Related papers: A simple regulatory architecture allows learning t…
Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two components parameterized by observable coordinates: a static…
It has long been known that antibiotic treatment will not completely kill off a bacteria population. For many species a small fraction of bacteria is not sensitive to antibiotics. These bacteria are said to persist. Recently it has been…
Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…
Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are `simple'…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
When working with large biological data sets, exploratory analysis is an important first step for understanding the latent structure and for generating hypotheses to be tested in subsequent analyses. However, when the number of variables is…
A robotic swarm that is required to operate for long periods in a potentially unknown environment can use both evolution and individual learning methods in order to adapt. However, the role played by the environment in influencing the…
Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods.…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Biological and living systems process information across spatiotemporal scales, exhibiting the hallmark ability to constantly modulate their behavior to ever-changing and complex environments. In the presence of repeated stimuli, a…