Related papers: Delay Line as a Chemical Reaction Network
A single dynamical system with time-delayed feedback can emulate networks. This property of delay systems made them extremely useful tools for Machine Learning applications. Here we describe several possible setups, which allow emulating…
Complex balanced mass-action systems (CBMASs) are of great importance in the filed of biochemical reaction networks. However analyzing the persistence of these networks with high dimensions and time delays poses significant challenges. To…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
The current biochemical information processing systems behave in a predetermined manner because all features are defined during the design phase. To make such unconventional computing systems reusable and programmable for biomedical…
Delay differential equations are used as a model when the effect of past states has to be taken into account. In this work we consider delay models of chemical reaction networks with mass action kinetics. We obtain a sufficient condition…
In this work, we introduce a new type of linear classifier that is implemented in a chemical form. We propose a novel encoding technique which simultaneously represents multiple datasets in an array of microliter-scale chemical mixtures.…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
Delayed interactions are a common property of coupled natural systems and therefore arise in a variety of different applications. For instance, signals in neural or laser networks propagate at finite speed giving rise to delayed…
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind…
Atomized chemical knowledge, such as functional group information of molecules and reactions, plays a pivotal intermediate role in the reasoning process that connects molecular structures with their properties and reactivities. While large…
With the increasing complexity of time-delayed systems, the diversification of boundary types of chemical reaction systems poses a challenge for persistence analysis. This paper focuses on delayed complex balanced mass action systems…
Chemists in search of structure-property relationships face great challenges due to limited high quality, concordant datasets. Machine learning (ML) has significantly advanced predictive capabilities in chemical sciences, but these modern…
Linear conjugacy offers a new perspective to broaden the scope of stable biochemical reaction networks to the systems linearly conjugated to the well-established complex balanced mass action systems ($\ell$cCBMASs). This paper addresses the…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication…
Prediction and control of chemical mixing are vital for many scientific areas such as subsurface reactive transport, climate modeling, combustion, epidemiology, and pharmacology. Due to the complex nature of mixing in heterogeneous and…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…