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

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

Intermediation for technology diffusion and user innovation in a developing rural economy:a social learning perspective

Technology intermediaries are seen as potent vehicles for addressing perennial problems in transferring technology from university to industry in developed and developing countries. This paper examines what constitutes effective user-end intermediation in a low-technology, developing economy context, which is an under-researched topic. The social learning in technological innovation framework is extended using situated learning theory in a longitudinal instrumental case study of an exemplar technology intermediation programme. The paper documents the role that academic-related research and advisory centres can play as intermediaries in brokering, facilitating and configuring technology, against the backdrop of a group of small-scale pisciculture businesses in a rural area of Colombia. In doing so, it demonstrates how technology intermediation activities can be optimized in the domestication and innofusion of technology amongst end-users. The design components featured in this instrumental case of intermediation can inform policy making and practice relating to technology transfer from university to rural industry. Future research on this subject should consider the intermediation components put forward, as well as the impact of such interventions, in different countries and industrial sectors. Such research would allow for theoretical replication and help improve technology domestication and innofusion in different contexts, especially in less-developed countries

Spectral Shape of Relaxations in Silica Glass

Precise low-frequency light scattering experiments on silica glass are presented, covering a broad temperature and frequency range (9 GHz < \nu < 2 THz). For the first time the spectral shape of relaxations is observed over more than one decade in frequency. The spectra show a power-law low-frequency wing of the relaxational part of the spectrum with an exponent $\alpha$ proportional to temperature in the range 30 K < T < 200 K. A comparison of our results with those from acoustic attenuation experiments performed at different frequencies shows that this power-law behaviour rather well describes relaxations in silica over 9 orders of magnitude in frequency. These findings can be explained by a model of thermally activated transitions in double well potentials.Comment: 4 pages, 3 figures, submitted to Phys. Rev. Let

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

Phase transitions and configuration space topology

Equilibrium phase transitions may be defined as nonanalytic points of thermodynamic functions, e.g., of the canonical free energy. Given a certain physical system, it is of interest to understand which properties of the system account for the presence of a phase transition, and an understanding of these properties may lead to a deeper understanding of the physical phenomenon. One possible approach of this issue, reviewed and discussed in the present paper, is the study of topology changes in configuration space which, remarkably, are found to be related to equilibrium phase transitions in classical statistical mechanical systems. For the study of configuration space topology, one considers the subsets M_v, consisting of all points from configuration space with a potential energy per particle equal to or less than a given v. For finite systems, topology changes of M_v are intimately related to nonanalytic points of the microcanonical entropy (which, as a surprise to many, do exist). In the thermodynamic limit, a more complex relation between nonanalytic points of thermodynamic functions (i.e., phase transitions) and topology changes is observed. For some class of short-range systems, a topology change of the M_v at v=v_t was proved to be necessary for a phase transition to take place at a potential energy v_t. In contrast, phase transitions in systems with long-range interactions or in systems with non-confining potentials need not be accompanied by such a topology change. Instead, for such systems the nonanalytic point in a thermodynamic function is found to have some maximization procedure at its origin. These results may foster insight into the mechanisms which lead to the occurrence of a phase transition, and thus may help to explore the origin of this physical phenomenon.Comment: 22 pages, 6 figure

Deregulation of methylation of transcribed-ultra conserved regions in colorectal cancer and their value for detection of adenomas and adenocarcinomas

Expression of Transcribed Ultraconserved Regions (T-UCRs) is often deregulated in cancer. The present study assesses the expression and methylation of three T-UCRs (Uc160, Uc283 and Uc346) in colorectal cancer (CRC) and explores the potential of T-UCR methylation in circulating DNA for the detection of adenomas and adenocarcinomas. Expression levels of Uc160, Uc283 and Uc346 were lower in neoplastic tissues from 64 CRC patients (statistically significant for Uc160, p<0.001), compared to non-malignant tissues, while methylation levels displayed the inverse pattern (p<0.001, p=0.001 and p=0.004 respectively). In colon cancer cell lines, overexpression of Uc160 and Uc346 led to increased proliferation and migration rates. Methylation levels of Uc160 in plasma of 50 CRC, 59 adenoma patients, 40 healthy subjects and 12 patients with colon inflammation or diverticulosis predicted the presence of CRC with 35% sensitivity and 89% specificity (p=0.016), while methylation levels of the combination of all three T-UCRs resulted in 45% sensitivity and 74.3% specificity (p=0.013). In conclusion, studied T-UCRs’ expression and methylation status are deregulated in CRC while Uc160 and Uc346 appear to have a complicated role in CRC progression. Moreover their methylation status appears a promising non-invasive screening test for CRC, provided that the sensitivity of the assay is improved

Photoprocesses in protoplanetary disks

Circumstellar disks are exposed to intense ultraviolet radiation from the young star. In the inner disks, the UV radiation can be enhanced by more than seven orders of magnitude compared with the average interstellar field, resulting in a physical and chemical structure that resembles that of a dense photon-dominated region (PDR). This intense UV field affects the chemistry, the vertical structure of the disk, and the gas temperature, especially in the surface layers of the disk. The parameters which make disks different from traditional PDRs are discussed, including the shape of the UV radiation field, grain growth, the absence of PAHs, the gas/dust ratio and the presence of inner holes. New photorates for selected species, including simple ions, are presented. Also, a summary of available cross sections at Lyman alpha 1216 A is made. Rates are computed for radiation fields with color temperatures ranging from 4000 to 30,000 K, and can be applied to a wide variety of astrophysical regions including exo-planetary atmospheres. The importance of photoprocesses is illustrated for a number of representative disk models, including disk models with grain growth and settling.Comment: A website with the final published version and all photodissociation cross sections and rates can be found at http://www.strw.leidenuniv.nl/~ewine/phot

Perturbation analysis of weakly discrete kinks

We present a perturbation theory of kink solutions of discrete Klein-Gordon chains. The unperturbed solutions correspond to the kinks of the adjoint partial differential equation. The perturbation theory is based on a reformulation of the discrete chain problem into a partial differential equation with spatially modulated mass density. The first order corrections to the kink solutions are obtained analytically and are shown to agree with exact numerical results. We discuss the problem of calculating the Peierls-Nabarro barrier.Comment: 13 pages, 6 figures, REVTE

Reexamination of the long-range Potts model: a multicanonical approach

We investigate the critical behavior of the one-dimensional q-state Potts model with long-range (LR) interaction $1/r^{d+\sigma}$, using a multicanonical algorithm. The recursion scheme initially proposed by Berg is improved so as to make it suitable for a large class of LR models with unequally spaced energy levels. The choice of an efficient predictor and a reliable convergence criterion is discussed. We obtain transition temperatures in the first-order regime which are in far better agreement with mean-field predictions than in previous Monte Carlo studies. By relying on the location of spinodal points and resorting to scaling arguments, we determine the threshold value $\sigma_c(q)$ separating the first- and second-order regimes to two-digit precision within the range $3 \leq q \leq 9$. We offer convincing numerical evidence supporting $\sigma_c(q)Comment: 18 pages, 18 figure