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Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins, allosteric effects have been observed in experiments with DNA as well. In these experiments two or more proteins bind at distinct DNA sites and interact indirectly with each other, via a mechanism mediated by the linker DNA molecule. We develop a mechanical model of DNA/protein interactions which predicts three distinct mechanisms of allostery. Two of these involve an enthalphy-mediated allostery, while a third mechanism is entropy driven. We analyze experiments of DNA allostery and highlight the distinctive signatures allowing one to identify which of the proposed mechanisms best fits the data.

While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence length increases with the distance. Here, we derive the formula by Wu et al. using a non-local twistable wormlike chain which introduces couplings between distal sites. Finally, we show that the same formula can account for the length-scale dependence of the torsional persistence length and is, in fact, applicable to any kind of polymer model with non-local couplings., Comment: 3 pages, 1 Figure

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 included

The steady-state phase diagram of the one-dimensional reaction-diffusion model 2A -> 3A, 2A -> 0 is studied through the non-hermitian density matrix renormalization group. In the absence of single-particle diffusion the model reduces to the pair-contact process, which has a phase transition in the universality class of Directed Percolation (DP) and an infinite number of absorbing steady states. When single-particle diffusion is added, the number of absorbing steady states is reduced to two and the model does not show DP critical behaviour anymore. The exponents $��=��_{\|}/��_{\perp}$ and $��/��_{\perp}$ are calculated numerically. The value of $��/��_{\perp}$ is close to the value of the Parity Conserving universality class, in spite of the absence of local conservation laws., Substantially revised version, RevTeX, 10 Pages and 5 PostScript figures included

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., 11 pages, RevTeX, 6 PostScript figures included. Manuscript substantially extended, details on the analytical and numerical calculations added. To appear in Phys. Rev. B

Networks of steps, seen in STM observations of vicinal surfaces on Au and Pt (110), are analyzed. A simple model is introduced for the calculation of the free energy of the networks as function of the slope parameters, valid at low step densities. It predicts that the networks are unstable, or at least metastable, against faceting and gives an equilibrium crystal shape with sharp edges either between the (110) facet and rounded regions or between two rounded regions. Experimental observations of the equilibrium shapes of Au or Pt crystals at sufficiently low temperatures, i.e. below the deconstruction temperature of the (110) facet, could check the validity of these predictions., 14 pages, RevTex, uses epsf.sty, the file rotate.sty is included. To appear in the Proceedings of the Traverse City workshop on The Dynamics of Crystal Surfaces (August 1996); this work is an extension of Phys. Rev. Lett. {\bf 76}, 4191 (1996)

The phase diagram of the staggered six vertex, or body centered solid on solid model, is investigated by transfer matrix and finite size scaling techniques. The phase diagram contains a critical region, bounded by a Kosterlitz-Thouless line, and a second order line describing a deconstruction transition. In part of the phase diagram the deconstruction line and the Kosterlitz-Thouless line approach each other without merging, while the deconstruction changes its critical behaviour from Ising-like to a different universality class. Our model has the same type of symmetries as some other two-dimensional models, such as the fully frustrated XY model, and may be important for understanding their phase behaviour. The thermal behaviour for weak staggering is intricate. It may be relevant for the description of surfaces of ionic crystals of CsCl structure., Comment: 13 pages, RevTex, 1 Postscript file with all figures, to be published in Phys. Rev. B