1,578 research outputs found
Pathways to Economic Mobility: Key Indicators
Outlines how indicators of social, human, and financial capital affect an individual's chances of moving up or down the economic ladder. Analyzes data on family structure, community, education, race/ethnicity, health, home ownership, and other factors
Paradigms for computational nucleic acid design
The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape
Dynamical mechanism of atrial fibrillation: a topological approach
While spiral wave breakup has been implicated in the emergence of atrial
fibrillation, its role in maintaining this complex type of cardiac arrhythmia
is less clear. We used the Karma model of cardiac excitation to investigate the
dynamical mechanisms that sustain atrial fibrillation once it has been
established. The results of our numerical study show that spatiotemporally
chaotic dynamics in this regime can be described as a dynamical equilibrium
between topologically distinct types of transitions that increase or decrease
the number of wavelets, in general agreement with the multiple wavelets
hypothesis. Surprisingly, we found that the process of continuous excitation
waves breaking up into discontinuous pieces plays no role whatsoever in
maintaining spatiotemporal complexity. Instead this complexity is maintained as
a dynamical balance between wave coalescence -- a unique, previously
unidentified, topological process that increases the number of wavelets -- and
wave collapse -- a different topological process that decreases their number.Comment: 15 pages, 14 figure
Thermodynamic Analysis of Interacting Nucleic Acid Strands
Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality
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
Phase Synchronization and Polarization Ordering of Globally-Coupled Oscillators
We introduce a prototype model for globally-coupled oscillators in which each
element is given an oscillation frequency and a preferential oscillation
direction (polarization), both randomly distributed. We found two collective
transitions: to phase synchronization and to polarization ordering. Introducing
a global-phase and a polarization order parameters, we show that the transition
to global-phase synchrony is found when the coupling overcomes a critical value
and that polarization order enhancement can not take place before global-phase
synchrony. We develop a self-consistent theory to determine both order
parameters in good agreement with numerical results
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
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
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
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
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