arXiv subjects

Zhen Zhang

Publications and source records attributed to Zhen Zhang.

At least 19 recordsLinked to original sources

arXiv2026

RAGTIMER 1.0: Rapid Rare-Event Partial State Space Construction for Stochastic VAS (extended version)

Transient reachability analysis of rare events in Continuous-Time Stochastic Vector Addition Systems (CTSVAS) such as Chemical Reaction Networks (CRNs) has proven a formidable challenge to cutting-edge tools. Underlying a CTSVAS is a continuous-time Markov chain (CTMC), and CTMC transient reachability analysis calls for Probabilistic Model Checking (PMC). This analysis requires the explicit representation of a model's entire state space. Rare events occur with extremely low probability, compounding the challenge of probabilistic analysis. In CRNs, it is imperative to verify the probability of rare events; even a low concentration of a species can have pathological consequences. This paper presents the RAGTIMER 1.0 tool, which efficiently builds a partial state space for a CTSVAS by enumerating traces to a rare event of interest and expanding them to exploit concurrency and cycles, providing a guaranteed lower bound on the probability of a rare event. Guaranteed lower bounds are particularly useful in synthetic biological applications because they indicate how and when a rare event can be experimentally observed. RAGTIMER is an attractive alternative to existing rare event analysis methods for CTSVAS models. It outperforms existing PMC tools and refutes multiple probability estimates from rare-event stochastic simulation on multiple challenging CRN models. RAGTIMER uses optimized data structures, a simple input format, and memory-safe Rust code to improve the scalability and accessibility of PMC for industry professionals.

cs.FL↗

arXiv2026

RealSimLoop: Online Real-to-Sim Adaptation via Differentiable Reduced-Order Simulation with Vision Feedback

Real-world observations of deformable objects are often sparse or surface-level, while downstream tasks require hidden physical quantities such as internal deformation, stress fields, and interaction forces. Physics-based simulation can recover these quantities, but online real-to-sim adaptation remains challenging due to costly full-space optimization, limited feedback, and time-varying material properties. To address these challenges, we propose RealSimLoop, a differentiable framework for online real-to-sim adaptation using vision data as physical feedback. Our approach achieves quasi-real-time performance by executing differentiable simulation within a reduced-order neural subspace, drastically accelerating the optimization loop. We couple this efficient dynamics model with differentiable rendering, enabling direct gradient backpropagation that leverages high-fidelity pixel data to refine physical parameters such as material stiffness. Furthermore, by employing a sliding-window objective function, RealSimLoop enables robust online adaptation, allowing the system to track time-varying material properties and effectively bridge the real-to-sim gap arising from model reduction or unmodeled dynamics. Extensive experiments demonstrate that our method outperforms conventional offline methods, and we validate the framework's versatility in downstream applications, including external force prediction and 3D stress field reconstruction with novel view synthesis.

cs.GR↗

arXiv2026

Effective particle size governs structure and dynamics in rough hard-particle fluids

We numerically investigate how particle surface roughness affects the static and dynamic properties of a hard-particle fluid across a wide range of densities, rho. These simulations of a simple model of granular systems reveal that, although the amplitude and coverage of surface corrugation significantly influence the rho-dependence of system properties, the qualitative behavior of this dependence remains unchanged. These findings can be described quantitatively by introducing an effective particle size, which enables a direct mapping of the rough particle systems to equivalent hard-disk systems. Analytical calculations provide an explicit form of this mapping, and allow us to predict the static and dynamic properties of rough particles using standard liquid-state theories for hard disks.

cond-mat.soft↗

arXiv2026

Connecting heterogeneous dynamics with local entropy

Establishing a robust and physically interpretable link between static structure and heterogeneous relaxation dynamics remains a fundamental challenge in glass physics. Here, we introduce a weighted pair-entropy descriptor based on the conventional two-body excess entropy. For this, we multiply the integrand used to calculate the excess entropy by a weight function that is directly related to the length scale of the pair correlation function. This multiplication does not affect the contribution of the short range order to the local excess entropy, but allows to take into account the structure present on intermediate distances, i.e., the medium-range order. For a canonical two-dimensional Lennard-Jones glass former, the resulting descriptor exhibits a strong correlation with particle-level dynamical propensity at long times (multiples of the alpha-relaxation time), with a maximum structure--dynamics correlation reaching about 0.9, substantially outperforming the predictive power of the conventional local pair excess entropy. These results demonstrate that incorporating a physically motivated structural length scale into entropy-based descriptors markedly enhances their predictive power while preserving physical interpretability. Our findings provide a simple and general framework for investigating structure--dynamics correlations in glass-forming systems.

cond-mat.dis-nn↗

arXiv2026

Efficient primal--dual splitting methods for a Poisson-constrained JKO scheme for Poisson-Nernst-Planck models

The Poisson--Nernst--Planck (PNP) equations strongly couple ionic transport and electrostatic interactions through the Poisson equation, posing substantial numerical challenges under small permittivity and complex potential boundary conditions. Underlying these equations is a natural Wasserstein gradient-flow structure, in which the Poisson equation serves as a local realization of the nonlocal electrostatic interaction energy. Exploiting this structure, we formulate each time step as a constrained convex minimization problem where the ionic continuity equations and the Poisson equation are incorporated as linear constraints, allowing the concentrations, fluxes, and electrostatic potential to be updated simultaneously. The variational structure of the scheme intrinsically guarantees the dissipation of the original free energy, mass conservation, and nonnegativity of ionic concentrations under general electrostatic boundary conditions. Moreover, the framework is structurally modular: extending from classical to modified PNP models with steric interactions and concentration-gradient corrections requires only modifying the energy functional, while all structure-preserving properties are automatically retained. To efficiently solve the resulting large-scale constrained problems, we develop preconditioned and transformed primal--dual algorithms equipped with tailored fast dual solvers, namely DCT-based direct and Schur-complement iterative methods, that exploit the coupled block structure of the PDE constraints. Numerical experiments on classical and modified PNP systems demonstrate the accuracy and structure-preserving properties of the scheme, and show that the proposed algorithms converge reliably in strongly coupled small-permittivity regimes without significant growth in computational cost.

math.NA↗

arXiv2026

DP-JMRNet: A Deep Unfolding Network for Differential Phase Preservation in Sparse Bitemporal SAR Reconstruction

Complex SAR imagery is usually visualized and evaluated mainly through its magnitude. Phase is retained in the complex data but is rarely treated as a direct image-quality objective. Existing sparse reconstruction methods typically focus on magnitude fidelity and single-epoch complex reconstruction accuracy. However, the phase difference between two acquisitions is what drives line-of-sight deformation retrieval in InSAR, from ground subsidence monitoring to earthquake deformation mapping. This paper proposes the Differential-Phase-Oriented Joint Masked Reconstruction Network (DP-JMRNet), which uses deep unfolding to reconstruct the two epochs jointly from masked observations under a differential-phase objective. An exchange-equivariant interaction module makes the reconstruction independent of epoch ordering. A coherence-aware gate opens cross-epoch sharing in coherent regions and closes it where the two epochs disagree. On simulated bitemporal SAR data, DP-JMRNet attains the lowest differential-phase RMSE at 30\%, 40\%, and 50\% sampling rate, while maintaining competitive amplitude and complex-image fidelity. This corresponds to a 47.5\%--51.3\% reduction over the best baseline, achieved with one third of its parameters. The same trend is validated on three Sentinel-1 scenes. A systematic study of acquisition design further shows that sharing the same aperture support across epochs is necessary for phase fidelity, whereas optimizing the sampling mask does not improve the differential phase. The code and data are available at https://github.com/JasonBao05/coherent-sar-unfolding.

eess.SP↗

arXiv2026

AffectSim: A Controllable Interactive 3D Simulation Benchmark for Embodied Affective Perception

Existing affective benchmarks largely consist of fixed recordings whose observation conditions are determined before inference, making it difficult to systematically study how embodied sensing influences affective perception. We introduce AffectSim, a controllable interactive 3D simulation benchmark for embodied affective perception. Rather than treating affective samples as fixed recordings, AffectSim instantiates emotion-expressive human motions as replayable 3D episodes in which distance, orientation, occlusion, scene geometry, and agent viewpoint can be systematically varied while preserving the underlying behavior and emotion label. AffectSim contains 27{,}647 episodes across five emotion categories and 57 scenes. Its factorized design separates affective behavior from observation conditions, supporting controlled re-observation of the same behavior as well as agent-controlled sensing in an executable 3D environment. To demonstrate this capability, we instantiate embodied emotion perception under matched initial (P-Init), reference (P-Ref), and actively acquired (A-Obs) observations. Across 24 frozen perception-model configurations, P-Ref substantially outperforms P-Init, while a simple two-stage active-observation baseline improves 21 of 24 configurations. Mean Macro-F1 increases from 9.89% to 11.70% for open-source models and from 22.61% to 24.26% for closed-source models, recovering 32.0% and 20.1% of their respective P-Ref--P-Init gaps. Episode-level recovery and path-aware evaluation further characterize the current baseline beyond aggregate recognition performance. These results demonstrate the value of making affective observation controllable and establish AffectSim as an initial platform for studying embodied affective perception through interactive 3D simulation.

cs.HC↗

arXiv2026

FrontierChallenge: Evaluating Scientific Workflow Completion

Scientific agents increasingly analyze data, execute code, and produce research artifacts, yet most benchmarks emphasize final answers, isolated programs, or a single domain. We introduce FrontierChallenge, a cross-domain benchmark comprising 300 end-to-end scientific workflows. In this paper, we release and evaluate 97 of these tasks, spanning quantum chemistry, molecular dynamics, materials characterization, analytical chemistry, life science, and electrochemistry/environment. Each task provides fixed inputs and specifies a bundle of required scientific deliverables. We evaluate twelve frontier models with three agent scaffolds. Pass Rate measures the fraction of tasks satisfying the full-completion criterion, while Avg. Score captures partial progress. Each of the best-performing configurations completed only 20 of the 97 released tasks, yielding a Pass Rate of 20.6%. Partial progress translated especially poorly into complete delivery in analytical chemistry and electrochemistry/environment: Avg. Scores reached 87.6 and 94.9, but the highest Pass Rates were only 4% and 0%. Among non-passing Claude Code trajectories, 75.5% still ended with language claiming completion. Complementary HDS6 process scores correlate strongly with task outcomes, supporting FrontierChallenge as a benchmark of Heavy Duty Solver capabilities. These findings show that neither high partial scores nor confident claims of completion reliably indicate that a scientific task has been fully delivered, highlighting the need to evaluate end-to-end workflow execution and the completeness of scientific deliverables together.

cs.AI↗

arXiv2026

Mapping metallic d-wave altermagnetism across the TiNiSi structural family

The prospect of using altermagnets as switchable sources of perpendicularly polarized spin currents has intensified the search for candidate materials, yet metallic d-wave systems with sizable spin-splitter responses remain scarce. Here, we identify an empirical magnetic motif that supports metallic d-wave altermagnetism in the TiNiSi structural family: ferromagnetically ordered zigzag chains with antiferromagnetic interchain coupling in a relatively low-symmetry crystal environment. The TiNiSi structure type combines this motif with broad chemical flexibility and competing magnetic ground states. By combining first-principles screening of thermodynamic stability and magnetic ground states across 280 ternary systems, we identify 16 metallic d-wave altermagnets. This set recovers four experimentally known members---WFeB, NbMnP, TaMnP, and NbMnAs---and yields 12 new predictions, of which ScMnP, TaMnAs, ScMnAs, MoMnAs, MoMnSi, and WMnSi are the most promising. Noncollinear calculations indicate that the collinear altermagnetic configuration is the ground state across them. Each of the six leading new candidates has a nonzero spin-splitter angle and a finite anomalous Hall conductivity. Notably, ScMnP and TaMnAs exhibit strong spin-splitter responses despite modest altermagnetic band splitting. These results establish TiNiSi-type metallic d-wave altermagnets as a chemically versatile platform for efficient charge-to-spin conversion and provide an empirical magnetic-motif-guided route to identifying further candidates.

cond-mat.mtrl-sci↗

arXiv2026

Nanoscale silicon sensor - guided new insights into early metabolic response of Escherichia coli to ampicillin

Antibiotic killing is often attributed to inhibition of specific cellular targets, yet metabolic processes can strongly influence drug efficacy. However, the relationship between metabolic responses and antibiotic lethality remains incompletely understood. Here, we employed silicon nanowire field-effect transistor (SiNWFET) sensors to monitor real-time metabolic responses of Escherichia coli to ampicillin (AMP). AMP treatment induced a biphasic extracellular pH signature, characterized by rapid acidification followed by alkalization. Metabolomic analyses revealed that the initial acidification resulted from organic acid secretion, whereas the subsequent alkalization was associated with altered amino acid metabolism and formate flux. Using metabolic and respiratory mutants, we found that these extracellular signatures reflected pathway-specific metabolic rewiring that predicted bacterial killing. AMP lethality strongly correlated with ATP dynamics and formate secretion: strains exhibiting larger AMP-induced ATP increases and greater formate secretion showed enhanced susceptibility. In contrast to literature, changes in NADH and NADPH levels did not support redox stress as the primary bacterial-killing mechanism. Together, our findings identify formate metabolism as a key pathway underlying the elevated ATP levels associated with AMP bactericidal activity. These results demonstrate that SiNWFET sensors provide a versatile label-free tool for probing antibiotic mechanisms, rapidly assessing bacterial susceptibility, and potentially guiding antimicrobial therapy development.

physics.ins-det↗

arXiv2026

Mutually phase-stable tunable attosecond soft X-ray attosecond pulses from a free-electron laser

We demonstrate the production of mutually phase-stable attosecond X-ray pulse pairs with tunable relative time delays and phases in a cascaded X-ray free-electron laser. We showcase the method in an experiment at the LCLS-II, in which a shaped electron beam is used in a split undulator configuration to generate the two attosecond pulses. We achieve mutual phase stability by reusing microbunching generated in the first undulator in order to seed the FEL process in the second at a detuned frequency. We measure controllable temporal delays between the two pulses directly in the time domain using angular streaking of photoelectrons, with a step size of 250 attoseconds. We then show that the behavior of the X-ray spectrum is consistent with phase stability between the two pulses, with a relative phase that can be easily tuned using inter-undulator phase shifters. This method is particularly well-suited to few to ten eV energy separations and sub to few femtosecond time delays, which are ideal for experiments in the soft X-ray regime for pushing the limits of our models for molecular dynamics and exerting direct coherent control over quantum systems.

physics.acc-ph↗

arXiv2026

Cross-View Correspondence Is a Measurement Intervention: Two-Sided Validation for Agent Evaluation and Credit Assignment

Agent evaluations and trace-based learning often compare outputs across transformed views through a post-response correspondence treated as neutral preprocessing. We show that this correspondence is a measurement intervention: omitting it can manufacture sensitivity, an over-aggressive map can manufacture invariance, and multiple optimal correspondences can leave mechanism labels and signed learning credit unidentified. We develop a validity theory and audit with three components: two-sided validation of nuisance removal and response preservation, all-optima identification of downstream conclusions, and uncertainty propagation after validity is established. We characterize the linear feasibility boundary for response-preserving nuisance removal, compute sharp ranges over exact-optimum correspondence sets, and give a distribution-free certificate that retains a credit coordinate only when all exact optima agree on its nonzero sign. Across public code and SQL pipelines, two deterministic optimal tracebacks disagree on temporal localization for 55.9% of 1,586 nonzero trajectory pairs; two frozen 800-rollout tool-use audits, including a task-and-seed-disjoint replication, expose exact-optimum reversals of intended turn-level credit, although a clean public quick-start subset shows none. A pre-registered transport gate failed on natural responses; frozen corrected and held-out controls then show that a map calibrated only on benign examples erases every retained harmful response, while two-sided validation selects response-preserving alternatives. Cross-view correspondence must therefore be declared, validated, and propagated into uncertainty before agent evaluation or credit assignment supports a point conclusion.

cs.LG↗

arXiv2026

CompCPZ: Preserving Multi-Modal Intent in Language-Guided Robot Manipulation

A robot asked to "place the cup near the red plate or the blue plate" may reach the centroid between them and appear geometrically successful, while satisfying neither disjunct of the instruction. This silent semantic failure exposes a structural limitation of language-conditioned robot policies: representations that collapse a disjunctive instruction into a single connected set cannot preserve all feasible modes, and planners that commit to one action degrade under run-time mode uncertainty. We address this limitation with CompCPZ, a sound algebraic layer that language-conditioned learning systems wrap to recover multi-modal disjunctive representation, recursively composing per-primitive constrained polynomial zonotope enclosures along the language parse tree with distribution-free conformal coverage and sub-millisecond runtime. On a closed-loop ManiSkill3 tabletop-manipulation benchmark, CompCPZ outperforms convex set baselines, multi-peak decoders, and a zero-shot vision-language-action model (1,900/1,918 paired wins, p << 10^(-30)); the same compiler also transfers without retuning to planar real-robot trials on a Unitree Go2 quadruped under motion capture. These results suggest that compositional language grounding should be evaluated not only by reaching a decoded target, but by whether the represented feasibility set preserves the connected-component structure of the user's intent.

cs.RO↗

arXiv2026

Electromagnetic World Model for 6G: A Unified Framework for Joint Environment Reconstruction and Channel Prediction

The integration of sensing, communication, and intelligence is becoming a key enabler for sixth generation (6G) wireless systems, where intelligent terminals are expected to simultaneously support efficient link establishment and reliable environmental sensing. However, existing studies mainly exploit sensing information or communication information to address a single task, such as channel prediction or environment reconstruction. Motivated by the shared dependence of optical and radio-frequency signals on the surrounding environment, we propose the electromagnetic world model (EMWM), the first unified framework for joint environment reconstruction and channel prediction. EMWM learns a common electromagnetic representation with the potential to provide a modeling foundation for 6G tasks. Specifically, partial channel state information (CSI) and multi-view red-green-blue (RGB) images are encoded into CSI and visual tokens and jointly processed by a hierarchical world-model backbone with local and global aggregation. Based on the learned representation, a mixture-of-experts (MoE)-based CSI prediction head reconstructs the complete CSI, while a depth prediction head estimates multi-view depth maps that are further converted into three-dimensional (3D) point clouds. Moreover, a large-scale multi-modal dataset is constructed based on a campus digital twin. Experimental results show that EMWM outperforms conventional neural network and large language model (LLM) baselines in both CSI prediction and environment reconstruction, achieving a squared generalized cosine similarity (SGCS) of 0.9699 for CSI prediction while demonstrating robustness across different signal-to-noise ratio (SNR) conditions and zero-shot generalization at 28 GHz.

eess.SP↗

arXiv2026

Probing Variations in Earth's Ionosphere Using Pulsars

We present high cadence 10-minute rotation measure (RM) monitoring of PSR~J0814+7429 using the LOw-Frequency ARray, aiming to probe ionospheric variability along the pulsar line of sight (LoS). By separating the ionospheric contribution from the observed RM, we quantitatively reconstruct the diurnal variation of the ionospheric electron density along the pulsar LoS based on the World Magnetic Model. The derived variations exhibit clear solar-driven modulation, including the ionospheric noontime bite-out phenomenon, and show good agreement with the LoS total electron content reconstructed from independent global vertical total electron content maps. These results demonstrate the feasibility of using pulsars as probes of temporal variations in the electron density of the Earth's ionosphere.

astro-ph.HE↗

arXiv2026

Hybrid Probabilistic Zonotopes for Identifiable and Refinable Predictive Uncertainty

Probabilistic prediction heads in neural networks typically output either a Gaussian mixture or a single conformal region. Neither separates the distinct sources of uncertainty often present in real prediction tasks: a discrete choice among modes, bounded systematic drift within the chosen mode, and irreducible stochastic noise. We introduce the Hybrid Probabilistic Zonotope (HProbZ), an output head that represents these three sources as binary, bounded, and stochastic generators of a zonotope, and admits a closed-form likelihood by convolution. Sharing the bounded generator across prediction steps couples future predictions algebraically, so observing one step refines the predictive distribution at every remaining step in a single forward pass. We establish that the three generators are identifiable from the likelihood up to permutation, and that an HProbZ density is representationally distinct from any finite Gaussian mixture. The same shared structure provides analytic per-mode risk and distribution-free multi-modal conformal sets at inference time. Empirical analysis on representative prediction benchmarks supports the effectiveness of the design relative to same-encoder mixture baselines, while offering structural properties that mixture or convex-conformal predictors do not jointly provide.

cs.LG↗

arXiv2026

Matrix Zonotopic Attention: A Context-Adaptive Value Projection for Set Transformers

Multi-head attention combines an input-dependent softmax routing with an input-independent linear value projection, so the per-sample operator mapping aggregated values to outputs is the same for every input set. We study the consequences of this asymmetry for permutation-invariant set targets. We introduce the Transformation Degrees of Freedom (TDOF) of a target operator, a complexity measure counting the input-dependent directions an exact representation requires, and present a depth-separation analysis showing that context-rigid attention needs depth proportional to the target's TDOF, whereas a single layer with a context-adaptive value family can represent the same target. Building on this analysis, we propose Matrix Zonotopic Attention (MZAttn), which replaces the fixed value projection with a context-adaptive matrix-zonotope family: a centre matrix plus a sum of generator matrices weighted by input-dependent gates. The construction reduces to standard multi-head attention at initialisation, preserves permutation equivariance, and admits a data-driven reachability interpretation. Experiments on a range of set-prediction tasks are consistent with the TDOF prediction that the architectural advantage is selective: it appears on targets that depend on the input set in a high-rank, sparsely combinatorial way, and is small on aggregate-statistic targets where parameter-matched standard attention is already competitive.

cs.LG↗

arXiv2026

Optimizing Parameterized Physics-Informed Neural Networks to Solve Multilayered Static Linear Elastic PDEs

Designing multilayered materials for controlled deformation is heavily bottlenecked by the immense computational costs and time of traditional, industrial-grade finite element methods (FEM). This excessive expense severely limits design space exploration and gradient-based optimization. To streamline the workflow, we propose a framework for parameterized physics-informed neural networks (P2INNs). The framework encompasses three core components: I. a FEM baseline with a Hex8 element and trilinear basis functions, II. a P2INN displacement field model across variable material stiffness and layer thicknesses, and III. FEM-referenced evaluation. The PINN enforces static linear elasticity via Navier-Cauchy residuals with training strategies that prioritize physics, including layerwise PDE decomposition, interface continuity penalty, and compliance aware scaling. For one-layer, pure physics-driven configurations, the PINN achieves a mean volume MAE of 1.56% and worst-case volume MAE of 2.87% against the FEM benchmark. For three-layer configurations with controlled supervised training, the PINN achieves a mean volume MAE of 2.53% and worst-case volume MAE of 4.66%, meeting the near-5% worst-case volume-MAE target for preliminary design-space exploration. The trained P2INN model remains a lightweight model with a simple forward pass for future calculations, creating an alternative to traditional FEM. By drastically reducing the need for expensive FEM evaluations, this approach could accelerate the inverse design and optimization of advanced layered architectures for protective structures in various load-heavy or potentially collision-heavy fields.

cs.CE↗