Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview

A Nicolle, S Deng, M Ihme… - Journal of Chemical …, 2024 - ACS Publications
Artificial Neural Networks (ANNs) are transforming how we understand chemical mixtures,
providing an expressive view of the chemical space and multiscale processes. Their …

Environmental conditions drive self-organization of reaction pathways in a prebiotic reaction network

WE Robinson, E Daines, P van Duppen, T de Jong… - Nature Chemistry, 2022 - nature.com
The evolution of life from the prebiotic environment required a gradual process of chemical
evolution towards greater molecular complexity. Elaborate prebiotically relevant synthetic …

Hidden concepts in the history and philosophy of origins-of-life studies: A workshop report

C Mariscal, A Barahona, N Aubert-Kato… - Origins of Life and …, 2019 - Springer
In this review, we describe some of the central philosophical issues facing origins-of-life
research and provide a targeted history of the developments that have led to the …

Kinetic and thermodynamic evidences of the Diels-Alder cycloaddition and Pechmann condensation as key mechanisms of hydrochar formation during hydrothermal …

H Sudibyo, B Budhijanto, L Marbelia, F Güleç… - Chemical Engineering …, 2024 - Elsevier
We investigated the kinetics and thermodynamics of the Diels-Alder cycloaddition and
Pechmann condensation to evaluate the significance of both mechanisms toward hydrochar …

A software package for chemically inspired graph transformation

JL Andersen, C Flamm, D Merkle, PF Stadler - … Ehrig, Held as Part of STAF …, 2016 - Springer
Chemical reaction networks can be automatically generated from graph grammar
descriptions, where transformation rules model reaction patterns. Because a molecule graph …

An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions

A Arya, J Ray, S Sharma, RC Simbron, A Lozano… - Chemical …, 2022 - pubs.rsc.org
A central question in origins of life research is how non-entailed chemical processes, which
simply dissipate chemical energy because they can do so due to immediate reaction kinetics …

Chemical transformation motifs—modelling pathways as integer hyperflows

JL Andersen, C Flamm, D Merkle… - IEEE/ACM transactions …, 2017 - ieeexplore.ieee.org
We present an elaborate framework for formally modelling pathways in chemical reaction
networks on a mechanistic level. Networks are modelled mathematically as directed multi …

An intermediate level of abstraction for computational systems chemistry

JL Andersen, C Flamm, D Merkle… - … Transactions of the …, 2017 - royalsocietypublishing.org
Computational techniques are required for narrowing down the vast space of possibilities to
plausible prebiotic scenarios, because precise information on the molecular composition …

An automated scientist to design and optimize microbial strains for the industrial production of small molecules

AH Singh, BB Kaufmann-Malaga, JA Lerman… - bioRxiv, 2023 - biorxiv.org
Engineering microbes to synthesize molecules of societal value has historically been a time
consuming and artisanal process, with the synthesis of each new non-native molecule …

Spaces of mathematical chemistry

G Restrepo - Theory in Biosciences, 2024 - Springer
In an effort to expand the domain of mathematical chemistry and inspire research beyond
the realms of graph theory and quantum chemistry, we explore five mathematical chemistry …