Related papers: Emergence of information transmission in a prebiot…
This paper describes a design of a molecular propagation system in molecular communication. Molecular communication is a new communication paradigm where biological and artificially-created nanomachines communicate over a short distance…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Information-theoretic description of the signal transmitter, the channel and receiver is extended to the network of self-organizing dissipative structures consisting of a source, a reservoir and a sink. The information generation by the…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…
It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and…
Trajectory mutual information is frequently used to quantify information transfer in biochemical systems. Tractable solutions of the trajectory mutual information can be obtained via the widely used Linear-Noise Approximation (LNA) using…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
We investigate the time evolution process of one selected (initially prepared by optical pumping) vibrational molecular state, coupled to all other intra-molecular vibrational states of the same molecule, and also to its environment.…
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…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…