Cluster States Research Articles

Mapping Dynamic Protein Clustering with AIEgen-Active Chemigenetic Probe.

Protein clustering/disassembling is a fundamental process in biomolecular condensates, playingcrucial roles in cell fate decision and cellular homeostasis. However, the inherent features of protein clustering, especially for its reversible behavior and subtle microenvironment variation, present significant hurdles in probe chemistry for tracking protein clustering dynamics. Herein, we report a bilateral-tailored chemigenetic probe, in which an "amphiphilic" AIEgenQMSO3Cl is covalently conjugated to a protein tag that is genetically fused to protein-of-interest (POI). Prior to target POI, the probeachieves a completely dark state in both aqueous environment and lipophilic organelles, ensuring an ultra-low background-interference. Upon reaching POI, the combination of synthetic molecule and genetically encoded protein allows for protein clustering-dependent ultra-sensitive response, with a substantial lighting-up fluorescence (67.5-fold) as protein transitions from disassembling to clustering state. Such ultra-high signal-to-noise ratio enables to monitor the dynamic and fate of IRE1clustering/disassembling under both acute and chronic endoplasmic reticulum (ER) stress. For the first time, we have demonstrated the use of chemigenetic probe to reveal therapy-induced ER stress and screen drugs inthree-dimensional scenario: microviscosity change, clustering dynamic, and cluster morphology. This chemigenetic probe design strategy would greatly facilitate the advancement of mapping protein dynamics in cell homeostasis and medicine research.

Quantum Private Comparison Protocol with Cluster States

Quantum Private Comparison Protocol with Cluster States

Excited cluster states: A new source for proton number fluctuations in the high baryon density regime

Excited cluster states: A new source for proton number fluctuations in the high baryon density regime

Plasmon Dynamics in Nanoclusters: Dephasing Revealed by Excited States Evaluation.

The photocatalytic efficiency of materials such as graphene and noble metal nanoclusters depends on their plasmon lifetimes. Plasmon dephasing and decay in these materials is thought to occur on ultrafast time scales, ranging from a few femtoseconds to hundreds of femtoseconds and longer. Here we focus on understanding the dephasing and decay pathways of excited states in small lithium and silver clusters and in plasmonic states of the π-conjugated molecule anthracene, providing insights that are crucial for interpreting optical properties and photophysics. To do this, we study the time dependence of the electronic density matrix of these molecules using a new approach that expresses the density matrix in terms of TDDFT eigenstates (ESs) of the TDDFT Hamiltonian. This approach, which involves combining linear response time-dependent density functional theory (LR-TDDFT) and real-time time-dependent density functional theory (RT-TDDFT), leads to an analysis of the electron dynamics in terms of ESs, rather than individual molecular orbital (MO) transitions as has typically been done. This circumvents the complexities and subjective biases that traditional MO-based analysis provides. We find in an analysis of the induced dipole moment in these molecules that what had previously been considered to be energy relaxation is actually dephasing associated with the eigenstates that are stationary after the excitation pulse is turned off. We conclude that the ES-basis analysis has significant potential to advance understanding of the electron dynamics of plasmonic nanomaterials, aiding their optimization for photocatalytic and technological applications.

Supercritical Water: Density-Independent Angular Jumps.

Molecular dynamics simulations were employed to investigate the reorientation dynamics of water molecules under supercritical conditions. Our findings indicate that supercritical water consists of a fluctuating assembly of water clusters of varying sizes. The reorientational motions are characterized by large angular displacements and occur on fast time scales. We found that the decreasing density of supercritical water correlates with a decrease in the number of angular jumps as more water molecules were found in isolated or small clustered states at lower densities. Notably, the amplitude of rotational jumps in relative coordinates does not depend much on the density of supercritical water at a given temperature.

Entangled states from arborescent knots

In this paper we discuss how to use arborescent knots to construct entangled multiqubit states. We show that Bell-states, GHZ-states and cluster states can be constructed from such knots. The latter are particularly interesting since they form a base for the measurement-based quantum computers. Published by the American Physical Society 2024

Local Energy Minima and Density of Energy Barriers in Dense Clusters of Magnetic Nanoparticles

In this paper, we focus on the properties of local energy minima and energy barriers in immobilized dense clusters of magnetic nanoparticles. Understanding of these features is highly interesting both for the fundamental physics of disordered systems with long-range interparticle interaction and for numerous applications of modern ferrofluids consisting of such clusters. In particular, it is needed to predict the ac-susceptibility of these systems and their magnetization relaxation after a sudden change in the external field, because both processes occur via magnetization jumps over energy barriers that separate the energy minima. Due to the exponential increase in the corresponding jump time with barrier height (tsw∼exp(ΔE/kT)), direct Langevin dynamics simulations of this process are not feasible. For this reason, we have developed efficient numerical methods both for finding as many energy minima as possible and for the reliable evaluation of energy barriers between them. Our results for the distribution of overlaps between the local energy minima imply that there is no spin-glass state in such clusters even when they consist of particles with a small anisotropy. Further, we show that the distributions of energy barrier heights are qualitatively different for clusters of particles with small, intermediate, and large anisotropies, which has important consequences for the magnetization dynamics of these systems.

Beyond water stress: Exploring the wastewater-irrigation for sustainable Agriculture

Abstract Water management is one of the crucial factors that impact the globally. As droughts become more frequent due to global warming, of this limited resource becomes increasingly important. Lately, tion of wastewater for irrigation purposes is considered a game that in many cases, wastewater treatment is poorly studied. This the EU member states water management practices based on the FAO Kruskal-Wallis test of the clustered countries revealed that the the most attention to wastewater treatment within the EU. Even oped countries treat quite low amount of wastewater, and based on are more likely to face water scarcity, the applied methods did not between the water stress levels of the clustered member states. cal tests highlighted that the various water stress levels of the not be connected with the utilization of the existing irrigation results, increasing the application of the built-out system may cient to serve and even increase the operation of the agricultural putting additional strain on the resources in the short term. of wastewater-based irrigation systems could be useful in those lization of the existing irrigation system is already high, or face Since we are still learning how to deal with this new resource, the of less contaminated water sources like collected rainwater or the development of the new system. This promising approach could significantly to several Sustainable Development Goals but also hance and over time even supersede the current method. Highlights for public administration, management and planning: The research analyzes water management practices across the member states using FAO’s Aquastat database. The study found that developing EU regions pay more attention to ment compared to more developed regions, which treat a lower ater despite facing water scarcity risks. The EU countries’ diverse water stress levels could not be of the current irrigation system. In short term, the built-out the demand of the agricultural production without increasing sure on the limited resources. The wastewater-based innovations should utilize less contaminated like collected rainwater or greywater in more water-stressed the development of a new sustainable irrigation system.

High-Mode Coupling Yields Multicoherent-Phase Phenomena in Nonlocally Coupled Oscillators.

Capturing the intricate dynamics of partially coherent patterns in coupled oscillator systems is vibrant and one of the crucial areas of nonlinear sciences. Considering higher-order Fourier modes in the coupling, we discover a novel type of clustered coherent state in phase models, where inside the coherent region oscillators are further split into q dynamically equivalent subgroups with a 2π/q phase difference between two neighboring subgroups, forming a multicoherent-phase (MUP) chimera state. Both a self-consistency analysis and the Ott-Antonsen dimension reduction techniques are used to theoretically derive these solutions, whose stability are further demonstrated by spectral analysis. The universality of MUP effects is demonstrated by generalized twisted states and higher-order spatial swarm chimera states of swarmalators which are beyond pure phase models since oscillators can move in space.

Similarity between oxygen evolution in photosystem II and oxygen reduction in cytochrome c oxidase via proton coupled electron transfers. A unified view of the oxygenic life from four electron oxidation–reduction reactions

Basic concepts and theoretical foundations of broken symmetry (BS) and post BS methods for strongly correlated electron systems (SCES) such as electron-transfer (ET) diradical, multi-center polyradicals with spin frustration are described systematically to elucidate structures, bonding and reactivity of the high-valent transition metal oxo bonds in metalloenzymes: photosystem II (PSII) and cytochrome c oxidase (CcO). BS hybrid DFT (HDFT) and DLPNO coupled-cluster (CC) SD(T0) computations are performed to elucidate electronic and spin states of CaMn4Ox cluster in the key step for oxygen evolution, namely S4 [S3 with Mn(IV) = O + Tyr161-O radical] state of PSII and PM [Fe(IV) = O + HO-Cu(II) + Tyr161-O radical] step for oxygen reduction in CcO. The cycle of water oxidation catalyzed by the CaMn4Ox cluster in PSII and the cycle of oxygen reduction catalyzed by the CuA-Fea-Fea3-CuB cluster in CcO are examined on the theoretical grounds, elucidating similar concerted and/or stepwise proton transfer coupled electron transfer (PT-ET) processes for the four-electron oxidation in PSII and four-electron reduction in CcO. Interplay between theory and experiments have revealed that three electrons in the metal sites and one electron in tyrosine radical site are characteristic for PT-ET in these biological redox reaction systems, indicating no necessity of harmful Mn(V) = O and Fe(V) = O bonds with strong oxyl-radical character. Implications of the computational results are discussed in relation to design of artificial systems consisted of earth abundant transition metals for water oxidation.Graphical abstract

Quantum Private Comparison Based on Four-Particle Cluster State

A quantum private comparison (QPC) protocol enables two parties to securely compare their private data without disclosing the actual values to one another, utilizing quantum mechanics to maintain confidentiality. Many current QPC protocols mainly concentrate on comparing the equality of private information between two users during a single execution, which restricts their scalability. To overcome this limitation, we present an efficient QPC protocol aimed at evaluating the equality of private information between two groups of users in one execution. This is achieved by leveraging the entanglement correlations present in each particle of a four-particle cluster state. In our approach, users encode their private data using bit flip or phase shift operators on the quantum sequence they receive, which is then sent back to a semi-trusted party which then determines whether the secrets of the two groups are equal and communicates the results to the users. By employing this method and facilitating the distributed transmission of the quantum sequence, our protocol achieves a qubit efficiency of 50%. Security analyses reveal that neither external attacks nor insider threats can successfully compromise the confidentiality of private data.

A multi-task genetic programming approach for online multi-objective container placement in heterogeneous cluster

Owing to the potential for fast deployment, containerization technology has been widely used in web applications based on microservice architecture. Online container placement aims to improve resource utilization and meet other service quality requirements of cloud data centers. Most current heuristic and hyper-heuristic methods for container placement rely on single allocation rules, which are inefficient in heterogeneous cluster scenarios. Moreover, some container placement tasks often have similar characteristics (e.g., resource request types and physical machine types), but traditional single-task optimization modeling cannot exploit potential common knowledge, resulting in repeated optimization during resource allocation. Therefore, a new multi-task genetic programming method is proposed to solve the online multi-objective container placement problem (MOCP-MTGP). This method considers selecting appropriate allocation rules according to the types of resource requests and cluster status. MOCP-MTGP can automatically generate multiple groups of allocation rules from historical workload patterns and different cluster states, and capture the similarities between all online tasks to guide the transfer of general knowledge during optimization. Comprehensive experiments show that the proposed algorithm can improve the resource utilization of clusters, reduce the number of physical machines, and effectively meet resource constraints and high availability requirements.

Abstract 4142799: Central role of LIM domain binding 3 (LDB3) protein in Tetralogy of Fallot assessed by single-nuclei multiome profiling of paediatric right ventricular samples

Background and aims: Tetralogy of Fallot (TOF; EC: 1565/2019) is the most common cyanotic congenital heart defect with a world-wide incidence of 0.02–0.04%. The pathophysiological mechanisms driven by variable genetic background are poorly understood. We applied the single-nuclei multiome profiling, composed of ATAC and RNA-seq from the same nuclei, of right ventricular samples of children with TOF. The final aim was to define cell types and characterize gene regulation states in different cell clusters including activation and maturation. Methods: Right ventricular samples were prospectively gathered during routinely performed cardiac surgery for TOF correction (EC: 1565/2019). In total, six paediatric patient samples were processed, and on average ~1,500 nuclei were sequenced per sample. Data was analysed using Scanpy to cluster and annotate cells, pycisTopic to identify cell stats and cis-regulatory topics, and SCENIC+ for enhancer-driven gene Regulatory network (eRegulon) construction. Results: Through manual annotation, using published markers, we identified cell types including cardiomyocyte, fibroblast, endothelial, pericyte, immune and neuronal cells. From this, we observed cell type specific expression, with overexpression of decorin in fibroblasts, PTPRC in immune cells, and neurexin genes in neuronal cells found. Differential expression analysis highlighted patient specific patterns of expression, of which gene set enrichment showed enrichment for genes associated with actomyosin structure organisation, dilated cardiomyopathy and cardiac muscle contraction. Integration of the gene expression data with the ATAC-seq data, across all patients, allowed for the construction of eRegulons networks. In detail, in the cardiomyocyte-annotated clusters, we identified enrichment of MEF2, MEIS2 and EPAS1 family enhancers with a central role of LIM domain binding 3 protein (LDB3, associated with cytoskeletal actin and muscle alpha-actin binding) (Fig. 1). Conclusion: Single nuclei multiome profiling of paediatric right ventricular TOF samples identified several patient specific patterns of expression and regulatory networks, related to the development of cyanotic congenital heart disease, and sheds light to the potential drivers of TOF.

Electrochemically Gated Frustrated Lewis Pair Chemistry in Electric Double Layer.

The recent discovery of frustrated Lewis pairs (FLPs) during the activation of small molecules has inspired extensive research across the full span of chemical science. Owing to the nature of weak interactions, it is experimentally challenging to directly observe and modulate FLP at the molecular scale. Here we design a boron cluster anion building block (B10H82-) and organic amine cations ([NR4]+, R= -CH3, -C2H5) as the FLP to prove the feasibility of controlling their interaction in the electric double layer (EDL) via an electrochemical strategy. In situ single-molecule electrical measurements and Raman monitoring of B10H82--[NR4]+ FLP formed at the positively charged Au(111) electrode surface, in contrast to the free-standing B10H82- near or below the potential of zero charge (PZC). Furthermore, this FLP chemistry leads to a shift in the local density of states of boron clusters towards the EF for enhancing electron transport, providing a new prototype of a reversible single-cluster switch that digitally switches upon controlling FLP chemistry in the electric double layer.

Electrochemically Gated Frustrated Lewis Pair Chemistry in Electric Double Layer

AbstractThe recent discovery of frustrated Lewis pairs (FLPs) during the activation of small molecules has inspired extensive research across the full span of chemical science. Owing to the nature of weak interactions, it is experimentally challenging to directly observe and modulate FLP at the molecular scale. Here we design a boron cluster anion building block (B10H82−) and organic amine cations ([NR4]+, R=−CH3, −C2H5) as the FLP to prove the feasibility of controlling their interaction in the electric double layer (EDL) via an electrochemical strategy. In situ single‐molecule electrical measurements and Raman monitoring of B10H82−−[NR4]+ FLP formed at the positively charged Au(111) electrode surface, in contrast to the free‐standing B10H82− near or below the potential of zero charge (PZC). Furthermore, this FLP chemistry leads to a shift in the local density of states of boron clusters towards the EF for enhancing electron transport, providing a new prototype of a reversible single‐cluster switch that digitally switches upon controlling FLP chemistry in the electric double layer.

Multimode squeezed state for reconfigurable quantum networks at telecommunication wavelengths

Continuous variable encoding of quantum information requires the deterministic generation of highly correlated quantum states of light in the form of quantum networks, which, in turn, necessitates the controlled generation of a large number of squeezed modes. In this paper, we present an experimental source of multimode squeezed states of light at telecommunication wavelengths. Generation at such wavelengths is especially important as it can enable quantum information processing, communication, and sensing beyond the laboratory scale. We use a single-pass spontaneous parametric down-conversion process in a nonlinear waveguide pumped with the second harmonic of a femtosecond laser. Our measurements reveal significant squeezing in more than 21 frequency modes, with a maximum squeezing value exceeding 2.5 dB. We demonstrate multiparty entanglement by measuring the state's covariance matrix. Finally, we show the source reconfigurability by preparing few-node cluster states and measure their nullifier squeezing level. These results pave the way for a scalable implementation of continuous variable quantum information protocols at telecommunication wavelengths, particularly for multiparty, entanglement-based quantum communications. Moreover, the source is compatible with additional pulse-by-pulse multiplexing, which can be utilized to construct the necessary three-dimensional entangled structures for quantum computing protocols. Published by the American Physical Society 2024

Information Propagation in Hypergraph-Based Social Networks.

Social networks, functioning as core platforms for modern information dissemination, manifest distinctive user clustering behaviors and state transition mechanisms, thereby presenting new challenges to traditional information propagation models. Based on hypergraph theory, this paper augments the traditional SEIR model by introducing a novel hypernetwork information dissemination SSEIR model specifically designed for online social networks. This model accurately represents complex, multi-user, high-order interactions. It transforms the traditional single susceptible state (S) into active (Sa) and inactive (Si) states. Additionally, it enhances traditional information dissemination mechanisms through reaction process strategies (RP strategies) and formulates refined differential dynamical equations, effectively simulating the dissemination and diffusion processes in online social networks. Employing mean field theory, this paper conducts a comprehensive theoretical derivation of the dissemination mechanisms within the SSEIR model. The effectiveness of the model in various network structures was verified through simulation experiments, and its practicality was further validated by its application on real network datasets. The results show that the SSEIR model excels in data fitting and illustrating the internal mechanisms of information dissemination within hypernetwork structures, further clarifying the dynamic evolutionary patterns of information dissemination in online social hypernetworks. This study not only enriches the theoretical framework of information dissemination but also provides a scientific theoretical foundation for practical applications such as news dissemination, public opinion management, and rumor monitoring in online social networks.

Engineering of hyperentangled complex quantum networks

Abstract We propose a novel scheme to engineer the atomic hyperentangled cluster and ring graph states invoking cavity-QED technique for applicative relevance to quantum biology and quantum communications utilizing the complex quantum networks. These states are engineered using both external quantized momenta states and energy levels of neutral atoms under off-resonant and resonant Atomic Bragg Diffraction (ABD) technique. The study of dynamical capacity and potential efficiency have certainly enhanced the range of usefulness of these states. In order to assess the operational behavior of such states when subjected to a realistic noise environment has also been simulated, demonstrating long enough sustainability of the proposed states. Moreover, experimental feasibility of the proposed scheme has also been elucidated under the prevailing cavity-QED research scenario.

Industrial Heritage and Cultural Clusters: More Than a Temporary Affair?

The transformation of industrial heritage buildings into cultural clusters has emerged as a prominent topic of academic research in urban planning, urban studies, heritage conservation, and architecture. Cultural clusters, defined as geographically concentrated cultural activities and organisations, have become a key instrument in urban regeneration, fostering economic growth and cultural development. Despite the benefits that cultural clusters offer in terms of fostering cultural activity, they often prove to be short-lived due to various external factors, including urban regeneration pressures, shifts in policy, and changes in zoning regulations. This thematic issue presents seven case studies that offer insights into the current state of cultural clusters, their transient nature, and the conditions necessary to guarantee their long-term sustainability in industrial heritage sites. The research is particularly relevant in light of the mounting pressure on urban land, where industrial heritage sites are frequently repurposed for residential, commercial, or industrial purposes.

A quantum group signature scheme with reusable keys based on four-particle Cluster states

Abstract With the continuous development of quantum technology, researchers are constantly improving the research on quantum signatures. In the public-key cryptosystem, a quantum group signature scheme based on four-particle Cluster states is proposed. In this scheme, the four-particle Cluster states are used as quantum channels. The signer randomly generates his private key according to the public key generated by the group manager, and uses the private key to sign. The verifier uses the public key to verify the signature. The features of the scheme are as follows: the public key and private key can be reused, thus reducing the number of keys that need to be saved by the communication parties; The length of the message to be signed does not need to be the same as the length of the public and private keys, which increases the flexibility of the signature; The random sequence is used in the signature process to ensure the unpredictability of the key, thus improving the security of the scheme; The scheme has unforgeability and non-repudiation.