Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Selectively exciting quasi-normal modes in open disordered systems.

ABSTRACT: Transmission through disordered samples can be controlled by illuminating a sample with waveforms corresponding to the eigenchannels of the transmission matrix (TM). But can the TM be exploited to selectively excite quasi-normal modes and so control the spatial profile and dwell time inside the medium? We show in microwave and numerical studies that spectra of the TM can be analyzed into modal transmission matrices of rank unity. This makes it possible to enhance the energy within a sample by a factor equal to the number of channels. Limits to modal selectivity arise, however, from correlation in the speckle patterns of neighboring modes. In accord with an effective Hamiltonian model, the degree of modal speckle correlation grows with increasing modal spectral overlap and non-orthogonality of the modes of non-Hermitian systems. This is observed when the coupling of a sample to its surroundings increases, as in the crossover from localized to diffusive waves.

SUBMITTER: Davy M

PROVIDER: S-EPMC6226460 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Selectively exciting quasi-normal modes in open disordered systems.

Davy Matthieu M Genack Azriel Z AZ

Nature communications 20181109 1

Transmission through disordered samples can be controlled by illuminating a sample with waveforms corresponding to the eigenchannels of the transmission matrix (TM). But can the TM be exploited to selectively excite quasi-normal modes and so control the spatial profile and dwell time inside the medium? We show in microwave and numerical studies that spectra of the TM can be analyzed into modal transmission matrices of rank unity. This makes it possible to enhance the energy within a sample by a ...[more]

PMID: 30413690

Similar Datasets

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires.

Project description:Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder.

| S-EPMC5379752 | biostudies-literature

Intrinsically disordered proteins: modes of binding with emphasis on disordered domains.

Project description:Our notions of protein function have long been determined by the protein structure-function paradigm. However, the idea that protein function is dictated by a prerequisite complementarity of shapes at the binding interface is becoming increasingly challenged. Interactions involving intrinsically disordered proteins (IDPs) have indicated a significant degree of disorder present in the bound state, ranging from static disorder to complete disorder, termed 'random fuzziness'. This review assesses the anatomy of an IDP and relates how its intrinsic properties permit promiscuity and allow for the various modes of interaction. Furthermore, a mechanistic overview of the types of disordered domains is detailed, while also relating to a recent example and the kinetic and thermodynamic principles governing its formation.

| S-EPMC8492171 | biostudies-literature

Classifying the Binding Modes of Disordered Proteins.

Project description:Disordered proteins often act as interaction hubs in cellular pathways, via the specific recognition of a distinguished set of partners. While disordered regions can adopt a well-defined conformation upon binding, the coupled folding to binding model does not explain how interaction versatility is achieved. Here, I present a classification scheme for the binding modes of disordered protein regions, based on their conformational heterogeneity in the bound state. Binding modes are defined as (i) disorder-to-order transitions leading to a well-defined bound state, (ii) disordered binding leading to a disordered bound state and (iii) fuzzy binding when the degree of disorder in the bound state may vary with the partner or cellular conditions. Fuzzy binding includes polymorphic bound structures, conditional folding and dynamic binding. This classification scheme describes the structural continuum of complexes involving disordered regions as well as their context-dependent interaction behaviors.

| S-EPMC7697186 | biostudies-literature

<i>Q</i>-Factor Optimization of Modes in Ordered and Disordered Photonic Systems Using Non-Hermitian Perturbation Theory.

Project description:The quality factor, Q, of photonic resonators permeates most figures of merit in applications that rely on cavity-enhanced light-matter interaction such as all-optical information processing, high-resolution sensing, or ultralow-threshold lasing. As a consequence, large-scale efforts have been devoted to understanding and efficiently computing and optimizing the Q of optical resonators in the design stage. This has generated large know-how on the relation between physical quantities of the cavity, e.g., Q, and controllable parameters, e.g., hole positions, for engineered cavities in gaped photonic crystals. However, such a correspondence is much less intuitive in the case of modes in disordered photonic media, e.g., Anderson-localized modes. Here, we demonstrate that the theoretical framework of quasinormal modes (QNMs), a non-Hermitian perturbation theory for shifting material boundaries, and a finite-element complex eigensolver provide an ideal toolbox for the automated shape optimization of Q of a single photonic mode in both ordered and disordered environments. We benchmark the non-Hermitian perturbation formula and employ it to optimize the Q-factor of a photonic mode relative to the position of vertically etched holes in a dielectric slab for two different settings: first, for the fundamental mode of L3 cavities with various footprints, demonstrating that the approach simultaneously takes in-plane and out-of-plane losses into account and leads to minor modal structure modifications; and second, for an Anderson-localized mode with an initial Q of 200, which evolves into a completely different mode, displaying a threefold reduction in the mode volume, a different overall spatial location, and, notably, a 3 order of magnitude increase in Q.

| S-EPMC10436348 | biostudies-literature

Extreme Foaming Modes for SCF-Plasticized Polylactides: Quasi-Adiabatic and Quasi-Isothermal Foam Expansion.

Project description:The experimental evidence on depressurization foaming of the amorphous D,L-polylactide, which is plasticized by subcritical (initial pressures below the critical value) or supercritical (initial pressures above the critical value) carbon dioxide at a temperature above the critical value, relates to two extreme cases: a slow quasi-isothermal foam expansion, and a rapid quasi-adiabatic expansion. Under certain conditions, the quasi-isothermal mode is characterized by the non-monotonic dependencies of the foam volume on the external pressure that are associated with the expansion-to-shrinkage transition. The quasi-adiabatic and quasi-isothermal expansions are characterized by a significant increase in the degree of foam expansion under conditions where the CO2 initial pressure approaches the critical value. The observed features are interpreted in terms of the energy balance in the foam volume and the phenomenological model based on the equation of the foam state. The expansion-to-shrinkage condition is based on the relationship between the average bubble radius and the pressure derivative of the surface tension for the plasticized polylactide. The maximum expansion ratio of the rapidly foamed polylactide in the vicinity of the critical point is interpreted in terms of the maximum decrement of the specific internal energy of the foaming agent (carbon dioxide) in the course of depressurization.

| S-EPMC7284874 | biostudies-literature

Research on a Novel Exciting Method for a Sandwich Transducer Operating in Longitudinal-Bending Hybrid Modes.

Project description:A novel exciting method for a sandwich type piezoelectric transducer operating in longitudinal-bending hybrid vibration modes is proposed and discussed, in which the piezoelectric elements for the excitations of the longitudinal and bending vibrations share the same axial location, but correspond to different partitions. Whole-piece type piezoelectric plates with three separated partitions are used, in which the center partitions generate the first longitudinal vibration, while the upper and lower partitions produce the second bending vibration. Detailed comparisons between the proposed exciting method and the traditional one were accomplished by finite element method (FEM) calculations, which were further verified by experiments. Compared with the traditional exciting method using independent longitudinal ceramics and bending ceramics, the proposed method achieves higher electromechanical coupling factors and larger vibration amplitudes, especially for the bending vibration mode. This novel exciting method for longitudinal-bending hybrid vibrations has not changed the structural dimensions of the sandwich transducer, but markedly improves the mechanical output ability, which makes it very helpful and meaningful in designing new piezoelectric actuators operated in longitudinal-bending hybrid vibration modes.

| S-EPMC5539521 | biostudies-other

Identifying the significance of nonlinear normal modes.

Project description:Nonlinear normal modes (NNMs) are widely used as a tool for understanding the forced responses of nonlinear systems. However, the contemporary definition of an NNM also encompasses a large number of dynamic behaviours which are not observed when a system is forced and damped. As such, only a few NNMs are required to understand the forced dynamics. This paper firstly demonstrates the complexity that may arise from the NNMs of a simple nonlinear system-highlighting the need for a method for identifying the significance of NNMs. An analytical investigation is used, alongside energy arguments, to develop an understanding of the mechanisms that relate the NNMs to the forced responses. This provides insight into which NNMs are pertinent to understanding the forced dynamics, and which may be disregarded. The NNMs are compared with simulated forced responses to verify these findings.

| S-EPMC5378240 | biostudies-literature

Normal Modes Expose Active Sites in Enzymes.

Project description:Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

| S-EPMC5225006 | biostudies-literature

Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes.

Project description:We present what to our knowledge is a new method of optimized torsion-angle normal-mode analysis, in which the normal modes move along curved paths in Cartesian space. We show that optimized torsion-angle normal modes reproduce protein conformational changes more accurately than Cartesian normal modes. We also show that orthogonalizing the displacement vectors from torsion-angle normal-mode analysis and projecting them as straight lines in Cartesian space does not lead to better performance than Cartesian normal modes. Clearly, protein motion is more naturally described by curved paths in Cartesian space.

| S-EPMC3244061 | biostudies-literature

Dynamic disorder in quasi-equilibrium enzymatic systems.

Project description:Conformations and catalytic rates of enzymes fluctuate over a wide range of timescales. Despite these fluctuations, there exist some limiting cases in which the enzymatic catalytic rate follows the macroscopic rate equation such as the Michaelis-Menten law. In this paper we investigate the applicability of macroscopic rate laws for fluctuating enzyme systems in which catalytic transitions are slower than ligand binding-dissociation reactions. In this quasi-equilibrium limit, for an arbitrary reaction scheme we show that the catalytic rate has the same dependence on ligand concentrations as obtained from mass-action kinetics even in the presence of slow conformational fluctuations. These results indicate that the timescale of conformational dynamics--no matter how slow--will not affect the enzymatic rate in quasi-equilibrium limit. Our numerical results for two enzyme-catalyzed reaction schemes involving multiple substrates and inhibitors further support our general theory.

| S-EPMC2927515 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data