Related papers: Optimal Information Encoding in Chemical Reaction …
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
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…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
Quantum systems are the ultimate touchstone for the production of random sequences of numbers. Spatially spread entangled systems allow the generation of identical random sequences in remote locations. The impossibility of observing a…
We investigate optimal encoding and retrieval of digital data, when the storage/communication medium is described by quantum mechanics. We assume an m-ary alphabet with arbitrary prior distribution, and an n-dimensional quantum system.…
Interacting random field of probabilities links Kolmogorov law 0-1 and Bayesian probabilities observing Markov diffusion process under Yes-No actions of random impulse. These objective probabilities measure virtual probing impulses…
We show that real-value approximations of Kolmogorov-Chaitin (K_m) using the algorithmic Coding theorem as calculated from the output frequency of a large set of small deterministic Turing machines with up to 5 states (and 2 symbols), is in…
One of the most fundamental problems in distribution testing is the identity testing problem: given samples $x_1,\ldots,x_s$, the goal is to determine whether the samples are drawn from a target distribution $\mathcal{D}$. When…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Chemputation reframes synthesis as the programmable execution of reaction code on a universally re-configurable hardware graph. Here we prove that a chemputer equipped with a finite, but extensible, set of reagents, catalysts and process…
Predicting monomer reactivity ratios is crucial for controlling monomer sequence distribution in copolymers and their properties. Traditional experimental methods of determining reactivity ratios are time-consuming and resource-intensive,…
According to Kolmogorov complexity, every finite binary string is compressible to a shortest code -- its information content -- from which it is effectively recoverable. We investigate the extent to which this holds for infinite binary…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
Optimal operation of chemical processes is vital for energy, resource, and cost savings in chemical engineering. The problem of optimal operation can be tackled with reinforcement learning, but traditional reinforcement learning methods…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…