Zipping and collapse of diblock copolymers

Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.Comment: 12 pages, RevTeX and 14 PostScript figures include

A simple model of DNA denaturation and mutually avoiding walks statistics

Recently Garel, Monthus and Orland (Europhys. Lett. v 55, 132 (2001)) considered a model of DNA denaturation in which excluded volume effects within each strand are neglected, while mutual avoidance is included. Using an approximate scheme they found a first order denaturation. We show that a first order transition for this model follows from exact results for the statistics of two mutually avoiding random walks, whose reunion exponent is c > 2, both in two and three dimensions. Analytical estimates of c due to the interactions with other denaturated loops, as well as numerical calculations, indicate that the transition is even sharper than in models where excluded volume effects are fully incorporated. The probability distribution of distances between homologous base pairs decays as a power law at the transition.Comment: 7 Pages, RevTeX, 8 Figure

Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model

While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb concerning oligo length, overall similarity, and continuous stretches, the final behavior is difficult to predict. The aim of this study was to investigate the effect of well-defined mismatches on hybridization specificity using CodeLink Activated Slides, and to study quantitatively the relation between hybridization intensity and Gibbs free energy (Delta G), taking the mismatches into account. Our data clearly showed a correlation between the hybridization intensity and Delta G of the oligos over three orders of magnitude for the hybridization intensity, which could be described by the Langmuir model. As Delta G was calculated according to the nearest-neighbor model, using values related to DNA hybridizations in solution, this study clearly shows that target-probe hybridizations on microarrays with a three-dimensional coating are in quantitative agreement with the corresponding reaction in solution. These results can be interesting for some practical applications. The correlation between intensity and Delta G can be used in quality control of microarray hybridizations by designing probes and corresponding RNA spikes with a range of Delta G values. Furthermore, this correlation might be of use to fine-tune oligonucleotide design algorithms in a way to improve the prediction of the influence of mismatching targets on microarray hybridizations.Comment: 32 pages on a single pdf fil

Physics-based analysis of Affymetrix microarray data

We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained before for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin, rather than being a problem with the proposed model.Comment: 11 pages, 10 figure

The quantitative genetics of incipient speciation: Heritability and genetic correlations of skeletal traits in populations of diverging favia fragum ecomorphs

Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h 2) in a suite of measurements that define corallite architecture, and could partition additive and nonadditive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h 2 estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h 2 were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution

Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions are consistent with first order thermal denaturation in both cases. Results for end-segments show a coexistence of two distinct power laws in the relative distributions, which is not foreseen by a recent approach in which DNA is treated as a homogeneous network of linear polymer segments. This unexpected feature, and the discrepancies with such an approach, are explained in terms of a refined scaling picture in which a precise distinction is made between network branches representing single stranded and effective double stranded segments.Comment: 8 pages, 8 figure

Construction of a matrix product stationary state from solutions of finite size system

Stationary states of stochastic models, which have $N$ states per site, in matrix product form are considered. First we give a necessary condition for the existence of a finite $M$-dimensional matrix product state for any ${N,M}$. Second, we give a method to construct the matrices from the stationary states of small size system when the above condition and $N\le M$ are satisfied. Third, the method by which one can check that the obtained matrices are valid for any system size is presented for the case where $M=N$ is satisfied. The application of our methods is explained using three examples: the asymmetric exclusion process, a model studied in [F. H. Jafarpour: J. Phys. A: Math. Gen. 36 (2003) 7497] and a hybrid of both of the models.Comment: 22 pages, no figure. Major changes: sec.3 was shortened; the list of references were changed. This is the final version, which will appear in J.Phys.

Boundary and Bulk Phase Transitions in the Two Dimensional Q > 4 State Potts Model

The surface and bulk properties of the two-dimensional Q > 4 state Potts model in the vicinity of the first order bulk transition point have been studied by exact calculations and by density matrix renormalization group techniques. For the surface transition the complete analytical solution of the problem is presented in the $Q \to \infty$ limit, including the critical and tricritical exponents, magnetization profiles and scaling functions. According to the accurate numerical results the universality class of the surface transition is independent of the value of Q > 4. For the bulk transition we have numerically calculated the latent heat and the magnetization discontinuity and we have shown that the correlation lengths in the ordered and in the disordered phases are identical at the transition point.Comment: 11 pages, RevTeX, 6 PostScript figures included. Manuscript substantially extended, details on the analytical and numerical calculations added. To appear in Phys. Rev.

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

UV Absorption Cross Sections of Nitrous Oxide (N2O) and Carbon Tetrachloride (CCl4) Between 210 and 350 K and the Atmospheric Implications

Absorption cross sections of nitrous oxide (N2O) and carbon tetrachloride (CCl4) are reported at five atomic UV lines (184.95, 202.548, 206.200, 213.857, and 228.8 nm) at 27 temperatures in the range 210-350 K. In addition, UV absorption spectra of CCl4 are reported between 200-235 nm as a function of temperature (225-350 K). The results from this work are critically compared with results from earlier studies. For N2O, the present results are in good agreement with the current JPL recommendation enabling a reduction in the estimated uncertainty in the N2O atmospheric photolysis rate. For CCl4, the present cross section results are systematically greater than the current recommendation at the reduced temperatures most relevant to stratospheric photolysis. The new cross sections result in a 5-7% increase in the modeled CCl4 photolysis loss, and a slight decrease in the stratospheric lifetime, from 51 to 50 years, for present day conditions. The corresponding changes in modeled inorganic chlorine and ozone in the stratosphere are quite small. A CCl4 cross section parameterization for use in 37 atmospheric model calculations is presented