相关论文: Context in Synthetic Biology: Memory Effects of En…

Associative learning is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was early recognized to be a general trait of complex multicellular organisms but also found in "simpler"…

Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…

We show that in the generic situation where a biological network, e.g. a protein interaction network, is in fact a subnetwork embedded in a larger "bulk" network, the presence of the bulk causes not just extrinsic noise but also memory…

We consider the problem of designing synthetic cells to achieve a complex goal (e.g., mimicking the immune system by seeking invaders) in a complex environment (e.g., the circulatory system), where they might have to change their control…

While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…

Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…

Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…

The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…

A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to…

Many active systems display nematic order, while interacting with their environment. In this work, we show theoretically how environment-stored memory acts an effective external field that aligns active nematics. The coupling to the…

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…

The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…

Understanding the basic operational logics of the nervous system is essential to advancing neuroscientific research. However, theoretical efforts to tackle this fundamental problem are lacking, despite the abundant empirical data about the…

We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…

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…

In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…

The exchange of information between an open quantum system and its environment allows us to discriminate among different kinds of dynamics, in particular detecting memory effects to characterize non-Markovianity. Here, we investigate the…

The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…

Synthetic reverberating activity patterns are experimentally generated by stimulation of a subset of neurons embedded in a spontaneously active network of cortical cells in-vitro. The neurons are artificially connected by means of…

Cells maintain a stable size as they grow and divide. Inspired by the available experimental data, most proposed models for size homeostasis assume size control mechanisms that act on a timescale of one generation. Such mechanisms lead to…