Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Symmetry breaking gives rise to energy spectra of three states of matter.

ABSTRACT: A fundamental task of statistical physics is to start with a microscopic Hamiltonian, predict the system's statistical properties and compare them with observable data. A notable current fundamental challenge is to tell whether and how an interacting Hamiltonian predicts different energy spectra, including solid, liquid and gas phases. Here, we propose a new idea that enables a unified description of all three states of matter. We introduce a generic form of an interacting phonon Hamiltonian with ground state configurations minimising the potential. Symmetry breaking SO(3) to SO(2), from the group of rotations in reciprocal space to its subgroup, leads to emergence of energy gaps of shear excitations as a consequence of the Goldstone theorem, and readily results in the emergence of energy spectra of solid, liquid and gas phases.

SUBMITTER: Bolmatov D

PROVIDER: S-EPMC3786290 | biostudies-other | 2013

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

The glassy random laser: replica symmetry breaking in the intensity fluctuations of emission spectra.

Project description:The behavior of a newly introduced overlap parameter, measuring the correlation between intensity fluctuations of waves in random media, is analyzed in different physical regimes, with varying amount of disorder and non-linearity. This order parameter allows to identify the laser transition in random media and describes its possible glassy nature in terms of emission spectra data, the only data so far accessible in random laser measurements. The theoretical analysis is performed in terms of the complex spherical spin-glass model, a statistical mechanical model describing the onset and the behavior of random lasers in open cavities. Replica Symmetry Breaking theory allows to discern different kinds of randomness in the high pumping regime, including the most complex and intriguing glassy randomness. The outcome of the theoretical study is, eventually, compared to recent intensity fluctuation overlap measurements demonstrating the validity of the theory and providing a straightforward interpretation of qualitatively different spectral behaviors in different random lasers.

| S-EPMC4663759 | biostudies-literature

Symmetry breaking in gastruloid development

Project description:We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 0 to 120h hours.

2023-04-29 | GSE229513 | GEO

Symmetry breaking in gastruloid development

Project description:We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 24 to 84 hours with 12 hours intervals.

2021-09-04 | GSE183255 | GEO

Three-dimensional structures and symmetry breaking in viscoelastic cross-channel flow.

Project description:Using holographic particle tracking, we report the three-dimensional flow structure organizing the viscoelastic instability in cross-channel flow. Beyond a critical Wi, the advective core flow undergoes an out-of-plane instability marked by the emergence of tertiary flow, resembling that of the toroidal vortices in Taylor-Couette geometry. The out-of-plane flow component distorts the separatrix between the impinging inflow streams, triggering symmetry breaking normal to the extension plane. As extensional rate increases, progressively higher order modes of the separatrix are observed, akin to Euler buckling of a rigid column. The disturbances propagate upstream via stress fluctuations despite viscous dissipation. These complex flow structures may be generic to elastic turbulence in mixed flows.

| S-EPMC7799373 | biostudies-literature

Spontaneous mirror-symmetry breaking induces inverse energy cascade in 3D active fluids.

Project description:Classical turbulence theory assumes that energy transport in a 3D turbulent flow proceeds through a Richardson cascade whereby larger vortices successively decay into smaller ones. By contrast, an additional inverse cascade characterized by vortex growth exists in 2D fluids and gases, with profound implications for meteorological flows and fluid mixing. The possibility of a helicity-driven inverse cascade in 3D fluids had been rejected in the 1970s based on equilibrium-thermodynamic arguments. Recently, however, it was proposed that certain symmetry-breaking processes could potentially trigger a 3D inverse cascade, but no physical system exhibiting this phenomenon has been identified to date. Here, we present analytical and numerical evidence for the existence of an inverse energy cascade in an experimentally validated 3D active fluid model, describing microbial suspension flows that spontaneously break mirror symmetry. We show analytically that self-organized scale selection, a generic feature of many biological and engineered nonequilibrium fluids, can generate parity-violating Beltrami flows. Our simulations further demonstrate how active scale selection controls mirror-symmetry breaking and the emergence of a 3D inverse cascade.

| S-EPMC5338532 | biostudies-literature

Excited States, Symmetry Breaking, and Unphysical Solutions in State-Specific CASSCF Theory.

Project description:State-specific electronic structure theory provides a route toward balanced excited-state wave functions by exploiting higher-energy stationary points of the electronic energy. Multiconfigurational wave function approximations can describe both closed- and open-shell excited states and avoid the issues associated with state-averaged approaches. We investigate the existence of higher-energy solutions in complete active space self-consistent field (CASSCF) theory and characterize their topological properties. We demonstrate that state-specific approximations can provide accurate higher-energy excited states in H2 (6-31G) with more compact active spaces than would be required in a state-averaged formalism. We then elucidate the unphysical stationary points, demonstrating that they arise from redundant orbitals when the active space is too large or symmetry breaking when the active space is too small. Furthermore, we investigate the singlet-triplet crossing in CH2 (6-31G) and the avoided crossing in LiF (6-31G), revealing the severity of root flipping and demonstrating that state-specific solutions can behave quasi-diabatically or adiabatically. These results elucidate the complexity of the CASSCF energy landscape, highlighting the advantages and challenges of practical state-specific calculations.

| S-EPMC10226133 | biostudies-literature

Symmetry breaking meets multisite modification.

Project description:Multisite modification is a basic way of conferring functionality to proteins and a key component of post-translational modification networks. Additional interest in multisite modification stems from its capability of acting as complex information processors. In this paper, we connect two seemingly disparate themes: symmetry and multisite modification. We examine different classes of random modification networks of substrates involving separate or common enzymes. We demonstrate that under different instances of symmetry of the modification network (invoked explicitly or implicitly and discussed in the literature), the biochemistry of multisite modification can lead to the symmetry being broken. This is shown computationally and consolidated analytically, revealing parameter regions where this can (and in fact does) happen, and characteristics of the symmetry-broken state. We discuss the relevance of these results in situations where exact symmetry is not present. Overall, through our study we show how symmetry breaking (i) can confer new capabilities to protein networks, including concentration robustness of different combinations of species (in conjunction with multiple steady states); (ii) could have been the basis for ordering of multisite modification, which is widely observed in cells; (iii) can significantly impact information processing in multisite modification and in cell signalling networks/pathways where multisite modification is present; and (iv) can be a fruitful new angle for engineering in synthetic biology and chemistry. All in all, the emerging conceptual synthesis provides a new vantage point for the elucidation and the engineering of molecular systems at the junction of chemical and biological systems.

| S-EPMC8439660 | biostudies-literature

Entropy gives rise to topologically associating domains.

Project description:We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.

| S-EPMC4937343 | biostudies-literature

Mechanochemical symmetry breaking in Hydra aggregates.

Project description:Tissue morphogenesis comprises the self-organized creation of various patterns and shapes. Although detailed underlying mechanisms are still elusive in many cases, an increasing amount of experimental data suggests that chemical morphogen and mechanical processes are strongly coupled. Here, we develop and test a minimal model of the axis-defining step (i.e., symmetry breaking) in aggregates of the Hydra polyp. Based on previous findings, we combine osmotically driven shape oscillations with tissue mechanics and morphogen dynamics. We show that the model incorporating a simple feedback loop between morphogen patterning and tissue stretch reproduces a wide range of experimental data. Finally, we compare different hypothetical morphogen patterning mechanisms (Turing, tissue-curvature, and self-organized criticality). Our results suggest the experimental investigation of bigger (i.e., multiple head) aggregates as a key step for a deeper understanding of mechanochemical symmetry breaking in Hydra.

| S-EPMC4423050 | biostudies-literature

Breaking the Symmetry in Molecular Nanorings.

Project description:Because of their unique electronic properties, cyclic molecular structures ranging from benzene to natural light-harvesting complexes have received much attention. Rigid π-conjugated templated porphyrin nanorings serve as excellent model systems here because they possess well-defined structures that can readily be controlled and because they support highly delocalized excitations. In this study, we have deliberately modified a series of six-porphyrin nanorings to examine the impact of lowering the rotational symmetry on their photophysical properties. We reveal that as symmetry distortions increase in severity along the series of structures, spectral changes and an enhancement of radiative emission strength occur, which derive from a transfer of oscillator strength into the lowest (k = 0) state. We find that concomitantly, the degeneracy of the dipole-allowed first excited (k = ±1) state is lifted, leading to an ultrafast polarization switching effect in the emission from strongly symmetry-broken nanorings.

| S-EPMC4745607 | 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