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

Development of reclaimed potable water quality criteria

In order to minimize launch requirements necessary to meet the demands of long-term spaceflight, NASA will reuse water reclaimed from various on-board sources including urine, feces, wash water and humidity condensate. Development of reclamation systems requires the promulgation of water quality standards for potable reuse of the reclaimed water. Existing standards for domestic U.S. potable water consumption were developed, but do not consider the peculiar problems associated with the potable reuse of recycled water. An effort was made to: (1) define a protocol by which comprehensive reclaimed water potability/palatability criteria can be established and updated; and (2) continue the effort to characterize the organic content of reclaimed water in the Regenerative Life Support Evaluation

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

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

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

Reentrant phase diagram and pH effects in cross-linked gelatin gels

Experimental results have shown that the kinetics of bond formation in chemical crosslinking of gelatin solutions is strongly affected not only by gelatin and reactant concentrations but also by the solution pH. We present an extended numerical investigation of the phase diagram and of the kinetics of bond formation as a function of the pH, via Monte Carlo simulations of a lattice model for gelatin chains and reactant agent in solution. We find a reentrant phase diagram, namely gelation can be hindered either by loop formation, at low reactant concentrations, or by saturation of active sites of the chains via formation of single bonds with crosslinkers, at high reactant concentrations. The ratio of the characteristic times for the formation of the first and of the second bond between the crosslinker and an active site of a chain is found to depend on the reactant reactivity, in good agreement with experimental data.Comment: 8 pages, 8 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

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

First Order Phase Transition of a Long Polymer Chain

We consider a model consisting of a self-avoiding polygon occupying a variable density of the sites of a square lattice. A fixed energy is associated with each $90^\circ$-bend of the polygon. We use a grand canonical ensemble, introducing parameters $\mu$ and $\beta$ to control average density and average (total) energy of the polygon, and show by Monte Carlo simulation that the model has a first order, nematic phase transition across a curve in the $\beta$-$\mu$ plane.Comment: 11 pages, 7 figure