We show how to design different couplings between a single ion trapped in harmonic potential and an environment. The coupling is due the absorption of laser photon subsequent spontaneous emission. variation frequencies intensities allows one ``engineer'' select master equation describing motion ion.

We show how to fully characterize a quantum process in an open system. particularize the procedure case of universal two-qubit gate computer. illustrate method with numerical simulation ion trap

Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for management of natural microbiomes design synthetic consortia. Specifically, it poorly understood whether functions can be quantitatively predicted from traits species monoculture. Inspired by study complex genetic interactions, we have examined how amylolytic rate combinatorial assemblages six starch-degrading soil bacteria depend on separate...

It is now recognized that molecular circuits with positive feedback can induce two different gene expression states (bistability) under the very same cellular conditions. Whether, and how, cells make use of coexistence a larger number stable (multistability) however largely unknown. Here, we first examine how autoregulation, common attribute genetic master regulators, facilitates multistability in two-component circuits. A systematic exploration these modules' parameter space reveals classes...

Genetic oscillators based on the interaction of a small set molecular components have been shown to be involved in regulation cell cycle, circadian rhythms, or response several signaling pathways. Uncovering functional properties such then becomes important for understanding these cellular processes and characterization fundamental more complex clocks. Here, we show how dynamics minimal two-component oscillator is drastically affected by its genetic implementation. We consider repressor...

Cell competition is a short-range cell-cell interaction leading to the proliferation of winner cells at expense losers, although either cell type shows normal growth in homotypic environments. Drosophila Myc (dMyc; Dm-FlyBase) potent inducer wing epithelia, but its role ovary germline stem niche unknown. Here, we show that (GSCs) with relative lower levels dMyc are replaced by GSCs higher dMyc. By contrast, dMyc-overexpressing outcompete wild-type without affecting total numbers. We also...

We propose a scheme to perform fundamental two-qubit gate between two trapped ions using ideas from atom interferometry. As opposed the considered by J. I. Cirac and P. Zoller, [Phys. Rev. Lett. 74, 4091 (1995)], it does not require laser cooling motional ground state.

The interaction of a trapped ion with laser beam in the strong excitation regime is analyzed. In this regime, variety non--classical states motion can be prepared either by using pulses well defined area, or an adiabatic passage scheme based on variation frequency. We show how these used to investigate fundamental properties quantum mechanics. also study possible applications system build interferometer.

Feedback-based control methods determine the behavior of cellular systems, an example being autogenous control, regulation production a protein by itself. This strategy was theoretically shown to be superior equivalent but nonautogenously regulated system when based on repressor. Although some its advantages were later confirmed with isolated synthetic circuits, superiority in natural networks remains untested. Here, we use SOS DNA repair Escherichia coli, where is part single-input module,...

Why do some groups of physically linked genes stay over long evolutionary periods? Although several factors are associated with the formation gene clusters in eukaryotic genomes, particular contribution each feature to clustering maintenance remains unclear.We quantify strength proposed a yeast lineage. First we identify magnitude variable determine linkage conservation by using comparator species at different distances Saccharomyces cerevisiae. For adjacent pairs, line null simulations,...

It is widely acknowledged that development shapes phenotypes, yet the extent to which genes with similar expression patterns during lead equivalent organismal phenotypes when mutated remains unclear. Here, we propose addressing this issue, term 𝒟evelopment-to-𝒫henotype, or 𝒟-𝒫, rule, by leveraging single-cell gene atlases and phenotypic ontologies, using Caenorhabditis elegans as a model system. This framework quantifies proportionality between developmental similarities, demonstrating...

Abstract By applying a graph-based algorithm to yeast protein-interaction networks we have extracted modular structures and show that they can be validated using information from the phylogenetic conservation of network components. We module cores, parts with highest intramodular connectivity, are biologically relevant components networks. These constituents correlate only weakly other levels organization. also discuss how such could used for finding targets antimicrobial drugs.

Coupling the control of expression stochasticity (noise) to ability change (plasticity) can alter gene function and influence adaptation. A number factors, such as transcription re-initiation, strong chromatin regulation or genome neighboring organization, underlie this coupling. However, these factors do not necessarily combine in equivalent ways strengths all genes. Can we identify then alternative architectures that modulate distinct linkage noise plasticity? Here first show regulation,...

Abstract Understanding the link between community composition and function is a major challenge in microbial ecology, with implications for management of natural microbiomes design synthetic consortia. For this purpose, it critical to understand extent which functions properties can be predicted from species traits what role played by complex interactions. Inspired study genetic interactions fitness landscapes, here we have examined how amylolytic combinatorial assemblages seven...

Exploring the degree to which phenotypic variation, influenced by intrinsic nonlinear biological mechanisms, can be accurately captured using statistical methods is essential for advancing our comprehension of complex systems and predicting their functionality. Here, we examine this issue combining a computational model gene regulation networks with linear additive prediction model, akin polygenic scores utilized in genetic analyses. Inspired variational framework quantitative genetics,...

Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by rise cheaters that do not contribute but just consume common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, result instead in persistence cooperation is prospect has yet remained largely unexplored. Here, we show demographic collapse induced population can actually rescue cooperation, clear illustration how...

The specific binding of regulatory proteins to DNA sequences exhibits no clear patterns association between amino acids (AAs) and nucleotides (NTs). This complexity protein-DNA interactions raises the question whether a simple set wide-coverage recognition rules can ever be identified. Here, we analyzed this issue using extensive LacI family transcriptional factors (TFs). We searched for by introducing new approach phylogenetic footprinting, based on pervasive presence local regulation in...

Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information subjected molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic enhances transfer in the presence multiple circuit copies. The result due contribution generation autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors correlate redundant units...

In the commons, communities whose growth depends on public good, individuals often rely surprisingly simple strategies, or heuristics, to decide whether contribute shared resource (at risk of exploitation by free-riders). Although this appears a limitation, we show here how four heuristics lead sustainable when coupled specific ecological constraints. The two simplest ones-contribute permanently switch stochastically between contributing not-are first shown bring sustainability good...

Abstract The fitness impact of loss-of-function mutations is generally assumed to reflect the loss specific molecular functions associated with perturbed gene. Here, we propose that rewiring transcriptome upon deleterious gene inactivation frequently nonspecific and mimics stereotypic responses external environmental change. Consequently, transcriptional response deletion could be suboptimal incur an extra cost. Analysis transcriptomes ∼1,500 single-gene Saccharomyces cerevisiae strains...

Transcriptional networks are constituted by a collection of building blocks known as network motifs. Why do motifs appear? An adaptive model motif emergence was recently questioned in favor neutralist scenarios. Here, we provide new picture assembly Escherichia coli which partially clarifies these contrasting explanations. This is based on characterizing the linkage between and sensing or response specificity their constituent transcriptional factors (TFs). We find that influences...

Abstract By integrating positive and negative feedback loops, biological systems establish intricate gene expression patterns linked to multistability, pulsing, oscillations. This depends on the specific characteristics of each interlinked feedback, thus one would expect additional programs be found. Here, we investigate such program associated with an antagonistic transcriptional autoregulatory motif derived from multiple antibiotic resistance ( mar ) system Escherichia coli . We studied...