arXiv subjects

Limei Xu

Publications and source records attributed to Limei Xu.

At least 19 recordsLinked to original sources

arXiv2026

PRAXIS: Case-distilled and code-verified AI agents for biological research

Large language models are moving scientific research from text assistance toward agentic workflows, yet biological research requires strong object validation, methodological suitability, reproducibility, and auditability. Prompt engineering, general RAG, or tool use alone cannot reliably produce domain-specific scientific judgment. Here, we present PRAXIS, a verifiable biological research agent framework driven by literature learning and case distillation. PRAXIS converts research experience, failure boundaries, domain rules, and executable procedures into structured long-term memory. By coordinating successful cases, negative cases, rules, and skills, PRAXIS supports problem definition, object validation, method selection, workflow execution, result interpretation, and review feedback across diverse biocomputational tasks. We instantiated PRAXIS as an agent suite for biomedical computing and evaluated it through object validation, case retrieval, memory ablation, public benchmarks, and cross-agent workflows. The results show that case-based learning improves method selection, error suppression, and workflow organization in complex biological research tasks. Rather than replacing scientists, PRAXIS provides a general pathway for transforming research experience into executable, auditable, and transferable agent capabilities.

q-bio.QM↗

arXiv2026

MDAgent: A Multi-Agent Framework for End-to-End Molecular Dynamics Research

Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software operation or parameter setup, but in translating experimental questions into executable, interpretable, and reviewable computational workflows. Here, we present MDAgent, a multi-agent system for end-to-end molecular dynamics research. The system integrates problem understanding, literature-guided strategy design, simulation execution, trajectory analysis, mechanistic interpretation, and quality supervision into a unified workflow, enabling agents not only to run simulations but also to generate research-oriented computational plans and analytical reports. We further introduce a case-based learning mechanism based on Skill and Memory, which stores reusable knowledge from prior tasks, including parameter choices, operational rules, analytical logic, and problem-solving pathways, thereby supporting cross-task transfer without retraining the underlying model. Across multiple representative molecular simulation tasks, MDAgent achieved stable end-to-end performance with improved strategic adaptability, interpretability, and generalization. In an independent complex task involving conformational transitions of TMEM16F and XKR8, the system successfully completed system design, simulation, and mechanistic analysis for large membrane proteins. These results show that combining multi-agent collaboration with case-based learning can transform MD agents from workflow automation tools into scientific question-oriented computational research systems, providing a scalable framework for AI-driven automated research.

q-bio.QM↗

arXiv2026

Kinetics of Stacking Order Evolution During Heterogeneous Ice Formation

The selection of stacking order in a broad range of close-packed polymorphic materials remains a challenging enigma. Using in situ cryogenic transmission electron microscopy, we uncover the atomistic mechanisms governing the vapour deposition growth of ice. We find that the heterogeneous ice nucleation and growth undergoes recrystallization accompanied by bifurcation, reflecting a coherent epitaxial transition from a cubic-ice embryonic core to hexagonal-ice prismatic dendrites, with intermediate stacking-disordered layers serving as a dynamic fluctuating bridge. Supported by molecular dynamics simulations, these phenomena are attributed to a surface-constrained, symmetry-breaking crystallization preference aligned with the principle of minimizing free energy. Our results highlight the critical role of the combined effects of surface and symmetry in shaping ice crystallization, providing fresh insights into crystal growth mechanisms and guiding principles for the design of advanced materials.

cond-mat.mtrl-sci↗

arXiv2026

Topological physics in quantum critical systems

Topology forms a cornerstone in modern condensed matter and statistical physics, offering a new framework to classify the phases and phase transitions beyond the traditional Landau paradigm. However, it is widely believed that topological properties are destroyed when the bulk energy gap closes, making it highly nontrivial to consider topology in gapless quantum critical systems. To address these challenges, recent advancements have sought to generalize the notion of topology to systems without a bulk energy gap, including quantum critical points and critical phases, collectively referred to as gapless symmetry-protected topological states. Extending topology to gapless quantum critical systems challenges the traditional belief in condensed matter physics that topological edge states are typically tied to the presence of a bulk energy gap. Furthermore, it suggests that topology plays a crucial role in classifying quantum phase transitions even if they belong to the same universality class, fundamentally enriching the textbook understanding of phase transitions. Given its importance, here we give a pedagogical review of the current progress of topological physics in quantum critical systems. We introduce the topological properties of quantum critical points and generalize them to stable critical phases, both for noninteracting and interacting systems. Additionally, we discuss further generalizations and future directions, including higher dimensions, nonequilibrium phase transitions, and realizations in modern experiments.

cond-mat.str-el↗

arXiv2025

Unveiling the amorphous ice layer during premelting using AFM integrating machine learning

Premelting plays a key role across physics, chemistry, materials and biology sciences but remains poorly understood at the atomic level due to surface characterization limitations. We report the discovery of a novel amorphous ice layer (AIL) preceding the quasi-liquid layer (QLL) during ice premelting, enabled by a machine learning framework integrating atomic force microscopy (AFM) with molecular dynamics simulations. This approach overcomes AFM's depth and signal limitations, allowing for three-dimensional surface structure reconstruction from AFM images. It further enables structural exploration of premelting interfaces across a wide temperature range that are experimentally inaccessible. We identify the AIL, present between 121-180K, displaying disordered two-dimensional hydrogen-bond network with solid-like dynamics. Our findings refine the ice premelting phase diagram and offering new insights into the surface growth dynamic, dissolution and interfacial chemical reactivity. Methodologically, this work establishes a novel framework for AFM-based 3D structural discovery, marking a significant leap in our ability to probe complex disordered interfaces with unprecedented precision and paving the way for future disciplinary research, including surface reconstruction, crystallization, ion solvation, and biomolecular recognition.

cond-mat.mtrl-sci↗

arXiv2023

Machine learning aided atomic structure identification of interfacial ionic hydrates from atomic force microscopy images

Relevant to broad applied fields and natural processes, interfacial ionic hydrates has been widely studied by ultrahigh-resolution atomic force microscopy (AFM). However, the complex relationship between AFM signal and the investigated system makes it difficult to determine the atomic structure of such complex system from AFM images alone. Using machine learning, we achieved precise identification of the atomic structures of interfacial water/ionic hydrates based on AFM images, including the position of each atom and the orientation of water molecules. Furthermore, it was found that structure prediction of ionic hydrates can be achieved cost-effectively by transfer learning using neural network (NN) trained with easily available interfacial water data. Thus, this work provides an efficient and economical methodology which not only opens up avenues to determine atomic structures of more complex systems from AFM images, but may also help to interpret other science-wide studies involving sophisticated experimental results.

cond-mat.mes-hall↗

arXiv2023

Non-Hermitian strongly interacting Dirac fermions: a quantum Monte-Carlo study

Exotic quantum phases and phase transition in the strongly interacting Dirac systems has attracted tremendous interests. On the other hand, non-Hermitian physics, usually associated with dissipation arising from the coupling to environment, emerges as a frontier of modern physics in recent years. In this letter, we investigate the interplay between non-Hermitian physics and strong correlation in Dirac-fermion systems. We develop a sign-problem-free projector quantum Monte-Carlo (QMC) algorithm for the non-Hermitian interacting fermionic systems. Employing state-of-the-art projector QMC simulation, we decipher the ground-state phase diagram of the Honeycomb Hubbard model in the presence non-Hermitian asymmetric spin resolved hopping processes. Intriguingly, the antiferromagnetic ordering induced by Hubbard interaction is enhanced by the non-Hermitian asymmetric hopping. More remarkably, our study reveals that critical properties of the quantum phase transition between Dirac semi-metal and AF ordered phases are consistent with the XY universality class in Hermitian system, implying Hermiticity is emergent at the quantum critical point. The numerically-exact QMC approach utilized in this study is easily applied to other non-Hermitian interacting fermionic models, hence paving a new avenue to investigating quantum many-body physics in non-Hermitian systems.

cond-mat.str-el↗

arXiv2023

Quantum criticality of a $\mathbb{Z}_{3}$ symmetric spin chain with long-range interactions

Based on large-scale density matrix renormalization group techniques, we investigate the critical behaviors of quantum three-state Potts chains with long-range interactions. Using fidelity susceptibility as an indicator, we obtain a complete phase diagram of the system. The results show that as the long-range interaction power $α$ increases, the critical points $f_{c}^{*}$ shift towards lower values. In addition, the critical threshold $α_{c}(\approx 1.43$) of the long-range interaction power is obtained for the first time by a non-perturbative numerical method. This indicates that the critical behavior of the system can be naturally divided into two distinct universality classes, namely the long-range ($α\textless α_c$) and short-range ($α\textgreater α_c$) universality classes, qualitatively consistent with the classical $ϕ^{3}$ effective field theory. This work provides a useful reference for further research on phase transitions in quantum spin chains with long-range interaction.

cond-mat.str-el↗

arXiv2022

Emergence of Competing Orders and Possible Quantum Spin Liquid in SU(N) Fermions

In the past decades, tremendous efforts have been made towards understanding the exotic physics emerging from competition between various ordering tendencies in strongly correlated systems. Employing state-of-the-art quantum Monte-Carlo simulation, we investigate an interacting SU($N$) fermionic model with varying interaction strength and value of $N$, and unveil the ground-state phase diagram of the model exhibiting a plethora of exotic phases. For small value of $N$, namely $N=2,3$, the ground state is antiferromagnetic (AFM) phase, whereas in the large-$N$ limit, valence bound solid (VBS) order is dominant. For the intermediate value of $N$ such as $N=4$, remarkably, our study reveals distinct VBS orders appear in the weak and strong coupling regimes. More fantastically, the competition between staggered and columnar VBS ordering tendencies gives rise to a Mott insulating phase without spontaneously symmetry breaking (SSB), existing in a large interacting parameter regime, which is consistent with a gapped quantum spin liquid. Our study not only provides a platform to investigate the fundamental physics of quantum many-body systems, but also offers a novel route towards searching for exotic states of matter such as quantum spin liquid in realistic quantum materials.

cond-mat.str-el↗

arXiv2022

Conformal Boundary Conditions of Symmetry-Enriched Quantum Critical Spin Chains

Some quantum critical states cannot be smoothly deformed into each other without either crossing some multicritical points or explicitly breaking certain symmetries even if they belong to the same universality class. This brings up the notion of ``symmetry-enriched'' quantum criticality. While recent works in the literature focused on critical states with robust degenerate edge modes, we propose that the conformal boundary condition (b.c.) is a more generic characteristic of such quantum critical states. We show that in two families of quantum spin chains, which generalize the Ising and the three-state Potts models, the quantum critical point between a symmetry-protected topological phase and a symmetry-breaking order realizes a conformal b.c. distinct from the simple Ising and Potts chains. Furthermore, we argue that the conformal b.c. can be derived from the bulk effective field theory, which realizes a novel bulk-boundary correspondence in symmetry-enriched quantum critical states.

cond-mat.str-el↗

arXiv2022

Fidelity susceptibility as a diagnostic of the commensurate-incommensurate transition: A revisit of the programmable Rydberg chain

In recent years, programmable Rydberg-atom arrays have been widely used to simulate new quantum phases and phase transitions, generating great interest among theorists and experimentalists. Based on the large-scale density matrix renormalization group method, the ground-state phase diagram of one-dimensional Rydberg chains is investigated with fidelity susceptibility as an efficient diagnostic method. We find that the competition between Rydberg blockade and external detuning produces unconventional phases and phase transitions. As the Rydberg blockade radius increases, the phase transition between disordered and density-wave ordered phases changes from the standard Potts universality class to an unconventional chiral one. As the radius increases further (above Potts point but still close to the tip of the lobe), a very narrow intermediate floating-phase region begins to appear. A concise physical picture is also provided to illustrate the numerical results. Compared with previous studies, this work brings more evidence for commensurate-incommensurate quantum phase transitions in programmable quantum simulators from the perspective of quantum information, showing that fidelity susceptibility can be used to study such phase transitions.

cond-mat.str-el↗

arXiv2022

Topology of vibrational modes predict plastic events in glasses

The plastic deformation of crystalline materials can be understood by considering their structural defects such as disclinations and dislocations. Although glasses are also solids, their structure resembles closely the one of a liquid and hence the concept of structural defects becomes ill-defined. As a consequence it is very challenging to rationalize on a microscopic level the mechanical properties of glasses close to the yielding point and to relate plastic events with structural properties. Here we investigate the topological characteristics of the eigenvector field of the vibrational excitations of a two-dimensional glass model, notably the geometric arrangement of the topological defects as a function of vibrational frequency. We find that if the system is subjected to a quasistatic shear, the location of the resulting plastic events correlate strongly with the topological defects that have a negative charge. Our results provide thus a direct link between the structure of glasses prior their deformation and the plastic events during deformation.

cond-mat.dis-nn↗

arXiv2022

Onset of metallic transition in molecular liquid hydrogen

Liquid-liquid phase transition of hydrogen is at the center of hydrogen phase diagram as a promising route towards emergent properties such as the Wigner-Huntington metallization, superconductivity, and superfluidity. Here we report a study on the liquid-liquid phase transition of hydrogen using the state-of-the-art diffusion quantum Monte Carlo and density functional theory calculations. Our results suggest that the metallization process happens at lower pressures and temperatures compared to the structural phase transition of molecular to atomic hydrogen. The consequence is that metallized molecular hydrogen is stable at a wide range of pressures and temperatures. Our study breaks the conventional assumption that metallization coinciding with dissociation of hydrogen molecule, and the molecular metallic hydrogen liquid phase is likely to become the frontier of studying hydrogen phase transitions.

cond-mat.mtrl-sci↗

arXiv2020

Hydration of NH$_4^+$ in Water: Bifurcated Hydrogen Bonding Structures and Fast Rotational Dynamics

Understanding the hydration and diffusion of ions in water at the molecular level is a topic of widespread importance. The ammonium ion (NH$_4^+$) is an exemplar system that has received attention for decades because of its complex hydration structure and relevance in industry. Here we report a study of the hydration and the rotational diffusion of NH$_4^+$ in water using ab initio molecular dynamics simulations and quantum Monte Carlo calculations. We find that the hydration structure of NH$_4^+$ features bifurcated hydrogen bonds, which leads to a rotational mechanism involving the simultaneous switching of a pair of bifurcated hydrogen bonds. The proposed hydration structure and rotational mechanism are supported by existing experimental measurements, and they also help to rationalize the measured fast rotation of NH$_4^+$ in water. This study highlights how subtle changes in the electronic structure of hydrogen bonds impacts the hydration structure, which consequently affects the dynamics of ions and molecules in hydrogen bonded systems.

physics.comp-ph↗

arXiv2018

Stretched and compressed exponentials in the relaxation dynamics of a metallic glass-forming melt

The relaxation dynamics of glass-forming systems shows a multitude of features that are absent in normal liquids, such as non-exponential relaxation and a strong temperature-dependence of the relaxation time. Connecting these dynamic properties to the microscopic structure of the system is very challenging because of the presence of the structural disorder. Here we use computer simulations of a metallic glass-former to establish such a connection. By probing the temperature and wave-vector dependence of the intermediate scattering function we find that the relaxation dynamics of the glassy melt is directly related to the local arrangement of icosahedral structures: Isolated icosahedra give rise to a flow-like stretched exponential relaxation whereas clusters of icosahedra lead to a compressed exponential relaxation that is reminiscent to the one found in a solid. Our results show that in metallic glass-formers these two types of relaxation processes can coexist and give rise to a surprisingly complex dynamics, insight that will allow to get a deeper understanding of the outstanding mechanical properties of metallic glasses.

cond-mat.dis-nn↗

arXiv2017

X-ray absorption of liquid water by advanced ab initio methods

Oxygen K-edge X-ray absorption spectra of liquid water are computed based on the configurations from advanced ab initio molecular dynamics simulations, as well as an electron excitation theory from the GW method. One one hand, the molecular structures of liquid water are accurately predicted by including both van der Waals interactions and hybrid functional (PBE0). On the other hand, the dynamic screening effects on electron excitation are approximately described by the recently developed enhanced static Coulomb hole and screened exchange approximation by Kang and Hybertsen [Phys. Rev. B 82, 195108 (2010)]. The resulting spectra of liquid water are in better quantitative agreement with the experimental spectra due to the softened hydrogen bonds and the slightly broadened spectra originating from the better screening model.

cond-mat.soft↗

arXiv2017

Local connectivity modulates multi-scale relaxation dynamics in a metallic glass-forming system

The structural description for the intriguing link between the fast vibrational dynamics and slow diffusive dynamics in glass-forming systems is one of the most challenging issues in physical science. Here, in a model of metallic supercooled liquid, we find that local connectivity as an atomic-level structural order parameter tunes the short-time vibrational excitations of the icosahedrally coordinated particles and meanwhile modulates their long-time relaxation dynamics changing from stretched to compressed exponentials, denoting a dynamic transition from subdiffusive to hyperdiffusive motions of such particles. Our result indicates that long-time dynamics has an atomic-level structural origin which is related to the short-time dynamics, thus suggests a structural bridge to link the fast vibrational dynamics and the slow structural relaxation in glassy materials.

cond-mat.dis-nn↗

arXiv2017

Submolecular-resolution non-invasive imaging of interfacial water with atomic force microscopy

Scanning probe microscopy (SPM) has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly non-invasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip-water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states without inducing any disturbance. This work may open up new possibility of studying the intrinsic structure and electrostatics of ice or water on bulk insulating surfaces, ion hydration and biological water with atomic precision.

physics.chem-ph↗