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

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 ν=1\nu =1 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, $\nu=1$. 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 $\nu$ 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 $\nu=1$

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 ($\nu <1$) 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 $T<2$ K. We find that its binding energy scales like $e^{2}/l$, where $l$ 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 $d$ between the photo-excited hole and the plane of the two-dimensional electron gas. When $d$ 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 $d$ 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

A modular RNA delivery system comprising spherical nucleic acids built on endosome-escaping polymeric nanoparticles

Nucleic acid therapeutics require delivery systems to reach their targets. Key challenges to be overcome include avoidance of accumulation in cells of the mononuclear phagocyte system and escape from the endosomal pathway. Spherical nucleic acids (SNAs), in which a gold nanoparticle supports a corona of oligonucleotides, are promising carriers for nucleic acids with valuable properties including nuclease resistance, sequence-specific loading and control of receptor-mediated endocytosis. However, SNAs accumulate in the endosomal pathway and are thus vulnerable to lysosomal degradation or recycling exocytosis. Here, an alternative SNA core based on diblock copolymer PMPC25–PDPA72 is investigated. This pH-sensitive polymer self-assembles into vesicles with an intrinsic ability to escape endosomes via osmotic shock triggered by acidification-induced disassembly. DNA oligos conjugated to PMPC25–PDPA72 molecules form vesicles, or polymersomes, with DNA coronae on luminal and external surfaces. Nucleic acid cargoes or nucleic acid-tagged targeting moieties can be attached by hybridization to the coronal DNA. These polymeric SNAs are used to deliver siRNA duplexes against C9orf72, a genetic target with therapeutic potential for amyotrophic lateral sclerosis, to motor neuron-like cells. By attaching a neuron-specific targeting peptide to the PSNA corona, effective knock-down is achieved at doses of 2 particles per cell