arXiv subjects

Zhaoxi Sun

Publications and source records attributed to Zhaoxi Sun.

5 recordsLinked to original sources

arXiv2026

AI-driven ionic liquid discovery with unified chemical intelligence

The rational discovery of functional solvents remains challenging because macroscopic solvent behaviors emerge from complex many-body interactions across vast chemical spaces. Ionic Liquids (ILs) constitute one of the most chemically diverse solvent families, yet their exceptional structural tunability remains only partially explored owing to the limitations of existing experimental and computational approaches. Here we introduce AIonopedia, a large-language-model-orchestrated agentic framework for IL research. Built around a domain-specific multimodal foundation model, it integrates information retrieval, chemical reasoning and autonomous tool execution within a unified architecture. Pretrained on large-scale unlabeled corpora and fine-tuned using over 80,000 curated measurements, AIonopedia learns expressive joint representations of multicomponent ionic systems, enabling accurate prediction across diverse physicochemical properties. Through a series of literature-grounded evaluations, AIonopedia exhibits robust out-of-distribution generalization, while many-body-expansion-based analysis provides physically grounded explanations of structure-property relationships. By coupling molecular screening and optimization with wet-lab validation in a closed-loop workflow, AIonopedia identifies high-performance ILs and reveals transferable design principles for the capture of various volatile organic compounds. This work establishes an end-to-end AI-driven paradigm for understanding and exploring complex ionic systems, demonstrating the promise of chemically specialized foundation models as a generalizable strategy for scientific discovery.

cs.AI↗

arXiv2026

AGATE: Provenance-Based Runtime Defense Against Compositional Attacks on LLM Agents

LLM agents can produce harmful effects through sequences of ordinary operations. Judging such actions requires establishing both the authority that permits them and the origin of the data they carry. We present AGATE, an authorization and data-provenance gate at instrumented agent-harness boundaries. Operator declarations and host approval events ground authorization; delegated actions are constrained by grants that bind to exact parameters, expire, and permit a limited number of uses. Source registration connects observed inputs to subsequent transfers, while an effect ledger tracks repeated requests. Deterministic checks make decisions without an LLM in the decision path and retain their grounds with execution evidence for forensic replay. Adapters integrate three production harnesses -- DeepSeek Harness, OpenCode, and OpenClaw -- without modifying host code, translating each host's native observation and veto points into a single shared gate interface; the judgment core is identical in all three, and only enforcement depth differs. Our evaluation combines 153 exercised attack-chain records with deployment, utility, and reconstruction experiments. The deployment observations expose how tool declarations and data checks govern business actions, including a bypass through parameter rewriting. Six of eleven benign file-processing scenarios contain denial events, revealing the utility cost of content-based provenance policies. Across 252 runs on 63 sanitized scenarios, replay agrees with live graph projections for all 63 scenarios on each of two platforms. These results establish the feasibility of provenance-based runtime judgment and identify content transformation, legitimate reuse, and observation coverage as concrete limits.

cs.CR↗

arXiv2021

Clustering-based convergence diagnostic for multi-modal identification in parameter estimation of chromatography model with parallel MCMC

Uncertainties from experiments and models render multi-modal difficulties in model calibrations. Bayesian inference and \textsc{mcmc} algorithm have been applied to obtain posterior distributions of model parameters upon uncertainty. However, multi-modality leads to difficulty in convergence criterion of parallel \textsc{mcmc} sampling chains. The commonly applied $\widehat{R}$ diagnostic does not behave well when multiple sampling chains are evolving to different modes. Both partitional and hierarchical clustering methods has been combined to the traditional $\widehat{R}$ diagnostic to deal with sampling of target distributions that are rough and multi-modal. It is observed that the distributions of binding parameters and pore diffusion of particle parameters are multi-modal. Therefore, the steric mass-action model used to describe ion-exchange effects of the model protein, lysozyme, on the \textsc{sp} Sepharose \textsc{ff} stationary phase might not be fully capable in certain experimental conditions, as model uncertainty from steric mass-action would result in multi-modality.

math.NA↗

arXiv2020

Model-based process design of a ternary protein separation using multi-step gradient ion-exchange SMB chromatography

Model-based process design of ion-exchange simulated moving bed (IEX-SMB) chromatography for center-cut separation of proteins is studied. Use of nonlinear binding models that describe more accurate adsorption behaviours of macro-molecules could make it impossible to utilize triangle theory to obtain operating parameters. Moreover, triangle theory provides no rules to design salt profiles in IEX-SMB. In the modelling study here, proteins (i.e., ribonuclease, cytochrome and lysozyme) on the chromatographic columns packed with strong cation-exchanger SP Sepharose FF is used as an example system. The general rate model with steric mass-action kinetics was used; two closed-loop IEX-SMB network schemes were investigated (i.e., cascade and eight-zone schemes). Performance of the IEX-SMB schemes was examined with respect to multi-objective indicators (i.e., purity and yield) and productivity, and compared to a single column batch system with the same amount of resin utilized. A multi-objective sampling algorithm, Markov Chain Monte Carlo (MCMC), was used to generate samples for constructing the Pareto optimal fronts. MCMC serves on the sampling purpose, which is interested in sampling the Pareto optimal points as well as those near Pareto optimal. Pareto fronts of the three schemes provide the full information of trade-off between the conflicting indicators of purity and yield. The results indicate the cascade IEX-SMB scheme and the integrated eight-zone IEX-SMB scheme have the similar performance that both outperforms the single column batch system.

cs.CE↗

arXiv2018

A theoretical interpretation of variance-based convergence criteria in perturbation-based theories

In QM/MM indirect free energy simulation, QM/MM corrections can be obtained from integration of partial derivatives of alchemical Hamiltonians or from perturbation-based estimators including free energy perturbation (FEP) and acceptance ratio methods. With FEP or exponential averaging, researchers tend to only sample MM states and calculate single point energy to get the free energy estimates. In this case the sample size hysteresis arises and the convergence is determined by bias elimination rather than variance minimization. Various criteria are proposed to evaluate the convergence issue and numerical studies are reported. It has been found that criteria including variance of distribution, effective sample size, information entropies and so on can be used and they are variance-of-distribution-dependent. However, no theoretical interpretation is presented. In this paper we present theoretical interpretations to dig the underlying statistical nature behind the problem. The convergence criteria are proven to be related with variance of distribution in Gaussian approximated Exponential averaging. Further, we prove that these estimators are nonlinearly dependent on the variance of the free energy estimate. As these estimators are often orders of magnitude overestimated, the variance of the FEP estimate is orders of magnitude underestimated. Hence, computing this statistical uncertainty is meaningless. In numerical calculation from timeseries data the effective sample size is bounded by 1 and N and thus the variance of the free energy estimate is proven to be bounded by 0 and 1 (kBT)2 for EXP and 0 and 2 (kBT)2 for BAR, which indicates an inevitable underestimation. Specifically, the upper bounds for these estimators are sample-size dependent. The effective sample size is proven to be a function of the overlap scalar, from which the range of the overlap scalar can also be derived.

physics.chem-ph↗