180 research outputs found
Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
The design space for a self-assembled multicomponent objects ranges from a
solution in which every building block is unique to one with the minimum number
of distinct building blocks that unambiguously define the target structure.
Using a novel pipeline, we explore the design spaces for a set of structures of
various sizes and complexities. To understand the implications of the different
solutions, we analyse their assembly dynamics using patchy particle simulations
and study the influence of the number of distinct building blocks and the
angular and spatial tolerances on their interactions on the kinetics and yield
of the target assembly. We show that the resource-saving solution with minimum
number of distinct blocks can often assemble just as well (or faster) than
designs where each building block is unique. We further use our methods to
design multifarious structures, where building blocks are shared between
different target structures. Finally, we use coarse-grained DNA simulations to
investigate the realisation of multicomponent shapes using DNA nanostructures
as building blocks.Comment: 12 page
The Formal Language and Design Principles of Autonomous DNA Walker Circuits.
Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions
Coarse-grained modelling of DNA-RNA hybrids
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is
based on two previously developed coarse-grained models\unicode{x2014}oxDNA
and oxRNA. The model naturally reproduces the physical properties of hybrid
duplexes including their structure, persistence length and force-extension
characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we
fit the model's thermodynamic properties to experimental data using both
average-sequence and sequence-dependent parameters. To demonstrate the model's
applicability we provide three examples of its use\unicode{x2014}calculating
the free energy profiles of hybrid strand displacement reactions, studying the
resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.Comment: 15 pages, 10 figure
Coarse-grained modelling of DNA-RNA hybrids
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami
An Anderson-Fano Resonance and Shake-Up Processes in the Magneto-Photoluminescence of a Two-Dimensional Electron System
We report an anomalous doublet structure and low-energy satellite in the
magneto-photoluminescence spectra of a two-dimensional electron system. The
doublet structure moves to higher energy with increasing magnetic field and is
most prominent at odd filling factors 5 and 3. The lower-energy satellite peak
tunes to lower energy for increasing magnetic field between filling factor 6
and 2. These features occur at energies below the fundamental band of
recombination originating from the lowest Landau level and display striking
magnetic field and temperature dependence that indicates a many-body origin.
Drawing on a recent theoretical description of Hawrylak and Potemski, we show
that distinct mechanisms are responsible for each feature.Comment: 14 pages including 5 figures. To appear in the April 15th edition of
Phy. Rev. B. rapid com
Evidence of Skyrmion excitations about in n-Modulation Doped Single Quantum Wells by Inter-band Optical Transmission
We observe a dramatic reduction in the degree of spin-polarization of a
two-dimensional electron gas in a magnetic field when the Fermi energy moves
off the mid-point of the spin-gap of the lowest Landau level, . This
rapid decay of spin alignment to an unpolarized state occurs over small changes
to both higher and lower magnetic field. The degree of electron spin
polarization as a function of is measured through the magneto-absorption
spectra which distinguish the occupancy of the two electron spin states. The
data provide experimental evidence for the presence of Skyrmion excitations
where exchange energy dominates Zeeman energy in the integer quantum Hall
regime at
Skyrmionic excitons
We investigate the properties of a Skyrmionic exciton consisting of a
negatively charged Skyrmion bound to a mobile valence hole. A variational wave
function is constructed which has the generalized total momentum P as a good
quantum number. It is shown that the Skyrmionic exciton can have a larger
binding energy than an ordinary magnetoexciton and should therefore dominate
the photoluminescence spectrum in high-mobility quantum wells and
heterojunctions where the electron-hole separation exceeds a critical value.
The dispersion relation for the Skyrmionic exciton is discussed.Comment: 9 pages, RevTex, 2 PostScript figures. Replaced with version to
appear in Phys. Rev. B Rapid Communications. Short discussion of variational
state adde
Charged exctions in the fractional quantum Hall regime
We study the photoluminescence spectrum of a low density ()
two-dimensional electron gas at high magnetic fields and low temperatures. We
find that the spectrum in the fractional quantum Hall regime can be understood
in terms of singlet and triplet charged-excitons. We show that these spectral
lines are sensitive probes for the electrons compressibility. We identify the
dark triplet charged-exciton and show that it is visible at the spectrum at
K. We find that its binding energy scales like , where is
the magnetic length, and it crosses the singlet slightly above 15 T.Comment: 10 pages, 5 figure
Theory of Exciton Recombination from the Magnetically Induced Wigner Crystal
We study the theory of itinerant-hole photoluminescence of two-dimensional
electron systems in the regime of the magnetically induced Wigner crystal. We
show that the exciton recombination transition develops structure related to
the presence of the Wigner crystal. The form of this structure depends strongly
on the separation between the photo-excited hole and the plane of the
two-dimensional electron gas. When is small compared to the magnetic
length, additional peaks appear in the spectrum due to the recombination of
exciton states with wavevectors equal to the reciprocal lattice vectors of the
crystal. For larger than the magnetic length, the exciton becomes strongly
confined to an interstitial site of the lattice, and the structure in the
spectrum reflects the short-range correlations of the Wigner crystal. We derive
expressions for the energies and the radiative lifetimes of the states
contributing to photoluminescence, and discuss how the results of our analysis
compare with experimental observations.Comment: 10 pages, no figures, uses Revtex and multicol.st
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