Related papers: Optimal Information Encoding in Chemical Reaction …
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Drawing on various notions from theoretical computer science, we present a novel numerical approach, motivated by the notion of algorithmic probability, to the problem of approximating the Kolmogorov-Chaitin complexity of short strings. The…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or identically repeated sequences, for example,…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Hinging on ideas from physical-layer network coding, some promising proposals of coded random access systems seek to improve system performance (while preserving low complexity) by means of packet repetitions and decoding of linear…
We develop a semidefinite programming method for the optimization of quantum networks, including both causal networks and networks with indefinite causal structure. Our method applies to a broad class of performance measures, defined…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
How to artificially encode observer in universal information coding structure like DNA ? It requires naturally creating information Bits and natural encoding triplet code enables recognizing other encoded information. These Bits become…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
I investigate dense coding with a general mixed state on the Hilbert space $C^{d}\otimes C^{d}$ shared between a sender and receiver. The following result is proved. When the sender prepares the signal states by mutually orthogonal unitary…
We study chemical reaction networks with discrete state spaces, such as the standard continuous time Markov chain model, and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
Collective information processing is fundamental in various biological systems, where the cooperation of multiple cells results in complex functions beyond individual capabilities. A distinctive example is collective exploration where…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Stochastic models of chemical reaction networks are an important tool to describe and analyze noise effects in cell biology. When chemical species and reaction rates in a reaction system have different orders of magnitude, the associated…
Reaction networks are a general formalism for describing collections of classical entities interacting in a random way. While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar…
We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the…