UC Riverside

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated VAN-DAMME code, we carried out QOC calculations of systems containing 10 - 15 qubits, which showed that our GPU implementation is 18.4× faster than the corresponding CPU implementation. Our GPU-accelerated enhancements allow efficient calculations of multi-qubit systems, which can be used for the efficient implementation of QOC applications across multiple domains. Program summary: Program Title: VAN-DAMME CPC Library link to program files:: https://doi.org/10.17632/zcgw2n5bjf.1 Licensing provisions: GNU General Public License 3 Programming language: C++ and CUDA Nature of problem: The VAN-DAMME software package utilizes GPU-accelerated routines and new algorithmic improvements to compute optimized time-dependent magnetic fields that can drive a system from a known initial qubit configuration to a specified target state with a large (≈1) transition probability. Solution method: Quantum control, GPU acceleration, analytic gradients, matrix exponential, and gradient ascent optimization.

The fungal genus Neonectria contains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority of Neonectria spp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies for Neonectria magnoliae NRRL 64651 and Neonectria punicea NRRL 64653.

Polymer/ceramic nanocomposites integrated the advantages of both polymers and ceramics for a wide range of biomedical applications, such as bone tissue repair. Here, we reported triphasic poly(lactic-co-glycolic acid) (PLGA, LA/GA = 90:10) nanocomposites with improved dispersion of hydroxyapatite (HA) and magnesium oxide (MgO) nanoparticles using a process that integrated the benefits of ultrasonic energy and dual asymmetric centrifugal mixing. We characterized the microstructure and composition of the nanocomposites and evaluated the effects of the HA/MgO ratios on degradation behavior and cell-material interactions. The PLGA/HA/MgO nanocomposites were composed of 70 wt % PLGA and 30 wt % nanoparticles made of 20:10, 25:5, and 29:1% by weight of HA and MgO, respectively. The results showed that the nanocomposites had a homogeneous nanoparticle distribution and as-designed elemental composition. The cell study indicated that reducing the MgO content in the triphasic nanocomposite increased the BMSC adhesion density under both direct and indirect contact conditions. Specifically, after the 24 and 48 h of culture, the PLGA/HA/MgO group with a weight ratio of 70:29:1 (P70/H29/M1) exhibited the greatest average cell adhesion density under direct and indirect contact conditions among triphasic nanocomposites. During a 28-day degradation study, the mass loss of triphasic nanocomposites was 18 ± 2% for P70/H20/M10, 9 ± 2% for P70/H25/M5, and 7 ± 1% for P70/H29/M1, demonstrating that MgO nanoparticles accelerated the degradation of the nanocomposites. Postculture analysis showed that the pH values and Mg2+ ion concentrations in the media increased with increasing MgO content in the nanocomposites. Triphasic nanocomposites provided different degradation profiles that can be tuned for different biomedical applications, especially when a shorter or longer period of degradation would be desirable for optimal bone tissue regeneration. The concentration and ratio of nanoparticles should be adjusted and optimized when other polymers with different degradation modes and rates are used in the nanocomposites.

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BACKGROUND: X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in development and cancer. METHODS: Kdm6a was knocked out (KO) using CRISPR/Cas9 gene editing in hybrid female mouse embryonic stem (ES) cells derived either from a 129 × Mus castaneus (cast) cross or a BL6 x cast cross. In one of the lines a transcriptional stop signal inserted in Tsix results in completely skewed X silencing upon differentiation. The effects of both homozygous and heterozygous Kdm6a KO on Xist expression during the onset of XCI were measured by RT-PCR and RNA-FISH. Changes in gene expression and in H3K27me3 enrichment were investigated using allele-specific RNA-seq and Cut&Run, respectively. KDM6A binding to the Xist gene was characterized by Cut&Run. RESULTS: We observed impaired upregulation of Xist and reduced coating of the Xi during early stages of differentiation in Kdm6a KO cells, both homozygous and heterozygous, suggesting a threshold effect of KDM6A. This was associated with aberrant overexpression of genes from the Xi after differentiation, indicating loss of X inactivation potency. Consistent with KDM6A having a direct role in Xist regulation, we found that the histone demethylase binds to the Xist promoter and KO cells show an increase in H3K27me3 at Xist, consistent with reduced expression. CONCLUSIONS: These results reveal a novel female-specific role for the X-linked histone demethylase, KDM6A in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation. X chromosome inactivation is a female-specific mechanism that evolved to balance sex-linked gene dosage between females (XX) and males (XY) by silencing one X chromosome in females. X inactivation begins with the upregulation of the long noncoding RNA Xist on the future inactive X chromosome. While most genes become silenced on the inactive X chromosome some genes escape inactivation and thus have higher expression in females compared to males, suggesting that escape genes may have female-specific functions. One such gene encodes the histone demethylase KDM6A which function is to turn on gene expression by removing repressive histone modifications. In this study, we investigated the role of KDM6A in the regulation of Xist expression during the onset of X inactivation. We found that KDM6A binds to the Xist gene to remove repressive histone marks and facilitate its expression in early development. Indeed, depletion of KDM6A prevents upregulation of Xist due to abnormal persistence of repressive histone modifications. In turn, this results in aberrant overexpression of genes from the inactive X chromosome. Our findings point to a novel mechanism of Xist regulation during the initiation of X inactivation, which may lead to new avenues of treatment to alleviate congenital disorders such as Kabuki syndrome and sex-biased immune disorders where X-linked gene dosage is perturbed.

Food packaging (FP) is essential for preserving food quality, safety, and extending shelf-life. However, growing concerns about the environmental and health impacts of conventional packaging materials, particularly per- and polyfluoroalkyl substances (PFAS) and microplastics, are driving a major transformation in FP design. PFAS, synthetic compounds with dual hydro- and lipophobicity, have been widely employed in food packaging materials (FPMs) to impart desirable water and grease repellency. However, PFAS bioaccumulate in the human body and have been linked to multiple health effects, including immune system dysfunction, cancer, and developmental problems. The detection of microplastics in various FPMs has raised significant concerns regarding their potential migration into food and subsequent ingestion. This comprehensive review examines the current landscape of FPMs, their functions, and physicochemical properties to put into perspective why there is widespread use of PFAS and microplastics in FPMs. The review then addresses the challenges posed by PFAS and microplastics, emphasizing the urgent need for sustainable and bio-based alternatives. We highlight promising advancements in sustainable and renewable materials, including plant-derived polysaccharides, proteins, and waxes, as well as recycled and upcycled materials. The integration of these sustainable materials into active packaging systems is also examined, indicating innovations in oxygen scavengers, moisture absorbers, and antimicrobial packaging. The review concludes by identifying key research gaps and future directions, including the need for comprehensive life cycle assessments and strategies to improve scalability and cost-effectiveness. As the FP industry evolves, a holistic approach considering environmental impact, functionality, and consumer acceptance will be crucial in developing truly sustainable packaging solutions.

Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds of effector proteins inside eukaryotic cells to ensure intracellular replication. Our understanding of the molecular functions of the largest pathogenic arsenal known to the bacterial world remains incomplete. By leveraging advancements in 3D protein structure prediction, we provide a comprehensive structural analysis of 368 L. pneumophila effectors, representing a global atlas of predicted functional domains summarized in a database ( https://pathogens3d.org/legionella-pneumophila ). Our analysis identified 157 types of diverse functional domains in 287 effectors, including 159 effectors with no prior functional annotations. Furthermore, we identified 35 cryptic domains in 30 effector models that have no similarity with experimentally structurally characterized proteins, thus, hinting at novel functionalities. Using this analysis, we demonstrate the activity of thirteen functional domains, including three cryptic domains, predicted in L. pneumophila effectors to cause growth defects in the Saccharomyces cerevisiae model system. This illustrates an emerging strategy of exploring synergies between predictions and targeted experimental approaches in elucidating novel effector activities involved in infection.

Visual perceptual learning (VPL), the training-induced improvement in visual tasks, has long been considered the product of neural plasticity at early and local stages of signal processing. However, recent evidence suggests that multiple networks and mechanisms, including stimulus- and task-specific plasticity, concur in generating VPL. Accordingly, early models of VPL, which characterized learning as being local and mostly involving early sensory areas, such as V1, have been updated to embrace these newfound complexities, acknowledging the involvement on parietal (i.e. intra-parietal sulcus) and frontal (i.e. dorsolateral prefrontal cortex) areas, in aspects concerning decision-making, feedback integration and task structure. However, evidence of multiple brain regions differentially involved in different aspects of learning is thus far mostly correlational, emerging from electrophysiological and neuroimaging techniques. To directly address these multiple components of VPL, we propose to use a causal neuromodulation technique, namely transcranial random noise stimulation, to selectively modulate the activity of different brain regions suggested to be involved in various aspects of learning. Specifically, we will target a region in the occipital cortex, which has been associated with stimulus-specific plasticity, and one in the parietal cortex, which has been associated with task-specific plasticity, in a between-subject design. Measures of transfer of learning to untrained stimuli and tasks will be used to evaluate the role of different regions and test for double dissociations between learning effects and stimulated area, shedding lights on learning mechanisms in the visual system. Evidence of dissociable mechanisms of learning can help refine current models of VPL and may help develop more effective visual training and rehabilitation protocols.

The floating phase, a critical incommensurate phase, has been theoretically predicted as a potential intermediate phase between crystalline ordered and disordered phases. In this study, we investigate the different quantum phases that arise in ladder arrays comprising up to 92 neutral-atom qubits and experimentally observe the emergence of the quantum floating phase. We analyze the site-resolved Rydberg state densities and the distribution of state occurrences. The site-resolved measurement reveals the formation of domain walls within the commensurate ordered phase, which subsequently proliferate and give rise to the floating phase with incommensurate quasi-long-range order. By analyzing the Fourier spectra of the Rydberg density-density correlations, we observe clear signatures of the incommensurate wave order of the floating phase. Furthermore, as the experimental system sizes increase, we show that the wave vectors approach a continuum of values incommensurate with the lattice. Our work motivates future studies to further explore the nature of commensurate-incommensurate phase transitions and their non-equilibrium physics.