Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Topologically protected modes in non-equilibrium stochastic systems.

ABSTRACT: Non-equilibrium driving of biophysical processes is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enzymatic specificity and maintenance of coherent oscillations. Elucidating the relation between energy consumption and organization remains an important and open question in non-equilibrium statistical mechanics. Here we report that steady states of systems with non-equilibrium fluxes can support topologically protected boundary modes that resemble similar modes in electronic and mechanical systems. Akin to their electronic and mechanical counterparts, topological-protected boundary steady states in non-equilibrium systems are robust and are largely insensitive to local perturbations. We argue that our work provides a framework for how biophysical systems can use non-equilibrium driving to achieve robust function.

SUBMITTER: Murugan A

PROVIDER: S-EPMC5234070 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Topologically protected modes in non-equilibrium stochastic systems.

Murugan Arvind A Vaikuntanathan Suriyanarayanan S

Nature communications 20170110

Non-equilibrium driving of biophysical processes is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enzymatic specificity and maintenance of coherent oscillations. Elucidating the relation between energy consumption and organization remains an important and open question in non-equilibrium statistical mechanics. Here we report that steady states of systems with non-e ...[more]

PMID: 28071644

Similar Datasets

Brownian motion in non-equilibrium systems and the Ornstein-Uhlenbeck stochastic process.

Project description:The Ornstein-Uhlenbeck stochastic process is an exact mathematical model providing accurate representations of many real dynamic processes in systems in a stationary state. When applied to the description of random motion of particles such as that of Brownian particles, it provides exact predictions coinciding with those of the Langevin equation but not restricted to systems in thermal equilibrium but only conditioned to be stationary. Here, we investigate experimentally single particle motion in a two-dimensional granular system in a stationary state, consisting of 1 mm stainless balls on a plane circular surface. The motion of the particles is produced by an alternating magnetic field applied perpendicular to the surface of the container. The mean square displacement of the particles is measured for a range of low concentrations and it is found that following an appropriate scaling of length and time, the short-time experimental curves conform a master curve covering the range of particle motion from ballistic to diffusive in accordance with the description of the Ornstein-Uhlenbeck model.

| S-EPMC5626708 | biostudies-literature

Topologically protected states in one-dimensional continuous systems and Dirac points.

Project description:We study a class of periodic Schrödinger operators on ℝ that have Dirac points. The introduction of an "edge" via adiabatic modulation of a periodic potential by a domain wall results in the bifurcation of spatially localized "edge states," associated with the topologically protected zero-energy mode of an asymptotic one-dimensional Dirac operator. The bound states we construct can be realized as highly robust transverse-magnetic electromagnetic modes for a class of photonic waveguides with a phase defect. Our model captures many aspects of the phenomenon of topologically protected edge states for 2D bulk structures such as the honeycomb structure of graphene.

| S-EPMC4066501 | biostudies-other

Coupling of Higgs and Leggett modes in non-equilibrium superconductors.

Project description:In equilibrium systems amplitude and phase collective modes are decoupled, as they are mutually orthogonal excitations. The direct detection of these Higgs and Leggett collective modes by linear-response measurements is not possible, because they do not couple directly to the electromagnetic field. In this work, using numerical exact simulations we show for the case of two-gap superconductors, that optical pump-probe experiments excite both Higgs and Leggett modes out of equilibrium. We find that this non-adiabatic excitation process introduces a strong interaction between the collective modes, which is absent in equilibrium. Moreover, we propose a type of pump-probe experiment, which allows to probe and coherently control the Higgs and Leggett modes, and thus the order parameter directly. These findings go beyond two-band superconductors and apply to general collective modes in quantum materials.

| S-EPMC4919519 | biostudies-literature

Topologically protected elastic waves in phononic metamaterials.

Project description:Surface waves in topological states of quantum matter exhibit unique protection from backscattering induced by disorders, making them ideal carriers for both classical and quantum information. Topological matters for electrons and photons are largely limited by the range of bulk properties, and the associated performance trade-offs. In contrast, phononic metamaterials provide access to a much wider range of material properties. Here we demonstrate numerically a phononic topological metamaterial in an elastic-wave analogue of the quantum spin Hall effect. A dual-scale phononic crystal slab is used to support two effective spins for phonons over a broad bandwidth, and strong spin-orbit coupling is realized by breaking spatial mirror symmetry. By preserving the spin polarization with an external load or spatial symmetry, phononic edge states are shown to be robust against scattering from discrete defects as well as disorders in the continuum, demonstrating topological protection for phonons in both static and time-dependent regimes.

| S-EPMC4659837 | biostudies-literature

Topologically protected Dirac plasmons in a graphene superlattice.

Project description:Topological optical states exhibit unique immunity to defects, rendering them ideal for photonic applications. A powerful class of such states is based on time-reversal symmetry breaking of the optical response. However, existing proposals either involve sophisticated and bulky structural designs or can only operate in the microwave regime. Here we show a theoretical demonstration for highly confined topologically protected optical states to be realized at infrared frequencies in a simple two-dimensional (2D) material structure-a periodically patterned graphene monolayer-subject to a magnetic field of only 2 tesla. In our graphene honeycomb superlattice structures, plasmons exhibit substantial nonreciprocal behavior at the superlattice junctions under moderate static magnetic fields, leading to the emergence of topologically protected edge states and localized bulk modes. This approach is simple and robust for realizing topologically nontrivial optical states in 2D atomic layers, and could pave the way for building fast, nanoscale, defect-immune photonic devices.

| S-EPMC5665919 | biostudies-literature

Spectral Analysis of a Non-Equilibrium Stochastic Dynamics on a General Network.

Project description:Unravelling underlying complex structures from limited resolution measurements is a known problem arising in many scientific disciplines. We study a stochastic dynamical model with a multiplicative noise. It consists of a stochastic differential equation living on a graph, similar to approaches used in population dynamics or directed polymers in random media. We develop a new tool for approximation of correlation functions based on spectral analysis that does not require translation invariance. This enables us to go beyond lattices and analyse general networks. We show, analytically, that this general model has different phases depending on the topology of the network. One of the main parameters which describe the network topology is the spectral dimension [Formula: see text]. We show that the correlation functions depend on the spectral dimension and that only for [Formula: see text] > 2 a dynamical phase transition occurs. We show by simulation how the system behaves for different network topologies, by defining and calculating the Lyapunov exponents on the graph. We present an application of this model in the context of Magnetic Resonance (MR) measurements of porous structure such as brain tissue. This model can also be interpreted as a KPZ equation on a graph.

| S-EPMC6156338 | biostudies-literature

Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks.

Project description:Many biochemical reaction networks are inherently multiscale in time and in the counts of participating molecular species. A standard technique to treat different time scales in the stochastic kinetics framework is averaging or quasi-steady-state analysis: it is assumed that the fast dynamics reaches its equilibrium (stationary) distribution on a time scale where the slowly varying molecular counts are unlikely to have changed. We derive analytic equilibrium distributions for various simple biochemical systems, such as enzymatic reactions and gene regulation models. These can be directly inserted into simulations of the slow time-scale dynamics. They also provide insight into the stimulus-response of these systems. An important model for which we derive the analytic equilibrium distribution is the binding of dimer transcription factors (TFs) that first have to form from monomers. This gene regulation mechanism is compared to the cases of the binding of simple monomer TFs to one gene or to multiple copies of a gene, and to the cases of the cooperative binding of two or multiple TFs to a gene. The results apply equally to ligands binding to enzyme molecules.

| S-EPMC4208355 | biostudies-literature

Mechanosensitive non-equilibrium supramolecular polymerization in closed chemical systems.

Project description:Chemical fuel-driven supramolecular systems have been developed showing out-of-equilibrium functions such as transient gelation and oscillations. However, these systems suffer from undesired waste accumulation and they function only in open systems. Herein, we report non-equilibrium supramolecular polymerizations in a closed system, which is built by viologens and pyranine in the presence of hydrazine hydrate. On shaking, the viologens are quickly oxidated by air followed by self-assembly of pyranine into micrometer-sized nanotubes. The self-assembled nanotubes disassemble spontaneously over time by the reduced agent, with nitrogen as the only waste product. Our mechanosensitive dissipative system can be extended to fabricate a chiral transient supramolecular helix by introducing chiral-charged small molecules. Moreover, we show that shaking induces transient fluorescence enhancement or quenching depending on substitution of viologens. Ultrasound is introduced as a specific shaking way to generate template-free reproducible patterns. Additionally, the shake-driven transient polymerization of amphiphilic naphthalenetetracarboxylic diimide serves as further evidence of the versatility of our mechanosensitive non-equilibrium system.

| S-EPMC10227035 | biostudies-literature

Topologically protected surface states in a centrosymmetric superconductor β-PdBi2.

Project description:The topological aspects of electrons in solids can emerge in real materials, as represented by topological insulators. In theory, they show a variety of new magneto-electric phenomena, and especially the ones hosting superconductivity are strongly desired as candidates for topological superconductors. While efforts have been made to develop possible topological superconductors by introducing carriers into topological insulators, those exhibiting indisputable superconductivity free from inhomogeneity are very few. Here we report on the observation of topologically protected surface states in a centrosymmetric layered superconductor, β-PdBi2, by utilizing spin- and angle-resolved photoemission spectroscopy. Besides the bulk bands, several surface bands are clearly observed with symmetrically allowed in-plane spin polarizations, some of which crossing the Fermi level. These surface states are precisely evaluated to be topological, based on the Z2 invariant analysis in analogy to three-dimensional strong topological insulators. β-PdBi2 may offer a solid stage to investigate the topological aspect in the superconducting condensate.

| S-EPMC4633943 | biostudies-literature

Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics.

Project description:Many chemical reaction networks in biological systems present complex oscillatory dynamics. In systems such as regulatory gene networks, cell cycle, and enzymatic processes, the number of molecules involved is often far from the thermodynamic limit. Although stochastic models based on the probabilistic approach of the Chemical Master Equation (CME) have been proposed, studies in the literature have been limited by the challenges of solving the CME and the lack of computational power to perform large-scale stochastic simulations. In this paper, we show that the infinite set of stationary moment equations describing the stochastic Brusselator and Schnakenberg oscillatory reactions networks can be truncated and solved using maximization of the entropy of the distributions. The results from our numerical experiments compare with the distributions obtained from well-established kinetic Monte Carlo methods and suggest that the accuracy of the prediction increases exponentially with the closure order chosen for the system. We conclude that maximum entropy models can be used as an efficient closure scheme alternative for moment equations to predict the non-equilibrium stationary distributions of stochastic chemical reactions with oscillatory dynamics. This prediction is accomplished without any prior knowledge of the system dynamics and without imposing any biased assumptions on the mathematical relations among species involved.

| S-EPMC6424531 | 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