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

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

Recommendation of RILEM TC 261-CCF: test method to determine the flexural creep of fibre reinforced concrete in the cracked state

[EN] To date there is no clear consensus about how creep of cracked FRC structural elements should be considered. In recent years, different methodologies have been developed for multiple stress cases. The absence of a standardised methodology to evaluate flexural creep in the cracked state has hindered general comparisons and conclusions that could lead to significant advances in this topic. Since 2014, the study of the creep behaviour of cracked FRC has been coordinated by the RILEM TC 261-CCF. All the available creep methodologies were analysed in terms of procedure, equipment and results. A comprehensive Round-Robin Test (RRT) on the creep behaviour of cracked sections of FRC was proposed and undertaken by a total of 19 participant laboratories from 14 countries all over the world. The analysis and conclusions of the RRT results and the different methodologies provided the basis for this recommendation. This recommendation focuses on the test method to evaluate the flexural creep of FRC specimens in the cracked state. Guidelines on specimen production, detailed test equipment, experimental setup and test procedure as well as the definitions of the most relevant parameters are provided.Llano-Torre, A.; Serna Ros, P. (2021). Recommendation of RILEM TC 261-CCF: test method to determine the flexural creep of fibre reinforced concrete in the cracked state. Materials and Structures. 54(3):1-20. https://doi.org/10.1617/s11527-021-01675-0S120543Theodorakopoulos D (1995) Creep characteristics of glass reinforced cement under flexural loading. Cement Concr Compos 17:267–279Chanvillard G, Roque O (1999) Behaviour of fibre reinforced concrete cracked section under sustained load. High Performance Fiber Reinforced Cement Composites (HPFRCC 3) Mainz, Germany, pp 239–250, RILEM PRO 06Kurt S, Balaguru P (2000) Post crack creep of polymeric fibre-reinforced concrete in flexure. Cem Concr Res 30(2):183–190Mackay J, Trottier JF (2004) Post-crack behavior of steel and synthetic FRC under flexural creep. In: Shotcrete, Proc. 2nd Intnl. Conf. on Engineering, Cairns, Australia (2004), pp 183–192Kusterle W (2009) Viscous material behaviour of solids- creep of polymer fibre reinforced concrete. In: Proc. 5th Central European Congress on Concrete Engineering. obv, Baden, pp 95–100Arango S, Serna P, Martí-Vargas JR, García-Taengua E (2012) A test method to characterize flexural creep behaviour of pre-cracked FRC specimens. Exp Mech 52(8):1067–1078Zerbino RL, Barragan BE (2012) Long-term behaviour of cracked steel fibre-reinforced concrete beams under sustained loading. ACI Mater J 109(2):215–224Abrishambaf A, Barros JAO, Cunha VMCF (2015) Time-dependent flexural behaviour of cracked steel fibre reinforced self-compacting concrete panels. Cem Concr Res 72:21–36Buratti N, Mazzotti C (2016) Experimental tests on the long-term behaviour of SFRC and MSFRC in bending and direct tension. In: Proceedings of the BEFIB 2016, 9th RILEM international symposium on fiber reinforced concrete, pp. 163–174, Vancouver, Canada, 19–21 Sept 2016Babafemi AJ, Boshoff WP (2015) Tensile creep of macro-synthetic fibre reinforced concrete (MSFRC) under uni-axial tensile loading. Cement Concr Compos 55:62–69Vrijdaghs R, di Prisco M, Vandewalle L (2018) Uniaxial tensile creep of a cracked polypropylene fiber reinforced concrete. Mater Struct 51:5. https://doi.org/10.1617/s11527-017-1132-5Vasanelli E, Micelli F, Aiello MA, Plizzari G (2013) Long term behaviour of FRC flexural beams under sustained load. Eng Struct 56:1858–1867Bernard ES (2010) Influence of fibre type on creep deformation of cracked fibre-reinforced shotcrete panels. ACI Mater J 107(5):474–480EFNARC (2012) Testing sprayed concrete—Creep test on square panelLarive C, Rogat D, Chamoley D, Regnard A, Pannetier T, Thuaud C (2016) Influence of fibres on the creep behaviour of reinforced sprayed concrete. In: Proceedings of ITA World Tunnel Congress WTC 2016, April 22‐28, San Francisco, United StatesMonetti DH, Llano-Torre A, Torrijos MC, Giaccio G, Zerbino R, Martí-Vargas JR, Serna P (2019) Long-term behavior of cracked fiber reinforced concrete under service conditions. Construct Build Mater; 196:649–658. https://doi.org/10.1016/j.conbuildmat.2018.10.230Llano-Torre A., Martí-Vargas JR, Serna P (2020) Flexural and compressive creep behavior of UHPFRC specimens. Construct Build Mater; 244:118254. https://doi.org/10.1016/j.conbuildmat.2020.118254Serna P, Llano-Torre A and Cavalaro S H P (ed) (2017) Creep behaviour in cracked sections of fibre reinforced concrete: proceedings of the international RILEM Workshop FRC-CREEP 2016. RILEM bookseries 14 (Dordrecht: Springer)Llano-Torre A, Serna P, Cavalaro SHP (2016) International round robin test on creep behavior of FRC supported by the RILEM TC 261-CCF. In: Proceedings of the BEFIB 2016, 9th RILEM international symposium on fiber reinforced concrete, pp 127–140, Vancouver, Canada, 19–21 Sept 2016Serna P, Llano-Torre A, García-Taengua E, Martí-Vargas JR (2015) Database on the long-term behaviour of FRC: a useful tool to achieve overall conclusions. In: Proceedings of the 10th international conference on mechanics and physics of Creep, Shrinkage, and Durability of Concrete and Concrete Structures, Vienna, September 2015, pp 1544–1553Llano-Torre A., Serna P. (eds) Round-Robin test on creep behaviour in cracked sections of FRC: experimental program, results and database analysis. RILEM State-of-the-Art Reports. Springer. https://doi.org/10.1007/978-3-030-72736-9ASTM International (2015) C1812/C1812M-15e1 Standard Practice for Design of Journal Bearing Supports to be Used in Fiber Reinforced Concrete Beam Tests. West Conshohocken, PA; ASTM International. https://doi.org/10.1520/C1812_C1812M-15E0

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

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

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

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

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

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

Stacking Interactions in Denaturation of DNA Fragments

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the \emph{adenine-thymine} rich portions of the fragment. The harmonic stacking coupling shifts, along the $T$-axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.Comment: European Physical Journal E (2011) in pres