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

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

Fixed Point of the Finite System DMRG

The density matrix renormalization group (DMRG) is a numerical method that optimizes a variational state expressed by a tensor product. We show that the ground state is not fully optimized as far as we use the standard finite system algorithm, that uses the block structure B**B. This is because the tensors are not improved directly. We overcome this problem by using the simpler block structure B*B for the final several sweeps in the finite iteration process. It is possible to increase the numerical precision of the finite system algorithm without increasing the computational effort.Comment: 6 pages, 4 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

Mentoring First-Year Distance Education Students in Taxation Studies

Research indicates that the dropout rate for fi rst-year students in universities is traditionally higher than for later years,1 with external or distance students posing the highest risk of withdrawal from studies of any group.2 This has been the case with the Bachelor of Taxation (BTax) in the Australian School of Taxation (Atax), Faculty of Law at the University of New South Wales (UNSW). The BTax program is offered nationally in an off-campus delivery mode and focuses on teaching taxation and commercial law as well as economics and accounting. The majority of its students are in fulltime employment, studying part-time; and generally students are in their late 20s to early 40s. A range of support measures, including student peer mentoring, has been successfully employed in Australia and elsewhere as a strategy to support fi rst-year university students in their studies

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

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Numerical Latent Heat Observation of the q=5 Potts Model

Site energy of the five-state ferromagnetic Potts model is numerically calculated at the first-order transition temperature using corner transfer matrix renormalization group (CTMRG) method. The calculated energy of the disordered phase $U^{+}$ is clearly different from that of the ordered phase $U^{-}$. The obtained latent heat $L = U^{-} - U^{+}$ is 0.027, which quantitatively agrees with the exact solution.Comment: 2 pages, Latex(JPSJ style files are included), 2 ps figures, submitted to J. Phys. Soc. Jpn.(short note

The Density Matrix Renormalization Group technique with periodic boundary conditions

The Density Matrix Renormalization Group (DMRG) method with periodic boundary conditions is introduced for two dimensional classical spin models. It is shown that this method is more suitable for derivation of the properties of infinite 2D systems than the DMRG with open boundary conditions despite the latter describes much better strips of finite width. For calculation at criticality, phenomenological renormalization at finite strips is used together with a criterion for optimum strip width for a given order of approximation. For this width the critical temperature of 2D Ising model is estimated with seven-digit accuracy for not too large order of approximation. Similar precision is reached for critical indices. These results exceed the accuracy of similar calculations for DMRG with open boundary conditions by several orders of magnitude.Comment: REVTeX format contains 8 pages and 6 figures, submitted to Phys. Rev.