Related papers: Support for Eschenmoser's Glyoxylate Scenario
Several aspects of mathematical astrobiology are discussed. It is argued that around the time of the origin of life the handedness of biomolecules must have established itself through an instability. Possible pathways of producing a certain…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Large linear systems are ubiquitous in modern computational science and engineering. The main recipe for solving them is the use of Krylov subspace iterative methods with well-designed preconditioners. Recently, GNNs have been shown to be a…
Graph Convolutional Networks (GCNs) achieve great success in non-Euclidean structure data processing recently. In existing studies, deeper layers are used in CCNs to extract deeper features of Euclidean structure data. However, for…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
Would another origin of life resemble Earth's biochemical use of amino acids? Here we review current knowledge at three levels: 1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis?…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
The managed-metabolism hypothesis suggests that a cooperation barrier must be overcome if self-producing chemical organizations are to transition from non-life to life. This barrier prevents un-managed, self-organizing, autocatalytic…
Nitriles play a key role as molecular precursors in prebiotic experiments based on the RNA-world scenario for the origin of life. These chemical compounds could have been partially delivered to the young Earth from extraterrestrial objects,…
Conspectus: The ability to navigate in chemical gradients, called chemotaxis, is crucial for the survival of microorganisms. It allows them to find food and to escape from toxins. Many microorganisms can produce the chemicals to which they…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Generative models in drug discovery have recently gained attention as efficient alternatives to brute-force virtual screening. However, most existing models do not account for synthesizability, limiting their practical use in real-world…
In recent years, the continued detection of complex organic molecules of prebiotic interest has refueled the interest on a panspermic origin of life. The prebiotic molecule glyceraldehyde is proposed to be formed from (Z)-1,2-ethenediol, a…
A class of preconditioners is introduced to enhance geometry optimisation and transition state search of molecular systems. We start from the Hessian of molecular mechanical terms, decompose it and retain only its positive definite part to…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to…
A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from…