2,802 research outputs found
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 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 monomers, as well as for the special case of polymers,
where , 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 . Our results show that, even though in three dimensions
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
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