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A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Pattern formation in biological tissues plays an important role in the development of living organisms. Since the classical work of Alan Turing, a pre-eminent way of modelling has been through reaction-diffusion mechanisms. More recently,…
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…
Since the Hadean era of Earth's history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical…
Questions about information encoded by the brain demand statistical frameworks for inferring relationships between neural firing and features of the world. The landmark discovery of grid cells demonstrates that neurons can represent spatial…
Nuclear physics is ideal to test and develop techniques to describe the microscopic dynamics of quantum many-body systems. At low energy, nuclear dynamics is described with non-relativistic approaches based on the mean-field approximation…
Retrosynthesis is a major task for drug discovery. It is formulated as a graph-generating problem by many existing approaches. Specifically, these methods firstly identify the reaction center, and break target molecule accordingly to…
This paper presents BioNeRF, a biologically plausible architecture that models scenes in a 3D representation and synthesizes new views through radiance fields. Since NeRF relies on the network weights to store the scene's 3-dimensional…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network model of integrate and…
Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…
Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation,…