Related papers: DNA-based chemical compiler
A compiler approach for generating low-level computer code from high-level input for discontinuous Galerkin finite element forms is presented. The input language mirrors conventional mathematical notation, and the compiler generates…
Interacting with computers is a ubiquitous activity for millions of people. Repetitive or specialized tasks often require creation of small, often one-off, programs. End-users struggle with learning and using the myriad of domain-specific…
The emergence of foundational models and generative artificial intelligence (GenAI) is poised to transform productivity in scientific computing, especially in code development, refactoring, and translating from one programming language to…
DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In…
Artificial Neural Networks (ANN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of potential energy surfaces (PES) and spectroscopic predictions.…
Reimplementing solutions to previously solved software engineering problems is not only inefficient but also introduces inadequate and error-prone code. Many existing methods achieve impressive performance on this issue by using…
A unified mathematical language for medicine and science will be presented. Using this language, models for DNA replication, protein synthesis, chemical reactions, neurons and a cardiac cycle of a heart have been built. Models for Turing…
Two networks are said to be linearly conjugate if the solution of their dynamic equations can be transformed into each other by a positive linear transformation. The study on dynamical equivalence in chemical kinetic systems was initiated…
A quantum compiler is a software program for decomposing ("compiling") an arbitrary unitary matrix into a sequence of elementary operations (SEO). The author of this paper is also the author of a quantum compiler called Qubiter. Qubiter…
Manin, Feynman, and Deutsch have viewed quantum computing as a kind of universal physical simulation procedure. Much of the writing about quantum logic circuits and quantum Turing machines has shown how these machines can simulate an…
Memory compilers are necessary tools to boost the design procedure of digital circuits. However, only a few are available to academia. Resistive Random Access Memory (RRAM) is characterised by high density, high speed, non volatility and is…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
Chemical reactor networks (CRNs) enable simulations of combustion reactors with detailed chemical kinetics and strongly simplified flow structure. In this paper, the implementation of a reactor component with less idealized flow structure,…
Visual Quality Inspection plays a crucial role in modern manufacturing environments as it ensures customer safety and satisfaction. The introduction of Computer Vision (CV) has revolutionized visual quality inspection by improving the…
DNA profiles are made up from multiple series of electrophoretic signal measuring fluorescence over time. Typically, human DNA analysts 'read' DNA profiles using their experience to distinguish instrument noise, artefactual signal, and…
In his 1984 Turing Award lecture, Ken Thompson showed that a compiler could be maliciously altered to insert backdoors into programs it compiles and perpetuate this behavior by modifying any compiler it subsequently builds. Thompson's hack…
We present a uniform method for translating an arbitrary nondeterministic finite automaton (NFA) into a deterministic mass action input/output chemical reaction network (I/O CRN) that simulates it. The I/O CRN receives its input as a…