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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…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
We present a geometric framework to study the growth-division dynamics of cells and protocells, and demonstrate that self-reproduction emerges only when a system's growth dynamics and division strategy are mutually compatible. Using several…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…
Any search for present or past life beyond Earth should consider the initial processes and related environmental controls that might have led to its start. As on Earth, such an understanding lies well beyond how simple organic molecules…
We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure…
Despite the harsh conditions of the interstellar medium, chemistry thrives in it, especially in star forming regions where several interstellar complex organic molecules (iCOMs) have been detected. Yet, how these species are synthesised is…
Retrosynthesis, which aims to identify viable synthetic pathways for target molecules by decomposing them into simpler precursors, is often treated as a search problem. However, its complexity arises from multi-branched tree-structured…
In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…
Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two…
Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks, and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…
Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
A mystery about the origins of life is which molecular structures $-$ and what spontaneous processes $-$ drove the autocatalytic transition from simple chemistry to biology? Using the HP lattice model of polymer sequence spaces leads to the…