1,720,986 research outputs found
On a simple case of possible non-deterministic chaotic behavior in compartment theory of biological observables
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Recurrence Quantification Analysis in structure/function relationships in proteins: an overview of a general methodology applied to the case of beta-lactamase
No full textProtein structure-function relationships have been increasingly scrutinized by a variety of correlational and information theoretic measures. In an effort to extend this methodology, a technique originally developed in non-linear science, recurrence quantification analysis, was combined with traditional principal components analysis to study a large number (56) of TEM-1 beta-lactamase mutants. The hydrophobicity profiles corresponding to the primary structure of 13 naturally occurring mutations partially impairing function, together with 43 artificial non-tolerated mutations were subjected to discriminant analysis, derived from the results of recurrence quantification analysis, coupled to a principal exponents extraction. Eleven (85%) of the naturally occurring mutants and 36 (84%) of the artificial mutants were correctly classified (p < 0.0001). We conclude that this technique may be useful in protein engineering and, in general, in structure-function studies of biopolymers
On the Constructive Role of Noise in Spatial Systems
No full textThe detection of weak signals has made a dramatic advance with the recognition of the constructiverole that noise can play in the study of weak periodic signals. In this paper we show that the enhancement of weak signals has a wider reach, and is not confined to dynamical systems. In particular, the addition of artificial noise to a principal components analysis of a geographical problem permitted the discrimination between very weak but informative components, and the noise inherent in the data. The mechanism involved is discussed
Recurrence quantification analysis as a tool for characterization of molecular dynamics simulations.
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Measures of coupling strength and synchronization in non linear interaction of heart rate and systolic blood pressure in the cardiovascular control system
No full textMental states follow quantum mechanics during perception and cognition of ambiguous figures
No full textAbstract. Processes undergoing quantum mechanics exhibit quantum interference e®ects.
In this case, quantum probabilities result to be di®erent from classical ones because they
contain an additional so called quantum interference term. We use ambiguous ̄gures to
analyse if during perception-cognition by human subjects we can observe violation of the
classical probability ̄eld and the presence of quantum interference. The experiments,
conducted on a group of 256 subjects, evidence that we indeed have such a quantum e®ect.
Therefore, mental states, during perception and cognition of ambiguous ̄gures, appear to
follow quantum mechanics
Non linear signal analysis methods in the elucidation of protein sequence/structure relationships
No full textWe tried to present the general meaning and scope
of the application of signal analysis methods to
protein sequence-structure relationships. In our
opinion, the dominant character of this nascent field
concerns the number of the contributing disciplines,
both in terms of methodological (the data analysis
techniques come directly from engineering, applied
mathematics, computational physics) and theoretical
influence (the basic assumptions informing the various
approaches coming from molecular biology, evolutionary
genetics, physical chemistry, biochemistry).
As eloquently discussed in the Laughlin et al. paper
entitled “The Middle Way” (P. Proc. Natl.
Acad. Sci. U.S.A. 2000, 97, 32) the frontiers of science
are rapidly shifting from the investigation of the basic
bricks of matter to the elucidation of mesoscopic
principles of organization. The study of proteins is perhaps the most typical
“mesoscopic” investigation field with its mixing of
basic physical laws, empirical results, and qualitative
descriptions.4 In this review we describe a particular
approach that adopts an empirical style typical of
medicinal chemistry, letting general principles emerge
from the practical solution of local cases
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