Nova Reader - Subject https://www.novareader.co Default RSS Feed en-us Newgen KnowledgeWorks <![CDATA[Phenomenology of quantum turbulence in superfluid helium]]> https://www.novareader.co/book/isbn/10.1073/pnas.2018406118 Quantum turbulence—the stochastic motion of quantum fluids such as 4He and 3He-B, which display pure superfluidity at zero temperature and two-fluid behavior at finite but low temperatures—has been a subject of intense experimental, theoretical, and numerical studies over the last half a century. Yet, there does not exist a satisfactory phenomenological framework that captures the rich variety of experimental observations, physical properties, and characteristic features, at the same level of detail as incompressible turbulence in conventional viscous fluids. Here we present such a phenomenology that captures in simple terms many known features and regimes of quantum turbulence, in both the limit of zero temperature and the temperature range of two-fluid behavior.

]]> <![CDATA[Establishment of heterochromatin in domain-size-dependent bursts]]> https://www.novareader.co/book/isbn/10.1073/pnas.2022887118 How repressive heterochromatic states propagate along chromosomes and are subsequently maintained for many cell divisions remain important unanswered questions in biology. Combining mathematical modeling and single-cell measurements, we find that heterochromatin does not propagate in a purely linear manner as often assumed. Rather, sudden transitions can affect large domains globally at once. We suggest this is due to long-range interactions that bring distant nucleosomes close to each other to facilitate their modification. This supports the notion that the compartmentalization of chromatin components within the nucleus and the folding of chromatin into loops dynamically control heterochromatin propagation in three dimensions by bringing nucleosomes and their modifiers into close proximity.

Methylation of histone H3K9 is a hallmark of epigenetic silencing in eukaryotes. Nucleosome modifications often rely on positive feedback where enzymes are recruited by modified nucleosomes. A combination of local and global feedbacks has been proposed to account for some dynamic properties of heterochromatin, but the range at which the global feedbacks operate and the exact mode of heterochromatin propagation are not known. We investigated these questions in fission yeast. Guided by mathematical modeling, we incrementally increased the size of the mating-type region and profiled heterochromatin establishment over time. We observed exponential decays in the proportion of cells with active reporters, with rates that decreased with domain size. Establishment periods varied from a few generations in wild type to >200 generations in the longest region examined, and highly correlated silencing of two reporters located outside the nucleation center was observed. On a chromatin level, this indicates that individual regions are silenced in sudden bursts. Mathematical modeling accounts for these bursts if heterochromatic nucleosomes facilitate a deacetylation or methylation reaction at long range, in a distance-independent manner. A likely effector of three-dimensional interactions is the evolutionarily conserved Swi6HP1 H3K9me reader, indicating the bursting behavior might be a general mode of heterochromatin propagation.

]]> <![CDATA[Deep generative selection models of T and B cell receptor repertoires with soNNia]]> https://www.novareader.co/book/isbn/10.1073/pnas.2023141118 The adaptive immune system relies on many types of B and T cells, whose functions are reflected in the distinct molecular features of their receptor sequences. Here, we introduce an inference framework, soNNia, which integrates interpretable knowledge-based models of immune receptor generation with flexible and powerful deep learning approaches to characterize sequence determinants of receptor function. Using soNNia, we characterize sequence-specific selection associated with receptors harvested from different cell types and tissues. We quantify synergetic interactions between the molecular features of the paired chains making up the receptor. Lastly, we develop a selection-based classifier to identify T cells specific to distinct pathogenic epitopes. Our approach provides a molecular understanding for how sequence determines the specific functionality of immune receptors.

Subclasses of lymphocytes carry different functional roles to work together and produce an immune response and lasting immunity. Additionally to these functional roles, T and B cell lymphocytes rely on the diversity of their receptor chains to recognize different pathogens. The lymphocyte subclasses emerge from common ancestors generated with the same diversity of receptors during selection processes. Here, we leverage biophysical models of receptor generation with machine learning models of selection to identify specific sequence features characteristic of functional lymphocyte repertoires and subrepertoires. Specifically, using only repertoire-level sequence information, we classify CD4+ and CD8+ T cells, find correlations between receptor chains arising during selection, and identify T cell subsets that are targets of pathogenic epitopes. We also show examples of when simple linear classifiers do as well as more complex machine learning methods.

]]> <![CDATA[Hidden order and multipolar exchange striction in a correlated <i>f</i>-electron system]]> https://www.novareader.co/book/isbn/10.1073/pnas.2025317118 Second-order phase transitions in solids occur due to spontaneous symmetry breaking with an order parameter continuously emerging from the disordered high-temperature phase. In some materials, the phase transitions are clearly detected in thermodynamic functions (e.g., specific heat), but the microscopic order parameters remain “hidden” from researchers, in some cases for decades. Here, we show how such hidden-order parameters can be unambiguously identified and the corresponding ordered phase fully described using a first-principles many-body linear response theory. Considering the canonical “hidden-order” system neptunium dioxide, we also identify an unconventional mechanism of spontaneous multipolar exchange striction that induces an anomalous volume contraction of the hidden-order phase in NpO2.

The nature of order in low-temperature phases of some materials is not directly seen by experiment. Such “hidden orders” (HOs) may inspire decades of research to identify the mechanism underlying those exotic states of matter. In insulators, HO phases originate in degenerate many-electron states on localized f

or d
shells that may harbor high-rank multipole moments. Coupled by intersite exchange, those moments form a vast space of competing order parameters. Here, we show how the ground-state order and magnetic excitations of a prototypical HO system, neptunium dioxide NpO2, can be fully described by a low-energy Hamiltonian derived by a many-body ab initio force theorem method. Superexchange interactions between the lowest crystal-field quadruplet of Np4+ ions induce a primary noncollinear order of time-odd rank 5 (triakontadipolar) moments with a secondary quadrupole order preserving the cubic symmetry of NpO2. Our study also reveals an unconventional multipolar exchange striction mechanism behind the anomalous volume contraction of the NpO2 HO phase.

]]> <![CDATA[Evidence of ideal excitonic insulator in bulk MoS<sub>2</sub> under pressure]]> https://www.novareader.co/book/isbn/10.1073/pnas.2010110118 We claim that MoS2
under pressure becomes the long-sought “excitonic insulator” (EI). This is a permanent condensate of excitons, electron–hole pairs bound by Coulomb interaction, which form in the absence of optical excitation. A surge of experimental claims has recently addressed layered materials, because of reduced Coulomb screening. However, the transition to the putative EI is ubiquitously accompanied by the softening of a phonon inducing a structural change; therefore it remains unclear whether the observed phase is excitonic or instead stabilized by electron–phonon interaction. Our calculations show that MoS2
for a range of applied pressure is unstable against the generation of excitons but stable against lattice distortion: We predict that the EI is an antiferroelectric, electronic density wave.

Spontaneous condensation of excitons is a long-sought phenomenon analogous to the condensation of Cooper pairs in a superconductor. It is expected to occur in a semiconductor at thermodynamic equilibrium if the binding energy of the excitons—electron (e

) and hole (h
) pairs interacting by Coulomb force—overcomes the band gap, giving rise to a new phase: the “excitonic insulator” (EI). Transition metal dichalcogenides are excellent candidates for the EI realization because of reduced Coulomb screening, and indeed a structural phase transition was observed in few-layer systems. However, previous work could not disentangle to which extent the origin of the transition was in the formation of bound excitons or in the softening of a phonon. Here we focus on bulk MoS2
and demonstrate theoretically that at high pressure it is prone to the condensation of genuine excitons of finite momentum, whereas the phonon dispersion remains regular. Starting from first-principles many-body perturbation theory, we also predict that the self-consistent electronic charge density of the EI sustains an out-of-plane permanent electric dipole moment with an antiferroelectric texture in the layer plane: At the onset of the EI phase, those optical phonons that share the exciton momentum provide a unique Raman fingerprint for the EI formation. Finally, we identify such fingerprint in a Raman feature that was previously observed experimentally, thus providing direct spectroscopic confirmation of an ideal excitonic insulator phase in bulk MoS2
above 30 GPa.

]]> <![CDATA[Transverse spin dynamics in structured electromagnetic guided waves]]> https://www.novareader.co/book/isbn/10.1073/pnas.2018816118 We formulate and experimentally validate a set of spin–momentum equations which are analogous to the Maxwell’s equations and govern spin–orbit coupling in electromagnetic guided waves. The Maxwell-like spin–momentum equations reveal the spin–momentum locking, the chiral spin texture of the field, Berry phase, and the spin–orbit interaction in the optical near field. The observed spin–momentum behavior can be extended to other classical waves, such as acoustic, fluid, gas, and gravitational waves.

Spin–momentum locking, a manifestation of topological properties that governs the behavior of surface states, was studied intensively in condensed-matter physics and optics, resulting in the discovery of topological insulators and related effects and their photonic counterparts. In addition to spin, optical waves may have complex structure of vector fields associated with orbital angular momentum or nonuniform intensity variations. Here, we derive a set of spin–momentum equations which describes the relationship between the spin and orbital properties of arbitrary complex electromagnetic guided modes. The predicted photonic spin dynamics is experimentally verified with four kinds of nondiffracting surface structured waves. In contrast to the one-dimensional uniform spin of a guided plane wave, a two-dimensional chiral spin swirl is observed for structured guided modes. The proposed framework opens up opportunities for designing the spin structure and topological properties of electromagnetic waves with practical importance in spin optics, topological photonics, metrology and quantum technologies and may be used to extend the spin-dynamics concepts to fluid, acoustic, and gravitational waves.

]]> <![CDATA[Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study]]> https://www.novareader.co/book/isbn/10.1073/pnas.2025263118 Bacteria inactivation by ultraviolet light is caused due to the formation of thymine dimers that inhibit DNA replication. We have used spectroscopic means for the identification of thymine dimer(s) that may pave the way for fast and definite identification of the ratio of live and dead bacteria, as suggested by our previous spectroscopic studies. In the present study, the dissociation of thymine to thymine dimers and (6-4) photoproducts was detected by means of a Raman, absorption, and synchronous fluorescence study. These data provide a fast method for determining, in situ, the reaction mechanism and final photoproducts formed as a function of UV irradiation dose.

In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.

]]> <![CDATA[Metastable–solid phase diagrams derived from polymorphic solidification kinetics]]> https://www.novareader.co/book/isbn/10.1073/pnas.2017809118 Kinetic stabilization of metastable phases in rapidly cooled metals and alloys has been established in experiments for decades. However, atomistic theories that can quantitatively predict the solidification conditions that produce nonequilibrium phases are still in their infancy. Recent advances in pulsed power/laser technologies, as well as in situ characterization, have brought to bear unprecedented understanding of matter at extreme temperatures and pressures. However, accurate predictions of kinetic stabilization of metastable phases that are necessary for physical interpretation of these experiments are lacking. This work provides a blueprint for development of kinetic phase maps of materials undergoing rapid solidification from first principles. Through atomistic simulations, the phases dominating nucleation are identified, and their kinetic stabilities during the growth stage are characterized.

Nonequilibrium processes during solidification can lead to kinetic stabilization of metastable crystal phases. A general framework for predicting the solidification conditions that lead to metastable-phase growth is developed and applied to a model face-centered cubic (fcc) metal that undergoes phase transitions to the body-centered cubic (bcc) as well as the hexagonal close-packed phases at high temperatures and pressures. Large-scale molecular dynamics simulations of ultrarapid freezing show that bcc nucleates and grows well outside of the region of its thermodynamic stability. An extensive study of crystal–liquid equilibria confirms that at any given pressure, there is a multitude of metastable solid phases that can coexist with the liquid phase. We define for every crystal phase, a solid cluster in liquid (SCL) basin, which contains all solid clusters of that phase coexisting with the liquid. A rigorous methodology is developed that allows for practical calculations of nucleation rates into arbitrary SCL basins from the undercooled melt. It is demonstrated that at large undercoolings, phase selections made during the nucleation stage can be undone by kinetic instabilities amid the growth stage. On these bases, a solidification–kinetic phase diagram is drawn for the model fcc system that delimits the conditions for macroscopic grains of metastable bcc phase to grow from the melt. We conclude with a study of unconventional interfacial kinetics at special interfaces, which can bring about heterogeneous multiphase crystal growth. A first-order interfacial phase transformation accompanied by a growth-mode transition is examined.

]]> <![CDATA[Do we understand the solid-like elastic properties of confined liquids?]]> https://www.novareader.co/book/isbn/10.1073/pnas.2021288118 <![CDATA[Universal law for the vibrational density of states of liquids]]> https://www.novareader.co/book/isbn/10.1073/pnas.2022303118 An analytical derivation of the vibrational density of states (DOS) of liquids, and, in particular, of its characteristic linear in frequency low-energy regime, has always been elusive because of the presence of an infinite set of purely imaginary modes—the instantaneous normal modes (INMs). By combining an analytic continuation of the Plemelj identity to the complex plane with the overdamped dynamics of the INMs, we derive a closed-form analytic expression for the low-frequency DOS of liquids. The obtained result explains, from first principles, the widely observed linear in frequency term of the DOS in liquids, whose slope appears to increase with the average lifetime of the INMs. The analytic results are robustly confirmed by fitting simulations data for Lennard-Jones liquids, and they also recover the Arrhenius law for the average relaxation time of the INMs, as expected.

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