Related papers: Satisfiability, sequence niches, and molecular cod…
Molecular processes of neuronal learning have been well-described. However, learning mechanisms of non-neuronal cells have not been fully understood at the molecular level. Here, we discuss molecular mechanisms of cellular learning,…
Cooperative interactions among the binding of multiple signaling molecules is a common mechanism for enhancing the sensitivity of biological signaling systems. It is widely assumed that this increase in sensitivity of the mean response…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…
Signaling pathways and networks determine the ability to communicate in systems ranging from living cells to human society. We investigate how the network structure constrains communication in social-, man-made and biological networks. We…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
Biological and artificial systems encode information through several complex nonlinear operations, making their exact study a formidable challenge. These internal mechanisms often take place across multiple timescales and process external…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
Cellular automata are one-dimensional arrays of interconnected interacting finite automata. We investigate one of the weakest classes, the real-time one-way cellular automata, and impose an additional restriction on their inter-cell…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
Self-organization of proteins in space and time is of crucial importance for the functioning of cellular processes. Often, this organization takes place in the presence of strong random fluctuations due to the small number of molecules…
Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative -- or correlated -- activity in neural populations, and in the…
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…
Brains learn to represent information from a large set of stimuli, typically by weak supervision. Unsupervised learning is therefore a natural approach for exploring the design of biological neural networks and their computations.…