Arizona State University
Beyond Center
Suspensions of the aerobic bacteria Bacilus subtilis develop patterns and flows from the interplay of motility, chemotaxis and buoyancy. In sessile drops, such bioconvectively driven flows carry plumes down the slanted meniscus and... more
Experiments and mathematical modeling show that complex flows driven by unexpected flagellar arrangements are induced when peritrichously flagellated bacteria are confined in a thin layer of fluid, between asymmetric boundaries. The... more
Aerobic bacteria often live in thin fluid layers near solid–air–water contact lines, in which the biology of chemotaxis, metabolism, and cell–cell signaling is intimately connected to the physics of buoyancy, diffusion, and mixing. Using... more
Nearly close-packed populations of the swimming bacterium Bacillus subtilis form a collective phase, the “Zooming BioNematic” (ZBN). This state exhibits large-scale orientational coherence, analogous to the molecular alignment of nematic... more
Recent experiments have shown large-scale dynamic coherence in suspensions of the bacterium B. subtilis, characterized by quorum polarity, collective parallel swimming of cells. To probe mechanisms leading to this, we study the response... more
The emergence of nontrivial collective behavior in networks of coupled chaotic maps is investigated by means of a nonlinear mutual prediction method. The resulting prediction error is used to measure the amount of information that a local... more
At high cell concentrations, bacterial suspensions are known to develop a state of collective swimming (the “zooming bionematic phase,” or ZBN) characterized by transient, recurring regions of coordinated motion greatly exceeding the size... more
Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is... more
"An algorithm for mutual prediction between time series is used to define an estimator that quantifies the amount of information that is transfered among different degrees of freedom of a system. It is presented a numerical example were... more
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems (Camp- bell, 1974; Auletta et al., 2008; Davies, 2006b, 2012;... more
We introduce and solve a 'null model' of stochastic metastatic colonization. The model is described by a single parameter θ: the ratio of the rate of cell division to the rate of cell death for a disseminated tumour cell in a given... more
Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical... more
Aerobic bacteria often live in thin fluid layers near solid-air-water contact lines, where the biology of chemotaxis, metabolism, and cell-cell signaling is intimately connected to the physics of buoyancy, diffusion, and mixing. Using the... more
Although cancer is one of the most intensively studied phenomena in biology and occurs in almost all multicellular species (1, 2), an explanation for its existence and properties within the context of evolutionary history has received... more
The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. SIM employs error-prone polymerases resulting in mutations concentrated around DNA double-strand breaks with... more
Résumé/Abstract An algorithm for mutual prediction between time series is used to define an estimator that quantifies the amount of information that is transfered among diffent degrees of freedom of a system. It is presented a numerical... more
We introduce and solve a 'null model' of stochastic metastatic colonization. The model is described by a single parameter θ: the ratio of the rate of cell division to the rate of cell death for a disseminated tumour cell in a given... more
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems (Camp-