scholarly journals Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity

2019 ◽  
Vol 36 (9) ◽  
pp. 2053-2068 ◽  
Author(s):  
She Zhang ◽  
Hongchun Li ◽  
James M Krieger ◽  
Ivet Bahar
Keyword(s):  
High Frequency ◽  
Family Members ◽  
Network Models ◽  
Intermediate Frequency ◽  
Functional Differentiation ◽  
Global Dynamics ◽  
Structural Variations ◽  
Mode Spectrum ◽  
Large Ensembles ◽  
Premise Structure

AbstractRecent studies have drawn attention to the evolution of protein dynamics, in addition to sequence and structure, based on the premise structure-encodes-dynamics-encodes-function. Of interest is to understand how functional differentiation is accomplished while maintaining the fold, or how intrinsic dynamics plays out in the evolution of structural variations and functional specificity. We performed a systematic computational analysis of 26,899 proteins belonging to 116 CATH superfamilies. Characterizing cooperative mechanisms and convergent/divergent features that underlie the shared/differentiated dynamics of family members required a methodology that lends itself to efficient analyses of large ensembles of proteins. We therefore introduced, SignDy, an integrated pipeline for evaluating the signature dynamics of families based on elastic network models. Our analysis confirmed that family members share conserved, highly cooperative (global) modes of motion. Importantly, our analysis discloses a subset of motions that sharply distinguishes subfamilies, which lie in a low-to-intermediate frequency regime of the mode spectrum. This regime has maximal impact on functional differentiation of families into subfamilies, while being evolutionarily conserved among subfamily members. Notably, the high-frequency end of the spectrum also reveals evolutionary conserved features across and within subfamilies; but in sharp contrast to global motions, high-frequency modes are minimally collective. Modulation of robust/conserved global dynamics by low-to-intermediate frequency fluctuations thus emerges as a versatile mechanism ensuring the adaptability of selected folds and the specificity of their subfamilies. SignDy further allows for dynamics-based categorization as a new layer of information relevant to distinctive mechanisms of action of subfamilies, beyond sequence or structural classifications.

scholarly journals High-frequency homogenization for periodic media

2010 ◽  
Vol 466 (2120) ◽  
pp. 2341-2362 ◽  
Author(s):  
R. V. Craster ◽  
J. Kaplunov ◽  
A. V. Pichugin
Keyword(s):  
High Frequency ◽  
Wave Equations ◽  
Standing Waves ◽  
Low Frequency ◽  
Homogenization Theory ◽  
Periodic Media ◽  
Mode Spectrum ◽  
Bloch Mode ◽  
Long Wavelength Asymptotics ◽  
Model Equations

An asymptotic procedure based upon a two-scale approach is developed for wave propagation in a doubly periodic inhomogeneous medium with a characteristic length scale of microstructure far less than that of the macrostructure. In periodic media, there are frequencies for which standing waves, periodic with the period or double period of the cell, on the microscale emerge. These frequencies do not belong to the low-frequency range of validity covered by the classical homogenization theory, which motivates our use of the term ‘high-frequency homogenization’ when perturbing about these standing waves. The resulting long-wave equations are deduced only explicitly dependent upon the macroscale, with the microscale represented by integral quantities. These equations accurately reproduce the behaviour of the Bloch mode spectrum near the edges of the Brillouin zone, hence yielding an explicit way for homogenizing periodic media in the vicinity of ‘cell resonances’. The similarity of such model equations to high-frequency long wavelength asymptotics, for homogeneous acoustic and elastic waveguides, valid in the vicinities of thickness resonances is emphasized. Several illustrative examples are considered and show the efficacy of the developed techniques.

scholarly journals Greybody Factors for Schwarzschild Black Holes: Path-Ordered Exponentials and Product Integrals

Universe ◽  
2018 ◽  
Vol 4 (9) ◽  
pp. 93 ◽  
Author(s):  
Finnian Gray ◽  
Matt Visser
Keyword(s):  
Black Holes ◽  
High Frequency ◽  
Low Frequency ◽  
Intermediate Frequency ◽  
General Context ◽  
Matrix Formalism ◽  
Barrier Penetration ◽  
Frequency Regime ◽  
Transfer Matrix Formalism ◽  
Numerical Approaches

In earlier work concerning the sparsity of the Hawking flux, we found it necessary to re-examine what is known regarding the greybody factors of black holes, with a view to extending and expanding on some old results from the 1970s. Focusing specifically on Schwarzschild black holes, we have re-calculated and re-assessed the greybody factors using a path-ordered-exponential approach, a technique which has the virtue of providing a pedagogically useful semi-explicit formula for the relevant Bogoliubov coefficients. These path-ordered-exponentials, being based on a variant of the “transfer matrix” formalism, are closely related to so-called “product integrals”, leading to quite straightforward and direct numerical evaluation, while side-stepping any need for numerically solving the relevant ordinary differential equations. Furthermore, while considerable analytic information is already available regarding both the high-frequency and low-frequency asymptotics of these greybody factors, numerical approaches seem better adapted to finding suitable “global models” for these greybody factors in the intermediate frequency regime, where most of the Hawking flux is actually concentrated. Working in a more general context, these path-ordered-exponential techniques are also likely to be of interest for generic barrier-penetration problems.

scholarly journals Development of a Job-Exposure Matrix for Assessment of Occupational Exposure to High-Frequency Electromagnetic Fields (3 kHz–300 GHz)

2019 ◽  
Vol 63 (9) ◽  
pp. 1013-1028
Author(s):  
Lucile Migault ◽  
Joseph D Bowman ◽  
Hans Kromhout ◽  
Jordi Figuerola ◽  
Isabelle Baldi ◽  
...  
Keyword(s):  
Occupational Exposure ◽  
Electromagnetic Fields ◽  
High Frequency ◽  
Health Management ◽  
Large Population ◽  
Intermediate Frequency ◽  
Epidemiological Studies ◽  
Coding System ◽  
Job Exposure Matrix ◽  
Field Exposure

Abstract Objectives The aim of this work was to build a job-exposure matrix (JEM) using an international coding system and covering the non-thermal intermediate frequency (IF) (3–100 kHz, named IFELF), thermal IF (100 kHz–10 MHz, named IFRF), and radiofrequency (RF) (>10 MHz) bands. Methods Detailed occupational data were collected in a large population-based case–control study, INTEROCC, with occupations coded into the International Standard Classification of Occupations system 1988 (ISCO88). The subjects’ occupational source-based ancillary information was combined with an existing source-exposure matrix and the reference levels of the International Commission on Non-Ionizing Radiation Protection (ICNIRP) for occupational exposure to calculate estimates of level (L) of exposure to electric (E) and magnetic (H) fields by ISCO88 code and frequency band as ICNIRP ratios (IFELF) or squared ratios (IFRF and RF). Estimates of exposure probability (P) were obtained by dividing the number of exposed subjects by the total number of subjects available per job title. Results With 36 011 job histories collected, 468 ISCO88 (four-digit) codes were included in the JEM, of which 62.4% are exposed to RF, IFRF, and/or IFELF. As a reference, P values for RF E-fields ranged from 0.3 to 65.0% with a median of 5.1%. L values for RF E-fields (ICNIRP squared ratio) ranged from 6.94 × 10−11 to 33.97 with a median of 0.61. Conclusions The methodology used allowed the development of a JEM for high-frequency electromagnetic fields containing exposure estimates for the largest number of occupations to date. Although the validity of this JEM is limited by the small number of available observations for some codes, this JEM may be useful for epidemiological studies and occupational health management programs assessing high-frequency electromagnetic field exposure in occupational settings.

scholarly journals Global Dynamics of Intact AMPA and NMDA Receptors using Elastic Network Models

2016 ◽  
Vol 110 (3) ◽  
pp. 382a
Author(s):  
Ji Young Lee ◽  
Anindita Dutta ◽  
James Krieger ◽  
Javier Garcia-Nafria ◽  
Ingo Greger ◽  
...  
Keyword(s):  
Nmda Receptors ◽  
Network Models ◽  
Global Dynamics ◽  
Elastic Network ◽  
Elastic Network Models ◽  
Ampa And Nmda Receptors

COMBINATORIAL FRACTAL GEOMETRY WITH A BIOLOGICAL APPLICATION

Fractals ◽  
2006 ◽  
Vol 14 (02) ◽  
pp. 133-142 ◽  
Author(s):  
JOHN KONVALINA ◽  
IGOR KONFISAKHAR ◽  
JACK HEIDEL ◽  
JIM ROGERS
Keyword(s):  
Fractal Geometry ◽  
Boolean Network ◽  
Biological Systems ◽  
Sierpinski Gasket ◽  
Network Models ◽  
Combinatorial Problem ◽  
Higher Dimensions ◽  
Global Dynamics ◽  
Biological Application ◽  
Sierpiński Gasket

The solution to a deceptively simple combinatorial problem on bit strings results in the emergence of a fractal related to the Sierpinski Gasket. The result is generalized to higher dimensions and applied to the study of global dynamics in Boolean network models of complex biological systems.

Dynamics of the brain at global and microscopic scales: Neural networks and the EEG

1996 ◽  
Vol 19 (2) ◽  
pp. 285-295 ◽  
Author(s):  
J. J. Wright ◽  
D. T. J. Liley
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Models ◽  
Cellular Neural Network ◽  
Information Storage ◽  
Cortical Activation ◽  
Global Dynamics ◽  
Neural Network Models ◽  
Neuronal Interactions ◽  
Neural Interactions

AbstractThere is some complementarity of models for the origin of the electroencephalogram (EEG) and neural network models for information storage in brainlike systems. From the EEG models of Freeman, of Nunez, and of the authors' group we argue that the wavelike processes revealed in the EEG exhibit linear and near-equilibrium dynamics at macroscopic scale, despite extremely nonlinear – probably chaotic – dynamics at microscopic scale. Simulations of cortical neuronal interactions at global and microscopic scales are then presented. The simulations depend on anatomical and physiological estimates of synaptic densities, coupling symmetries, synaptic gain, dendritic time constants, and axonal delays. It is shown that the frequency content, wave velocities, frequency/wavenumber spectra and response to cortical activation of the electrocorticogram (ECoG) can be reproduced by a “lumped” simulation treating small cortical areas as single-function units. The corresponding cellular neural network simulation has properties that include those of attractor neural networks proposed by Amit and by Parisi. Within the simulations at both scales, sharp transitions occur between low and high cell firing rates. These transitions may form a basis for neural interactions across scale. To maintain overall cortical dynamics in the normal low firing-rate range, interactions between the cortex and the subcortical systems are required to prevent runaway global excitation. Thus, the interaction of cortex and subcortex via corticostriatal and related pathways may partly regulate global dynamics by a principle analogous to adiabatic control of artificial neural networks.

Artificial Higher Order Neural Network Models

2016 ◽  
pp. 241-311
Author(s):  
Ming Zhang
Keyword(s):  
Neural Network ◽  
High Frequency ◽  
Learning Algorithm ◽  
Network Models ◽  
Higher Order ◽  
Neural Network Models ◽  
Ultra High Frequency

This chapter introduces the background of HONN model developing history and overview 24 applied artificial higher order neural network models. This chapter provides 24 HONN models and uses a single uniform HONN architecture for ALL 24 HONN models. This chapter also uses a uniform learning algorithm for all 24 HONN models and uses a uniform weight update formulae for all 24 HONN models. In this chapter, Polynomial HONN, Trigonometric HONN, Sigmoid HONN, SINC HONN, and Ultra High Frequency HONN structure and models are overviewed too.

Anatomical Characteristics and Potential Gene Mutation Sites of a Familial Recurrent Patellar Dislocation

2021 ◽  
Author(s):  
Qi-hao Zhang ◽  
Yan Zhang ◽  
Rui-xuan He ◽  
Xin-guang Wang
Keyword(s):  
Knee Joint ◽  
High Frequency ◽  
Patellar Dislocation ◽  
Family Members ◽  
Patella Dislocation ◽  
Recurrent Patellar Dislocation ◽  
Anatomical Characteristics ◽  
Synonymous Mutations ◽  
Pathogenic Genes ◽  
Pathogenic Gene

Abstract Background Recurrent patellar dislocation is the result of anatomical alignment and imbalance of restraint of bone and soft tissue. To investigate the anatomical characteristics of the knee joint in a family of patients with recurrent patella dislocation, and to screen the possible pathogenic genes in this family by whole exon sequencing in 4 patients and 4 healthy subjects, so as to provide theoretical basis for the pathogenesis of this disease. Methods The data related to patella dislocation were measured by imaging data. The peripheral blood DNA of related family members was extracted for full exon sequencing, and then the sequencing results were compared with the human database. By filtering out synonymous mutations and high-frequency mutations, and then integrating single nucleotide non-synonymous mutations of family members, disease-causing genes were found. Results All patients in this family have different degree of abnormal knee anatomy, which is closely related to patella dislocation. The sequencing results of patients and normal persons in this patella dislocation family were compared and analyzed, and the data were filtered through multiple biological databases. Find HOXB9(NM_024017.4:p.Glu135Gly/c.404A>G),COL1A1(NM_000088.3:p.Ala1256 Thr/c.3766G>A),GNPAT(NM_014236.3:p.Asp519Gly/c1556A>G),NANS(NM_018946.3:p.Glu68Asp/c.204G>C),SLC26A2(NM_000112.3:p.Thr689Ser/c.2065A>T) are not synonymous mutations (MISSENSE). Through Sanger sequencing, HOXB9 and SLC26A2 genes were found to be the pathogenic genes of this family with recurrent patella dislocation. Conclusions The anatomical structure of the knee joint of patients with recurrent patellar dislocation in this family is obviously abnormal. HOXB9 mutation may be the high frequency pathogenic gene of recurrent patella dislocation in this family, while COL1A1, GNPAT, NAans, SLC26A2 gene may be the sporadical pathogenic gene.

Research on the Intermediate Frequency Receiver of L-Band

2014 ◽  
Vol 1056 ◽  
pp. 193-196
Author(s):  
Shuang Zhao ◽  
Yun Qing Liu
Keyword(s):  
High Frequency ◽  
High Reliability ◽  
Rapid Development ◽  
Intermediate Frequency ◽  
Low Power Consumption ◽  
Frequency Signal ◽  
High Frequency Signal ◽  
Wireless Receiver ◽  
Rf Receiver ◽  
L Band

With the rapid development of wireless communications, there are more and more ​​stringent requirements on the wireless receiver, such as low power consumption, high reliability, low price, as well as smaller size. The design of RF receiver is the key to achieve this goal. According to the actual needs of the project, a double conversion IF receiver is designed. At first, the high frequency signal is changed to a higher IF, and the second output is a zero-IF signal. Experimental results show that the receiver has 100dB gain and a flat bandwidth.

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