arXiv subjects

Zhiping Xu

Publications and source records attributed to Zhiping Xu.

At least 19 recordsLinked to original sources

arXiv2026

Bioinfoysis Technical Report

Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.

cs.AI↗

arXiv2026

Rippled graphene pores as fluidic memristive devices with synaptic and neuromorphic functionalities

Nanofluidic memristive devices work with nanoscale pores and ions dissolved in water, which harness the ionic memory effect aiming to store and process information. These devices share the same charge carriers as biological systems and bring hope for better emulating the neural functions and developing ionic circuits for neuromorphic applications. Specially, theory and experiments suggest that nanoconfinement is essential for inducing a memory effect, which places limit on the pore size to nm-scale or smaller. Such devices are difficult to scale up with precision and operate with long-term stability. Here, we show that a micrometer size pore, generally expected to exhibit a linear ion transport, can display a pronounced memory effect, if its rim is wrapped by strongly curved and tightly stacked graphene. We attribute the observation to slow ion dynamics confined in the rippled graphene edges. The devices are easy to scale up and integrate into fluidic circuits. The memory effect is ion-selective and exhibits long endurance comparable to the lifetime of synaptic proteins, which enables reversible modification of the conductance states using programmable voltage spikes and various electrolytes over a long time, akin to biological synaptic plasticity. Thanks to this plasticity, our devices and their integrated circuits enable storing, transmitting and processing information with high reliability, fidelity and accuracy, as evidenced in the identification of both greyscale and color images, and in the real-time analysis of emulated neural signals. Our results highlight nanoscale morphology of the pore wall as an important parameter regulating ion transport and indicate that the stringent nanoconfinement for ionic memory can be lifted from restricting the pore size to designing its rim structure. The devices and their integrated circuits may find use in ionic neuromorphic applications.

cond-mat.mtrl-sci↗

arXiv2026

Observation of robust macroscale structural superlubricity

Structural superlubricity (SSL) promises nearly frictionless and wearless sliding, but has until now been considered a special and extreme interfacial phenomenon limited to micro- and nanoscale contacts. Here, we demonstrate robust macroscale SSL within a single sub-millimeter graphite contact. Previously reported near-zero friction coefficients, where friction is nearly independent of normal load, have only been observed at microscale contacts under low loads. Our system expands both contact size and load into the macroscopic regime, exhibiting friction coefficients that fluctuate around zero and reach values as low as $10^{-6}$ across a broad load range from 1 mN to 0.5 N. Negative friction coefficients are also observed. Similar behavior is observed at graphite/MoS$_2$ interfaces, indicating that macroscale SSL is a generalizable phenomenon across flat layered materials. These findings overturn long-standing scaling limitations and establish macroscale SSL as a paradigm-shifting platform for next-generation mechanical and electromechanical systems.

cond-mat.mtrl-sci↗

arXiv2025

Atomically-precise synthesis and simultaneous integration of 2D transition metal dichalcogenides enabled by nano-confinement

Two-dimensional (2D) materials, such as graphene, transition metal dichalcogenides (TMDs), and hBN, exhibit intriguing properties that are sensitive to their atomic-scale structures and can be further enriched through van der Waals (vdW) integration. However, the precise synthesis and clean integration of 2D materials remain challenging. Here, using graphene or hBN as a vdW capping layer, we create a nano-confined environment that directs the growth kinetics of 2D TMDs (e.g., NbSe2 and MoS2), enabling precise formation of TMD monolayers with tailored morphologies, from isolated monolayer domains to large-scale continuous films and intrinsically-patterned rings. Moreover, Janus S-Mo-Se monolayers are synthesized with atomic precision via vdW-protected bottom-plane chalcogen substitution. Importantly, our approach simultaneously produces ultraclean vdW interfaces. This in situ encapsulation reliably preserves air-sensitive materials, as evidenced by the enhanced superconductivity of nano-confined NbSe2 monolayers. Altogether, our study establishes a versatile platform for the controlled synthesis and integration of 2D TMDs for advanced applications.

cond-mat.mtrl-sci↗

arXiv2025

Predicting Brain Morphogenesis via Physics-Transfer Learning

Brain morphology is shaped by genetic and mechanical factors and is linked to biological development and diseases. Its fractal-like features, regional anisotropy, and complex curvature distributions hinder quantitative insights in medical inspections. Recognizing that the underlying elastic instability and bifurcation share the same physics as simple geometries such as spheres and ellipses, we developed a physics-transfer learning framework to address the geometrical complexity. To overcome the challenge of data scarcity, we constructed a digital library of high-fidelity continuum mechanics modeling that both describes and predicts the developmental processes of brain growth and disease. The physics of nonlinear elasticity from simple geometries is embedded into a neural network and applied to brain models. This physics-transfer approach demonstrates remarkable performance in feature characterization and morphogenesis prediction, highlighting the pivotal role of localized deformation in dominating over the background geometry. The data-driven framework also provides a library of reduced-dimensional evolutionary representations that capture the essential physics of the highly folded cerebral cortex. Validation through medical images and domain expertise underscores the deployment of digital-twin technology in comprehending the morphological complexity of the brain.

q-bio.NC↗

arXiv2025

On-Device Control of Electronic Friction

Friction causes mechanical energy dissipation and material degradation in machinery and devices. While phononic friction is well understood via anharmonic lattice dynamics, the physics of electronic friction remains unclear due to challenges in separating electronic degrees of freedom from phononic ones in experiments and analyzing the non-equilibrium interactions between ionic movement and electronic dynamics in theory. To tackle this problem, we construct a sliding device featuring 2D crystalline interfaces that possess ultra-smooth and minimally interacting surfaces, achieving the state of structural superlubricity with no wear and minimal friction. Using electrical and mechanical controls, we tuned the nature of interfacial electronic coupling and charge densities in materials in an on-device setting, which allows us to disentangle the electron and phonon contributions to friction. Our experimental data and theoretical analysis supported by first-principles calculations demonstrate that electronic friction can well surpass phononic contributions and dominate energy dissipation at structural superlubricity contacts. These findings offer fresh insights into the mechanism of electronic friction and promising opportunities for friction control in device applications.

cond-mat.mes-hall↗

arXiv2025

Mechanical Performance Database for Low-Temperature Alloys

Low-temperature alloys are important for a wide spectrum of modern technologies ranging from liquid hydrogen, and superconductivity to quantum technology. These applications push the limit of material performance into extreme coldness, often demanding a combination of strength and toughness to address various challenges. Steel is one of the most widely used materials in cryogenic applications. With the deployment in aerospace liquid hydrogen storage and the transportation industry, aluminum and titanium alloys are also gaining increasing attention. Emerging medium-entropy alloys (MEAs) and high-entropy alloys (HEAs) demonstrate excellent low-temperature mechanical performance with a much-expanded space of material design. A database of low-temperature metallic alloys is collected from the literature and hosted in an open repository. The workflow of data collection includes automated extraction based on machine learning and natural language processing, supplemented by manual inspection and correction, to enhance data extraction efficiency and database quality. The product datasets cover key performance parameters including yield strength, tensile strength, elongation at fracture, Charpy impact energy, as well as detailed information on materials such as their types, chemical compositions, processing and testing conditions. Data statistics are analyzed to elucidate the research and development patterns and clarify the challenges in both scientific exploration and engineering deployment.

cond-mat.mtrl-sci↗

arXiv2025

Neural Network Modeling of Microstructure Complexity Using Digital Libraries

Microstructure evolution in matter is often modeled numerically using field or level-set solvers, mirroring the dual representation of spatiotemporal complexity in terms of pixel or voxel data, and geometrical forms in vector graphics. Motivated by this analog, as well as the structural and event-driven nature of artificial and spiking neural networks, respectively, we evaluate their performance in learning and predicting fatigue crack growth and Turing pattern development. Predictions are made based on digital libraries constructed from computer simulations, which can be replaced by experimental data to lift the mathematical overconstraints of physics. Our assessment suggests that the leaky integrate-and-fire neuron model offers superior predictive accuracy with fewer parameters and less memory usage, alleviating the accuracy-cost tradeoff in contrast to the common practices in computer vision tasks. Examination of network architectures shows that these benefits arise from its reduced weight range and sparser connections. The study highlights the capability of event-driven models in tackling problems with evolutionary bulk-phase and interface behaviors using the digital library approach.

cs.LG↗

arXiv2025

Discovering High-Strength Alloys via Physics-Transfer Learning

Predicting the strength of materials requires considering various length and time scales, striking a balance between accuracy and efficiency. Peierls stress measures material strength by evaluating dislocation resistance to plastic flow, reliant on elastic lattice responses and crystal slip energy landscape. Computational challenges due to the non-local and non-equilibrium nature of dislocations prohibit Peierls stress evaluation from state-of-the-art material databases. We propose a data-driven framework that leverages neural networks trained on force field simulations to understand crystal plasticity physics, predicting Peierls stress from material parameters derived via density functional theory computations, which are otherwise computationally intensive for direct dislocation modeling. This physics transfer approach successfully screen the strength of metallic alloys from a limited number of single-point calculations with chemical accuracy. Guided by these predictions, we fabricate high-strength binary alloys previously unexplored, utilizing high-throughput ion beam deposition techniques. The framework extends to problems facing the accuracy-performance dilemma in general by harnessing the hierarchy of physics of multiscale models in materials sciences.

cond-mat.mtrl-sci↗

arXiv2024

Disentangling Electronic and Phononic Thermal Transport Across 2D Interfaces

Electrical and thermal transport across material interfaces is key for 2D electronics in semiconductor technology, yet their relationship remains largely unknown. We report a theoretical proposal to separate electronic and phononic contributions to thermal conductance at 2D interfaces, which is validated by non-equilibrium Green's function calculations and molecular dynamics simulations for graphene-gold contacts. Our results reveal that while metal-graphene interfaces are transparent for both electrons and phonons, non-covalent graphene interfaces block electronic tunneling beyond two layers but not phonon transport. This suggests that the Wiedemann-Franz law can be experimentally tested by measuring transport across interfaces with varying graphene layers.

cond-mat.mes-hall↗

arXiv2024

On the Edge Roughness of Two-Dimensional Materials

This study examines the roughness of mechanically cleaved edges in 2D crystals and glasses using molecular dynamics simulations with chemically accurate machine-learning force fields. Our results show that ultra-flat armchair and zigzag edges can be achieved in graphene by aligning the loading direction with specific lattice orientations. Deviations from these orientations create kinks between the atomically smooth armchair and zigzag segments, with increased irregularities when dynamic effects are considered. Fracture mechanics analysis highlights the kinetic and dynamic factors contributing to crack deflection and edge roughening. In three-atom-thick 2D silica crystals, the relationship between edge morphologies and cleavage conditions is modified by their bilayer structure and sublattice asymmetry. In 2D silica glasses, this correlation is further disrupted by topological disorder. These insights are crucial for minimizing edge roughness in 2D materials, which is essential for their performance in mechanical and electronic applications.

cond-mat.mtrl-sci↗

arXiv2024

Strength of 2D Glasses Explored by Machine-Learning Force Fields

The strengths of glasses are intricately linked to their atomic-level heterogeneity. Atomistic simulations are frequently used to investigate the statistical physics of this relationship, compensating for the limited spatiotemporal resolution in experimental studies. However, theoretical insights are limited by the complexity of glass structures and the accuracy of the interatomic potentials used in simulations. Here, we investigate the strengths and fracture mechanisms of 2D silica, with all structural units accessible to direct experimental observation. We develop a neural network force field for fracture (NN-F$^{3}$) based on the deep potential-smooth edition (DeepPot-SE) framework. Representative atomic structures across crystals, nanocrystalline, paracrystalline, and continuous random network glasses are studied. We find that the virials or bond lengths control the initialization of bond-breaking events, creating nanoscale voids in the vitreous network. However, the voids do not necessarily lead to crack propagation due to a disorder-trapping effect, which is stronger than the lattice-trapping effect in a crystalline lattice and occurs over larger length and time scales. Fracture initiation proceeds with void growth and coalescence, and advances through a bridging mechanism. The fracture patterns are shaped by subsequent trapping and cleavage steps, often guided by voids forming ahead of the crack tip. These heterogeneous processes result in atomically smooth facets in crystalline regions and rough, amorphous edges in the glassy phase. These insights into 2D crystals and glasses, both sharing SiO$_{2}$ chemistry, highlight the pivotal role of atomic-level structures in determining fracture kinetics and path selection in materials.

cond-mat.mtrl-sci↗

arXiv2024

Cooperating Cracks in Two-Dimensional Crystals

The pattern development of multiple cracks in extremely anisotropic solids such as bilayer or multilayer two-dimensional (2D) crystals contains rich physics, which, however, remains largely unexplored. We studied crack interaction across neighboring 2D layers by transmission electron microscopy and molecular dynamics simulations. Parallel and anti-parallel ('En-Passant') cracks attract and repel each other in bilayer 2D crystals, respectively, in stark contrast to the behaviors of co-planar cracks. We show that the misfit between in-plane displacement fields around the crack tips results in non-uniform interlayer shear, which modifies the crack driving forces by creating an antisymmetric component of the stress intensity factor. The cross-layer interaction between cracks directly leads to material toughening, the strength of which increases with the shear stiffness and decreases with the crack spacings. Backed by the experimental findings and simulation results, a theory that marries the theory of linear elastic fracture mechanics and the shear-lag model is presented, which guides the unconventional approach to engineer fracture patterns and enhance material resistance to cracking.

cond-mat.mtrl-sci↗

arXiv2023

Electrified Fracture of Nanotube Films

Strong and conductive carbon nanotube films are ideal candidates for lightning-strike protection. Understanding their failure mechanisms by considering the anisotropic and single-fiber nature is essential to improve performance. Our experimental studies show that the single-layer, nanometer-thick films fail under electrification by crack nucleation and propagation, reminiscent of brittle and ductile fracture of materials under mechanical loads. Sharp and diffuse patterns of fracture are identified in aligned and non-woven films, respectively, signaling the strong effect of material anisotropy that is absent in common engineering materials. The fracture is driven by local Joule heating concentrated at the crack fronts instead of force-induced breakage, which is validated by experimental characterization and simulation results at both continuum and atomistic levels.

physics.app-ph↗

arXiv2023

On the Performance of LoRa Empowered Communication for Wireless Body Area Networks

To remotely monitor the physiological status of the human body, long range (LoRa) communication has been considered as an eminently suitable candidate for wireless body area networks (WBANs). Typically, a Rayleigh-lognormal fading channel is encountered by the LoRa links of the WBAN. In this context, we characterize the performance of the LoRa system in WBAN scenarios with an emphasis on the physical (PHY) layer and medium access control (MAC) layer in the face of Rayleigh-lognormal fading channels and the same spreading factor interference. Specifically, closed-form approximate bit error probability (BEP) expressions are derived for the LoRa system. The results show that increasing the SF and reducing the interference efficiently mitigate the shadowing effects. Moreover, in the quest for the most suitable MAC protocol for LoRa based WBANs, three MAC protocols are critically appraised, namely the pure ALOHA, slotted ALOHA, and carrier-sense multiple access. The coverage probability, energy efficiency, throughput, and system delay of the three MAC protocols are analyzed in Rayleigh-lognormal fading channel. Furthermore, the performance of the equal-interval-based and equal-area-based schemes is analyzed to guide the choice of the SF. Our simulation results confirm the accuracy of the mathematical analysis and provide some useful insights for the future design of LoRa based WBANs.

cs.IT↗

arXiv2023

A Planning-and-Exploring Approach to Extreme-Mechanics Force Fields

Extreme mechanical processes such as strong lattice distortion and bond breakage during fracture are ubiquitous in nature and engineering, which often lead to catastrophic failure of structures. However, understanding the nucleation and growth of cracks is challenged by their multiscale characteristics spanning from atomic-level structures at the crack tip to the structural features where the load is applied. Molecular simulations offer an important tool to resolve the progressive microstructural changes at crack fronts and are widely used to explore processes therein, such as mechanical energy dissipation, crack path selection, and dynamic instabilities (e.g., kinking, branching). Empirical force fields developed based on local descriptors based on atomic positions and the bond orders do not yield satisfying predictions of fracture, even for the nonlinear, anisotropic stress-strain relations and the energy densities of edges. High-fidelity force fields thus should include the tensorial nature of strain and the energetics of rare events during fracture, which, unfortunately, have not been taken into account in both the state-of-the-art empirical and machine-learning force fields. Based on data generated by first-principles calculations, we develop a neural network-based force field for fracture, NN-F$^3$, by combining pre-sampling of the space of strain states and active-learning techniques to explore the transition states at critical bonding distances. The capability of NN-F$^3$ is demonstrated by studying the rupture of h-BN and twisted bilayer graphene as model problems. The simulation results confirm recent experimental findings and highlight the necessity to include the knowledge of electronic structures from first-principles calculations in predicting extreme mechanical processes.

cond-mat.mtrl-sci↗

arXiv2023

Predicting Fatigue Crack Growth via Path Slicing and Re-Weighting

Predicting potential risks associated with the fatigue of key structural components is crucial in engineering design. However, fatigue often involves entangled complexities of material microstructures and service conditions, making diagnosis and prognosis of fatigue damage challenging. We report a statistical learning framework to predict the growth of fatigue cracks and the life-to-failure of the components under loading conditions with uncertainties. Digital libraries of fatigue crack patterns and the remaining life are constructed by high-fidelity physical simulations. Dimensionality reduction and neural network architectures are then used to learn the history dependence and nonlinearity of fatigue crack growth. Path-slicing and re-weighting techniques are introduced to handle the statistical noises and rare events. The predicted fatigue crack patterns are self-updated and self-corrected by the evolving crack patterns. The end-to-end approach is validated by representative examples with fatigue cracks in plates, which showcase the digital-twin scenario in real-time structural health monitoring and fatigue life prediction for maintenance management decision-making.

cs.LG↗

arXiv2023

A Data-Driven Approach to Morphogenesis under Structural Instability

Morphological development into evolutionary patterns under structural instability is ubiquitous in living systems and often of vital importance for engineering structures. Here we propose a data-driven approach to understand and predict their spatiotemporal complexities. A machine-learning framework is proposed based on the physical modeling of morphogenesis triggered by internal or external forcing. Digital libraries of structural patterns are constructed from the simulation data, which are then used to recognize the abnormalities, predict their development, and assist in risk assessment and prognosis. The capabilities to identify the key bifurcation characteristics and predict the history-dependent development from the global and local features are demonstrated by examples of brain growth and aerospace structural design, which offer guidelines for disease diagnosis/prognosis and instability-tolerant design.

nlin.PS↗