Related papers: New insights on the Dynamic Cellular Metabolism
We characterize the pre-softmax attention matrix $\mathbf{QK^\top}$ in transformers as an associative memory matrix encoding pairwise associations between input features. By decomposing this matrix into its symmetric and skew-symmetric…
Encoding models are used for predicting brain activity in response to sensory stimuli with the objective of elucidating how sensory information is represented in the brain. Encoding models typically comprise a nonlinear transformation of…
Hippocampal place and time cells encode spatial and temporal aspects of experience. Both have the same neural substrate, but have been modeled as having different functions and mechanistic origins, place cells as continuous attractors, and…
The task of modelling and forecasting a dynamical system is one of the oldest problems, and it remains challenging. Broadly, this task has two subtasks - extracting the full dynamical information from a partial observation; and then…
Regardless of the marked differences between biological and artificial neural systems, one fundamental similarity is that they are essentially dynamical systems that can learn to imitate other dynamical systems, without knowing their…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…
In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…
Cyclic patterns of neuronal activity are ubiquitous in animal nervous systems, and partially responsible for generating and controlling rhythmic movements such as locomotion, respiration, swallowing and so on. Clarifying the role of the…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Background: Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix and intracellular actions. By…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Quantum memory effects can be related to a bidirectional exchange of information between an open system and its environment, which in turn modifies the state and dynamical behavior of the last one. Nevertheless, non-Markovianity can also be…
Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data…
Attractor neural networks consider that neural information is stored as stationary states of a dynamical system formed by a large number of interconnected neurons. The attractor property empowers a neural system to encode information…
Living microorganisms have evolved dedicated sensory machinery to detect environmental perturbations, processing these signals through biochemical networks to guide behavior. Replicating such capabilities in synthetic active matter remains…
Continuous-Time Recurrent Neural Networks (CTRNNs) have been widely used for their capacity to model complex temporal behaviour. However, their internal dynamics often remain difficult to interpret. In this paper, we propose a new class of…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…