.Comment: 23 pages, latex, no figure

Controlling the energy flow in nonlinear lattices: a model for a thermal rectifier

We address the problem of heat conduction in 1-D nonlinear chains; we show that, acting on the parameter which controls the strength of the on site potential inside a segment of the chain, we induce a transition from conducting to insulating behavior in the whole system. Quite remarkably, the same transition can be observed by increasing the temperatures of the thermal baths at both ends of the chain by the same amount. The control of heat conduction by nonlinearity opens the possibility to propose new devices such as a thermal rectifier.Comment: 4 pages with figures included. Phys. Rev. Lett., to be published (Ref. [10] corrected

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