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International audience; Viruses are obligate parasites that rely on their host's cellular machinery for replication. To facilitate their replication cycle, many viruses have been shown to remodel the cellular architecture by inducing the formation of membraneless organelles (MLOs). Eukaryotic cells have evolved MLOs that are highly dynamic, self-organizing microenvironments that segregate biological processes and increase the efficiency of reactions by concentrating enzymes and substrates. In the context of viral infections, MLOs can be utilized by viruses to complete their replication cycle. This review focuses on the pathway used by the HIV-1 virus to remodel the nuclear landscape of its host, creating viral/host niches that enable efficient viral replication. Specifically, we discuss how the interaction between the HIV-1 capsid and the cellular factor CPSF6 triggers the formation of nuclear MLOs that support nuclear reverse transcription and viral integration in favored regions of the host chromatin. This review compiles current knowledge on the origin of nuclear HIV-MLOs and their role in early post-nuclear entry steps of the HIV-1 replication cycle.

Over the past decades, the relativistic density functional theory has been greatly developed and widely applied to investigate a variety of nuclear phenomena. In this paper, we briefly review the concept of covariant density functional theory in nuclear physics with a few latest applications in describing nuclear ground-state and excitation properties as well as nuclear dynamics. Moreover, attempts to build a microscopic and universal density functional are also discussed in terms of the successful fully self-consistent relativistic Brueckner–Hartree–Fock calculations.

Principles of genome folding and their relationship to function depend on understanding conformational changes of the chromatin fiber. Analysis of bulk chromatin motion at high resolution is still lacking. We developed Hi-D, a method to quantitatively map DNA dynamics for every pixel simultaneously over the entire nucleus from real-time fluorescence images. Hi-D combines reconstruction of chromatin motion using computer vision and classification of local diffusion processes by Bayesian inference. We found that DNA dynamics in the nuclear interior are spatially organized into 0.3-3μm domains of distinct types of diffusion was uncoupled from chromatin compaction. Reorganization of the network of dynamic domains between quiescent and active cells suggest that the microenvironment plays a predominant role in stochastic chromatin motion. Hi-D opens new perspectives towards understanding of chromatin organization placing global motion of nuclear molecules in the context of nuclear architecture.

Treballs Finals de Grau de Física, Facultat de Física, Universitat de Barcelona, Curs: 2022, Tutors: Amy E. M. Beedle, Jaume Casademunt Viader, In this project we studied the influence of fibrillar adhesions formation on nuclear dynamics and cell migration in human fibroblasts. We first show that their formation is a migrationdependent process that is not observed when fibroblasts are confined. Then, we present significant evidence that in absence of fibrillar adhesions nuclei align with the long axis of the cell less effectively. Moreover, we present promising data that show that nuclear positioning and cell migration arealso altered in these conditions. In conclusion, we establish that fibrillar adhesions formation is a potentially important parameter of nuclear and cellular dynamics in migrating human fibroblasts

We analytically study quantum dissipative dynamics described by the Caldirola-Kanai model with inter-particle interactions. We have found that the dissipative quantum dynamics of the Caldirola-Kanai model can be exactly mapped to a dissipationless quantum dynamics under a negative external harmonic potential, even when the particles are strongly interacting. In particular, we show that the mapping is valid for the unitary Fermi gas, which is relevant for cold atoms and nuclear matters., 12 pages

While most contemporary analyses of South Asian nuclear dynamics acknowledge the presence of a strategic triangle between the region’s three nuclear players, the primary focus usually remains on th...

By means of time-lapse imaging, consistent patterns of nuclei movement in GV oocytes of SN and NSN types, differing in the chromatin configuration and the initial position of the nucleus, were established. Two types of movement specific for the GV oocyte nuclei were shown: directed motion from the periphery to the central region of the oocyte and oscillatory displacements in the central or peripheral region of the oocyte. It was noted that the nuclei of the NSN type oocytes with the initial position at the periphery hardly changed their position and oocytes died 3.5–4 h after the filming started.

The Variational Multi-Configurational Gaussian (vMCG) approach offers a framework to perform exact trajectory-based quantum dynamics. Herein we use two model vibronic coupling Hamiltonians of pyrazine to explore, for the first time, the influence of the coupling between the external field and the Gaussian basis functions (GBFs) in vMCG on the dynamics. We show that when the excitation pulse is short compared to the nuclear dynamics, vertical projection without a field and explicit description of the external field converge. For longer pulses, a sizeable change is observed. We demonstrate that comparatively few GBFs are sufficient to provide qualitative agreement to MCTDH dynamics and a quantitative agreement can be achieved using ∼100 GBFs. Longer pulses require more GBFs due to the prolonged coupling between the ground and excited states. Throughout this work the single set formalism offers the fastest convergence.

Since the beginning of 2018, the nuclear dynamics surrounding the Korean Peninsula have started to change rapidly and dramatically. The world is now watching a series of historic negotiations in which the denuclearization of the Korean Peninsula is to be discussed. Meanwhile, South Korea’s current nuclear policies look paradoxical, mainly in two ways. First, although the Moon Jae-in administration is adhering to its nuclear phaseout policy, the country’s nuclear capacity is likely to grow during his term. Second, South Korea is continuing its research on pyroprocessing – which can be controversial especially from a nonproliferation perspective – for its future spent fuel management while at the same time pursuing the denuclearization of the Korean Peninsula. This article describes the country’s current nuclear capacity, reviews the history of spent fuel management in South Korea, discusses differing views of nuclear elites and the Korean public on the nuclear phaseout and back-end fuel cycle policies, and explains how these paradoxes in current nuclear policies have emerged. The article concludes that South Korea faces nuclear policy dilemmas and that the current policy incoherence could worsen in the future because of contentious internal dynamics.

We investigate the interactions of weakly interacting massive particles (WIMPS) with nucleons in nuclear medium by taking into account the effect of nuclear dynamics. We derive the nonrelativistic effective operators starting from the relativistic mean-field approximation. Certain interactions receive non-negligible corrections, which may significantly change the sensitivities of WIMP-nucleus scattering cross section to these effective operators., 9 pages, 1 table

The chaotic nature of x-ray free-electron-laser pulses is a major bottleneck that has limited the joint temporal and spectral resolution of spectroscopic measurements. We show how to use the stochastic x-ray field statistics to overcome this difficulty by correlation signals averaged over independent pulse realizations. No control is required over the spectral phase of the pulse, enabling immediate application with existing, noisy x-ray free-electron-laser pulses. The proposed stimulated Raman technique provides the broad observation bandwidth and high time-frequency resolution needed for the observation of elementary molecular events. A model is used to simulate chaotic free-electron-laser pulses and calculate their correlation properties. The resulting joint temporal/spectral resolution is exemplified for a molecular model system with time-dependent frequencies and for the RNA base Uracil passing through a conical intersection. Ultrafast coherences, which represent a direct signature of the nonadiabatic dynamics, are resolved. The detail and depth of physical information accessed by the proposed stochastic signal are virtually identical to those obtained by phase-controlled pulses., 24 pages, 13 figures

We provide an exhaustive characterization of structural properties and nuclear dynamics in tungstic acid (WO3·H2O). To this end, we employ neutron and X-ray diffraction (ND and XRD) combined with inelastic neutron scattering (INS) and neutron Compton scattering (NCS) experiments, and we corroborate the analysis with extensive ab initio modeling. The first step in our analysis is the elucidation of the crystal structure based on the refinement of low-temperature powder ND data, extending the knowledge gained from XRD analysis of a mineral specimen of tungstite. These results are confronted with low-temperature INS experiments and zero-temperature phonon calculations. The analysis reveals an inconsistency in the definition of the structure of confined water with respect to crystallographic data, also showing a concomitant failure of the phonon calculations due to a strongly anharmonic confining potential. Extending the computational route toward ab initio MD (AIMD) simulations allows us to probe different structural configurations and provides an improved description of the vibrational dynamics as compared to high-resolution INS experiments, nevertheless, requiring the use of effective classical temperatures. The analysis of both INS and the NCS data reveals a remarkable similarity to the nuclear dynamics earlier reported for water confined in single-wall carbon nanotubes (SWNT), which has been qualitatively described as a new phase of ice. Our analysis reveals a strong two-dimensional hydrogen-bonding network, similar to the shell model for water in SWNT. The reported NCS data show narrowing of the hydrogen momentum distribution with respect to the reference ab initio calculations, indicating a great deal of conformational freedom due to spatial delocalization of protons in the ground state of the system, a clear signature of the quantum character of the nuclei., The authors gratefully acknowledge the financial support from the U.K. Science and Technologies Facilities Council (STFC), granting the beamtime on WISH, TOSCA, and VESUVIO. The authors also acknowledge the computing resources provided by the STFC Scientific Computing Department’s SCARF cluster. K.D. gratefully acknowledges financial support from the Gipuzkoako Foru Aldundia under Grant Number 2020-CIEN-000009-01. This work has been gratefully supported by PL-Grid Infrastructure and the PROMETHEUS facility.

A semi-classical transport model, namely, quantum molecular dynamics (QMD) model, is employed for the theoretical study of nuclear dynamics in case of 197Au+197Au collisions at different beam energies from 20 to 1000 MeV/nucleon and at impact parameters from b = 0 to 13 fm using soft equation of state (EOS). In particular, we study the energy and impact parameter dependence of various quantities like average and maximum density, collision rate and participant-spectator matter. Our findings clearly indicate a significant energy and impact parameter dependence of all quantities. Interestingly, we observed that the variation of the impact parameter leads to drastic change in the participant/spectator matter up to 400 MeV/nucleon, whereas beyond 400 MeV/nucleon, nearly impact parameter independent results are found.

International audience

PA28γ is a nuclear activator of the 20S proteasome, which is involved in the regulation of several essential cellular processes and angiogenesis. Over the past 20 years, many amino acid sites and motifs have been proven to play important roles in the characteristic functions of PA28γ. The number of binding partners and validated cellular functions of PA28γ have increased, which has facilitated the clarification of its involvement in different biological events. PA28γ is involved in the progression of various diseases, and its aberrant overexpression in cancer is remarkable. Patients with low levels of PA28γ expression have a higher survival rate than those with high levels of PA28γ expression, as has been shown for a wide variety of tumors. The functions of PA28γ in cancer can be divided into five main categories: cell proliferation, cell apoptosis, metastasis and invasion, cell nuclear dynamics that have relevance to angiogenesis, and viral infection. In this review, we focus on the role of PA28γ in cancer, summarizing its aberrant expression, prooncogenic effects and underlying mechanisms in various cancers, and we highlight the possible cancer-related applications of PA28γ, such as its potential use in the diagnosis, targeted treatment and prognostic assessment of cancer.

The human adenovirus (Ad) type 2/5 early region 4 (E4) ORF4 protein (E4orf4) exerts a remarkable tumor cell-selective killing activity in mammalian cells. This indicates that E4orf4 can target tumor cell-defining features and is a unique tool to probe cancer cell vulnerabilities. Recently, we found that E4orf4, through an interaction with the polarity protein PAR3, subverts nuclear envelope (NE) remodeling processes in a tumor cell-selective manner. In this Perspective, we outline mechanical signals that modify nuclear dynamics and tumor cell behavior to highlight potential mechanisms for E4orf4's tumoricidal activity. Through an analysis of E4orf4's cellular targets, we define a protein subnetwork that comprises phosphatase systems interconnected to polarity protein hubs, which could contribute to enhanced NE plasticity. We infer that elucidating E4orf4's protein network at a functional level could uncover key mechanisms of NE remodeling that define the tumor cell phenotype.

We report the results of a study aimed at inferring direct information on the repulsive three-nucleon potential $V^R_{ijk}$\textemdash driving the stiffness of the nuclear matter equation of state at supranuclear densities\textemdash from astrophysical observations. Using a Bayesian approach, we exploit the measurements of masses, radii and tidal deformabalities performed by the NICER satellite and the LIGO/Virgo collaboration, as well as the mass of the heaviest observed pulsar, to constrain the strength of $V^R_{ijk}$. The baseline of our analysis is the widely employed nuclear Hamiltonian comprising the Argonne $v_{18}$ nucleon-nucleon potential andthe Urbana IX model of three-nucleon potential. The numerical results, largely determined by the bound on the maximum mass, suggest that existing and future facilities have the potential to provide valuable new insight into microscopic nuclear dynamics at supranuclear densities., Discussion of the results extended. Various changes to match the version in press on Phys. Rev. C

We study two different methods to prepare excited states on a quantum computer, a key initial step to study dynamics within linear response theory. The first method uses unitary evolution for a short time $T=\mathcal{O}(\sqrt{1-F})$ to approximate the action of an excitation operator $\hat{O}$ with fidelity $F$ and success probability $P\approx1-F$. The second method probabilistically applies the excitation operator using the Linear Combination of Unitaries (LCU) algorithm. We benchmark these techniques on emulated and real quantum devices, using a toy model for thermal neutron-proton capture. Despite its larger memory footprint, the LCU-based method is efficient even on current generation noisy devices and can be implemented at a lower gate cost than a naive analysis would suggest. These findings show that quantum techniques designed to achieve good asymptotic scaling on fault tolerant quantum devices might also provide practical benefits on devices with limited connectivity and gate fidelity., 25 pages, 19 figures (some circuits shown as figures); small modifications; title changed; version accepted for publication

We develop a formalism to calculate electromagnetic (EM) transition rates for rotational-vibrational models of nuclei. The formalism is applied to recently proposed models of ¹²C and ¹⁶O which are inspired by nuclear dynamics in the Skyrme model. We compare the results to experimental data as well as other nuclear models. The results for ¹²C are in good agreement with the data across all models, making it difficult to differentiate the models. More experimental data is needed to do this, and we suggest which transitions would be most interesting to measure. The models of ¹⁶O are less successful in describing the data, and we suggest some possible improvements to our approximations which may help.

We propose a method for enacting the unitary time propagation of two interacting neutrons at leading order of chiral effective-field theory by efficiently encoding the nuclear dynamics into a single multilevel quantum device. The emulated output of the quantum simulation shows that, by applying a single gate that draws on the underlying characteristics of the device, it is possible to observe multiple cycles of the nuclear dynamics before the onset of decoherence. Owing to the signal's longevity, we can then extract spectroscopic properties of the simulated nuclear system. This allows us to validate the encoding of the nuclear Hamiltonian and the robustness of the simulation in the presence of quantum-hardware noise by comparing the extracted spectroscopic information to exact calculations. This work paves the way for transformative calculations of the dynamical properties of nuclei on near-term quantum devices.

Feshbach resonances corresponding to metastable vibrational states of the dipole-bound state (DBS) have been interrogated in real time for the first time. The state-specific autodetachment rates of the DBS of the phenoxide anion in the cryogenically cooled ion trap have been directly measured, giving $\ensuremath{\tau}\ensuremath{\sim}33.5\text{ }\text{ }\mathrm{ps}$ for the lifetime of the most prominent ${11}^{\ensuremath{'}1}$ mode ($519\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$). Overall, the lifetime of the individual DBS state is strongly mode dependent to give $\ensuremath{\tau}\ensuremath{\sim}5\text{ }\text{ }\mathrm{ps}$ for the ${18}^{\ensuremath{'}1}$ mode ($632\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$) and $\ensuremath{\tau}\ensuremath{\sim}12\text{ }\text{ }\mathrm{ps}$ for the ${11}^{\ensuremath{'}2}$ mode ($1036\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$). The qualitative trend of the experiment could be successfully explained by the Fermi's golden rule. Autodetachment of the ${11}^{\ensuremath{'}1}{18}^{\ensuremath{'}1}$ combination mode is found to be much accelerated ($\ensuremath{\tau}\ensuremath{\le}1.4\text{ }\text{ }\mathrm{ps}$) than expected, and its bifurcation dynamics into either the ${11}^{1}{18}^{0}$ or ${11}^{0}{18}^{1}$ state of the neutral core radical, according to the propensity rule of $\mathrm{\ensuremath{\Delta}}v=\ensuremath{-}1$, could be distinctly differentiated through the photoelectron images to provide the unprecedented deep insights into the interaction between electronic and nuclear dynamics of the DBS, challenging the most sophisticated theoretical calculations.

In this paper, we briefly review the studies on nuclear structure and nuclear dynamics using the Canonical-basis time-dependent Hartree-Fock-Bogoliubov (Cb-TDHFB) theory which is one of the time-dependent mean-field models which deal with nuclear pairing. At first, after a brief introduction of the time-dependent mean-field models, we explain the derivation and the properties of Cb-TDHFB equations. Next, we introduce the methods to study the nuclear linear responses and to simulate the nuclear collision in terms of the time-dependent mean-field models. Then, we display parts of the results obtained by using the time-dependent methods; Electric dipole ($E1$) excitation mode of $^{172}$Yb which is a heavy and prolate deformed open-shell nucleus, Systematic study of low-energy $E1$ mode, and Comparison of the simulations of the fusion reactions using time-dependent mean-field models with and without pairing correlation. Finally, we summarize the Cb-TDHFB activities and discuss its perspectives.

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that continuously carry thousands of nuclei in their spores and hyphae. This unique cellular biology raises fundamental questions regarding their nuclear dynamics. This review aims to address these by synthesizing current knowledge of nuclear content and behavior in these ubiquitous soil fungi. Overall, we find that that nuclear counts, as well as the nuclei shape and organization, vary drastically both within and among species in this group. By comparing these features with those of other fungi, we highlight unique aspects of the AMF nuclear biology that require further attention. The potential implications of the observed nuclear variability for the biology and evolution of these widespread plant symbionts are discussed.

Molecular frame angular distributions of electrons released by interatomic Coulombic decay of ${\mathrm{He}}^{+*}(2\ensuremath{\ell})\text{\ensuremath{-}}\mathrm{He}$ states are studied theoretically by means of electronic structure and nonadiabatic nuclear dynamics calculations. In previous experimental work [Phys. Rev. A 82, 063405 (2010)], distinct variations of the angular emission patterns have been observed for different ranges of kinetic-energy release of the fragment ions. Good agreement between the presently computed and these measured angular distributions can be achieved by assuming nonequal populations of ${}^{2}{\mathrm{\ensuremath{\Sigma}}}_{g/u}^{+}$ and ${}^{2}{\mathrm{\ensuremath{\Pi}}}_{g/u}$ decaying electronic states via initial shake-up ionization of the dimers.

International audience; A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.

Summary Cell divisions are essential for tissue growth. In pseudostratified epithelia, where nuclei are staggered across the tissue, each nucleus migrates apically before undergoing mitosis. Successful apical nuclear migration is critical for planar-orientated cell divisions in densely packed epithelia. Most previous investigations have focused on the local cellular mechanisms controlling nuclear migration. Inter-species and inter-organ comparisons of different pseudostratified epithelia suggest global tissue architecture may influence nuclear dynamics, but the underlying mechanisms remain elusive. Here, we use the developing Drosophila wing disc to systematically investigate, in a single epithelial type, how changes in tissue architecture during growth influence mitotic nuclear migration. We observe distinct nuclear dynamics at discrete developmental stages, as epithelial morphology changes. We use genetic and physical perturbations to show a direct effect of cell density on mitotic nuclear positioning. We find Rho kinase and Diaphanous, which facilitate mitotic cell rounding in confined cell conditions, are essential for efficient apical nuclear movement. Perturbation of Diaphanous causes increasing defects in apical nuclear migration as the tissue grows and cell density increases, and these defects can be reversed by acute physical reduction of cell density. Our findings reveal how the mechanical environment imposed on cells within a tissue alters the molecular and cellular mechanisms adopted by single cells for mitosis., Graphical Abstract, Highlights • Mitotic nuclear dynamics change as the Drosophila wing disc develops and grows • Cell density is the primary driver of the differences in mitotic nuclear dynamics • Mitotic rounding and nuclear dynamics depend on Dia in a density-dependent manner • Nuclear dynamic defects in Dia mutants can be reversed by physical perturbations, By using genetic and physical manipulations of cell packing, Kirkland et al. find a density-dependent regulation of mitotic nuclear dynamics in the developing Drosophila wing disc. Moreover, they show a differential requirement of Rok and Dia for mitotic rounding and apical nuclear positioning as cell density increases during development.

Theoretical frameworks used to qualitatively and quantitatively describe nuclear dynamics in solids are often based on the harmonic approximation. However, this approximation is known to become inaccurate or to break down completely in many modern functional materials. Interestingly, there is no reliable measure to quantify anharmonicity so far. Thus, a systematic classification of materials in terms of anharmonicity and a benchmark of methodologies that may be appropriate for different strengths of anharmonicity is currently impossible. In this work, we derive and discuss a statistical measure that reliably classifies compounds across temperature regimes and material classes by their "degree of anharmonicity". This enables us to distinguish "harmonic" materials, for which anharmonic effects constitute a small perturbation on top of the harmonic approximation, from strongly "anharmonic" materials, for which anharmonic effects become significant or even dominant and the treatment of anharmonicity in terms of perturbation theory is more than questionable. We show that the analysis of this measure in real and reciprocal space is able to shed light on the underlying microscopic mechanisms, even at conditions close to, e.g., phase transitions or defect formation. Eventually, we demonstrate that the developed approach is computationally efficient and enables rapid high-throughput searches by scanning over a set of several hundred binary solids. The results show that strong anharmonic effects beyond the perturbative limit are not only active in complex materials or close to phase transitions, but already at moderate temperatures in simple binary compounds., Comment: 17 figures, 2 tables, and 12 pages

The observation of the gravitational wave signal GW170817, consistent with emission from the inspiral of a binary neutron-star system, provided information on the tidal deformation of the participating stars. The available data may be exploited to constrain the equation of state of densenuclear matter, as well as to shed light on the underlying models describing nuclear dynamics at microscopic level. In this paper we compare the experimental results to the predictions of different theoretical models, based on non relativistic nuclear many-body theory, the relativistic field-theoretical formalism, and a more phenomenological approach constrained by observed nuclear properties. While the precision of the available data does not allow to resolve the degeneracy of the models, our analysis shows a distinct sensitivity to the star compactness predicted by the different equations of state, which turns out to be significantly affected by relativistic boost corrections to the nucleon-nucleon potential., Comment: Accepted for publication in Physical Review C

The paper describes the NRV web knowledge base on low-energy nuclear physics developed in the Joint Institute for Nuclear Research. The NRV knowledge base working through the Internet integrates a large amount of digitized experimental data on the properties of nuclei and nuclear reaction cross sections with a wide range of computational programs for modeling of nuclear properties and nuclear dynamics. Today, the NRV becomes a powerful instrument for nuclear physics research as well as for educational applications. Advantages of the functioning scheme of the knowledge base provide the synergy of coexistence of the experimental data and computational codes within one platform.

A procedure for diabatization of quantum-chemical data is proposed that allows one to surmount the problem of -shaped peaks of nonadiabatic matrix elements $$ $$ by passing to a hybrid diabatic representation of a system of coupled channel equations of nuclear dynamics with the use of model nonadiabatic matrix elements that approach initially specified matrix elements. Results of the application of this method within the framework of the Landau–Zener model are presented for the example of the CaH collision system.

"Where do we go from here?" is the underlying question regarding the future (perhaps foreseeable) developments in computational chemistry. Although this young discipline has already permeated practically all of chemistry, it is likely to become even more powerful with the rapid development of computational hard- and software.

Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the ‘gold standard’ for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.

Electron-nuclear dynamics of molecular high-order harmonic generation from H2 + and its isotopes has been theoretically investigated beyond the Born-Oppenheimer approximations. The results show that (i) due to the different ionisation probabilities and the harmonic emission times, the intensities of the harmonics from H2 + and its isotopes are very sensitive to the initial vibrational state, the pulse duration, and the pulse intensity. (ii) Due to the nonadiabatic effects in molecular high-order harmonic generation, the red-shifts of the harmonics can be found in the lower pulse intensity. With the increase of the pulse intensity, the harmonics are from the red-shifts to the blue-shifts. Moreover, as the pulse duration increases, the blue-shifts of the harmonics can be enhanced. As the initial vibrational state increases, the red-shifts of the harmonics can be decreased, whereas the blue-shifts of the harmonics can be enhanced. However, the shifts of the harmonics are decreased as the nuclear mass increases. (iii) Due to the coupled electron-nuclear dynamics in molecules, the spatial symmetry of the system is broken. As a result, non-odd harmonics can be generated at the larger internuclear distance. With the increase of the initial vibrational state or the nuclear mass, the generation of the non-odd harmonics can be enhanced and reduced, respectively. As the pulse duration or the pulse intensity increase, the generation of the non-odd harmonics can be enhanced. However, the intensities of the non-odd harmonics are decreased when using the longer pulse duration with the much higher laser intensity.

We show that molecular aggregation can strongly influence the nonradiative decay (NRD) lifetime of an electronic excitation. As a demonstrative example, we consider a transition-dipole-dipole-interacting dimer whose monomers have harmonic potential energy surfaces (PESs). Depending on the position of the NRD channel ($q_{\rm nr}$), we find that the NRD lifetime ($\tau_{\rm nr}^{\rm dim}$) can exhibit a completely different dependence on the intermolecular-interaction strength. We observe that (i) for $q_{\rm nr}$ near the Franck-Condon region, $\tau_{\rm nr}^{\rm dim}$ increases with the interaction strength; (ii) for $q_{\rm nr}$ near the minimum of the monomer excited PES, the intermolecular interaction has little influence on $\tau_{\rm nr}^{\rm dim}$; (iii) for $q_{\rm nr}$ near the classical turning point of the monomer nuclear dynamics, on the other side of the minimum, $\tau_{\rm nr}^{\rm dim}$ decreases with the interaction strength. Our findings suggest design principles for molecular systems where a specific fluorescence quantum yield is desired.

// Shalaka Chitale 1,2 and Holger Richly 1 1 Laboratory of Molecular Epigenetics, Institute of Molecular Biology, Mainz, Germany, Ackermannweg, Mainz, Germany 2 Faculty of Biology, Johannes Gutenberg University, Mainz, Germany Correspondence to: Holger Richly, email: // Keywords : nucleotide excision repair, DNA repair, ubiquitin, chromatin, nuclear dynamics Received : November 10, 2016 Accepted : February 15, 2017 Published : March 11, 2017 Abstract One of the major cellular DNA repair pathways is nucleotide excision repair (NER). It is the primary pathway for repair of various DNA lesions caused by exposure to ultraviolet (UV) light, such as cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. Although lesion-containing DNA associates with the nuclear matrix after UV irradiation it is still not understood how nuclear organization affects NER. Analyzing unscheduled DNA synthesis (UDS) indicates that NER preferentially occurs in specific nuclear areas, viz the nucleolus. Upon inducing localized damage, we observe migration of damaged DNA towards the nucleolus. Employing a LacR-based tethering system we demonstrate that H2A-ubiquitylation via the UV-RING1B complex localizes chromatin close to the nucleolus. We further show that the H2A-ubiquitin binding protein ZRF1 resides in the nucleolus, and that it anchors ubiquitylated chromatin along with XPC. Our data thus provide insight into the sub-nuclear organization of NER and reveal a novel role for histone H2A-ubiquitylation.

Duchenne muscular dystrophy (DMD) is a genetic disorder in which the absence of dystrophin leads to progressive muscle degeneration and weakness. Although the genetic basis is known, the pathophysiology of dystrophic skeletal muscle remains unclear. We examined nuclear movement in wild-type (WT) and muscular dystrophy mouse model for DMD (MDX) (dystrophin-null) mouse myofibers. We also examined expression of proteins in the linkers of nucleoskeleton and cytoskeleton (LINC) complex, as well as nuclear transcriptional activity via histone H3 acetylation and polyadenylate-binding nuclear protein-1. Because movement of nuclei is not only LINC dependent but also microtubule dependent, we analyzed microtubule density and organization in WT and MDX myofibers, including the application of a unique 3D tool to assess microtubule core structure. Nuclei in MDX myofibers were more mobile than in WT myofibers for both distance traveled and velocity. MDX muscle shows reduced expression and labeling intensity of nesprin-1, a LINC protein that attaches the nucleus to the microtubule and actin cytoskeleton. MDX nuclei also showed altered transcriptional activity. Previous studies established that microtubule structure at the cortex is disrupted in MDX myofibers; our analyses extend these findings by showing that microtubule structure in the core is also disrupted. In addition, we studied malformed MDX myofibers to better understand the role of altered myofiber morphology vs. microtubule architecture in the underlying susceptibility to injury seen in dystrophic muscles. We incorporated morphological and microtubule architectural concepts into a simplified finite element mathematical model of myofiber mechanics, which suggests a greater contribution of myofiber morphology than microtubule structure to muscle biomechanical performance.NEW & NOTEWORTHY Microtubules provide the means for nuclear movement but show altered organization in the muscular dystrophy mouse model (MDX) (dystrophin-null) muscle. Here, MDX myofibers show increased nuclear movement, altered transcriptional activity, and altered linkers of nucleoskeleton and cytoskeleton complex expression compared with healthy myofibers. Microtubule architecture was incorporated in finite element modeling of passive stretch, revealing a role of fiber malformation, commonly found in MDX muscle. The results suggest that alterations in microtubule architecture in MDX muscle affect nuclear movement, which is essential for muscle function.

Recently a coherence controlled (CC) approach to nonadiabatic dynamics was proposed by one of the authors based on the mapping between the decomposed classical state space and different types of nuclear dynamics. Here we elaborate the state-space decomposition scheme and the corresponding state-space-to-dynamics mapping of the CC approach in a general high-dimensional framework. In the CC formalism, dynamical properties such as the full electronic matrix can be evaluated by means of the ensemble of trajectories in the active state space, which consists of single-state domains and coherence domains. The feasibility of the state space decomposition and related mappings and the performance of the CC approach are demonstrated by the implementation to benchmark problems of nonadiabatic molecular dynamics in condensed phase including the spin-boson model and the excitation energy transfer problem in photosynthesis. The results obtained from the CC approach are in reasonably good agreement with exact or benchmark calculations, and it is also shown that the CC approach satisfies the detailed balance approximately and is capable of efficiently describing condensed phase nonadiabatic molecular dynamics at reasonable accuracy.

Repairing double-strand breaks (DSBs) is particularly challenging in pericentromeric heterochromatin, where the abundance of repeated sequences exacerbates the risk of ectopic recombination and chromosome rearrangements. Recent studies in Drosophila cells revealed that faithful homologous recombination repair of heterochromatic DSBs relies on the relocalization of DSBs to the nuclear periphery before Rad51 recruitment. Here we summarize the exciting progress in understanding this pathway, including conserved responses in mammalian cells and surprising similarities with mechanisms available in yeast to deal with DSBs in other sites that are difficult to repair, including other repeated sequences. We will also point out some of the most important open questions in the field and emerging evidence suggesting that deregulating these pathways might have dramatic consequences for human health.

We calculate the rovibrational states of the protonated methane molecular ion CH5+ for angular momenta up to J = 4. Our novel approach is based on a quantum graph description of the low-energy nuclear dynamics. Previous work on the quantum graph model neglected rotational degrees of freedom and so only described purely vibrational excitations. We extend this work significantly to give the first example of a full rovibrational quantum graph model. We compare our results to 7D variational calculations, finding good agreement for J ≤ 3. To the best of our knowledge, the J = 4 results are the first of their kind.

International audience; Nucleus position in cells can act as a developmental cue. Mammalian oocytes position their nucleus centrally using an F-actin-mediated pressure gradient. The biological significance of nucleus centering in mammalian oocytes being unknown, we sought to assess the F-actin pressure gradient effect on the nucleus. We addressed this using a dedicated computational 3D imaging approach, biophysical analyses, and a nucleus repositioning assay in mouse oocytes mutant for cytoplasmic F-actin. We found that the cytoplasmic activity, in charge of nucleus centering, shaped the nucleus while promoting nuclear envelope fluctuations and chromatin motion. Off-centered nuclei in F-actin mutant oocytes were misshaped with immobile chromatin and modulated gene expression. Restoration of F-actin in mutant oocytes rescued nucleus architecture fully and gene expression partially. Thus, the F-actin-mediated pressure gradient also modulates nucleus dynamics in oocytes. Moreover, this study supports a mechano-transduction model whereby cytoplasmic microfilaments could modulate oocyte transcriptome, essential for subsequent embryo development.

Mixed quantum–classical mechanical descriptions are critical to modeling coupled electron–nuclear dynamics, i.e., nonadiabatic molecular dynamics, relevant to photochemical and photophysical processes. We introduce an efficient description of such dynamics in terms of an effective Hamiltonian that not only properly captures electron–nuclear correlation effects but also helps develop an efficient computational method. In particular, we introduce a coupled Gaussian wavepacket parametrization of the nuclear wave function, which generalizes the Ehrenfest approach to account for electron–nuclei correlations. We test this new approach, Ehrenfest-Plus, on a suite of model problems that probe electron–nuclear correlation in nonadiabatic transitions. The high accuracy of our approach, combined with mixed quantum–classical efficiency, opens a path for improved simulation of nonadiabatic molecular dynamics in realistic molecular systems.

We review theoretical methods which can be used for the simulation of time-dependent electronic and nuclear dynamics of gas-phase molecules beyond the Born-Oppenheimer approximation. We concentrate on methods which allow for a description of extensive electronic excitation and ionization. Particular emphasis is placed on the extended multiconfiguration time-dependent Hartree-Fock (Ex-MCTDHF) method. We provide a derivation of the equations of motion of the Ex-MCTDHF method, and discuss its advantages and disadvantages over the methods based on the Born-Huang expansion.

Time-dependent Hartree-Fock (TDHF) theory has been a powerful tool in describing a variety of complex nuclear dynamics microscopically without empirical parameters. In this contribution, recent advances in nuclear dynamics studies with TDHF and its extensions are briefly reviewed, along the line with the study of multinucleon transfer (MNT) reactions. The latter lies at the core of this Research Topic, whose application for production of extremely neutron-rich nuclei has been extensively discussed in recent years. Having in mind the ongoing theoretical developments, it is envisaged how microscopic theories may contribute to the future MNT study., Comment: 13 pages, 1 figure; An invited mini review to be published in: Research Topic "Structure, Reaction and Production Mechanism of Extremely Neutron-Rich Nuclei" (ed.) N. Wang, A. Bonaccorso, and S.-G. Zhou, in Frontiers in Physics, section Nuclear Physics

In this paper, the ultrafast dissociation following Cl 2p core–shell excitation into the 10a1* antibonding orbital in CH2Cl2 and CD2Cl2 molecules is studied. It is observed the presence of atomic Auger lines associated to the decay of dissociated Cl* atoms. The choice of CH2Cl2 and CD2Cl2 molecules to study the competition between the atomic and molecular Auger decays, allow us to probe nuclear dynamics and electron relaxation occurring on a comparable time scale, keeping other parameters identical.In this paper, the ultrafast dissociation following Cl 2p core–shell excitation into the 10a1* antibonding orbital in CH2Cl2 and CD2Cl2 molecules is studied. It is observed the presence of atomic Auger lines associated to the decay of dissociated Cl* atoms. The choice of CH2Cl2 and CD2Cl2 molecules to study the competition between the atomic and molecular Auger decays, allow us to probe nuclear dynamics and electron relaxation occurring on a comparable time scale, keeping other parameters identical.

We present a combined experimental and theoretical study of the Auger-emission spectrum following double core ionization and excitation of gas-phase water molecules with hard-x-ray synchrotron radiation above the O $K^{−2}$ threshold. We observe an indication of ultrafast proton motion occurring within the 1.5 fs lifetime of the double-core-hole (DCH) states in water. Furthermore, we have identified symmetric and antisymmetric dissociation modes characteristic for particular DCH states. Our results serve as a fundamental reference for state-of-the-art studies of DCH dynamic processes in liquid water both at synchrotron and free-electron-laser facilities.