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Automatic differentiation represents a paradigm shift in scientific programming, where evaluating both functions and their derivatives is required for most applications. By removing the need to explicitly derive expressions for gradients,…
Multi-LLM collaboration promises accurate, robust, and context-aware solutions, yet existing approaches rely on implicit selection and output assessment without analyzing whether collaborating models truly complement or conflict. We…
We introduce expandable partial propensity direct method (EPDM) - a new exact stochastic simulation algorithm suitable for systems involving many interacting molecular species. The algorithm is especially efficient for sparsely populated…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
We introduce MetaChem, a language for representing and implementing Artificial Chemistries. We motivate the need for modularisation and standardisation in representation of artificial chemistries. We describe a mathematical formalism for…
Thermodynamic simulation of chemical and metallurgical systems is the only method to predict their equilibrium composition and is the most important application of chemical thermodynamics. The conventional strategy of simulation is always…
The simple genetic algorithm is proposed for the simulation of quantum many body dynamics. It uses the selection of entangled quantum states and has the inbuilt absolute decoherence that comes from the limitation of classical memory. It…
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…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Computational chemistry tools are widely used to study the behaviour of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation,…
Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the origin of life. In this work we define a P system based artificial graph chemistry to understand the principles…
Chemistry laboratory automation aims to increase throughput, reproducibility, and safety, yet many existing systems still depend on frequent human intervention. Advances in robotics have reduced this dependency, but without a structured…
Laboratory experiments play a key role in deciphering the chemistry of the interstellar medium (ISM) and the role that product complex organic molecules (COMs) may play in the origins of life. However, to date, most studies in experimental…
An analogy between combinatorial chemistry and Monte Carlo computer simulation is pursued. Examples of how to design libraries for both materials discovery and protein molecular evolution are given. For materials discovery, the concept of…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…
In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect…
Combining quantum computers with classical compute power has become a standard means for developing algorithms that are eventually supposed to beat any purely classical alternatives. While in-principle advantages for solution quality or…
A new tool for modeling electrochemical kinetics is presented. An extension of the Stochastic Simulation Algorithm framework to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a…