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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

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.

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.

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 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.

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

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.

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.

Here we develop a microscopic approach aimed at the description of a suite of physical effects related to carrier transport in, and the optical properties of, halide perovskites. Our theory is based on the description of the nuclear dynamics to all orders and goes beyond the common assumption of linear electron-phonon coupling in describing the carrier dynamics and band gap characteristics. When combined with first-principles calculations and applied to the prototypical MAPbI$_{3}$ system, our theory explains seemingly disparate experimental findings associated with both the charge-carrier mobility and optical absorption properties, including their temperature dependencies. Our findings demonstrate that orbital overlap fluctuations in the lead-halide structure plays a significant role in determining the optoelectronic features of halide perovskites.

The multi-configuration time-dependent Hartree (MCTDH) method was applied to study nuclear dynamics following transitions to a manifold of vibronically coupled ground 2A1 and excited 2A2 and 2B1 states of the pyridine radical cation (PRC). These states originate from ionization out of the highest occupied orbitals of pyridine, 7a1 (nσ), 1a2 (π), and 2b1 (π), respectively, and give rise to the lowest two photoelectron bands. We focus on various theoretical and computational aspects of the MCTDH method and methodology to calculate the spectrum, taking our study of the vibronically interacting 2A1, 2A2, and 2B1 states of PRC as an example. In particular, the choice of the single-particle functions (SPFs) and schemes to combine vibrational modes are discussed.

We illustrate the state of the art in time-dependent calculations on systems of chemical interest. In particular, our exposition covers the Gaussian multiconfiguration time-dependent Hartree/variational multiconfiguration Gaussian approach in nuclear dynamics, where the scope is that of explaining dynamical effects in various physicochemical processes. Conversely, the Rice–Ramsperger–Kassel–Marcus/master equation kinetic methods are also examined, used to calculate rate constants of gas phase processes (used in the modeling of combustion, atmospheric, and astrochemical processes).

Principles underlying the organization and operation of the NRV web knowledge base on low-energy nuclear physics (http://nrv.jinr.ru) are described. This base includes a vast body of digitized experimental data on the properties of nuclei and on cross sections for nuclear reactions that is combined with a wide set of interconnected computer programs for simulating complex nuclear dynamics, which work directly in the browser of a remote user. Also, the current situation in the realms of application of network information technologies in nuclear physics is surveyed. The potential of the NRV knowledge base is illustrated in detail by applying it to the example of an analysis of the fusion of nuclei that is followed by the decay of the excited compound nucleus formed.

Proton knockout reactions, in which the scattered beam particle and the outgoing nucleon are detected in coincidence, proved to be a very powerful tool for studying the properties of bound nucleons. The first generation of (e, e′p) data—collected over more than thirty years, starting in the early 1960s—have greatly contributed to establish the validity of the nuclear shell model, showing at the same time its limitations. More recent measurements, made possible by the availability of continuous electron beams of higher energy, have unambiguously demonstrated the occurrence of significant effects of nucleon-nucleon correlations, thus providing new insight into the nature of short-range nuclear dynamics.

Coulomb explosion of CO 2 , CO 2 → CO 2 2 + + 2e − → CO + + O + + 2e − , in phase-locked two-color ultrashort intense laser fields (800 nm and 400 nm, ∼10 14 W/cm 2 ) has been investigated by coincidence momentum imaging. The momentum images of the O + and CO + fragments show asymmetric distributions along the laser polarization direction depending on the relative phase of the two-color laser fields. The fragment asymmetry becomes most prominent (∼4%) at the relative phases providing the largest asymmetry of the electric field amplitude, with the O + fragments preferentially ejected to the stronger field side. The mechanism of the asymmetric bond breaking of the two equivalent C O bonds is discussed in terms of the nuclear dynamics in CO 2 2 + .

The ascomycete Sordaria macrospora has a long history as a model organism for studying fungal sexual development. Starting from an ascospore, sexual fruiting bodies (perithecia) develop within seven days and discharge new ascospores. Sexual development has been studied in detail, revealing genes required for perithecium formation and ascospore germination. However, the germination process per se has not yet been examined. Here I analyze nuclear dynamics during ascospore germination using a fluorescently labeled histone. Live-cell imaging revealed that nuclei are transported into germination vesicles that form on one side of the spore. Polar growth is established from these vesicles.

We propose a "backtracking" mechanism within Tully's fewest switches surface hopping (FSSH) algorithm, whereby whenever one detects consecutive (double) hops during a short period of time, one simply rewinds the dynamics backward in time. In doing so, one reduces the number of hopping events and comes closer to a truly fewest switches surface hopping approach with independent trajectories. With this algorithmic change, we demonstrate that surface hopping can be reasonably accurate for nuclear dynamics in a multidimensional configuration space with a complex-valued (i.e., not real-valued) electronic Hamiltonian; without this adjustment, surface hopping often fails. The added computational cost is marginal. Future research will be needed to assess whether or not this backtracking correction can improve the accuracy of a typical FSSH calculation with a real-valued electronic Hamiltonian (that ignores spin).

Aging is a progressive functional decline in organs and tissues over time and typically represents the accumulation of psychological and social changes in a human being. Diverse diseases, such as cardiovascular, musculoskeletal, and neurodegenerative disorders, are now understood to be caused by aging. While biological assessment of aging mainly focuses on the gradual changes that occur either on the molecular scale, for example, alteration of gene expression and epigenetic modification, or on larger scales, for example, changes in muscle strength and cardiac function, the mechanics that regulates the behavior of individual cells and interactions between the internal elements of cells, are largely missing. In this study, we show that the dynamic features of migrating cells across different human ages could help to establish the underlying mechanism of biological age-dependent cellular functional decline. To determine the relationship between cellular dynamics and human age, we identify the characteristic relationship between cell migration and nuclear motion which is tightly regulated by nucleus-bound cytoskeletal organization. This analysis demonstrates that actomyosin contractility-dependent nuclear motion plays a key role in cell migration. We anticipate this study to provide noble biophysical insights on biological aging in order to precisely diagnose age-related chronic diseases.

Concurrent neutron Compton scattering (NCS) and neutron diffraction experiments at temperatures between 70 K and 300 K have been performed on proton-conducting hydrated BaZr0.7Ce0.2Y0.1O3−δ (BZCY72) fabricated by spark plasma sintering. A combined neutron data analysis, augmented with density functional theory modelling of lattice dynamics, has enabled, for the first time, a mass-selective appraisal of the combined thermal and nuclear quantum effect on nuclear dynamics and thermodynamic stability of this technologically important proton conducting perovskite oxide. The analysis suggests that the nuclear dynamics in hydrated BZCY72 is a result of a subtle interplay of harmonic, anharmonic and thermal effects, with the increased anharmonic character of the lattice dynamics above the orthorhombic to rhombohedral phase transition at 85 K. The anharmonic effect seems to be most pronounced in the case of oxygen and cerium. The analysis of the proton momentum distribution reveals that the concentration of the hydrogen in the BZCY72 lattice is constant across the orthorhombic to rhombohedral phase transition and further down to the room temperature. Moreover, the average hydrogen concentration obtained from our analysis of the mass-resolved neutron Compton scattering data seems to be commensurate with the total vacancy concentration in the BZCY72 framework. The calculation of the vibrational enthalpy of both phases allows obtaining the value of the enthalpy of the orthorhombic to the rhombohedral phase transition of −3.1 ± 1 kJ mol−1. Finally, our analysis of the nuclear kinetic energy of the proton obtained from NCS and the oxygen-oxygen distance distributions obtained from ND allows to conclude that BZCY72 in both the orthorhombic and rhombohedral phase at 70 K and 100 K respectively falls into the category of the KDP-type crystals where proton is probably under the influence of a double-well potential and forms hydrogen bonds of moderate strength. The obtained results have important ramifications for this technological important material.

The relationship between electronic interactions and electronic decoherence is a fundamental problem in chemistry. Here we show that varying the electron-electron interactions does not affect the electronic decoherence in the pure-dephasing limit. In this limit, the effect of varying the electronic interactions is to rigidly shift in energy the diabatic potential energy surfaces without changing their shape, thus keeping the nuclear dynamics in these surfaces that leads to the electronic decoherence intact. This analysis offers a simple and intuitive understanding of previous theoretical and computational efforts to characterize the influence of electronic interactions on the decoherence and opens opportunities to study exact electronic decoherence with approximate electronic structure theories.

A key feature of Notch signaling is that it directs immediate changes in transcription via the DNA-binding factor CSL, switching it from repression to activation. How Notch generates both a sensitive and accurate response-in the absence of any amplification step-remains to be elucidated. To address this question, we developed real-time analysis of CSL dynamics including single-molecule tracking in vivo. In Notch-OFF nuclei, a small proportion of CSL molecules transiently binds DNA, while in Notch-ON conditions CSL recruitment increases dramatically at target loci, where complexes have longer dwell times conferred by the Notch co-activator Mastermind. Surprisingly, recruitment of CSL-related corepressors also increases in Notch-ON conditions, revealing that Notch induces cooperative or "assisted" loading by promoting local increase in chromatin accessibility. Thus, in vivo Notch activity triggers changes in CSL dwell times and chromatin accessibility, which we propose confer sensitivity to small input changes and facilitate timely shut-down.

Physical boundary conditions of the cell define its cytoskeletal organization and thus regulate the force balance on the nucleus. The boundary can be very precisely engineered by plating cells on micropatterned substrate of various geometries. Such modulations of cell shape and size impinge on nuclear morphology and dynamics. Understanding the regulation of nuclear dynamics is crucial for both physiological processes such as migration, wound healing, stem cell differentiation, and gene expression program and for disease conditions like cancer progression and laminopathies. In this chapter, we discuss the different types of nuclear dynamics, translation, rotation, and fluctuations of the nuclear envelope, forces contributing to such dynamics, and their implications in cell physiology.