Related papers: Metabolism, information, and viability in a simula…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
We present a new modeling approach for G protein coupled receptors signaling systems, that take into account the compartmentalization of receptors and their effectors, both at plasma membrane and in dynamic intra-cellular vesicles called…
Exploring nonlinear chemical dynamic systems for information processing has emerged as a frontier in chemical and computational research, seeking to replicate the brain's neuromorphic and dynamic functionalities. We have extensively…
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…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
We study a large number of physically-plausible arrangements of chromophores, generated via a computational method involving stochastic real-space transformations of a naturally occurring `reference' structure, illustrating our methodology…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Controlling the flow of excitons between organic molecules holds immense promise for various applications, including energy conversion, spectroscopy, photocatalysis, sensing, and microscopy. DNA nanotechnology has shown promise in achieving…
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here…
As a paradigm for heat conduction in 1 dimension, we propose a class of models represented by chains of identical cells, each one of which containing an energy storage device called a "tank". Energy exchange among tanks is mediated by…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
The cerebellum and cerebral cortex form tightly coupled circuits thought to support flexible and efficient temporal processing. How this interaction shapes cortical learning dynamics, and whether such heterogeneous modularity can benefit…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…
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…
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…
Quantum transport of charge or energy in networks with discrete sites is central to diverse quantum technologies, from molecular electronics to light harvesting and quantum opto-mechanical metamaterials. A one dimensional network can be…