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We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for the cases where the force is applied to only one strand or to both. Different assumptions on the monomer size of single and double stranded DNA lead to opposite conclusions as to whether DNA melts or not as it overstretches.
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We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsically accounts for the cooperativity related to the free energy penalty of bubble nucleation. The model describes both the unpairing and unstacking parts of the spectroscopically determined experimental melting curves. Furthermore, the model explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor (NN) type. We compute the partition function for the model through the transfer matrix formalism, which we also generalize to include non local chain entropy terms. This part introduces a new parametrization of the Yeramian-like transfer matrix approach to the Poland-Scheraga description of DNA melting. The model is exactly solvable in the homogeneous thermodynamic limit, and we calculate all observables without use of the grand partition function. As is well known, models of this class have a first order or continuous phase transition at the temperature of complete strand separation depending on the value of the exponent of the bubble entropy.
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs, subject to a tensile force applied at the end monomer of the chain while the other end is fixed at the origin of coordinates. The impact of bond non-linearity on the relaxation dynamics of the polymer at different degrees of stretching is treated analytically within the Gaussian self-consistent approach (GSC) and then compared to simulation results derived from two different methods: Monte-Carlo (MC) and Molecular Dynamics (MD). At low and medium degrees of chain elongation we find good agreement between GSC predictions and the Monte-Carlo simulations. However, for strongly stretched chains the MD method, which takes into account inertial effects, reveals two important aspects of the nonlinear interaction between monomers: (i) a coupling and energy transfer between the damped, oscillatory normal modes of the chain, and (ii) the appearance of non-vanishing contributions of a continuum of frequencies around the characteristic modes in the power spectrum of the normal mode correlation functions.
We study the effect of rapid quench to zero temperature in a model with competing interactions, evolving through conserved spin dynamics. In a certain regime of model parameters, we find that the model belongs to the broader class of kinetically constrained models, however, the dynamics is different from that of a glass. The system shows stretched exponential relaxation with the unusual feature that the relaxation time diverges as a power of the system size. Explicitly, we find that the spatial correlation function decays as $exp(-2r/sqrt{L})$ as a function of spatial separation $r$ in a system with $L$ sites in steady state, while the temporal auto-correlation function follows $exp(-(t/tau_L)^{1/2})$, where $t$ is the time and $tau_L$ proportional to $L$. In the coarsening regime, after time $t_w$, there are two growing length scales, namely $mathcal{L}(t_w) sim t_w^{1/2}$ and $mathcal{R}(t_w) sim t_w^{1/4}$; the spatial correlation function decays as $exp(-r/ mathcal{R}(t_w))$. Interestingly, the stretched exponential form of the auto-correlation function of a single typical sample in steady state differs markedly from that averaged over an ensemble of initial conditions resulting from different quenches; the latter shows a slow power law decay at large times.
Relaxation in glasses is often approximated by a stretched-exponential form: $f(t) = A exp [-(t/tau)^{beta}]$. Here, we show that the relaxation in a model of sheared non-Brownian suspensions developed by Corte et al. [Nature Phys. 4, 420 (2008)] can be well approximated by a stretched exponential with an exponent $beta$ that depends on the strain amplitude: $0.25 < beta < 1$. In a one-dimensional version of the model, we show how the relaxation originates from density fluctuations in the initial particle configurations. Our analysis is in good agreement with numerical simulations and reveals a functional form for the relaxation that is distinct from, but well approximated by, a stretched-exponential function.
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {em block length} $2n$ as well as on the {em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.
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