An information-bearing seed for nucleating algorithmic self-assembly

Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed molecule can determine which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramolecular structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, we present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form crystalline ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is 17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication

Delay Induced Excitability

We analyse the stochastic dynamics of a bistable system under the influence of time-delayed feedback. Assuming an asymmetric potential, we show the existence of a regime in which the systems dynamic displays excitability by calculating the relevant residence time distributions and correlation times. Experimentally we then observe this behaviour in the polarization dynamics of a vertical cavity surface emitting laser with opto-electronic feedback. Extending these observations to two-dimensional systems with dispersive coupling we finally show numerically that delay induced excitability can lead to the appearance of propagating wave-fronts and spirals.Comment: 5 pages, 6 figure

Utilization and Outcomes of Exposure Therapy in Child and Adolescent Usual Care.

Ph.D. Thesis. University of Hawaiʻi at Mānoa 2017

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required

Bifurcation analysis of a normal form for excitable media: Are stable dynamical alternans on a ring possible?

We present a bifurcation analysis of a normal form for travelling waves in one-dimensional excitable media. The normal form which has been recently proposed on phenomenological grounds is given in form of a differential delay equation. The normal form exhibits a symmetry preserving Hopf bifurcation which may coalesce with a saddle-node in a Bogdanov-Takens point, and a symmetry breaking spatially inhomogeneous pitchfork bifurcation. We study here the Hopf bifurcation for the propagation of a single pulse in a ring by means of a center manifold reduction, and for a wave train by means of a multiscale analysis leading to a real Ginzburg-Landau equation as the corresponding amplitude equation. Both, the center manifold reduction and the multiscale analysis show that the Hopf bifurcation is always subcritical independent of the parameters. This may have links to cardiac alternans which have so far been believed to be stable oscillations emanating from a supercritical bifurcation. We discuss the implications for cardiac alternans and revisit the instability in some excitable media where the oscillations had been believed to be stable. In particular, we show that our condition for the onset of the Hopf bifurcation coincides with the well known restitution condition for cardiac alternans.Comment: to be published in Chao

Helicoidal instability of a scroll vortex in three-dimensional reaction-diffusion systems

We study the dynamics of scroll vortices in excitable reaction-diffusion systems analytically and numerically. We demonstrate that intrinsic three-dimensional instability of a straight scroll leads to the formation of helicoidal structures. This behavior originates from the competition between the scroll curvature and unstable core dynamics. We show that the obtained instability persists even beyond the meander core instability of two-dimensional spiral wave.Comment: 4 pages, 5 figures, revte

Robust self-replication of combinatorial information via crystal growth and scission

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies

Breaking Synchrony by Heterogeneity in Complex Networks

For networks of pulse-coupled oscillators with complex connectivity, we demonstrate that in the presence of coupling heterogeneity precisely timed periodic firing patterns replace the state of global synchrony that exists in homogenous networks only. With increasing disorder, these patterns persist until they reach a critical temporal extent that is of the order of the interaction delay. For stronger disorder these patterns cease to exist and only asynchronous, aperiodic states are observed. We derive self-consistency equations to predict the precise temporal structure of a pattern from the network heterogeneity. Moreover, we show how to design heterogenous coupling architectures to create an arbitrary prescribed pattern.Comment: 4 pages, 3 figure

Diffusion-induced vortex filament instability in 3-dimensional excitable media

We studied the stability of linear vortex filaments in 3-dimensional (3D) excitable media, using both analytical and numerical methods. We found an intrinsic 3D instability of vortex filaments that is diffusion-induced, and is due to the slower diffusion of the inhibitor. This instability can result either in a single helical filament or in chaotic scroll breakup, depending on the specific kinetic model. When the 2-dimensional dynamics were in the chaotic regime, filament instability occurred via on-off intermittency, a failure of chaos synchronization in the third dimension.Comment: 5 pages, 5 figures, to appear in PRL (September, 1999

Protein-DNA computation by stochastic assembly cascade

The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan DNA sequence through a cascade of random nucleation and disassembly events that is mechanistically similar to the dynamic instability of microtubules. This iterative cascade is a multistage kinetic proofreading process that amplifies minute differences, even a single base change. Our measurements suggest that this stochastic Turing-like machine can compute certain integral transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/ http://www.pnas.org/content/99/18/11589.abstrac