Related papers: Support for Eschenmoser's Glyoxylate Scenario
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to…
The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…
Drug discovery is a complex, resource-intensive process requiring significant time and cost to bring new medicines to patients. Many generative models aim to accelerate drug discovery, but few produce synthetically accessible molecules.…
Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to…
Template directed replication of nucleic acids is at the essence of all living beings and a major milestone for any origin of life scenario. We here present an idealized model of prebiotic sequence replication, where binary polymers act as…
From medicines to materials, small organic molecules are indispensable for human well-being. To plan their syntheses, chemists employ a problem solving technique called retrosynthesis. In retrosynthesis, target molecules are recursively…
The emergence of autocatalytic sets of molecules seems to have played an important role in the origin of life context. Although the possibility to reproduce this emergence in laboratory has received considerable attention, this is still far…
Generative artificial intelligence has revolutionized the exploration of chemical space, yet a critical bottleneck remains that a substantial fraction of generated molecules is synthetically inaccessible. Current solutions, such as post-hoc…
Generating graphs with hierarchical structures remains a fundamental challenge due to the limitations of Euclidean geometry in capturing exponential complexity. Here we introduce \textbf{GGBall}, a novel hyperbolic framework for graph…
Autocatalytic sets are sets of entities that mutually catalyse each other's production through chemical reactions from a basic food source. Recently, the reflexively autocatalytic and food generated theory has introduced a formal definition…
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the…
Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present Generalist Molecular generative model (GenMol), a versatile framework…
A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The…
Context. The detection of NH2CH2CH2OH (ethanolamine) in molecular cloud G+0.693-0.027 adds an additional player to the prebiotic molecules discovered so far in the interstellar medium (ISM). As this molecule might be formed through…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
The famous Miller-Urey experiment, which provides essential information on the prebiotic synthesis of the molecules of life, still has many obscure points. In this paper, we want to suggest a way of possible future progress, which consists…