Related papers: Accurate control to run and stop chemical reaction…

Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations…

Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…

Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…

We study chemical oscillators in the presence of phase separation. By imposing timescale separation between slow reactions and fast diffusion, we define a dynamics at phase equilibrium for the relevant degrees of freedom. We demonstrate…

Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators remain elusive and lack a general framework. Using…

Bioreactors are widely used in many industries to generate a range of products using various host cells e.g., yeast, insect, and mammalian cells. Depending on the process, product, and host cell, some bioreactors exhibit sustained periodic…

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,…

Phase-separated liquid condensates can spatially organize and thereby regulate chemical processes. However, the physicochemical mechanisms underlying such regulation remain elusive as the intramolecular interactions responsible for phase…

Chemical reactions modeled by ordinary differential equations are finite-dimensional dissipative dynamical systems with multiple time-scales. They are numerically hard to tackle -- especially when they enter an optimal control problem as…

Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of…

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…

This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…

The precise control of complex reactions is critical for biological processes yet our inability to design for specific outcomes limits the development of synthetic analogues. Here, we leverage differentiable simulators to design nontrivial…

Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…

Robust coordination and organization in large ensembles of nonlinear oscillatory units play a vital role in a wide range of natural and engineered system. The control of self-organizing network-coupled systems has recently seen significant…

Oscillatory activity is ubiquitous in natural and engineered network systems. The interaction scheme underlying interdependent oscillatory components governs the emergence of network-wide patterns of synchrony that regulate and enable…

Electrical engineering and molecular programming share many of the same mathematical foundations. In this paper, we show how to send multiple signals through a single pair of chemical species using modulation and demodulation techniques…

Limit cycles are self-sustained, closed trajectories in phase space representing (un)-stable, periodic behavior in nonlinear dynamical systems. They underpin diverse natural phenomena, from neuronal firing patterns to engineering…

In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…

The exploration of deep neural networks for optimal control has gathered a considerable amount of interest in recent years. Here, we utilize deep reinforcement learning to control individual evolutions of coupled harmonic oscillators in an…