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Virtual, make-on-demand chemical libraries have transformed early-stage drug discovery by unlocking vast, synthetically accessible regions of chemical space. Recent years have witnessed rapid growth in these libraries from millions to…
A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of…
One of the stumbling blocks for studying the evolution of interstellar molecules is the lack of adequate knowledge of the rate co-efficients of various reactions which take place in the Interstellar medium and molecular clouds. Some of the…
Understanding the nature and hierarchy of on surface reactions is a major chal- lenge for designing coordination and covalent nanostructures by means of multistep synthetic routes. In particular, intermediates and final products are hard to…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
It is long debated if pre-biotic molecules are indeed present in the interstellar medium. Despite substantial works pointing to their existence, pre-biotic molecules are yet to be discovered with a complete confidence. In this paper, our…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
It is suggested that life originated in a three-step process referred to as the jigsaw model. RNA, proteins, or similar organic molecules polymerized in a dehydrated carbon-rich environment, on surfaces in a carbon-rich environment, or in…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
Earth is expected to have acquired a reduced proto-atmosphere enriched in H2 and CH4 through the accretion of building blocks that contain metallic Fe and/or the gravitational trapping of surrounding nebula gas. Such an early, wet, reduced…
Generative machine learning models for exploring chemical space have shown immense promise, but many molecules they generate are too difficult to synthesize, making them impractical for further investigation or development. In this work, we…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
In this study, we provide a relatively simple simulation framework for constructing artificial life (ALife) with both autonomous and evolutionary aspects by extending chemoton model. While the original chemoton incorporates metabolism,…
With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manfred Eigen. We investigate the dynamics of certain networks…
Preconditioning is at the heart of iterative solutions of large, sparse linear systems of equations in scientific disciplines. Several algebraic approaches, which access no information beyond the matrix itself, are widely studied and used,…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
A range of generative machine learning models for the design of novel molecules and materials have been proposed in recent years. Models that can generate three-dimensional structures are particularly suitable for quantum chemistry…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…