Related papers: Support for Eschenmoser's Glyoxylate Scenario
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
The functionality of catalysts, enzymes, and supramolecular assemblies emerges not from individual molecules alone, but from the subtle interplay between multiple components arranged in complex systems. Designing such systems is a grand…
Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
It has been pointed out that if an autocatalytic cycle produces primitive membrane chemicals, it can compose a self-maintaining proto cell. Moreover, it is known that a proto cell can divide itself spontaneously as it grows. An unsolved…
The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the…
The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address…
Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical…
Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is…
Extraterrestrial amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth are present in meteoritic samples. More recently, glycine (NH$_2$CH$_2$COOH), the simplest amino acid, was detected by…
Early theoretical work revealed that the simplest class of autocatalytic cycles, known as hypercycles, provide an elegant framework for understanding the evolution of mutualism. Furthermore, hypercycles are highly susceptible to parasites,…
In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
Chemical space exploration underlies drug discovery, yet most generative models treat chemical space as a fixed, implicitly learned distribution, focusing on sampling molecules rather than deliberately designing the space itself. We…
This article presents the results of a study concerning interstellar molecules which are useful for the bookkeeping of the organic content of the universe and for providing a glimpse into prebiotic conditions on Earth and in other…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
The formation of complex organic molecules in the interstellar medium (ISM) is central to astrochemistry and prebiotic chemistry, as these species may act as precursors to biomolecules essential for life. Although glyceraldehyde…
The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…
The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modelling how living systems first arose. It has been known for several decades that such networks will form…