A lattice polymer study of DNA renaturation dynamics

DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate limiting step) followed by a much faster zippering. We consider a lattice polymer model undergoing Rouse dynamics and focus on the nucleation of two diffusing strands. We study numerically the dependence of various nucleation rates on the strand lengths and on an additional local nucleation barrier. When the local barrier is sufficiently high, all renaturation rates considered scale with the length as predicted by Kramers' rate theory and are also in agreement with experiments: their scaling behavior is governed by exponents describing equilibrium properties of polymers. When the local barrier is lowered renaturation occurs in a regime of genuine non-equilibrium behavior and the scaling deviates from the rate theory prediction.Comment: 13 pages, 6 figures. To appear in Journal of Statistical Mechanic

Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays

Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs. free energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.Comment: 4 pages, 4 figure

Coexistence of excited states in confined Ising systems

Using the density-matrix renormalization-group method we study the two-dimensional Ising model in strip geometry. This renormalization scheme enables us to consider the system up to the size 300 x infinity and study the influence of the bulk magnetic field on the system at full range of temperature. We have found out the crossover in the behavior of the correlation length on the line of coexistence of the excited states. A detailed study of scaling of this line is performed. Our numerical results support and specify previous conclusions by Abraham, Parry, and Upton based on the related bubble model.Comment: 4 Pages RevTeX and 4 PostScript figures included; the paper has been rewritten without including new result

Equilibrium shapes and faceting for ionic crystals of body-centered-cubic type

A mean field theory is developed for the calculation of the surface free energy of the staggered BCSOS, (or six vertex) model as function of the surface orientation and of temperature. The model approximately describes surfaces of crystals with nearest neighbor attractions and next nearest neighbor repulsions. The mean field free energy is calculated by expressing the model in terms of interacting directed walks on a lattice. The resulting equilibrium shape is very rich with facet boundaries and boundaries between reconstructed and unreconstructed regions which can be either sharp (first order) or smooth (continuous). In addition there are tricritical points where a smooth boundary changes into a sharp one and triple points where three sharp boundaries meet. Finally our numerical results strongly suggest the existence of conical points, at which tangent planes of a finite range of orientations all intersect each other. The thermal evolution of the equilibrium shape in this model shows strong similarity to that seen experimentally for ionic crystals.Comment: 14 Pages, Revtex and 10 PostScript figures include

Crossover from reptation to Rouse dynamics in a one-dimensional model

A simple one-dimensional model is constructed for polymer motion. It exhibits the crossover from reptation to Rouse dynamics through gradually allowing hernia creation and annihilation. The model is treated by the density matrix technique which permits an accurate finite-size-scaling analysis of the behavior of long polymers.Comment: 5 Pages RevTeX and 5 PostScript figures included (to appear in Physical Review E

The generalized contact process with n absorbing states

We investigate the critical properties of a one dimensional stochastic lattice model with n (permutation symmetric) absorbing states. We analyze the cases with $n \leq 4$ by means of the non-hermitian density matrix renormalization group. For n=1 and n=2 we find that the model is respectively in the directed percolation and parity conserving universality class, consistent with previous studies. For n=3 and n=4, the model is in the active phase in the whole parameter space and the critical point is shifted to the limit of one infinite reaction rate. We show that in this limit the dynamics of the model can be mapped onto that of a zero temperature n-state Potts model. On the basis of our numerical and analytical results we conjecture that the model is in the same universality class for all $n \geq 3$ with exponents $z = \nu_\|/\nu_\perp = 2$, $\nu_\perp = 1$ and $\beta = 1$. These exponents coincide with those of the multispecies (bosonic) branching annihilating random walks. For n=3 we also show that, upon breaking the symmetry to a lower one ($Z_2$), one gets a transition either in the directed percolation, or in the parity conserving class, depending on the choice of parameters.Comment: 10 pages, RevTeX, and 10 PostScript figures include

Reptation in the Rubinstein-Duke model: the influence of end-reptons dynamics

We investigate the Rubinstein-Duke model for polymer reptation by means of density-matrix renormalization group techniques both in absence and presence of a driving field. In the former case the renewal time \tau and the diffusion coefficient D are calculated for chains up to N=150 reptons and their scaling behavior in N is analyzed. Both quantities scale as powers of N: $\tau \sim N^z$ and $D \sim 1/N^x$ with the asymptotic exponents z=3 and x=2, in agreement with the reptation theory. For an intermediate range of lengths, however, the data are well-fitted by some effective exponents whose values are quite sensitive to the dynamics of the end reptons. We find 2.7 <z< 3.3 and 1.8 <x< 2.1 for the range of parameters considered and we suggest how to influence the end reptons dynamics in order to bring out such a behavior. At finite and not too small driving field, we observe the onset of the so-called band inversion phenomenon according to which long polymers migrate faster than shorter ones as opposed to the small field dynamics. For chains in the range of 20 reptons we present detailed shapes of the reptating chain as function of the driving field and the end repton dynamics.Comment: RevTeX 12 Pages and 14 figure

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.Comment: 8 pages, 6 figure