An Analysis for Proving Temporal Properties of Biological Systems

2006 ◽  
pp. 234-252 ◽  
Author(s):  
Roberta Gori ◽  
Francesca Levi
Keyword(s):  
Biological Systems ◽  
Temporal Properties

scholarly journals A Stochastic Concurrent Constraint Based Framework to Model and Verify Biological Systems

2006 ◽  
Vol 9 (2) ◽  
Author(s):  
Carlos Olarte ◽  
Camilo Rueda
Keyword(s):  
Temporal Logic ◽  
Design Methodology ◽  
Biological Systems ◽  
Proof System ◽  
Binding Affinities ◽  
Concurrent Process ◽  
Underlying Process ◽  
Process Calculi ◽  
Temporal Properties ◽  
Molecular Components

Abstract Concurrent process calculi are powerful formalisms for modelling concurrent systems. The mathematical style underlying process cal- culi allow to both model and verify properties of a system, thus pro- viding a concrete design methodology for complex systems. ntcc , a constraints-based calculus for modeling temporal non-deterministic and asynchronous behaviour of processes has been proposed recently. Process interactions in ntcc can be determined by partial informa- tion (i.e. constraints) accumulated in a global store. ntcc has also an associated temporal logic with a proof system that can be conve- niently used to formally verify temporal properties of processes. We are interested in using ntcc to model the activity of genes in biological systems. In order to account for issues such as the basal rate of re- actions or binding affinities of molecular components, we believe that stochastic features must be added to the calculus. In this paper we propose an extension of ntcc with various stochastic constructs. We describe the syntax and semantics of this extension together with the new temporal logic and proof system associated with it. We show the relevance of the added features by modelling a non trivial biological system: the gene expression mechanisms of the λ virus. We argue that this model is both more elaborate and compact than the stochastic πcalculus model proposed recently for the same system.

Temporal properties of some biological systems and their fractal attractors

1989 ◽  
Vol 51 (6) ◽  
pp. 785-800 ◽  
Author(s):  
Emilia Gutierrez ◽  
Helena Almirall
Keyword(s):  
Biological Systems ◽  
Temporal Properties

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

Freeze-fracture cytochemistry: A goal set by Russell Steere in 1957

1993 ◽  
Vol 51 ◽  
pp. 60-61
Author(s):  
Nicholas J Severs
Keyword(s):  
Chemical Nature ◽  
Biological Systems ◽  
Freeze Fracture ◽  
Structural Components ◽  
Major Goal ◽  
Membrane Biology ◽  
Routine Application ◽  
The Future ◽  
Freeze Etching

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.

Seeking to uncover biology's chemical roots

2019 ◽  
Vol 3 (5) ◽  
pp. 435-443 ◽  
Author(s):  
Addy Pross
Keyword(s):  
Environmental Changes ◽  
Biological Systems ◽  
Significant Development ◽  
The Road ◽  
Physical Chemical ◽  
Systems Chemistry ◽  
Biological World ◽  
Inanimate Matter ◽  
The Origin Of Life ◽  
Opening Up

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.

Auditory Training to Improve Speech Perception and Self-Efficacy in Aging Adults

2020 ◽  
Vol 63 (4) ◽  
pp. 1270-1281
Author(s):  
Leah Fostick ◽  
Riki Taitelbaum-Swead ◽  
Shulamith Kreitler ◽  
Shelly Zokraut ◽  
Miriam Billig
Keyword(s):  
Speech Perception ◽  
Self Efficacy ◽  
Temporal Order Judgment ◽  
Auditory Training ◽  
Intensity Discrimination ◽  
Training Design ◽  
Auditory Temporal Processing ◽  
Temporal Properties ◽  
Computer Based ◽  
Aging Adults

Purpose Difficulty in understanding spoken speech is a common complaint among aging adults, even when hearing impairment is absent. Correlational studies point to a relationship between age, auditory temporal processing (ATP), and speech perception but cannot demonstrate causality unlike training studies. In the current study, we test (a) the causal relationship between a spatial–temporal ATP task (temporal order judgment [TOJ]) and speech perception among aging adults using a training design and (b) whether improvement in aging adult speech perception is accompanied by improved self-efficacy. Method Eighty-two participants aged 60–83 years were randomly assigned to a group receiving (a) ATP training (TOJ) over 14 days, (b) non-ATP training (intensity discrimination) over 14 days, or (c) no training. Results The data showed that TOJ training elicited improvement in all speech perception tests, which was accompanied by increased self-efficacy. Neither improvement in speech perception nor self-efficacy was evident following non-ATP training or no training. Conclusions There was no generalization of the improvement resulting from TOJ training to intensity discrimination or generalization of improvement resulting from intensity discrimination training to speech perception. These findings imply that the effect of TOJ training on speech perception is specific and such improvement is not simply the product of generally improved auditory perception. It provides support for the idea that temporal properties of speech are indeed crucial for speech perception. Clinically, the findings suggest that aging adults can be trained to improve their speech perception, specifically through computer-based auditory training, and this may improve perceived self-efficacy.

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