Quantum Dynamics of Water from Møller-Plesset Perturbation Theory via a Neural Network Potential

We report the static and dynamical properties of liquid water at the level of second-order Møller-Plesset per- perturbation theory (MP2) with classical and quantum nuclear dynamics using a neural network potential. We examined the temperature-dependent radial distribution functions, diffusion, and vibrational dynamics. MP2 theory predicts over-structured liquid water as well as a lower diffusion coefficient at ambient conditions compared to experiments, which may be attributed to the incomplete basis set. A better agreement with experimental structural properties and the diffusion constant are observed at an elevated temperature of 340 K from our simulations. Although the high-level electronic structure calculations are expensive, training a neural network potential requires only a few thousand frames. The approach is promising as it involves modest human effort and is straightforwardly extensible to other simple liquids.

Methods to Calculate Electronic Excited-state Dynamics For Molecules on Large Metal Clusters with Many States: Ensuring Fast Overlap Calculations and a Robust Choice of Phase

We present an efficient set of methods for propagating excited-state dynamics involving a large number of electronic states based on a CIS electronic state overlap scheme. Specifically, (i) following Head-Gordon et al, we implement an exact evaluation of the overlap of singly-excited electronic states at different nuclear geometries using a biorthogonal basis, and (ii) we employ a unified protocol for choosing the correct phase for each adiabat at each geometry. For many-electron systems, the combination of these techniques significantly reduces the computational cost of integrating the electronic Schrodinger equation and imposes minimal overhead on top of the underlying electronic structure calculation. As a demonstration, we calculate the electronic excited-state dynamics for a hydrogen molecule scattering off a silver metal cluster, focusing on high-lying excited states where many electrons can be excited collectively and crossings are plentiful. Interestingly, we find that the high-lying, plasmon-like collective excitation spectrum changes with nuclear dynamics, highlighting the need to simulate non-adiabatic nuclear dynamics and plasmonic excitations simultaneously. In the future, the combination of methods presented here should help theorists build a mechanistic understanding of plasmon-assisted charge transfer and excitation energy relaxation processes near a nanoparticle or metal surface.

Challenges in Nuclear Posture and Deterrence from India’s Perspective

South Asia comprises eight countries, among which India and Pakistan are two nuclear weapon powers marked by strained relations. Within this dynamic, this essay examines India’s nuclear path, in spite of its staunch support for a nuclear-weapon-free world. It covers Pakistan’s nuclear journey through proliferation and the logic for it to perpetrate state-sponsored terrorism against India, arguing that this serves as a major factor that could lead to war. Despite this potential, it also explains why South Asia is not the most dangerous nuclear flashpoint in the world. In addition to India and Pakistan, five other nuclear nations are present in the region, namely China, Russia, Israel, North Korea and the United States. As such, this essay discusses positive and negative effects of each of these powers on nuclear dynamics of the region. It concludes with recommendations for fostering strategic stability in South Asia.

Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity

Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.

XopQ induced stromule formation in Nicotiana benthamiana is causally linked to ETI signaling and depends on ADR1 and NRG1

In Nicotiana benthamiana, expression of the Xanthomonas effector XopQ triggers ROQ1-dependent ETI responses and in parallel accumulation of plastids around the nucleus and the formation of stromules. Both processes were proposed to contribute to ETI-related hypersensitive cell death and thereby to plant immunity. Whether these reactions are directly connected to ETI signaling events has not been tested. Here we utilized transient expression experiments to determine whether XopQ-mediated plastid reactions are a result of XopQ perception by ROQ1 or a consequence of XopQ virulence activity. We find that N. benthamiana mutants lacking ROQ1, both RNLs (NRG1 and ADR1) or EDS1, fail to elicit XopQ-dependent host cell death and stromule formation. Mutants lacking only NRG1 lost XopQ-dependent cell death but retained some stromule induction that was abolished in the RNL double mutant. This analysis aligns XopQ-induced stromules with the ETI signaling cascade but not to host programmed cell death. Furthermore, data reveal that XopQ-triggered plastid clustering is not strictly linked to stromule formation during ETI. Our data suggest that stromule formation, in contrast to chloroplast peri-nuclear dynamics, is an integral part of the N. benthamiana ETI response and that both RNL sub-types play a role in this ETI response.

Nucleophagy contributes to genome stability though TOP2cc and nucleolar components degradation

ABSTRACTThe nuclear architecture of mammalian cells can be altered as a consequence of anomalous accumulation of nuclear proteins or genomic alterations. Most of the knowledge about nuclear dynamics comes from studies on cancerous cells. How normal, healthy cells maintain genome stability avoiding accumulation of nuclear damaged material is less understood. Here we describe that primary mouse embryonic fibroblasts develop a basal level of nuclear buds and micronuclei, which increase after Etoposide-induced DNA Double-Stranded Breaks. These nuclear buds and micronuclei co-localize with autophagic proteins BECN1 and LC3 and with acidic vesicles, suggesting their clearance by nucleophagy. Some of the nuclear alterations also contain autophagic proteins and Type II DNA Topoisomerases (TOP2A and TOP2B), or nucleolar protein Fibrillarin, implying they are also targets of nucleophagy. We propose that a basal nucleophagy contributes to genome and nuclear stability and also in response to DNA damage and nucleolar stress.

Stalling interkinetic nuclear migration in curved pseudostratified epithelium of developing cochlea

The bending of epithelial tubes is a fundamental process in organ morphogenesis, driven by various multicellular behaviours. The cochlea in the mammalian inner ear is a representative example of spiral tissue architecture where the continuous bending of the duct is a fundamental component of its morphogenetic process. Although the cochlear duct morphogenesis has been studied by genetic approaches extensively, it is still unclear how the cochlear duct morphology is physically formed. Here, we report that nuclear behaviour changes are associated with the curvature of the pseudostratified epithelium during murine cochlear development. Two-photon live-cell imaging reveals that the nuclei shuttle between the luminal and basal edges of the cell is in phase with cell-cycle progression, known as interkinetic nuclear migration, in the flat region of the pseudostratified epithelium. However, the nuclei become stationary on the luminal side following mitosis in the curved region. Mathematical modelling together with perturbation experiments shows that this nuclear stalling facilitates luminal-basal differential growth within the epithelium, suggesting that the nuclear stalling would contribute to the bending of the pseudostratified epithelium during the cochlear duct development. The findings suggest a possible scenario of differential growth which sculpts the tissue shape, driven by collective nuclear dynamics.

Femtosecond X-ray absorption spectroscopy of pyrazine at the nitrogen K-edge: on the validity of the Lorentzian limit

We calculate the femtosecond X-ray absorption spectrum of pyrazine at the nitrogen K-edge including the wavepacket dynamics in both the valence and core-excited state manifolds. We do not invoke the widely used short-time (or Lorentzian) approximation which neglects the nuclear dynamics after the X-ray probe excitation. Instead, we calculate the X-ray-induced polarization in the time-domain where the optical pump as well as X-ray probe pulses are explicitly described. While the non-adiabatic population transfer following the optical excitation is well reproduced in the Lorentzian limit the transient X-ray absorption spectra obtained under this approximation lack some vibronic features, even when considering the short core-hole lifetime of nitrogen. We further demonstrate the effect of an increasingly longer pulse on the observed photo-triggered wavepacket dynamics which are blurred to the point that the X-ray probe response becomes effectively time-independent.

Cell cycle stage classification using phase imaging with computational specificity

Traditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.