812 research outputs found
Extreme Precision Antenna Reflector Study Results
Thermal and mechanical distortion degrade the RF performance of antennas. The complexity of future communications antennas requires accurate, dimensionally stable antenna reflectors and structures built from materials other than those currently used. The advantages and disadvantages of using carbon fibers in an epoxy matrix are reviewed as well as current reflector fabrications technology and adjustment. The manufacturing sequence and coefficient of thermal expansion of carbon fiber/borosilicate glass composites is described. The construction of a parabolic reflector from this material and the assembling of both reflector and antenna are described. A 3M-aperture-diameter carbon/glass reflector that can be used as a subassembly for large reflectors is depicted. The deployment sequence for a 10.5M-aperture-diameter antenna, final reflector adjustment, and the deployment sequence for large reflectors are also illustrated
Modelling the Self-Assembly of Virus Capsids
We use computer simulations to study a model, first proposed by Wales [1],
for the reversible and monodisperse self-assembly of simple icosahedral virus
capsid structures. The success and efficiency of assembly as a function of
thermodynamic and geometric factors can be qualitatively related to the
potential energy landscape structure of the assembling system. Even though the
model is strongly coarse-grained, it exhibits a number of features also
observed in experiments, such as sigmoidal assembly dynamics, hysteresis in
capsid formation and numerous kinetic traps. We also investigate the effect of
macromolecular crowding on the assembly dynamics. Crowding agents generally
reduce capsid yields at optimal conditions for non-crowded assembly, but may
increase yields for parameter regimes away from the optimum. Finally, we
generalize the model to a larger triangulation number T = 3, and observe more
complex assembly dynamics than that seen for the original T = 1 model.Comment: 16 pages, 11 figure
Force-induced rupture of a DNA duplex
The rupture of double-stranded DNA under stress is a key process in
biophysics and nanotechnology. In this article we consider the shear-induced
rupture of short DNA duplexes, a system that has been given new importance by
recently designed force sensors and nanotechnological devices. We argue that
rupture must be understood as an activated process, where the duplex state is
metastable and the strands will separate in a finite time that depends on the
duplex length and the force applied. Thus, the critical shearing force required
to rupture a duplex within a given experiment depends strongly on the time
scale of observation. We use simple models of DNA to demonstrate that this
approach naturally captures the experimentally observed dependence of the
critical force on duplex length for a given observation time. In particular,
the critical force is zero for the shortest duplexes, before rising sharply and
then plateauing in the long length limit. The prevailing approach, based on
identifying when the presence of each additional base pair within the duplex is
thermodynamically unfavorable rather than allowing for metastability, does not
predict a time-scale-dependent critical force and does not naturally
incorporate a critical force of zero for the shortest duplexes. Additionally,
motivated by a recently proposed force sensor, we investigate application of
stress to a duplex in a mixed mode that interpolates between shearing and
unzipping. As with pure shearing, the critical force depends on the time scale
of observation; at a fixed time scale and duplex length, the critical force
exhibits a sigmoidal dependence on the fraction of the duplex that is subject
to shearing.Comment: 10 pages, 6 figure
Coarse-grained modelling of supercoiled RNA
We study the behaviour of double-stranded RNA under twist and tension using
oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit
salt-dependence into the model allows us to directly compare our results to
data from recent single-molecule experiments. The model reproduces extension
curves as a function of twist and stretching force, including the buckling
transition and the behaviour of plectoneme structures. For negative
supercoiling, we predict denaturation bubble formation in plectoneme end-loops,
suggesting preferential plectoneme localisation in weak base sequences. OxRNA
exhibits a positive twist-stretch coupling constant, in agreement with recent
experimental observations.Comment: 8 pages + 5 pages Supplementary Materia
Evolutionary Dynamics in a Simple Model of Self-Assembly
We investigate the evolutionary dynamics of an idealised model for the robust
self-assembly of two-dimensional structures called polyominoes. The model
includes rules that encode interactions between sets of square tiles that drive
the self-assembly process. The relationship between the model's rule set and
its resulting self-assembled structure can be viewed as a genotype-phenotype
map and incorporated into a genetic algorithm. The rule sets evolve under
selection for specified target structures. The corresponding, complex fitness
landscape generates rich evolutionary dynamics as a function of parameters such
as the population size, search space size, mutation rate, and method of
recombination. Furthermore, these systems are simple enough that in some cases
the associated model genome space can be completely characterised, shedding
light on how the evolutionary dynamics depends on the detailed structure of the
fitness landscape. Finally, we apply the model to study the emergence of the
preference for dihedral over cyclic symmetry observed for homomeric protein
tetramers
Monodisperse self-assembly in a model with protein-like interactions
We study the self-assembly behaviour of patchy particles with `protein-like'
interactions that can be considered as a minimal model for the assembly of
viral capsids and other shell-like protein complexes. We thoroughly explore the
thermodynamics and dynamics of self assembly as a function of the parameters of
the model and find robust assembly of all target structures considered. Optimal
assembly occurs in the region of parameter space where a free energy barrier
regulates the rate of nucleation, thus preventing the premature exhaustion of
the supply of monomers that can lead to the formation of incomplete shells. The
interactions also need to be specific enough to prevent the assembly of
malformed shells, but whilst maintaining kinetic accessibility. Free-energy
landscapes computed for our model have a funnel-like topography guiding the
system to form the target structure, and show that the torsional component of
the interparticle interactions prevents the formation of disordered aggregates
that would otherwise act as kinetic traps.Comment: 11 pages; 10 figure
Coarse-grained simulations of DNA overstretching
We use a recently developed coarse-grained model to simulate the
overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the
model, about 6-7 pN higher than the experimental value at equivalent salt
conditions. Furthermore, the model reproduces the temperature dependence of the
overstretching force well. The mechanism of overstretching is always
force-induced melting by unpeeling from the free ends. That we never see S-DNA
(overstretched duplex DNA), even though there is clear experimental evidence
for this mode of overstretching under certain conditions, suggests that S-DNA
is not simply an unstacked but hydrogen-bonded duplex, but instead probably has
a more exotic structure.Comment: 11 pages, 11 figure
DNA nanotweezers studied with a coarse-grained model of DNA
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces
the basic thermodynamics of short strands: duplex hybridization,
single-stranded stacking and hairpin formation, and also captures the essential
structural properties of DNA: the helical pitch, persistence length and
torsional stiffness of double-stranded molecules, as well as the comparative
flexibility of unstacked single strands. We apply the model to calculate the
detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple
machine driven by hybridization and strand displacement.Comment: 4 pages, 5 figure
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