Kinetics and thermodynamics of first-order Markov chain copolymerization

We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment and detachment of monomers. Exact solutions are obtained for these kinetic equations in the steady regimes of multicomponent copolymerization and depolymerization. Thermodynamic equilibrium is identified as the state at which the growth velocity is vanishing on average and where detailed balance is satisfied. Away from equilibrium, the analytical expression of the thermodynamic entropy production is deduced in terms of the Shannon disorder per monomer in the copolymer sequence. The Mayo-Lewis equation is recovered in the fully irreversible growth regime. The theory also applies to Bernoullian chains in the case where the attachment and detachment rates only depend on the reacting monomer

Universal Formulae for Percolation Thresholds

A power law is postulated for both site and bond percolation thresholds. The formula writes $p_c=p_0[(d-1)(q-1)]^{-a}d^{\ b}$, where $d$ is the space dimension and $q$ the coordination number. All thresholds up to $d\rightarrow \infty$ are found to belong to only three universality classes. For first two classes $b=0$ for site dilution while $b=a$ for bond dilution. The last one associated to high dimensions is characterized by $b=2a-1$ for both sites and bonds. Classes are defined by a set of value for $\{p_0; \ a\}$. Deviations from available numerical estimates at $d \leq 7$ are within $\pm 0.008$ and $\pm 0.0004$ for high dimensional hypercubic expansions at $d \geq 8$. The formula is found to be also valid for Ising critical temperatures.Comment: 11 pages, latex, 3 figures not include

Force-induced misfolding in RNA

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.Comment: 28 pages, 11 figure

Clusterization, frustration and collectivity in random networks

We consider the random Erd{\H o}s--R\'enyi network with enhanced clusterization and Ising spins $s=\pm 1$ at the network nodes. Mutually linked spins interact with energy $J$. Magnetic properties of the system as dependent on the clustering coefficient $C$ are investigated with the Monte Carlo heat bath algorithm. For $J>0$ the Curie temperature $T_c$ increases from 3.9 to 5.5 when $C$ increases from almost zero to 0.18. These results deviate only slightly from the mean field theory. For $J<0$ the spin-glass phase appears below $T_{SG}$; this temperature decreases with $C$, on the contrary to the mean field calculations. The results are interpreted in terms of social systems.Comment: 10 pages, 6 figures; serious change of result

Dynamics and Thermodynamics of the Glass Transition

The principal theme of this paper is that anomalously slow, super-Arrhenius relaxations in glassy materials may be activated processes involving chains of molecular displacements. As pointed out in a preceding paper with A. Lemaitre, the entropy of critically long excitation chains can enable them to grow without bound, thus activating stable thermal fluctuations in the local density or molecular coordination of the material. I argue here that the intrinsic molecular-scale disorder in a glass plays an essential role in determining the activation rate for such chains, and show that a simple disorder-related correction to the earlier theory recovers the Vogel-Fulcher law in three dimensions. A key feature of this theory is that the spatial extent of critically long excitation chains diverges at the Vogel-Fulcher temperature. I speculate that this diverging length scale implies that, as the temperature decreases, increasingly large regions of the system become frozen and do not contribute to the configurational entropy, and thus ergodicity is partially broken in the super-Arrhenius region above the Kauzmann temperature $T_K$. This partially broken ergodicity seems to explain the vanishing entropy at $T_K$ and other observed relations between dynamics and thermodynamics at the glass transition.Comment: 20 pages, no figures, some further revision

A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.Comment: 15 pages, 15 figure

Monte Carlo simulations of the solid-liquid transition in hard spheres and colloid-polymer mixtures

Monte Carlo simulations at constant pressure are performed to study coexistence and interfacial properties of the liquid-solid transition in hard spheres and in colloid-polymer mixtures. The latter system is described as a one-component Asakura-Oosawa (AO) model where the polymer's degrees of freedom are incorporated via an attractive part in the effective potential for the colloid-colloid interactions. For the considered AO model, the polymer reservoir packing fraction is eta_p^r=0.1 and the colloid-polymer size ratio is q=sigma_p/\sigma=0.15 (with sigma_p and sigma the diameter of polymers and colloids, respectively). Inhomogeneous solid-liquid systems are prepared by placing the solid fcc phase in the middle of a rectangular simulation box creating two interfaces with the adjoined bulk liquid. By analyzing the growth of the crystalline region at various pressures and for different system sizes, the coexistence pressure p_co is obtained, yielding p_co=11.576 k_BT/sigma^3 for the hard sphere system and p_co=8.0 k_BT/sigma^3 for the AO model (with k_B the Boltzmann constant and T the temperature). Several order parameters are introduced to distinguish between solid and liquid phases and to describe the interfacial properties. From the capillary-wave broadening of the solid-liquid interface, the interfacial stiffness is obtained for the (100) crystalline plane, giving the values gamma=0.49 k_BT/sigma^2 for the hard-sphere system and gamma=0.95 k_BT/sigma^2 for the AO model.Comment: 11 pages, 13 figure

Grand canonical and canonical solution of self-avoiding walks with up to three monomers per site on the Bethe lattice

We solve a model of polymers represented by self-avoiding walks on a lattice which may visit the same site up to three times in the grand-canonical formalism on the Bethe lattice. This may be a model for the collapse transition of polymers where only interactions between monomers at the same site are considered. The phase diagram of the model is very rich, displaying coexistence and critical surfaces, critical, critical endpoint and tricritical lines, as well as a multicritical point. From the grand-canonical results, we present an argument to obtain the properties of the model in the canonical ensemble, and compare our results with simulations in the literature. We do actually find extended and collapsed phases, but the transition between them, composed by a line of critical endpoints and a line of tricritical points, separated by the multicritical point, is always continuous. This result is at variance with the simulations for the model, which suggest that part of the line should be a discontinuous transition. Finally, we discuss the connection of the present model with the standard model for the collapse of polymers (self-avoiding self-attracting walks), where the transition between the extended and collapsed phases is a tricritical point.Comment: 34 pages, including 10 figure

Local and chain dynamics in miscible polymer blends: A Monte Carlo simulation study

Local chain structure and local environment play an important role in the dynamics of polymer chains in miscible blends. In general, the friction coefficients that describe the segmental dynamics of the two components in a blend differ from each other and from those of the pure melts. In this work, we investigate polymer blend dynamics with Monte Carlo simulations of a generalized bond-fluctuation model, where differences in the interaction energies between non-bonded nearest neighbors distinguish the two components of a blend. Simulations employing only local moves and respecting a non-bond crossing condition were carried out for blends with a range of compositions, densities, and chain lengths. The blends investigated here have long-chain dynamics in the crossover region between Rouse and entangled behavior. In order to investigate the scaling of the self-diffusion coefficients, characteristic chain lengths $N_\mathrm{c}$ are calculated from the packing length of the chains. These are combined with a local mobility $\mu$ determined from the acceptance rate and the effective bond length to yield characteristic self-diffusion coefficients $D_\mathrm{c}=\mu/N_\mathrm{c}$. We find that the data for both melts and blends collapse onto a common line in a graph of reduced diffusion coefficients $D/D_\mathrm{c}$ as a function of reduced chain length $N/N_\mathrm{c}$. The composition dependence of dynamic properties is investigated in detail for melts and blends with chains of length twenty at three different densities. For these blends, we calculate friction coefficients from the local mobilities and consider their composition and pressure dependence. The friction coefficients determined in this way show many of the characteristics observed in experiments on miscible blends.Comment: 12 pages, 13 figures, editorial change

On the size and shape of excluded volume polymers confined between parallel plates

A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between two parallel plates with varying plate separation. We show that the non-monotonic behavior of the overall size of the chain as a function of plate-separation, seen in computer simulations and reproduced by earlier theories, can already be predicted on the basis of scaling arguments. However, the behavior of the size in a plane parallel to the plates, a quantity observed in recent experiments, is predicted to be monotonic, in contrast to the experimental findings. We analyze this problem in depth with a mean-field approach that maps the confined polymer onto an anisotropic Gaussian chain, which allows the size of the polymer to be determined separately in the confined and unconfined directions. The theory allows the analytical construction of a smooth cross-over between the small plate-separation de Gennes regime and the large plate-separation Flory regime. The results show good agreement with Langevin dynamics simulations, and confirm the scaling predictions.Comment: 15 pages, 3 figure