scholarly journals Applications of Information Theory Methods for Evolutionary Optimization of Chemical Computers

Entropy ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. 313 ◽  
Author(s):  
Jerzy Gorecki

It is commonly believed that information processing in living organisms is based on chemical reactions. However, the human achievements in constructing chemical information processing devices demonstrate that it is difficult to design such devices using the bottom-up strategy. Here I discuss the alternative top-down design of a network of chemical oscillators that performs a selected computing task. As an example, I consider a simple network of interacting chemical oscillators that operates as a comparator of two real numbers. The information on which of the two numbers is larger is coded in the number of excitations observed on oscillators forming the network. The parameters of the network are optimized to perform this function with the maximum accuracy. I discuss how information theory methods can be applied to obtain the optimum computing structure.

2017 ◽  
Vol 19 (42) ◽  
pp. 28808-28819 ◽  
Author(s):  
Konrad Gizynski ◽  
Jerzy Gorecki

We discuss chemical information processing considering dataset classifiers formed with a network of interacting droplets.


Author(s):  
Nikolay V. Ryzhkov ◽  
Konstantin G. Nikolaev ◽  
Artemii S. Ivanov ◽  
Ekaterina V. Skorb

Nowadays, information processing is based on semiconductor (e.g., silicon) devices. Unfortunately, the performance of such devices has natural limitations owing to the physics of semiconductors. Therefore, the problem of finding new strategies for storing and processing an ever-increasing amount of diverse data is very urgent. To solve this problem, scientists have found inspiration in nature, because living organisms have developed uniquely productive and efficient mechanisms for processing and storing information. We address several biological aspects of information and artificial models mimicking corresponding bioprocesses. For instance, we review the formation of synchronization patterns and the emergence of order out of chaos in model chemical systems. We also consider molecular logic and ion fluxes as information carriers. Finally, we consider recent progress in infochemistry, a new direction at the interface of chemistry, biology, and computer science, considering unconventional methods of information processing. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


Author(s):  
J. Gorecki ◽  
K. Gizynski ◽  
J. Guzowski ◽  
J. N. Gorecka ◽  
P. Garstecki ◽  
...  

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction–diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov–Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed.


2018 ◽  
Author(s):  
Christian D. Márton ◽  
Makoto Fukushima ◽  
Corrie R. Camalier ◽  
Simon R. Schultz ◽  
Bruno B. Averbeck

AbstractPredictive coding is a theoretical framework that provides a functional interpretation of top-down and bottom up interactions in sensory processing. The theory has suggested that specific frequency bands relay bottom-up and top-down information (e.g. “γ up, β down”). But it remains unclear whether this notion generalizes to cross-frequency interactions. Furthermore, most of the evidence so far comes from visual pathways. Here we examined cross-frequency coupling across four sectors of the auditory hierarchy in the macaque. We computed two measures of cross-frequency coupling, phase-amplitude coupling (PAC) and amplitude-amplitude coupling (AAC). Our findings revealed distinct patterns for bottom-up and top-down information processing among cross-frequency interactions. Both top-down and bottom-up made prominent use of low frequencies: low-to-low frequency (θ, α, β) and low frequency-to-high γ couplings were predominant top-down, while low frequency-to-low γ couplings were predominant bottom-up. These patterns were largely preserved across coupling types (PAC and AAC) and across stimulus types (natural and synthetic auditory stimuli), suggesting they are a general feature of information processing in auditory cortex. Moreover, our findings showed that low-frequency PAC alternated between predominantly top-down or bottom-up over time. Altogether, this suggests sensory information need not be propagated along separate frequencies upwards and downwards. Rather, information can be unmixed by having low frequencies couple to distinct frequency ranges in the target region, and by alternating top-down and bottom-up processing over time.1SignificanceThe brain consists of highly interconnected cortical areas, yet the patterns in directional cortical communication are not fully understood, in particular with regards to interactions between different signal components across frequencies. We employed a a unified, computationally advantageous Granger-causal framework to examine bi-directional cross-frequency interactions across four sectors of the auditory cortical hierarchy in macaques. Our findings extend the view of cross-frequency interactions in auditory cortex, suggesting they also play a prominent role in top-down processing. Our findings also suggest information need not be propagated along separate channels up and down the cortical hierarchy, with important implications for theories of information processing in the brain such as predictive coding.


Author(s):  
Philip Ball

‘The burning issue: molecules and energy’ describes how energy can be transferred through molecular reactions. Metabolic processes are the foundation of cellular life. All chemical reactions increase entropy (or disorder), but living cells maintain their order by carefully controlling metabolic reactions. In living organisms glucose is broken down into pyruvate through glycolysis. Pyruvate then enters the citric acid cycle, which is a series of reactions that generate electrons which generate ATP — the cell's ‘fuel’. Many scientists, most notably Alfred Nobel, have sought to develop molecules which contain huge amounts of energy safely. These molecules can be used to build civilization — or destroy life.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Olga Bozovic ◽  
Brankica Jankovic ◽  
Peter Hamm

AbstractAllosteric regulation is an innate control in most metabolic and signalling cascades that enables living organisms to adapt to the changing environment by tuning the affinity and regulating the activity of target proteins. For a microscopic understanding of this process, a protein system has been designed in such a way that allosteric communication between the binding and allosteric site can be observed in both directions. To that end, an azobenzene-derived photoswitch has been linked to the α3-helix of the PDZ3 domain, arguably the smallest allosteric protein with a clearly identifiable binding and allosteric site. Photo-induced trans-to-cis isomerisation of the photoswitch increases the binding affinity of a small peptide ligand to the protein up to 120-fold, depending on temperature. At the same time, ligand binding speeds up the thermal cis-to-trans back-isomerisation rate of the photoswitch. Based on the energetics of the four states of the system (cis vs trans and ligand-bound vs free), the concept of an allosteric force is introduced, which can be used to drive chemical reactions.


2015 ◽  
Vol 7 (12) ◽  
pp. 1487-1517 ◽  
Author(s):  
G. Pezzulo ◽  
M. Levin

How do regenerating bodies know when to stop remodeling? Bioelectric signaling networks guide pattern formation and may implement a somatic memory system. Deep parallels may exist between information processing in the brain and morphogenetic control mechanisms.


1989 ◽  
Vol 15 (4-5) ◽  
pp. 223-236 ◽  
Author(s):  
Peter Willett

This paper discusses the use of parallel computer hardware to increase the efficiency of processing in databases of text and chemical structures. After a general introduction to parallelism, two types of parallel computer are described: the ICL Distrib uted Array Processor and the INMOS Transputer. Experimen tal results are presented of the use of the DAP for cluster analysis, of the transputer for chemical substructure and maxi mal common substructure searching, and of both machines for text retrieval.


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