Complexity of Reconfiguration in Surface Chemical Reaction Networks

We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different ordered pair of species according to a predefined set of allowed transition rules (chemical reactions). In particular, two questions that are fundamental to the simulation of sCRNs are whether a given configuration of molecules can ever transform into another given configuration, and whether a given cell can ever contain a given species, given a set of transition rules. We show that these problems can be solved in polynomial time, are NP-complete, or are PSPACE-complete in a variety of different settings, including when adjacent species just swap instead of arbitrary transformation (swap sCRNs), and when cells can change species a limited number of times (k-burnout). Most problems turn out to be at least NP-hard except with very few distinct species (2 or 3)

Configuring robust DNA strand displacement reactions for in situ molecular analyses

The number of distinct biomolecules that can be visualized within individual cells and tissue sections via fluorescence microscopy is limited by the spectral overlap of the fluorescent dye molecules that are coupled permanently to their targets. This issue prohibits characterization of important functional relationships between different molecular pathway components in cells. Yet, recent improved understandings of DNA strand displacement reactions now provides opportunities to create programmable labeling and detection approaches that operate through controlled transient interactions between different dynamic DNA complexes. We examined whether erasable molecular imaging probes could be created that harness this mechanism to couple and then remove fluorophore-bearing oligonucleotides to and from DNA-tagged protein markers within fixed cell samples. We show that the efficiency of marker erasing via strand displacement can be limited by non-toehold mediated stand exchange processes that lower the rates that fluorophore-bearing strands diffuse out of cells. Two probe constructions are described that avoid this problem and allow efficient fluorophore removal from their targets. With these modifications, we show one can at least double the number of proteins that can be visualized on the same cells via reiterative in situ labeling and erasing of markers on cells

Shape replication through self-assembly and RNase enzymes

We introduce the problem of shape replication in the Wang tile self-assembly model. Given an input shape, we consider the problem of designing a self-assembly system which will replicate that shape into either a specific number of copies, or an unbounded number of copies. Motivated by practical DNA implementations of Wang tiles, we consider a model in which tiles consisting of DNA or RNA can be dynamically added in a sequence of stages. We further permit the addition of RNase enzymes capable of disintegrating RNA tiles. Under this model, we show that arbitrary genus-0 shapes can be replicated infinitely many times using only O(1) distinct tile types and O(1) stages. Further, we show how to replicate precisely n copies of a shape using O(log n) stages and O(1) tile types.National Science Foundation (U.S.) (NSF CAREER award CCF-0347776)United States. Dept. of Energy (DOE grant DE-FG02-04ER25647

Could climate change precipitate peace?

Growing interest in the social consequences of climate change has fueled speculation that global warming could lead to an increase in various forms of political violence. This article examines the effects of climate change on international conflict subsequent to the onset of European industrialization. Surprisingly, analysis at the system level suggests that global warming is associated with a reduction in interstate conflict. This naive relationship is suspect, however, as the increased consumption of carbon-based fuels is itself associated with changing patterns of politics and prosperity. In particular, economic development has been viewed as a cause of both climate change and interstate peace. Incorporating measures of development, democracy, cross-border trade, and international institutions reveals that systemic trends toward peace are actually best accounted for by the increase in average international income. The results imply that climate change, which poses a number of critical challenges for citizens and policymakers, need not be characterized as fundamentally a security issue, though climate change may have important security implications on the periphery of world politics. The analysis here also suggests that efforts to curb climate change should pay particular attention to encouraging clean development among middle-income states, as these countries are the most conflict prone. Ironically, stagnating economic development in middle-income states caused by efforts to combat climate change could actually realize fears of climate-induced warfare