Related papers: DNA-based chemical compiler
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
We introduce a novel approach to automatically synthesize a mathematical representation of the control algorithms implemented in industrial cyber-physical systems (CPS), given the embedded system binary. The output model can be used by…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Synthetic medical image generation has evolved as a key technique for neural network training and validation. A core challenge, however, remains in the domain gap between simulations and real data. While deep learning-based domain transfer…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
We study the model of continuous chemical reaction networks (CRNs), consisting of reactions such as $A+B \to C+D$ that can transform some continuous, nonnegative real-valued quantity (called a *concentration*) of chemical species $A$ and…
We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard consensus-based output convention have…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
SIMD||DNA is a model of DNA strand displacement allowing parallel in-memory computation on DNA storage. We show how to simulate an arbitrary 3-symbol space-bounded Turing machine with a SIMD||DNA program, giving a more direct and efficient…
An emerging application of Raman spectroscopy is monitoring the state of chemical reactors during biologic drug production. Raman shift intensities scale linearly with the concentrations of chemical species and thus can be used to…
The advent of simulation engines has revolutionized learning and operational efficiency for robots, offering cost-effective and swift pipelines. However, the lack of a universal simulation platform tailored for chemical scenarios impedes…
Support vector machines and kernel methods have recently gained considerable attention in chemoinformatics. They offer generally good performance for problems of supervised classification or regression, and provide a flexible and…
The decompiler is one of the most common tools for examining binaries without corresponding source code. It transforms binaries into high-level code, reversing the compilation process. Decompilers can reconstruct much of the information…
The goal of program synthesis is to automatically generate programs in a particular language from corresponding specifications, e.g. input-output behavior. Many current approaches achieve impressive results after training on randomly…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…