Related papers: Information propagation in time through allosteric…
Stochastic forces in natural systems are rarely isotropic. From hydrodynamically coupled colloids to chemical reaction networks, noise contributions are inherently correlated. Together with internal interactions and changing environments,…
The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
In many complex systems, the dynamic processes that take place on a network and the changes in the network topology are intertwined. Here, we propose a model of coevolutionary dynamics of information spreading which is accompanied with link…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
Understanding how the complex connectivity structure of the brain shapes its information-processing capabilities is a long-standing question. By focusing on a paradigmatic architecture, we study how the neural activity of excitatory and…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
Arterial blood pressure is a key vital sign for the health of the human body. As such, accurate and reproducible measurement techniques are necessary for successful diagnosis. Blood pressure measurement is an example of molecular…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…
Entanglement growth and out-of-time-order correlators (OTOC) are used to assess the propagation of information in isolated quantum systems. In this work, using large scale exact time-evolution we show that for weakly disordered…
Coordinated responses to environmental stimuli are critical for multicellular organisms. To overcome the obstacles of cell-to-cell heterogeneity and noisy signaling dynamics within individual cells, cells must effectively exchange…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
Complex systems with multiple processes evolving on different temporal scales are naturally described by multilayer networks, where each layer represents a different timescale. In this work, we show how the multilayer structure shapes the…
Biological neural systems encode and transmit information as patterns of activity tracing complex trajectories in high-dimensional state-spaces, inspiring alternative paradigms of information processing. Heteroclinic networks, naturally…
can evolve simultaneously. For the information-driven adaptive process, susceptible (infected) individuals who have abilities to recognize the disease would break the links of their infected (susceptible) neighbors to prevent the epidemic…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…