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

Asymptotic behavior of the entropy of chains placed on stripes

By using the transfer matrix approach, we investigate the asymptotic behavior of the entropy of flexible chains with $M$ monomers each placed on stripes. In the limit of high density of monomers, we study the behavior of the entropy as a function of the density of monomers and the width of the stripe, inspired by recent analytical studies of this problem for the particular case of dimers (M=2). We obtain the entropy in the asymptotic regime of high densities for chains with $M=2,..,9$ monomers, as well as for the special case of polymers, where $M\to\infty$, and find that the results show a regular behavior similar to the one found analytically for dimers. We also verify that in the low-density limit the mean-field expression for the entropy is followed by the results from our transfer matrix calculations

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

Binding branched and linear DNA structures: from isolated clusters to fully bonded gels

The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well defined valence, namely tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10{\deg}C to 55{\deg}C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel and as a cluster fluid depending on the selected r.Comment: 15 pages, 11 figure

Fractal dimension of domain walls in the Edwards-Anderson spin glass model

We study directly the length of the domain walls (DW) obtained by comparing the ground states of the Edwards-Anderson spin glass model subject to periodic and antiperiodic boundary conditions. For the bimodal and Gaussian bond distributions, we have isolated the DW and have calculated directly its fractal dimension $d_f$. Our results show that, even though in three dimensions $d_f$ is the same for both distributions of bonds, this is clearly not the case for two-dimensional (2D) systems. In addition, contrary to what happens in the case of the 2D Edwards-Anderson spin glass with Gaussian distribution of bonds, we find no evidence that the DW for the bimodal distribution of bonds can be described as a Schramm-Loewner evolution processes.Comment: 6 pages, 5 figures. Accepted for publication in PR

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.Comment: Revised version including supplemental material, 7 pages, 8 figure

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

Self-Assembly of Patchy Particles into Polymer Chains: A Parameter-Free Comparison between Wertheim Theory and Monte Carlo Simulation

We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory, a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameter and liquid state correlation functions. This theory has not been subjected to stringent tests against simulation data for ordering across the polymerization transition. We numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results

Solution of a model of SAW's with multiple monomers per site on the Husimi lattice

We solve a model of self-avoiding walks which allows for a site to be visited up to two times by the walk on the Husimi lattice. This model is inspired in the Domb-Joyce model and was proposed to describe the collapse transition of polymers with one-site interactions only. We consider the version in which immediate self-reversals of the walk are forbidden (RF model). The phase diagram we obtain for the grand-canonical version of the model is similar to the one found in the solution of the Bethe lattice, with two distinct polymerized phases, a tricritical point and a critical endpoint.Comment: 16 pages, including 6 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