Related papers: Multi-bit information storage by multisite phospho…
Living cells sense noisy biochemical signals crucial for survival, yet models incorporating intracellular signaling are limited. This study examines how cells sense chemotactic concentrations through phosphorylation readouts in Ca2+…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
Recent studies have shown that metaplastic synapses can retain information longer than simple binary synapses and are beneficial for continual learning. In this paper, we explore the multistate metaplastic synapse characteristics in the…
Digital data explosion drives a demand for robust and reliable data storage medium. Development of better digital storage device to accumulate Zetta bytes (1 ZB = $10^{21}$ bytes ) of data that will be generated in near future is a big…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
There is evidence that biological synapses have only a fixed number of discrete weight states. Memory storage with such synapses behaves quite differently from synapses with unbounded, continuous weights as old memories are automatically…
DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
The multiple futile cycle is a phosphorylation system in which a molecular substrate might be phosphorylated sequentially n times by means of an enzymatic mechanism. The system has been studied mathematically using reaction network theory…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…
It has recently been emphasized again that the very existence of stationary stable localized structures with short range interactions might allow to store information in non-equilibrium media, opening new perspectives on information…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
Replicating the computational functionalities and performances of the brain remains one of the biggest challenges for the future of information and communication technologies. Such an ambitious goal requires research efforts from the…