Chemical Information Processing Research Articles

Biologically Inspired Computation for Chemical Sensing

In this paper, we present how the achievements related to NEUROCHEM project (FP7, Bio-ICT, Grant number 216916) have increased the understanding of the olfactory system and helped to develop novel computing architectures and models for chemical sensing. We present the developed computational models of the olfactory pathway of vertebrates and insects to capture the mechanisms that underlie their chemical information processing abilities. To mimic the biological olfactory epithelium a large scale chemical sensor array has been developed. We also present a robot that demonstrates the chemical search task as a direct application of the computing paradigms extracted.

Enhanced selectivity and efficiency of coherent population transfer via a train of pulse pairs

We propose a way to significantly enhance selectivity and efficiency of coherent population transfer in a {Lambda}-type four-level system with a closely spaced doublet in the final state by using a train of counterintuitively ordered pump-Stokes pulse pairs. Due to temporal constructive and destructive quantum interference between the sequential transitions and subsequent coherent accumulation and annihilation in the time domain, the spectral resolution of selective and perfect population transfer to either of the final states can be improved by more than one order of magnitude as compared to the conventionally widely used stimulated Raman adiabatic passage and chirped adiabatic passage techniques, which can also be well understood as a result of the formation of a comblike structure of the pulse train spectrum in the frequency domain. Moreover, an arbitrary coherent superposition between the closely separated doublet can be achieved by suitably tuning the repetition period and detuning of the laser fields. This method has potential applications in control of chemical reactions and quantum information processing.

Ultrafast control of coherent population transfer with a train of femtosecond pulse pairs

Abstract We investigate the ultrafast control of coherent population transfer in a Λ-type three-level system with a train of pump–Stokes femtosecond pulse pairs, where the pulse sequences can be produced either by optical delay line or by pulse shaping with sinusoidal phase modulation. It is shown that when the pump and Stokes pulses in each pair are applied in the counterintuitive order, similar to that in the stimulated Raman adiabatic passage technique, due to temporal quantum interference (besides optical interference in the case of overlapped subpulses), ultrafast control of coherent population transfer can be achieved by scanning the inter-pair time delay or by changing the sinusoidal phase modulation parameters. This method has potential applications in ultrafast control of chemical reactions and quantum information processing.

Seamless integration of the PubChem database into an universal scriptable chemical information processing environment

Seamless integration of the PubChem database into an universal scriptable chemical information processing environment

Linking biological and artificial olfaction: biomimetic quartz crystal microbalance odor sensors

AbstractBiological olfaction is a powerful system enabling acquisition and processing of various chemical information from environment. Vast significance of the sense of smell is reflected in attempts to create instrumental techniques mimicking the biological system—artificial/machine olfaction. Following the biological systems, the artificial olfaction relies on arrays of gas sensors with broad specificities to odorants. Arguably, among available gas‐sensing technologies, the most suitable choices for artificial olfaction are acoustic wave sensors, including quartz crystal microbalance (QCM) gas/odor sensors. The short review herein presents basic information on organization and principles of biological and artificial olfaction systems as well as several methods for fabrication of biomimetic or bioinspired (QCM) sensors for artificial olfaction. Copyright © 2009 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.

Enzyme logic gates for assessing physiological conditions during an injury: Towards digital sensors and actuators

We describe preliminary results on an enzyme logic sensing system for a reliable assessment of the overall physiological condition during an injury. The new system consists of AND and XOR logic gates based on the concerted operation of tyrosinase, glucose oxidase, lactate dehydrogenase and microperoxidase-11. The enzyme logic system is activated by physiologically relevant concentrations of the input signals of biomarkers: norepinephrine, oxygen, glucose and lactate mimicking in vitro different injuries, including trauma brain injury and hemorrhagic shock. We anticipate that such biochemical logic gates will eventually facilitate decision-making towards the initiation of an optimal timely therapeutic intervention, leading to improved survival of injured soldiers and civilians. The biochemical logic system analyzing biomarker signals represents the first step towards digitally operating sensors and actuators with chemical information processing steps.

Experimental Investigation of Information Processing under Irreversible Brownian Conditions: Work/Time Analysis of Paper Chromatograms

A wet laboratory study of chemical information processing in Brownian (random walk) environments is presented. Point samples of adsorbed dyes were subject to diffusion on paper chromatography sheets; the resulting images were recorded digitally using an office scanner. The experiments enabled the measurement of four types of information along with the attendant costs of work and time. The data are examined for their statistical distribution and scaling properties and Fourier spectral components. Whereas theory, calculations, and reversible pathways were central to the previous paper, the present study is devoted to experiments and irreversible transformations. Overall, the results establish several key points about information of four varieties purchased in real-time Brownian venues. The points concern the kinetics of information, memory effects, and the distributions of information changes with energy.

Conditional genetic labeling of mitral cells of the mouse accessory olfactory bulb to visualize the organization of their apical dendritic tufts

Chemical information captured through the vomeronasal sensory neurons is transmitted to mitral cells in the accessory olfactory bulb (AOB). Morphological characterization of AOB mitral cells is crucial to reveal the mechanisms underlying pheromone and other chemical information processing. Here, we developed a conditional genetic approach to visualize single AOB mitral cells in mice and analyzed the distribution of their apical dendritic tufts and cell bodies. We found that there is a subpopulation of superficial AOB mitral cells with small cell bodies and simple dendritic arborization. We also showed that segregation of the anterior and posterior AOB appears incomplete at the level of the mitral cell positions. Furthermore, we demonstrated that significant population of the anterior AOB mitral cells has multiple apical dendritic tufts organized in a quite small range along the dorsal–ventral axis. These findings have important implications in how various chemical signals may be processed in the AOB.

MolDiA: A Novel Molecular Diversity Analysis Tool. 1. Principles and Architecture

We introduce the principles and the architecture of a user-friendly software named MOLDIA (Molecular Diversity Analysis) which aims to the comparison of diverse molecular data sets through an XML structured database of predefined fragments. The MOLDIA descriptors are composed of complex fingerprint-like structures, which enclose not only structural information but also physicochemical property data. The system architecture includes the use of customizable weights on molecular descriptors and different choices of similarity/diversity measures to analyze the given data sets. Intermolecular comparisons using Ullmann's algorithm were optimized by the use of fuzzy logic, generic atoms, and a whole system of chemical graph analysis. We have found that customizing the similarity/diversity computation using structural and/or properties weights and choosing the level of fuzziness of the molecular comparison allow the user to adapt the tool to particular needs and increases the possibilities of MolDiA applications. The implementation of XML Web technologies has proven to improve and ease the extraction, processing, and analysis of chemical information.

Functional neuroanatomy of the rhinophore of Archidoris pseudoargus

For sea slugs, chemosensory information represents an important sensory modality, because optical and acoustical information are limited. In the present study, we focussed on the neuroanatomy of the rhinophores and processing of olfactory stimuli in the rhinophore ganglion of Archidoris pseudoargus, belonging to the order of Nudibranchia in the subclass of Opisthobranchia. Histological techniques, fluorescent markers, and immunohistochemistry were used to analyse neuroanatomical features of the rhinophore. A large ganglion and a prominent central lymphatic channel are surrounded by longitudinal muscles. Many serotonin-immunoreactive (IR) processes were found around the centre and between the ganglion and the highly folded lobes of the rhinophore, but serotonin-IR cell bodies were absent inside the rhinophore. In contrast to the conditions recently found in Aplysia punctata, we found no evidence for the presence of olfactory glomeruli within the rhinophore. Using calcium-imaging techniques with Fura II as a calcium indicator, we found differential calcium responses in various regions within the ganglion to stimulation of the rhinophore with different amino acids. The lack of glomeruli in the rhinophores induces functional questions about processing of chemical information in the rhinophore.

Role of the paratrigeminal nucleus in nocifensive responses of rats to chemical, thermal and mechanical stimuli applied to the hind paw

Anatomical and immunohystochemical data suggest the paratrigeminal nucleus (Pa5) may play a role in nociceptive processing. The current study examines the influence of unilateral Pa5 lesion on nocifensive responses of conscious rats to noxious thermal (Hargreaves test), mechanical (electronic von Frey and Randall–Selitto tests), and chemical (formalin 2.5%; 50 μl) stimuli applied to the hind paw. Lesion of the Pa5 induced by ibotenic acid did not affect the latency for radiant heat-induced withdrawal of either paw. In contrast, the mean mechanical threshold for withdrawal of the contralateral (but not ipsilateral) paw in Pa5-lesioned rats was reduced by approximately 45% and 20%, in electronic von Frey and Randall–Selitto tests, respectively, when compared to sham-operated animals. Conversely, animals with Pa5 lesions injected with formalin in the contralateral paw spent less time engaged in focused (licking, biting or scratching the injected paw) and total nocifensive behavior (i.e., focused nocifensive behavior plus protection of the injected paw during movements) in both the first and second phases of the test [∼50% inhibition of each parameter during first phase (0–5 min) and at 20, 25, and 30 min of second phase, relative to the sham-operated group], but the number of paw-jerks was unaffected. Pa5 lesion also delayed the onset of second phase focused pain induced by formalin in the ipsilateral paw. The results suggest that the Pa5 integrates the supraspinal pain control system and plays a differential modulatory role in the central processing of mechanical and chemical nociceptive information.

Involvement of Forebrain Glucose-monitoring Neurons in Taste Information Processing: Electrophysiological and Behavioral Studies

The ventromedial hypothalamic nucleus (VMH), the nucleus accumbens (NAcc) and the mediodorsal and ventrolateral prefrontal (orbitofrontal) cortices (mdPFC and OBF, respectively), key structures of the forebrain limbic circuitry, are known to play important roles in various mechanisms of the homeostatic regulation (Oomura, 1980; Swanson and Mogenson, 1981; Neafsey, 1990). In previous studies, special chemoneurons, the so called ‘glucose-sensitive’ (GS) and ‘glucose-receptor’ (GR) neural cells have been discovered in the above regions, and these glucose-monitoring (GM) neurons, in addition to specifically change in activity in response to increase of the extracellular glucose concentration, have also been shown to be involved in various processes of the organization of feeding (Oomura et al., 1964; Oomura, 1980; Karadi et al., 1995, 2002). Despite an increasing amount of related data, however, very little is known yet about simultaneous ‘endogenous’ and ‘exogenous’ gustatory chemosensitivities of these GM cells. To elucidate the involvement of GM units in an integrative processing of complex chemical information, microelectrophysiological as well as behavioral investigations have been performed. Extracellular single neuron activity of the VMH, NAcc, mdPFC and OBF was recorded during (i) microelectrophoretic administration of D-glucose and other chemicals and (ii) gustatory stimulations as well. Recently conducted behavioral–biochemical experiments provided evidence for that the pancreatic β-cell destroying streptozotocin (STZ) (Like and Rossini, 1976) specifically damages the GM neurons if applied locally to these structures (Egyed et al., 2000; Karadi et al., 2000). In our other line of present studies, taste reactivity and taste associated learning ability were tested in STZ treated or control rats.

On one dimensional chemical diode and frequency generator constructed with an excitable surface reaction

The oxidation of carbon monoxide on a Pt(110) surface is considered as a medium for chemical information processing in which bits of information are represented by traveling pulses of high oxygen coverage. Using numerical simulations for a model of CO oxidation we demonstrate that in such system one dimensional chemical signal diode can be realized by setting a proper profile of temperature. We also show that a pulse splitting can occur on a temperature inhomogeneity. The phenomenon of pulse splitting can be used to construct one dimensional generator of a train of pulses with adjustable frequency.

The Estimation of Production Centers for Wakame Seaweed

Some scams of disguising imported food as domestic have been recently reported in Japan. Concerning wakame seaweed, which is indispensable in the Japanese diet, the situations is also the same. Most people would not be willing to consume them, if they are from other production areas. Analytical methods for determining the production centers are now definitely needed and such methods should be sensitive to determine any disguising. We found the feasibility using Visible-Nearinfraraed spectroscopy and some chemical information processing methods. In this analysis, we found a clear classification between the China, Kashiwazaki and others because we drew 3-D score plots of the principal component analysis after the variable selection using classification trees.

Lure of molecular electronics—from molecular switches to distributed molecular information processing media

There are two main directions in the development of devices for molecular information processing. The first includes attempts to elaborate molecular scale primitive elements such as molecular rectifiers, molecular switches and other devices. The most remarkable examples in this direction are the chiropticene molecular switch, protein-based associative processors and volumetric memories. The second direction is based on the concept of distributed molecular (chemical) information processing media. Chemical reaction-diffusion media represent information effective processing means capable of solving problems of high computational complexity. The distributed character and complex nonlinear dynamics of chemical reactions inherent in the media are the basis of high parallelism and complex logical operations carried out by the media as primitives. Photo-sensitive catalysts of the media reactions enable easy input of initial data, output of computational results and control of the dynamics (modes of functioning) of the media. It was found during the last decade that chemical reaction-diffusion media can be used effectively for image processing, finding the shortest paths in a labyrinth and solving some other problems of high computational complexity. Detailed analysis showed that designing a media with a multilevel architecture and suitable for performing evolutionary computations can be a promising way for further development of reaction-diffusion based devices.

A Bibliometric Study on Chemical Information and Computer Sciences Focusing on Literature of JCICS

A bibliometric approach was used to survey the state-of-the-art of research in the field of chemical information and computer sciences (CICS). By examining the CA database for the articles abstracted under the subsection "Chemical information, documentation, and data processing", Journal of Chemical Information and Computer Sciences (JCICS) was identified to have been the top journal in this subsection for the last 30 years. Based on this result, CA subsections and controlled index terms given to JCICS articles were analyzed to see trends in subjects and topics in the CICS field during the last two decades. These analyses revealed that the subjects of research in CICS have diversified from traditional information science and computer applications to chemistry to "molecular information sciences". The SCISEARCH database was used to grasp interdependency between JCICS and other key journals and also the international nature of JCICS in its publications and citedness.

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Complex functional attributes of amygdaloid gustatory neurons in the rhesus monkey.

To reveal specific functions of glucose-sensitive (GS) and glucose-insensitive (GIS) cells in chemical information processing, single neuron activity was recorded in the amygdaloid body (AMY) of macaques during: 1) gustatory stimulations and 2) micro-electrophoretic administration of chemicals. Of the 629 neurons tested, 56 (8.9%) responded to, usually two or more, taste qualities. Hedonically distinct tastants usually elicited opposite firing rate changes of the gustatory cells. Seventy percent of the gustatory responses were recorded from GS neurons (17% of all AMY cells). Catecholamines (CAs) induced discharge rate changes in a majority of taste-responsive neurons: The GS gustatory cells were suppressed by norepinephrine (in the form of noradrenaline HCl, NA), whereas the GIS taste-responsive neurons were facilitated by dopamine (DA). Furthermore, NA- and/or DA-antagonists were able to attenuate or suppress taste-elicited responses of several of these cells. These and previous data indicate a specific functional organization of AMY gustatory cells: The GS and GIS taste neurons appear to be involved in differential integration of feeding-associated humoral-metabolic, motivational and exogenous chemical information.

Self-evolution in a constructive binary string system.

We examine the qualitative dynamics of a catalytic self-organizing system of binary strings that is inspired by the chemical information processing metaphor. A string is interpreted in two different ways: either (a) as raw data or (b) as a machine that is able to process another string as data in order to produce a third one. This article focuses on the phenomena of evolution whose appearance is notable because no explicit mutation, recombination, or artificial selection operators are introduced. We call the system self-evolving because every variation is performed by the objects themselves in their machine form.

Parallel processing of chemical information in a local area network—II. A parallel cross-validation procedure for artificial neural networks

This paper describes a parallel cross-validation (PCV) procedure, for testing the predictive ability of multi-layer feed-forward (MLF) neural networks models, trained by the generalized delta learning rule. The PCV program has been parallelized to operate in a local area computer network. Development and execution of the parallel application was aided by the HYDRA programming environment, which is extensively described in Part I of this paper. A brief theoretical introduction on MLF networks is given and the problems, associated with the validation of predictive abilities, will be discussed. Furthermore, this paper comprises a general outline of the PCV program. Finally, the parallel PCV application is used to validate the predictive ability of an MLF network modeling a chemical non-linear function approximation problem which is described extensively in the literature.