Topological Interactions Research Articles

Understanding the interplay between extracellular matrix topology and tumor-immune interactions: Challenges and opportunities.

Modern cancer management comprises a variety of treatment strategies. Immunotherapy, while successful at treating many cancer subtypes, is often hindered by tumor immune evasion and T cell exhaustion as a result of an immunosuppressive tumor microenvironment (TME). In solid malignancies, the extracellular matrix (ECM) embedded within the TME plays a central role in T cell recognition and cancer growth by providing structural support and regulating cell behavior. Relative to healthy tissues, tumor associated ECM signatures include increased fiber density and alignment. These and other differentiating features contributed to variation in clinically observed tumor-specific ECM configurations, collectively referred to as Tumor-Associated Collagen Signatures (TACS) 1-3. TACS is associated with disease progression and immune evasion. This review explores our current understanding of how ECM geometry influences the behaviors of both immune cells and tumor cells, which in turn impacts treatment efficacy and cancer evolutionary progression. We discuss the effects of ECM remodeling on cancer cells and T cell behavior and review recent in silico models of cancer-immune interactions.

Nanoscale Multipatterning Zn,Co-ZIF@FeOOH for Eradication of Multidrug-Resistant Bacteria and Antibacterial Treatment of Wounds.

The rising incidence of infections caused by multidrug-resistant bacteria highlights the urgent need for innovative bacterial eradication strategies. Metal ions, such as Zn2+ and Co2+, have bactericidal effects by disrupting bacterial cell membranes and interfering with essential cellular processes. This has led to increased attention toward metal-organic frameworks (MOFs) as potential nonantibiotic bactericidal agents. However, the uniform and enhanced localized release of bactericidal metal ions remains a challenge. Herein, we introduce a nanoscale multipatterned Zn,Co-ZIF@FeOOH, featuring a multipod-like morphology with spiky corners, and dual-bactericidal metal ions. Compared to pure Zn,Co-ZIF, the multipod-like morphology of Zn,Co-ZIF@FeOOH exhibits enhanced adhesion toward bacterial surfaces via topological and multiple interactions of electrostatic interaction, significantly increasing the local release of Zn2+ and Co2+. Additionally, the spiky corners of the spindle-shaped FeOOH nanorods physically penetrate bacterial membranes, causing damage and further enhancing adhesion to bacteria. Nine Gram-negative and one Gram-positive bacteria were selected for in vitro test. Notably, the nanoscale multipatterned Zn,Co-ZIF@FeOOH exhibited high bactericidal efficacy against various multidrug-resistant bacteria, including extended-spectrum β-lactamase-producing (ESBL+) bacteria and carbapenem-resistant bacteria, performing well in both acidic and neutral environments. The wound healing activity of Zn,Co-ZIF@FeOOH was further demonstrated using female Balb/c mouse models infected with bacteria, where the materials show robust antibacterial efficacy and commendable biocompatibility. This study showcases the assembly of metal oxide/MOF composites for nanoscale multipatterning, aims at synergistic bacterial eradication and offers insights into developing nanomaterial-based strategies against multidrug-resistant bacteria.

Topological Interactions Between Homotopy and Dehn Twist Varieties

The topological Dehn twists have several applications in mathematical sciences as well as in physical sciences. The interplay between homotopy theory and Dehn twists exposes a rich set of properties. This paper generalizes the Dehn twists by proposing the notion of pre-twisted space, orientations of twists and the formation of pointed based space under a homeomorphic continuous function. It is shown that the Dehn twisted homotopy under non-retraction admits a left lifting property (LLP) through the local homeomorphism. The LLP extends the principles of Hurewicz fibration by avoiding pullback. Moreover, this paper illustrates that the Dehn twisted homotopy up to a base point in a based space can be formed by considering retraction. As a result, two disjoint continuous functions become point-wise continuous at the base point under retracted homotopy twists. Interestingly, the oriented Dehn twists of a pre-twisted space under homotopy retraction mutually commute in a contractible space.

Bose Metals, from Prediction to Realization.

Bose metals are metals made of Cooper pairs, which form at very low temperatures in superconducting films and Josephson junction arrays as an intermediate phase between superconductivity and superinsulation. We predicted the existence of this 2D metallic phase of bosons in the mid 1990s, showing that they arise due to topological quantum effects. The observation of Bose metals in perfectly regular Josephson junction arrays fully confirms our prediction and rules out alternative models based on disorder. Here, we review the basic mechanism leading to Bose metals. The key points are that the relevant vortices in granular superconductors are core-less, mobile XY vortices which can tunnel through the system due to quantum phase slips, that there is no charge-phase commutation relation preventing such vortices from being simultaneously out of condensate with charges, and that out-of-condensate charges and vortices are subject to topological mutual statistics interactions, a quantum effect that dominates at low temperatures. These repulsive mutual statistics interactions are sufficient to increase the energy of the Cooper pairs and lift them out of condensate. The result is a topological ground state in which charge conduction along edges and vortex movement across them organize themselves so as to generate the observed metallic saturation at low temperatures. This state is known today as a bosonic topological insulator.

Hypernetwork modeling and topology of high-order interactions for complex systems

Interactions among the underlying agents of a complex system are not only limited to dyads but can also occur in larger groups. Currently, no generic model has been developed to capture high-order interactions (HOI), which, along with pairwise interactions, portray a detailed landscape of complex systems. Here, we integrate evolutionary game theory and behavioral ecology into a unified statistical mechanics framework, allowing all agents (modeled as nodes) and their bidirectional, signed, and weighted interactions at various orders (modeled as links or hyperlinks) to be coded into hypernetworks. Such hypernetworks can distinguish between how pairwise interactions modulate a third agent (active HOI) and how the altered state of each agent in turn governs interactions between other agents (passive HOI). The simultaneous occurrence of active and passive HOI can drive complex systems to evolve at multiple time and space scales. We apply the model to reconstruct a hypernetwork of hexa-species microbial communities, and by dissecting the topological architecture of the hypernetwork using GLMY homology theory, we find distinct roles of pairwise interactions and HOI in shaping community behavior and dynamics. The statistical relevance of the hypernetwork model is validated using a series of in vitro mono-, co-, and tricultural experiments based on three bacterial species.

T0-spaces and the lower topology

Abstract The authors’ primary goal in this paper is to enhance the study of $T_0$ topological spaces by using the order of specialization of a $T_0$ -space to introduce the lower topology (with a subbasis of closed sets $\mathord{\uparrow } x$ ) and studying the interaction of the original topology and the lower topology. Using the lower topology, one can define and study new properties of the original space that provide deeper insight into its structure. One focus of study is the property R, which asserts that if the intersection of a family of finitely generated sets $\mathord{\uparrow } F$ , $F$ finite, is contained in an open set $U$ , then the same is true for finitely many of the family. We first show that property R is equivalent to several other interesting properties, for example, the property that all closed subsets of the original space are compact in the lower topology. We then find conditions under which these spaces are compact, well-filtered, and coherent, a weaker variant of stably compact spaces. We also investigate what have been called strong $d$ -spaces, develop some of their basic properties, and make connections with the earlier considerations involving spaces satisfying property R. Two key results we obtain are that if a dcpo $P$ with the Scott topology is a strong $d$ -space, then it is well-filtered, and if additionally the Scott topology of the product $P\times P$ is the product of the Scott topologies of the factors, then the Scott space of $P$ is sober. We also exhibit connections of this work with de Groot duality.

Observation of flat bands and Dirac cones in a pyrochlore lattice superconductor

Emergent phases often appear when the electronic kinetic energy is comparable to the Coulomb interactions. One approach to seek material systems as hosts of such emergent phases is to realize localization of electronic wavefunctions due to the geometric frustration inherent in the crystal structure, resulting in flat electronic bands. Recently, such efforts have found a wide range of exotic phases in the two-dimensional kagome lattice, including magnetic order, time-reversal symmetry breaking charge order, nematicity, and superconductivity. However, the interlayer coupling of the kagome layers disrupts the destructive interference needed to completely quench the kinetic energy. Here we demonstrate that an interwoven kagome network—a pyrochlore lattice—can host a three dimensional (3D) localization of electron wavefunctions. Meanwhile, the nonsymmorphic symmetry of the pyrochlore lattice guarantees all band crossings at the Brillouin zone X point to be 3D gapless Dirac points, which was predicted theoretically but never yet observed experimentally. Through a combination of angle-resolved photoemission spectroscopy, fundamental lattice model and density functional theory calculations, we investigate the novel electronic structure of a Laves phase superconductor with a pyrochlore sublattice, CeRu2. We observe evidence of flat bands originating from the Ce 4f orbitals as well as flat bands from the 3D destructive interference of the Ru 4d orbitals. We further observe the nonsymmorphic symmetry-protected 3D gapless Dirac cone at the X point. Our work establishes the pyrochlore structure as a promising lattice platform to realize and tune novel emergent phases intertwining topology and many-body interactions.

Kinetic Description of Swarming Dynamics with Topological Interaction and Transient Leaders

Kinetic Description of Swarming Dynamics with Topological Interaction and Transient Leaders

Non-local interaction in discrete Ricci curvature-induced biological aggregation

We investigate the collective dynamics of multi-agent systems in two- and three-dimensional environments generated by minimizing discrete Ricci curvature with local and non-local interaction neighbourhoods. We find that even a single effective topological neighbour suffices for significant order in a system with non-local topological interactions. We also explore topological information flow patterns and clustering dynamics using Hodge spectral entropy and mean Forman–Ricci curvature.

Flexible iontronics with super stretchability, toughness and enhanced conductivity based on collaborative design of high-entropy topology and multivalent ion-dipole interactions.

All-solid-state ionic conductive elastomers (ASSICEs) are emerging as a promising alternative to hydrogels and ionogels in flexible electronics. Nevertheless, the synthesis of ASSICEs with concomitant mechanical robustness, superior ionic conductivity, and cost-effective recyclability poses a formidable challenge, primarily attributed to the inherent contradiction between mechanical strength and ionic conductivity. Herein, we present a collaborative design of high-entropy topological network and multivalent ion-dipole interaction for ASSICEs, and successfully mitigate the contradiction between mechanical robustness and ionic conductivity. Benefiting from the synergistic effect of this design, the coordination, de-coordination, and intrachain transfer of Li+ are effectively boomed. The resultant ASSICEs display exceptional mechanical robustness (breaking strength: 7.45 MPa, fracture elongation: 2621%, toughness: 107.19 MJ m-3) and impressive ionic conductivity (1.15 × 10-2 S m-1 at 25 °C). Furthermore, these ASSICEs exhibit excellent environmental stability (fracture elongation exceeding 1400% at 50 °C or -60 °C) and recyclability. Significantly, the application of these ASSICEs in a strain sensor highlights their potential in various fields, including human-interface communication, aerospace vacuum measurement, and medical balloon monitoring.

A novel Co(II) complex with sulfamethoxazole ligand: Isostructuralism, non-covalent interactions, Hirshfeld surfaces, crystal voids and energy calculations

The crystal structure of [Co(H2O)6][Co(SMX)3]2 complex (SMX = sulfamethoxazole), hereafter CoSMXW, has been solved by X-ray diffraction methods. The complex CoSMXW was characterized by Infrared (IR), Raman, and UV-Vis spectroscopies. A comparison with the analogous Mn(II) complex, [Mn(H2O)6][Mn(SMX)3]2 (CSD refcode AJIFUW), indicates 3D isostructurality and packing similarity, as evident from X-ray diffraction and geometric descriptors such as dissimilarity index (X = 2.0 from XPac) and packing similarity (PSab = 0.3070 from CrystalCMP), respectively. This represents the first case of isostructurality observed among eleven metal complexes of sulfamethoxazole reported in the literature. A study of non-covalent interactions shows presence of structural motifs involving N-H…O and N-H…S (Motif I), N-H…O (Motif II), O-H…O and O-H…N (Motif III) H-bonds, as well as C-H…π contacts (Motif IV) for [Co(H2O)6][Co(SMX)3]2 and AJIFUW. Energy analysis using CrystalExplorer indicates that the strongest dimer involves Motifs I and II with total energy of -70.3 kcal/mol for CoSMXW, which is only 2.1 kcal/mol longer than that for AJIFUW. Hirshfeld surface (HS) analysis reveals meaningless effect of metal replacement on the intermolecular contacts, confirming the energetic results. The volume of the crystal voids and the percentage of free space were calculated as 862.35 Å3 and 11.8 % for CoSMXW, and 911.42 Å3 and 12.2 % for AJIFUW. 3D topology and hierarchy of interactions were analyzed with energy framework diagrams. Further, structural motifs, HS, crystal voids and intermolecular energies for the SMX free ligand (CSD refcode SLFNMB08) were also studied. Finally, the present study was complemented with DFT calculations to evaluate the strength and nature of the non-covalent interactions by using the quantum theory of atoms in molecules (QTAIM) and NCIplots computational tools. In addition, we have used the potential energy density predictor obtained from QTAIM analysis to investigate the relative contribution of each interaction to the formation of the assemblies.

Strain-induced antiferromagnetic domain switching via the spin Jahn-Teller effect

The spin Jahn-Teller effect, where a degeneracy of magnetic ground states is spontaneously lifted by structural distortions, lends itself to exploitation by the implied magnetoelastic coupling. CoTi2O5 hosts a frustrated topology of magnetic interactions that could realize such coupling, since the observed magnetic ground state requires a spontaneous monoclinic distortion of the crystal. Using resonant elastic x-ray scattering to simultaneously probe the magnetic structure and lattice distortion of CoTi2O5, we demonstrate near complete magnetic domain switching by an applied uniaxial stress that is conjugate to the monoclinic strain. Our results, supported by density functional theory calculations, confirm that CoTi2O5 displays spin Jahn-Teller effects that can be understood in terms of modulated Heisenberg exchange interactions, and demonstrate the potential functionality of spin Jahn-Teller materials in spintronic devices sensitive to uniaxial strain. Published by the American Physical Society 2024

Experiment and numerical investigation on beetle elytra inspired lattice structure: Enhanced mechanical properties and customizable responses

The elytra of the ironclad beetles possess very strong and toughness performance, to protect the body from catastrophic physical damage, owing to its unique curved geometry and layered microstructure. In this paper, inspired by the elytra of ironclad beetles, a novel configuration of lattice structure (IBCC) was developed. The digital light processing (DLP) with hard-tough resin was used to fabricate the lattice structures. The compression experiment and simulation were performed to investigate the mechanical response and deformation mechanism. The response surface model (RSM) was adopted to build a forward relationship between structure parameters and mechanical properties. A numerical method was developed to inversely design structure parameters of IBCC with “target” mechanical properties using genetic algorithm. The novel lattice structure exhibits superior stiffness and energy absorption than conventional BCC (body-centered cubic) and OCT (Octet) structures, under the same relative density. For example, IBCC shows a maximum 59% improvement (at ρ¯=9.60%) of stiffness, and a maximum 25% improvement (at ρ¯=7.40%) of SEA, with respect to OCT. Besides, the stress plateau of IBCC is more stable than OCT, even at relatively large compression strain. The superior mechanical response of the IBCC lattice structure is mainly ascribed to bio-inspired topological design and interaction effects of curved rods in the “V-shaped” region. Besides, the effectiveness of the proposed inverse design method is verified by three numerical cases. The proposed bio-inspired design strategy, mechanical enhancement mechanism, and customizable method will be helpful in expanding the prospects of lattice structures in future multifunctional application fields.

Biodiversity in changing environments: An external-driver internal-topology framework to guide intervention.

Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments.

Interactions Enable Thouless Pumping in a Nonsliding Lattice

A topological “Thouless” pump represents the quantized motion of particles in response to a slow, cyclic modulation of external control parameters. The Thouless pump, like the quantum Hall effect, is of fundamental interest in physics, because it links physically measurable quantities, such as particle currents, to geometric properties of the experimental system, which can be robust against perturbations and, thus, technologically useful. So far, experiments probing the interplay between topology and interparticle interactions have remained relatively scarce. Here, we observe a Thouless-type charge pump in which the particle current and its directionality inherently rely on the presence of strong interactions. Experimentally, we utilize a two-component Fermi gas in a dynamical superlattice which does not exhibit a sliding motion and remains trivial in the single-particle regime. However, when tuning interparticle interactions from zero to positive values, the system undergoes a transition from being stationary to drifting in one direction, consistent with quantized pumping in the first cycle. Remarkably, the topology of the interacting pump trajectory cannot be adiabatically connected to a noninteracting limit, highlighted by the fact that only one atom is transferred per cycle. Our experiments suggest that Thouless charge pumps are promising platforms to gain insights into interaction-driven topological transitions and topological quantum matter. Published by the American Physical Society 2024

LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data.

Reconstructing the topology of gene regulatory network from gene expression data has been extensively studied. With the abundance functional transcriptomic data available, it is now feasible to systematically decipher regulatory interaction dynamics in a logic form such as a Boolean network (BN) framework, which qualitatively indicates how multiple regulators aggregated to affect a common target gene. However, inferring both the network topology and gene interaction dynamics simultaneously is still a challenging problem since gene expression data are typically noisy and data discretization is prone to information loss. We propose a new method for BN inference from time-series transcriptional profiles, called LogicGep. LogicGep formulates the identification of Boolean functions as a symbolic regression problem that learns the Boolean function expression and solve it efficiently through multi-objective optimization using an improved gene expression programming algorithm. To avoid overly emphasizing dynamic characteristics at the expense of topology structure ones, as traditional methods often do, a set of promising Boolean formulas for each target gene is evolved firstly, and a feed-forward neural network trained with continuous expression data is subsequently employed to pick out the final solution. We validated the efficacy of LogicGep using multiple datasets including both synthetic and real-world experimental data. The results elucidate that LogicGep adeptly infers accurate BN models, outperforming other representative BN inference algorithms in both network topology reconstruction and the identification of Boolean functions. Moreover, the execution of LogicGep is hundreds of times faster than other methods, especially in the case of large network inference.

Designing multi-functional MoS2/rGO piezocatalysts based on bacteria-catalyst topological interactions and electron pump effects for efficient water disinfection

In catalytic technology, the capability of nanocatalysts to generate reactive species (ROS) and the rapid contact between ROS and target pollutants are critical for the catalytic reaction. Herein, we proposed an effective strategy to construct multi-functional MoS2/rGO piezocatalysts based on bacteria-catalyst topological interactions and electron pump effects, which possessed high carrier separation ability and adhesion to bacteria, ensuring the effective utilization of ROS. Attributed to the unique 3D heterogeneous structure and interface electronic structure, MoS2/rGO could completely inactivate 6.21 log10 cfu mL−1 of E. coli K-12 within 30 min under ultrasonic conditions, significantly faster than pure MoS2. It was demonstrated experimentally and theoretically that the introduction of rGO led to the generation of a large amount of ROS by enhancing the piezoelectric properties and conductivity of MoS2/rGO, while the topological interactions between MoS2/rGO and bacteria facilitated effective bacteria capture, improving the utilization of ROS. Additionally, Kelvin Probe Force Microscopy texting confirmed that rGO acts as an electron pump, effectively attracting electrons from bacterial cells, which disrupted bacterial metabolic processes, increased oxidative stress, and further enhanced the bactericidal effect. The mechanisms of topological interactions and electron pump effects elucidated in this work offer new insights into the design and understanding of efficient bactericidal materials in water purification applications.

Influence of atomic electronegativity on ESIPT behaviour for the BTDI and its derivatives: Theoretical exploration

In this work, we theoretically explored the influence of atomic electronegativity on excited-state intramolecular proton transfer (ESIPT) behavior among novel fluorescent probes BTDI and its derivatives (BODI and BSeDI). A thorough examination of the optimized structural parameters and infrared vibrational spectra reveals an enhancement in intramolecular hydrogen bonding within BTDI and its derivatives upon light excitation. This finding is further reinforced by topological analysis and interaction region indicator scatter plots, which underscores the sensitivity of atomic electronegativity to variations in hydrogen bonding strength. With regards to absorption and fluorescence spectra, the decrease in atomic electronegativity leads to a pronounced redshift, primarily attributed to the narrowing of the energy gap. Additionally, an analysis of potential energy curves and the exploration of intrinsic reaction coordinate paths based on transition state structures afford a deeper understanding of the mechanism underlying ESIPT and being modulated through the manipulation of atomic electronegativity. We anticipate that this work on atomic electronegativity regulating ESIPT behavior will serve as a catalyst for novel fluorescent probes in the future, offering fresh perspectives and insights.

ATI: Assemble topological interaction overcomes consistency–cohesion trade‐off in bird flocking

AbstractIn nature, various animal groups like bird flocks display proficient collective navigation achieved by maintaining high consistency and cohesion simultaneously. Both metric and topological interactions have been explored to ensure high consistency among groups. The topological interactions found in bird flocks are more cohesive than metric interactions against external perturbations, especially the spatially balanced topological interaction (SBTI). However, it is revealed that in complex environments, pursuing cohesion via existing interactions compromises consistency. The authors introduce an innovative solution, assemble topological interaction, to address this challenge. Contrasting with static interaction rules, the new interaction empowers individuals with self‐awareness to adapt to the complex environment by switching between interactions through visual cues. Most individuals employ high‐consistency k‐nearest topological interaction when not facing splitting threats. In the presence of such threats, some switch to the high‐cohesion SBTI to avert splitting. The assemble topological interaction thus transcends the limit of the trade‐off between consistency and cohesion. In addition, by comparing groups with varying degrees of these two features, the authors demonstrate that group effects are vital for efficient navigation led by a minority of informed agents. Finally, the real‐world drone‐swarm experiments validate the applicability of the proposed interaction to artificial robotic collectives.

Low and high-order topological disruption of functional networks in multiple system atrophy with freezing of gait: A resting-state study

ObjectiveFreezing of gait (FOG), a specific survival-threatening gait impairment, needs to be urgently explored in patients with multiple system atrophy (MSA), which is characterized by rapid progression and death within 10 years of symptom onset. The objective of this study was to explore the topological organisation of both low- and high-order functional networks in patients with MAS and FOG. MethodLow-order functional connectivity (LOFC) and high-order functional connectivity FC (HOFC) networks were calculated and further analysed using the graph theory approach in 24 patients with MSA without FOG, 20 patients with FOG, and 25 healthy controls. The relationship between brain activity and the severity of freezing symptoms was investigated in patients with FOG. ResultsRegarding global topological properties, patients with FOG exhibited alterations in the whole-brain network, dorsal attention network (DAN), frontoparietal network (FPN), and default network (DMN), compared with patients without FOG. At the node level, patients with FOG showed decreased nodal centralities in sensorimotor network (SMN), DAN, ventral attention network (VAN), FPN, limbic regions, hippocampal network and basal ganglia network (BG), and increased nodal centralities in the FPN, DMN, visual network (VIN) and, cerebellar network. The nodal centralities of the right inferior frontal sulcus, left lateral amygdala and left nucleus accumbens (NAC) were negatively correlated with the FOG severity. ConclusionThis study identified a disrupted topology of functional interactions at both low and high levels with extensive alterations in topological properties in MSA patients with FOG, especially those associated with damage to the FPN. These findings offer new insights into the dysfunctional mechanisms of complex networks and suggest potential neuroimaging biomarkers for FOG in patients with MSA.