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

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

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

Diversity-induced resonance in a system of globally coupled linear oscillators

The purpose of this paper to analyze in some detail the arguably simplest case of diversity-induced reseonance: that of a system of globally-coupled linear oscillators subjected to a periodic forcing. Diversity appears as the parameters characterizing each oscillator, namely its mass, internal frequency and damping coefficient are drawn from a probability distribution. The main ingredients for the diversity-induced-resonance phenomenon are present in this system as the oscillators display a variability in the individual responses but are induced, by the coupling, to synchronize their responses. A steady state solution for this model is obtained. We also determine the conditions under which it is possible to find a resonance effect.Comment: Reported at the XI International Workshop "Instabilities and Nonequilibrium Structures" Vina del Mar (Chile

Is J 133658.3-295105 a Radio Source at z >= 1.0 or at the Distance of M 83?

We present Gemini optical imaging and spectroscopy of the radio source J 133658.3-295105. This source has been suggested to be the core of an FR II radio source with two detected lobes. J 133658.3-295105 and its lobes are aligned with the optical nucleus of M 83 and with three other radio sources at the M 83 bulge outer region. These radio sources are neither supernova remnants nor H II regions. This curious configuration prompted us to try to determine the distance to J 133658.3-295105. We detected H_alpha emission redshifted by ~ 130 km s^-1 with respect to an M 83 H II region 2.5" east-southeast of the radio source. We do not detect other redshifted emission lines of an optical counterpart down to m_i = 22.2 +/- 0.8. Two different scenarios are proposed: the radio source is at z >= 2.5, a much larger distance than the previously proposed lower limit z >= 1.0, or the object was ejected by a gravitational recoil event from the M 83 nucleus. This nucleus is undergoing a strong dynamical evolution, judging from previous three-dimensional spectroscopy.Comment: 6 pages, 4 figure

Method of remotely characterizing thermal properties of a sample

A sample in a wind tunnel is radiated from a thermal energy source outside of the wind tunnel. A thermal imager system, also located outside of the wind tunnel, reads surface radiations from the sample as a function of time. The produced thermal images are characteristic of the heat transferred from the sample to the flow across the sample. In turn, the measured rates of heat loss of the sample are characteristic of the flow and the sample

Topological constraints on spiral wave dynamics in spherical geometries with inhomogeneous excitability

We analyze the way topological constraints and inhomogeneity in the excitability influence the dynamics of spiral waves on spheres and punctured spheres of excitable media. We generalize the definition of an index such that it characterizes not only each spiral but also each hole in punctured, oriented, compact, two-dimensional differentiable manifolds and show that the sum of the indices is conserved and zero. We also show that heterogeneity and geometry are responsible for the formation of various spiral wave attractors, in particular, pairs of spirals in which one spiral acts as a source and a second as a sink -- the latter similar to an antispiral. The results provide a basis for the analysis of the propagation of waves in heterogeneous excitable media in physical and biological systems.Comment: 5 pages, 6 Figures, major revisions, accepted for publication in Phys. Rev.

Optimization of supply diversity for the self-assembly of simple objects in two and three dimensions

The field of algorithmic self-assembly is concerned with the design and analysis of self-assembly systems from a computational perspective, that is, from the perspective of mathematical problems whose study may give insight into the natural processes through which elementary objects self-assemble into more complex ones. One of the main problems of algorithmic self-assembly is the minimum tile set problem (MTSP), which asks for a collection of types of elementary objects (called tiles) to be found for the self-assembly of an object having a pre-established shape. Such a collection is to be as concise as possible, thus minimizing supply diversity, while satisfying a set of stringent constraints having to do with the termination and other properties of the self-assembly process from its tile types. We present a study of what we think is the first practical approach to MTSP. Our study starts with the introduction of an evolutionary heuristic to tackle MTSP and includes results from extensive experimentation with the heuristic on the self-assembly of simple objects in two and three dimensions. The heuristic we introduce combines classic elements from the field of evolutionary computation with a problem-specific variant of Pareto dominance into a multi-objective approach to MTSP.Comment: Minor typos correcte

Noise Effects on Synchronized Globally Coupled Oscillators

The synchronized phase of globally coupled nonlinear oscillators subject to noise fluctuations is studied by means of a new analytical approach able to tackle general couplings, nonlinearities, and noise temporal correlations. Our results show that the interplay between coupling and noise modifies the effective frequency of the system in a non trivial way. Whereas for linear couplings the effect of noise is always to increase the effective frequency, for nonlinear couplings the noise influence is shown to be positive or negative depending on the problem parameters. Possible experimental verification of the results is discussed.Comment: 6 Pages, 4 EPS figures included (RevTeX and epsfig needed). Submitted to Phys. Re

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