Geometry Of Nucleus Research Articles

Schrödinger equation for the chiral geometry in atomic nuclei

The dynamical and spectral features of the chiral geometry in atomic nu clei are described by means of a triaxial rigid rotor Hamiltonian cranked by quasiparticle alignments. The problem is treated alternatively in the space of angular momentum states and using a Schr¨odinger equation for a continuous variable associated with an angular momentum projection. The later is con structed using a semiclassical approach. Numerical applications performed for various deformation and alignment conditions with both methods are compared in terms of energy levels and wave functions.

Effect of particle anisotropy on the thermodynamics and kinetics of ordering transitions in hard faceted particles.

Monte Carlo simulations were used to study the influence of particle aspect ratio on the kinetics and phase behavior of hard gyrobifastigia (GBF). First, the formation of a highly anisotropic nucleus shape in the isotropic-to-crystal transition in regular GBF is explained by the differences in interfacial free energies of various crystal planes and the nucleus geometry predicted by the Wulff construction. GBF-related shapes with various aspect ratios were then studied, mapping their equations of state, determining phase coexistence conditions via interfacial pinning, and computing nucleation free-energy barriers via umbrella sampling using suitable order parameters. Our simulations reveal a reduction of the kinetic barrier for isotropic-crystal transition upon an increase in aspect ratio, and that for highly oblate and prolate aspect ratios, an intermediate nematic phase is stabilized. Our results and observations also support two conjectures for the formation of the crystalline state from the isotropic phase: that low phase free energies at the ordering phase transition correlate with low transition barriers and that the emergence of a mesophase provides a steppingstone that expedites crystallization.

Critical Nucleus Size and Activation Energy of Ag Nucleation by Electrochemical Observation of Isolated Nucleation Events.

The induction times for electrodeposition of individual Ag nanoparticles on Pt nanodisk electrodes in acetonitrile were used to determine the critical nucleus size and activation energy barrier associated with the formation of Ag nuclei. Induction times for the nucleation and growth of a single Ag nanoparticle were determined following the application of a potential step to reduce Ag+ at overpotentials, η, ranging from -130 to -70 mV. Sufficiently small Pt electrodes (5.1 × 10-10-2.6 × 10-11 cm2) were used to ensure that the detection of a single Ag nucleation event occurred during the experimental observation time (150 ms-1000 s). Multiple measurements of Ag nucleation induction times were recorded to determine nucleation rates as a function of η using cumulative probability theory. Both classical nucleation theory (CNT) and the atomistic theory of electrochemical nucleation were employed to analyze experimental nucleation rates, without a requisite knowledge of the nucleus geometry or surface free energy. Using the CNT, the number of atoms comprising the critical size nucleus, Nc, was estimated to be 1-9 atoms for η ranging from -130 to -70 mV, in good agreement with 1-5 atoms obtained using atomistic theory. The experimental nucleation rates were also used to determine the activation energy barriers for nucleation from the CNT, which varied from 3.31 ± 0.05 to 13 ± 1 kT over the same range of η.

Geometrical Properties of the Nucleus and Chromosome Intermingling Are Possible Major Parameters of Chromosome Aberration Formation.

Ionizing radiation causes chromosome aberrations, which are possible biomarkers to assess space radiation cancer risks. Using the Monte Carlo codes Relativistic Ion Tracks (RITRACKS) and Radiation-Induced Tracks, Chromosome Aberrations, Repair and Damage (RITCARD), we investigated how geometrical properties of the cell nucleus, irradiated with ion beams of linear energy transfer (LET) ranging from 0.22 keV/μm to 195 keV/μm, influence the yield of simple and complex exchanges. We focused on the effect of (1) nuclear volume by considering spherical nuclei of varying radii; (2) nuclear shape by considering ellipsoidal nuclei of varying thicknesses; (3) beam orientation; and (4) chromosome intermingling by constraining or not constraining chromosomes in non-overlapping domains. In general, small nuclear volumes yield a higher number of complex exchanges, as compared to larger nuclear volumes, and a higher number of simple exchanges for LET < 40 keV/μm. Nuclear flattening reduces complex exchanges for high-LET beams when irradiated along the flattened axis. The beam orientation also affects yields for ellipsoidal nuclei. Reducing chromosome intermingling decreases both simple and complex exchanges. Our results suggest that the beam orientation, the geometry of the cell nucleus, and the organization of the chromosomes within are important parameters for the formation of aberrations that must be considered to model and translate in vitro results to in vivo risks.

Subnucleon fluctuations in coherent and incoherent ultra-peripheral AA collisions at LHC and RHIC with the Sartre event generator

Sartre~has been extensively used for describing photon-nuclei processes at the electron-ion collider (EIC) as well as ultra-peripheral collisions (UPC) at LHC and RHIC. Sartre is an event generator which implements the dipole model for DIS, and models the transverse geometry of the target nucleus or proton in coordinate space. It uses the Good-Walker mechanism for simulating fluctuations which contribute to the incoherent cross section for which the target breaks up after the interaction. With improved precision of UPC measurements in the last years, a detailed test of the dipole model has become possible, and Sartre's model was found lacking. In these proceedings we add subnucleon fluctuations to the nucleus and show that this is sufficient for describing the vast majority of the present measurements. We also find that for larger momentum transfers in the nucleus, which probes gluon fluctuations at higher resolution, the current complexity of the model may not suffice. Future measurements at the LHC, RHIC and especially the EIC has the potential to reveal these gluon vacuum fluctuations and glean novel insights into the self-interacting quantum field of QCD.

A simple pipeline for cell cycle kinetic studies in the root apical meristem.

Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification. Based on this approach, we characterized differences in cell volume, nucleus volume, and nucleus shape across different domains of the Arabidopsis RAM. We found that DNA replication patterns were cell layer and region dependent. G2 phase duration, which varied from 3.5 h in the pericycle to more than 4.5 h in the epidermis, was found to be associated with some features of nucleus geometry. Endocycle duration was determined as the time required to achieve 100% EdU-positive cells in the elongation zone and, as such, it was estimated to be in the region of 5 h for the epidermis and cortex. This experimental pipeline could be used to precisely map cell cycle duration in the RAM of mutants and in response to environmental stress in several plant species without the need for introgressing molecular cell cycle markers.

In-Situ Growth of Nucleus Geometry to Dual Types of Periodically Ringed Assemblies in Poly(nonamethylene terephthalate)

Monitoring of nucleus geometry and growth into dual types of periodically ring-banded morphology in poly(nonamethylene terephthalate) (PNT), respectively, Type-1 and Type-2, are done with detailed analyses using polarized-light optical microscopy (POM) in-situ CCD recording; the periodic assembly morphologies are characterized using atomic-force microscopy (AFM) and scanning electron microscopy (SEM). Different annealing treatments (Tmax = 110, 120, 130 °C) are accomplished at a crystallization temperature of 85 °C; effects on the nucleus geometry, number (25–10%) and volume fractions (33–15%) of Type-2 among two types of banded PNT spherulites are expounded. Growth of a specific type of periodically banded PNT spherulite is initiated from either highly elongated sheaf-like or well-rounded nuclei, with the final grown lamellae being self-packed as multi-shell structures. Nucleation geometry and crystallization parameters collectively lead to development of multiple types of banded PNT spherulites of different relative fractions.

NuSTAR view of heavily absorbed AGN: The R–NH correlation

Context. The nature of the putative torus and the outer geometry of active galactic nuclei (AGN) are still rather unknown and the subject of active research. Improving our understanding of them is crucial for developing a physical picture for the structure of AGN. Aims. The main goal of this work is to investigate the outer geometry of AGN by studying the observed hard X-ray spectrum of obscured sources. We primarily aim at researching the reflected emission in these sources. Methods. To that end, we analysed archived NuSTAR observations of a sample of nearby AGN, whose X-ray emission has been found to be heavily absorbed, with 1023 &lt; NH &lt; 2.5 × 1023 cm−2; the upper limit on NH was necessary due to the analysis we followed and the data quality. Fitting their emission with both a phenomelogical and a physical model, we investigated the relation between reflection and absorption. Results. The strength of reflected emission, as well as the equivalent width of the Fe Kα line, correlates with the absorption column density, which can be explained with a clumpy torus origin for the reflection in these sources. The shape of the observed correlation is found to be well reproduced when the effects of a clumpy torus with a variable filling factor are simulated. A similar increase in reflection seems to be featured even by sources with larger absorption, reaching the Compton thick (NH &gt; 1.5 × 1024 cm−2) regime.

Inferring chromosome radial organization from Hi-C data

BackgroundThe nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations.ResultsA number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells.ConclusionsOur analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.

Computational modelling of metal soap formation in historical oil paintings: the influence of fatty acid concentration and nucleus geometry on the induced chemo-mechanical damage

Metal soap formation is one of the most wide-spread degradation mechanisms observed in historical oil paintings, affecting works of art from museum collections worldwide. Metal soaps develop from a chemical reaction between metal ions present in the pigments and saturated fatty acids, which are released by the oil binder. The presence of large metal soap crystals inside paint layers or at the paint surface can be detrimental for the visual appearance of artworks. Moreover, metal soaps can possibly trigger mechanical damage, ultimately resulting in flaking of the paint. This paper departs from a recently proposed computational model to predict chemo-mechanical degradation in historical oil paintings, as presented in Eumelen et al. (J Mech Phys Solids 132:103683, 2019). The model describes metal soap formation and growth, which are phenomena that are driven by the diffusion of saturated fatty acids and proceed by a nucleation process from a crystalline nucleus of small size. This results into a chemically-induced strain in the paint, which may promote crack nucleation and propagation. The proposed model is here used to investigate the effects of saturated fatty acid concentration and initial nucleus geometry on the amount of chemo-mechanical damage generated. Numerical simulations show that both factors have a marginal influence on the growth rate of the metal soap crystal, but play a significant role on the extent of fracture induced in the paint.

Nitrogen Bubbles at Pt Nanoelectrodes in a Nonaqueous Medium: Oscillating Behavior and Geometry of Critical Nuclei.

Gas bubble evolution is present in many electrochemical and photoelectrochemical processes. We previously reported the formation of individual H2, N2, and O2 nanobubbles generated from electrocatalytic reduction of H+ and oxidation of N2H4 and H2O2, respectively, at Pt nanodisk electrodes in an aqueous solution. All the nanobubbles formed display a dynamic stationary state of a three-phase boundary with an invariant residual current. Here, we test the hypothesis that gas nanobubbles can also be electrogenerated in a nonaqueous medium. Interestingly, we found oscillating bubble behavior corresponding to nucleation, growth, and dissolution in dimethyl sulfoxide and methanol. One possible explanation of the oscillation mechanism is provided by the instable dynamic equilibrium between the gas influx due to supersaturation and outflux due to Laplace pressure. Furthermore, the critical gas concentrations for N2 nanobubble nucleation are estimated to be 148, 386, 200, and 16 times supersaturation and the contact angles of the critical nuclei to be 164°, 151°, 160°, and 174° in water, dimethyl sulfoxide, ethylene glycol, and methanol, respectively. This is the first report on electrochemical nucleation of gas bubbles in nonaqueous solvents. Our electrochemical gas bubble study based on a nanoelectrode platform has proven to be a prototypical example of single-entity electrochemistry.

Single-cell high-content imaging parameters predict functional phenotype of cultured human bone marrow stromal stem cells.

Cultured human bone marrow stromal (mesenchymal) stem cells (hBM‐MSCs) are heterogenous cell populations exhibiting variable biological properties. Quantitative high‐content imaging technology allows identification of morphological markers at a single cell resolution that are determinant for cellular functions. We determined the morphological characteristics of cultured primary hBM‐MSCs and examined their predictive value for hBM‐MSC functionality. BM‐MSCs were isolated from 56 donors and characterized for their proliferative and differentiation potential. We correlated these data with cellular and nuclear morphological features determined by Operetta; a high‐content imaging system. Cell area, cell geometry, and nucleus geometry of cultured hBM‐MSCs exhibited significant correlation with expression of hBM‐MSC membrane markers: ALP, CD146, and CD271. Proliferation capacity correlated negatively with cell and nucleus area and positively with cytoskeleton texture features. In addition, in vitro differentiation to osteoblasts as well as in vivo heterotopic bone formation was associated with decreased ratio of nucleus width to length. Multivariable analysis applying a stability selection procedure identified nuclear geometry and texture as predictors for hBM‐MSCs differentiation potential to osteoblasts or adipocytes. Our data demonstrate that by employing a limited number of cell morphological characteristics, it is possible to predict the functional phenotype of cultured hBM‐MSCs and thus can be used as a screening test for “quality” of hBM‐MSCs prior their use in clinical protocols.

Outgassing-induced acceleration of comet 67P/Churyumov-Gerasimenko

Context. Cometary activity affects the orbital motion and rotation state through sublimation-induced forces. The availability of precise rotation-axis orientation and position data from the Rosetta mission allows us to accurately determine the outgassing of comet Churyumov-Gerasimenko/67P (67P). Aims. We derived the observed non-gravitational acceleration of 67P directly from the trajectory of the Rosetta spacecraft. From the non-gravitational acceleration, we recovered the diurnal outgassing variations and study a possible delay of the sublimation response with respect to the peak of the solar illumination. This allowed us to compare the non-gravitational acceleration of 67P with expectations based on empirical models and common assumptions about the sublimation process. Methods. We used an iterative orbit refinement and Fourier decomposition of the diurnal activity to derive the outgassing-induced non-gravitational acceleration. The uncertainties of the data reduction were established by a sensitivity analysis of an ensemble of best-fit orbits for comet 67P. Results. We find that the Marsden non-gravitational acceleration parameters reproduce part of the non-gravitational acceleration, but need to be augmented by an analysis of the nucleus geometry and surface illumination to draw conclusions about the sublimation process on the surface. The non-gravitational acceleration closely follows the subsolar latitude (seasonal illumination), with a small lag angle with respect to local noon around perihelion. The observed minor changes of the rotation axis do not favor forced precession models for the non-gravitational acceleration. Conclusions. In contrast to the sublimation-induced torques, the non-gravitational acceleration does not place strong constraints on localized active areas on the nucleus. We find a close agreement of the orbit-deduced non-gravitational acceleration and the water production that is independently derived from Rosetta in situ measurements.

Influence of chromatin compaction on simulated early radiation-induced DNA damage using Geant4-DNA.

In this work, we present simulated double-strand breaks (DSBs) obtained for two human cell nucleus geometries. The first cell nucleus represents fibroblasts, filled with DNA molecules in different compaction forms: heterochromatin or euchromatin only. The second one represents an endothelial cell nucleus, either filled with heterochromatin only or with a uniform distribution of 48% of heterochromatin and 52% of euchromatin, obtained from measurements carried out at IRSN. Protons and alpha particles of different energies were used as projectiles. Each cell nucleus model includes a multi-scale description of the DNA target from the molecular level to the whole human genome representation. The cell nucleus models were generated using an extended version of the DnaFabric software in which a new model of euchromatin was implemented in addition to the existing model of heterochromatin. Thus, each nucleus model contains the complete human genome (a total of 6 Gbp) in the G0/G1 phase of the cycle, filled with a continuous chromatin fiber per chromosome that can take into account the heterochromatin and the euchromatin compaction. These geometries were then exported to a simulation chain using the Monte Carlo toolkit Geant4-DNA to perform computations of the physical, physicochemical, and chemical stages, in order to evaluate the influence of chromatin compaction on DSB induction and the contribution of direct and indirect damage, as well as DSB complexity. More direct damage and less indirect damage were observed in the heterochromatin than in the euchromatin. Nevertheless, no difference in terms of DSB complexity was observed between those formed in the heterochromatin or the euchromatin models. Yields of DSB/Gy/Gbp show an increase when both heterochromatin and euchromatin models are taken into account, compared to when only heterochromatin is considered. The results presented indicate that the chromatin compaction decreases DNA damage generated by ionizing radiation and thus, DNA compaction should be considered for the simulation of DNA repair and other cellular outcomes.

SIMULATION OF EARLY RADIATION-INDUCED DNA DAMAGE ON DIFFERENT TYPES OF CELL NUCLEI.

This work presents a comparison of simulated early radiation-induced DNA damage represented by yields of double-strand breaks (DSB) in three different human cell nuclei geometries representing fibroblasts, lymphocytes and endothelial cells for protons and alpha particles of different energies and for different irradiation configurations. Each cell nucleus model includes a multi-scale description of the DNA target from the molecular level to the whole human genome representation (6 Gbp) in the G0/G1 phase of the cell cycle and was generated with the DnaFabric software. The three nuclei differ in shape, volume, and therefore DNA density. A calculation chain based on Geant4-DNA that takes into account the physical, physico-chemical and chemical stages was used to simulate the irradiation of the different cell nuclei. Results show an increase of DSB/primary/μm with an increase of DNA density and an increase of DSB/Gy/Gbp with an increase of the cell nucleus volume which indicates that the cell nucleus shape and size have an impact on early DNA damage, which may play a role in latter effects.

Physical confinement alters sarcoma cell cycle progression and division

ABSTRACTTumor cells experience physical confinement on one or multiple axes, both in the primary tumor and at multiple stages during metastasis. Recent work has shown that confinement in a 3D spheroid alters nucleus geometry and delays cell division, and that vertical confinement impairs mitotic spindle rounding, resulting in abnormal division events. Meanwhile, the effects of bi-axial confinement on cell cycle progression has received little attention. Given the critical role of nuclear shape and mechanics in cell division, we hypothesized that bi-axial physical confinement of the cell body and nucleus would alter cell cycle progression. We used sarcoma cells stably expressing the fluorescence ubiquitination cell cycle indicator (FUCCI), along with fibronectin-coated microchannel devices, and explored the impact of bi-axial physical confinement on cell cycle progression. Our results demonstrate that bi-axial physical confinement reduces the frequency of cell division, which we found to be attributed to an arrest in the S/G2/M phase of the cell cycle, and increases the frequency of abnormal division events. Cell and nuclear morphology were both altered in confinement, with the most confining channels preventing cells from undergoing the normal increase in size from G1 to S/G2/M during cell cycle progression. Finally, our results suggest that confinement induces a mechanical memory to the cells, given our observation of lasting effects on cell division and morphology, even after cells exited confinement. Together, our results provide new insights into the possible impact of mechanical forces on primary and secondary tumor formation and growth.

Experimental Study of the Production of Eta Mesons and Kaons in Cu + Au Interactions at 200 GeV

The first traces of the formation of strongly interacting quark–gluon plasma (sQGP) were found in central collisions of heavy nuclei (A + A) in experiments on the RHIC collider. The quenching of hadron jets, which is seen as a reduction in the yield of particles in A + A collisions relative to their yield in proton–proton collisions, is one observable sign of sQGP formation. Asymmetrical Cu + Au collisions at 200 GeV, which are characterized by a distinct geometry of nucleus overlap that differs from the geometry in symmetrical collision systems (Au + Au or Cu + Cu), are of special interest in systematic studies of the quenching of hadron jets. The results are presented from measuring invariant transverse-momentum spectra and nuclear modification factors of mesons containing strange quarks in Cu + Au collisions at 200 GeV.

Anatomy into Interior Lamellar Assembly in Nuclei-Dependent Diversified Morphologies of Poly(l-lactic acid)

Sophisticated dissection into the interiors of the three different birefringent types of poly(l-lactic acid) (PLLA) spherulites via delicate fracturing across the thickness sections, coupled with proper etching techniques, was adopted to reveal the correlations between the diversified birefringence patterns and interior lamellae assembly. The three types of spherulites are circularly ringed spherulite (type 1), hexagon-shaped axialite (type 2), and circularly core–stripe dendrites (type 3). Such morphological diversification originates from different nuclei geometries. For all three different types (circularly ringed, hexagonal, and core–stripe) of PLLA aggregation into spherulites or dendrites/axialites, the dissected inner lamellar arrangement shares universal commonality of intersecting at a 60° angle in the intersection between different lamellar species, with distinct discontinuity in the grating structures being characteristic of all three types of aggregated PLLA spherulites. This kind of grating a...

Thermal Evolution of the Nucleus of the Comet 67P for 120 Years: Numerical Simulations

Abstract The purpose of this paper is to estimate to what temperatures and to what depth the outer layers of the cometary nuclei are heated for several dozen revolutions around the Sun, and what changes in the composition of the volatiles occur in this case. This is important because it is not clear how much the experimentally obtained results on the composition of cometary comes depend on how long the comet is in the current orbit. Our approach to this problem is based on using 3D model of the geometry and dynamics of a cometary nucleus that takes into account the diurnal rotation and orientation of the rotation axis relative to the Sun to simulate the irradiance to take value of temperature the surface of the nucleus and 1D thermal model of the porous ice-rock body. The results of the numerical simulation of heat propagation in the subsurface layers of some points the MA’AT region of the 67P core, obtained for the 20 orbital cycles (close to 130 years), are presented in this paper.

Complex geometry of nuclei and atoms

We propose a new geometrical model of matter, in which neutral atoms are modelled by compact, complex algebraic surfaces. Proton and neutron numbers are determined by a surface’s Chern numbers. Equivalently, they are determined by combinations of the Hodge numbers, or the Betti numbers. Geometrical constraints on algebraic surfaces allow just a finite range of neutron numbers for a given proton number. This range encompasses the known isotopes.