arXiv subjects

Zhen-Yu Yin

Publications and source records attributed to Zhen-Yu Yin.

5 recordsLinked to original sources

arXiv2026

Agent-MD: Selective LLM Intervention with Event-Driven Escalation for Stateful GCMC--MD Campaigns

Long-running molecular simulation campaigns require repeated continuation from saved states, provenance-aware progression, adaptive assessment, and occasional interpretation of workflow conditions that cannot be resolved safely by fixed rules. Here, we present Agent-MD, a framework that places large language model (LLM) reasoning selectively at campaign construction and event-triggered review, while routine simulation, analysis, continuation, archiving, and state progression are handled by a persistent rule-based campaign agent using approved policies and explicit state records. Agent-MD was demonstrated in a grand canonical Monte Carlo-molecular dynamics (GCMC-MD) water-vapor desorption campaign comprising five montmorillonite systems and three sequential relative-humidity states (RH = 0.9-0.3-0.1). Across 15 system-RH states, the workflow completed 120 segmented simulation cycles with state-specific sampling lengths and provenance-aware restart inheritance. Routine production required no live reasoning-agent invocation, while one state reached a review boundary; two preserved incidents were subsequently evaluated through blinded reasoning-agent replay, which identified the underlying workflow problems and recommended appropriate follow-up actions. The simulations also revealed distinct composition-dependent low-RH responses, with Ca-bearing montmorillonite retaining more interlayer water and maintaining a larger basal spacing than the Na- and K-bearing systems, while the highest-charge Na system retained more residual water under dry conditions. These results demonstrate that long-running scientific workflows need not place every operation inside an LLM reasoning loop: selective reasoning can instead be combined with deterministic execution, structured evidence, and validated control handoffs to provide reproducible and auditable agent-assisted molecular simulation.

cs.AI↗

arXiv2026

Unveiling the Role of Friction in Coarse-Grained Clay: A Hybrid Framework Integrating Long-Range Interactions and Granular Contact Mechanics

Given the predominant role of inter-particle physicochemical forces in governing clay behavior, researchers have increasingly utilized coarse-grained molecular dynamics (CGMD) simulations. However, inter-particle friction has been historically overlooked due to methodological limitations, and the extent to which this omission influences simulation accuracy remains an unresolved question. This study proposes a novel hybrid CGMD framework explicitly coupling long-range Buckingham potential with Hertzian granular contact mechanics. A baseline model was validated via isotropic compression, where the resulting compressibility and derived compression index (Cc) aligned with macroscopic geotechnical observations. Parametric analyses revealed that viscoelastic damping of particle contacts governs structural evolution. Elevated damping suppresses densification, trapping platelets in disorganized, high-void-ratio configurations. Furthermore, evaluating the interplay with thermal fluctuations underscores the necessity of precise temperature control to prevent such unphysical kinetic trapping. Finally, uniaxial compression tests demonstrate the critical importance of inter-particle friction. Explicit friction locks sliding interfaces and sustains significantly higher loads compared to frictionless models; the latter rely solely on geometric interlocking and ultimately exhibit unphysical fluid-like yielding. By bridging atomistic potentials with contact mechanics, this framework highlights the fundamental role of the inter-particle friction and offers essential guidelines for future multi-scale simulations of clay assemblies.

cond-mat.mtrl-sci↗

arXiv2024

Parsimonious Universal Function Approximator for Elastic and Elasto-Plastic Cavity Expansion Problems

Cavity expansion is a canonical problem in geotechnics, which can be described by partial differential equations (PDEs) and ordinary differential equations (ODEs). This study explores the potential of using a new solver, a physics-informed neural network (PINN), to calculate the stress field in an expanded cavity in the elastic and elasto-plastic regimes. Whilst PINNs have emerged as an effective universal function approximator for deriving the solutions of a wide range of governing PDEs/ODEs, their ability to solve elasto-plastic problems remains uncertain. A novel parsimonious loss function is first proposed to balance the simplicity and accuracy of PINN. The proposed method is applied to diverse material behaviours in the cavity expansion problem including isotropic, anisotropic elastic media, and elastic-perfectly plastic media with Tresca and Mohr-Coulomb yield criteria. The results indicate that the use of a parsimonious prior information-based loss function is highly beneficial to deriving the approximate solutions of complex PDEs with high accuracy. The present method allows for accurate derivation of solutions for both elastic and plastic mechanical responses of an expanded cavity. It also provides insights into how PINNs can be further advanced to solve more complex problems in geotechnical practice.

cs.CE↗

arXiv2024

A Novel Coupled bES-FEM Formulation with SUPG stabilization for Thermo-Hydro-Mechanical Analysis in Saturated Porous Media

Two primary types of numerical instabilities often occur in low-order finite element method (FEM) analyses of thermo-hydro-mechanical (THM) phenomena: (1) pressure oscillations arising improper interpolation of pressure and displacement fields; and (2) spatial oscillations induced by nonlinear convection terms in convection-dominated scenarios. In response to these issues, this paper proposes a novel stabilized edge-based smoothed FEM with a bubble function (bES-FEM) for THM analysis within saturated porous media. In the proposed framework, a cubic bubble function is first incorporated into ES-FEM to efficiently mitigate pressure oscillations that breach the Inf-Sup condition, and then the Streamline Upwind Petrov-Galerkin (SUPG) scheme is adopted in bES-FEM to effectively reduce the spurious oscillations in convection-dominated heat transfer scenarios. The accuracy of the bES-FEM with SUPG formulation for THM coupled problems is validated through a series of five benchmark tests. Moreover, the simulations of open-loop ground source energy systems demonstrate the proposed method's exceptional capability in tackling complex THM challenges in real-world applications. All the obtained results showcase the superiority of proposed bES-FEM with SUPG in eliminating the spatial and pressure oscillations, marking it as a promising tool for the exploration of coupled THM issues.

physics.geo-ph↗

arXiv2023

Gas flow and solid deformation in unconventional shale

Shale, a material that is currently at the heart of energy resource development, plays a critical role in the management of civil infrastructures. Whether it concerns geothermal energy, carbon sequestration, hydraulic fracturing, or waste storage, one is likely to encounter shale as it accounts for approximately 75\% of rocks in sedimentary basins. Despite the abundance of experimental data indicating the mechanical anisotropy of these formations, past research has often simplified the modeling process by assuming isotropy. In this study, the anisotropic elasticity model and the advanced anisotropic elastoplasticity model proposed by Semnani et al. (2016) and Zhao et al. (2018) were adopted in traditional gas production and strip footing problems, respectively. This was done to underscore the unique characteristics of unconventional shale. The first application example reveals the effects of bedding on apparent permeability and stress evolutions. In the second application example, we contrast the hydromechanical responses with a comparable case where gas is substituted by incompressible fluid. These novel findings enhance our comprehension of gas flow and solid deformation in shale.

physics.geo-ph↗