arXiv subjects

Xinpeng Xu

Publications and source records attributed to Xinpeng Xu.

At least 19 recordsLinked to original sources

arXiv2026

Geometric formulation of state-dependent Langevin dynamics using scalar free energy

Stochastic dynamics with state-dependent diffusion arise broadly in confined, anisotropic, and hydrodynamically coupled systems. The conventional Langevin equation contains a spurious drift associated with multiplicative noise. Since the restricted free energy is generally non-scalar, the covariance is not explicit. Here, we reformulate state-dependent Langevin dynamics using a scalar free energy and a diffusion metric defined by the inverse diffusion tensor. The conventional spurious drift is then expressed as a Christoffel contribution. Although our formulation is mathematically equivalent to the conventional one through the relation between the restricted and scalar free energies, it makes coordinate covariance explicit and enables the phenomenological construction of thermodynamic potentials directly from system symmetries. We demonstrate its consistency in representative examples of state-dependent diffusion arising from coordinate transformations, geometric confinement, and projection from curved to flat spaces.

cond-mat.soft↗

arXiv2026

Covariant Onsager and Onsager-Machlup principles for active and inertial dynamics

The Onsager principle provides a variational route to the phenomenological equations of dissipative dynamics through the minimization of the Rayleighian. We develop a covariant formulation of the Onsager principle for active and inertial systems, ensuring geometric consistency under coordinate transformations. To further incorporate thermal fluctuations, we formulate the Onsager-Machlup principle for active and inertial systems by considering the Onsager-Machlup functional and the corresponding path probability for stochastic trajectories. Requiring that the path probability obeys the detailed fluctuation theorem, we show that the extended Onsager-Machlup theory is consistent with stochastic thermodynamics. The extended OP and OMP offer a unified and useful variational framework for deriving the dynamical equations of active and inertial systems.

cond-mat.soft↗

arXiv2026

Onsager-variational formulation of diffuse-domain methods for computational modeling of microscale fluid-structure interactions

Direct numerical simulation of microscale fluid--structure interactions in multicomponent and multiphase flows requires methods that can represent moving boundaries together with fields constrained to evolving interfaces. Diffuse-domain methods (DDMs) address this geometric difficulty by replacing sharp surfaces with diffuse volumetric representations on regular computational domains. Here we formulate DDMs using Onsager's variational principle. Instead of extending sharp-interface equations and boundary conditions term by term, we embed sharp-surface free-energy and dissipation functionals into the bulk through a diffuse surface delta density and derive the governing equations from the Rayleighian. The framework distinguishes balance-law fields, internal nonconserved order parameters, and kinematic or constitutive rate variables. It also clarifies a key moving-surface distinction: conserved surface densities are transported by the full material surface velocity, whereas explicitly tangential vector and tensor internal variables require projected objective or co-rotational rates within their admissible tangential state spaces. For scalar transport on rigid and deformable interfaces, and for interfacial hydrodynamics near rigid walls, the formulation recovers established DDM models and their sharp-interface limits. The same variational construction yields coupled diffuse-domain models for multicomponent deformable vesicles with surface viscosity, tangential slip, and finite areal compressibility, and for active shells carrying chemical and tangential vector order. These results provide a unified route to thermodynamically consistent passive DDMs for interfacial and surface dynamics, while allowing active stresses through active work power. The framework is relevant to soft matter, microfluidic interfaces, biological membranes, and morphogenetic surface dynamics.

physics.bio-ph↗

arXiv2026

Neural optimization of the most probable paths of 3D active Brownian particles

We develop a variational neural-network framework to determine the most probable path (MPP) of a 3D active Brownian particle (ABP) by directly minimizing the Onsager-Machlup integral (OMI). To obtain the OMI, we use the Onsager-Machlup variational principle for active systems and construct the Rayleighian of the ABP by including its active power. This approach reveals geometric transitions of the MPP from in-plane I- and U-shaped paths to 3D helical paths as the final time and net displacement are varied. We also demonstrate that the initial and final boundary conditions have a significant impact on the MPPs. Our results show that neural optimization combined with the Onsager-Machlup variational principle provides an efficient and versatile framework for exploring optimal transition pathways in active and nonequilibrium systems.

cond-mat.soft↗

arXiv2025

Deep learning-based computational method for soft matter dynamics: Deep Onsager-Machlup method

A deep learning-based computational method is proposed for soft matter dynamics -- the deep Onsager-Machlup method (DOMM). It combines the brute forces of deep neural networks (DNNs) with the fundamental physics principle -- Onsager-Machlup variational principle (OMVP). In the DOMM, the trial solution to the dynamics is constructed by DNNs that allow us to explore a rich and complex set of admissible functions. It outperforms the Ritz-type variational method where one has to impose carefully-chosen trial functions. This capability endows the DOMM with the potential to solve rather complex problems in soft matter dynamics that involve multiple physics with multiple slow variables, multiple scales, and multiple dissipative processes. Actually, the DOMM can be regarded as an extension of the deep Ritz method (DRM) developed by E and Yu that uses DNNs to solve static problems in physics. In this work, as the first step, we focus on the validation of the DOMM as a useful computational method by using it to solve several typical soft matter dynamic problems: particle diffusion in dilute solutions, and two-phase dynamics with and without hydrodynamics. The predicted results agree very well with the analytical solution or numerical solution from traditional computational methods. These results show the accuracy and convergence of DOMM and justify it as an alternative computational method for solving soft matter dynamics.

cond-mat.soft↗

arXiv2025

EP250207b is not a collapsar fast X-ray transient. Is it due to a compact object merger?

Fast X-ray Transients (FXTs) are short-lived extra-galactic X-ray sources. Recent progress through multi-wavelength follow-up of Einstein Probe discovered FXTs has shown that several are related to collapsars, which can also produce gamma-ray bursts (GRBs). In this paper we investigate the nature of the FXT EP250207b. The VLT/MUSE spectra of a nearby (15.9 kpc in projection) lenticular galaxy reveal no signs of recent star formation. If this galaxy is indeed the host, EP250207b lies at a redshift of z=0.082, implying a peak observed absolute magnitude for the optical counterpart of M_r=-14.5. At the time when supernovae (SNe) would peak, it is substantially fainter than all SN types. These results are inconsistent with a collapsar origin for EP250207b. The properties favour a binary compact object merger driven origin. The X-ray, optical and radio observations are compared with predictions of several types of extra-galactic transients, including afterglow and kilonova models. The data can be fit with a slightly off-axis viewing angle afterglow. However, the late-time (~30 day) optical/NIR counterpart is too bright for the afterglow and also for conventional kilonova models. This could be remedied if that late emission is due to a globular cluster or the core of a (tidally disrupted) dwarf galaxy. If confirmed, this would be the first case where the multi-wavelength properties of an FXT are found to be consistent with a compact object merger origin, increasing the parallels between FXTs and GRBs. We finally discuss if the source could originate in a higher redshift host galaxy.

astro-ph.HE↗

arXiv2025

Simulation Method of Microscale Fluid-Structure Interactions: Diffuse-Resistance-Domain Approach

Direct numerical simulations (DNS) of microscale fluid-structure interactions (mFSI) in multicomponent multiphase flows pose many challenges, including the thermodynamic consistency of multiphysics couplings, tracking of moving interfaces, dynamics of moving triple-phase contact lines, and the coupling of multiphase hydrodynamics with phase transition dynamics. We propose and validate a generic DNS approach: Diffuse-Resistance-Domain (DRD) approach. It overcomes the above challenges by employing Onsager's variational principle (OVP) to formulate dynamic models and combining traditional diffuse-interface models for fluid-fluid interfacial dynamics with a novel implementation of complex fluid-solid interfacial conditions via smooth interpolations of dynamic-resistance coefficients across interfaces. After careful validation by numerous benchmark simulations, we simulated several cutting-edge, challenging mFSI problems across diverse fields. This generic DNS approach offers a promising tool for elucidating physical mechanisms, manipulating microscale fluid dynamics, and optimizing engineering processes across diverse fields.

physics.flu-dyn↗

arXiv2024

Detection of an Orphan X-ray Flare from a Blazar Candidate EP240709a with Einstein Probe

Blazars are often observed to flare across multiple wavelengths. Orphan flares from blazars have been only detected a few times, providing an opportunity to understand the structure of the jet in the accreting system. We report a remarkable orphan X-ray flare from a blazar candidate EP240709a, detected by Einstein Probe (EP) in July 2024. The multi-band spectral properties and variability support EP240709a as a high-energy peaked BL Lacertae-type object. The flux in 0.5-10 keV increases by at least 28 times to the value of low state in 2020, with non-detection of remarkable flaring in other bands during the same period. EP240709a exhibits the harder-when-brighter tendency in the X-ray band during the orphan flare, while its infrared-optical spectra are featureless. We employ one-zone and two-zone leptonic synchrotron self-Compton models to perform the spectral energy distribution fitting. Detecting this rare orphan flare shows the potential of EP in discovering peculiar activities from AGN in high-cadence X-ray sky surveys.

astro-ph.HE↗

arXiv2024

Elastic interactions compete with persistent cell motility to drive durotaxis

The directed migration of cells toward stiffer substrate regions or durotaxis is relevant to tissue development and tumor progression. Here, we introduce a phenomenological model for single cell durotaxis that incorporates both elastic deformation-mediated cell-substrate interactions and the stochasticity of cell migration. Our model is motivated by a key observation in an early demonstration of durotaxis: a single, contractile cell at a sharp interface between a softer and a stiffer region of an elastic substrate reorients and migrates towards the stiffer region. We model migrating cells as self-propelling, persistently motile agents that exert contractile traction forces on their elastic substrate. The resulting substrate deformations induce elastic interactions with mechanical boundaries, captured by an elastic potential. Cell dynamics are governed by two critical parameters: the strength of the traction-induced boundary interaction (A) and the persistence of cell motility (Pe). The resulting elastic forces and torques align cells perpendicular (parallel) to the boundary and accumulate (deplete) them at clamped (free) boundaries. A clamped boundary induces an attractive potential, promoting durotaxis, while a free boundary generates a repulsive potential, preventing anti-durotaxis. By analyzing steady-state position and orientation probabilities, we show how accumulation and depletion depend on elastic potential strength and motility. We compare our findings with biological microswimmers and other active particles that accumulate at confining boundaries. The model defines metrics for boundary accumulation and durotaxis, presenting a phase diagram with three regimes: durotaxis, adurotaxis, and motility-induced accumulation. Our model predicts how durotaxis depends on cell contractility and motility, offering insights and testable predictions for future experiments.

cond-mat.soft↗

arXiv2023

CryptoEval: Evaluating the Risk of Cryptographic Misuses in Android Apps with Data-Flow Analysis

The misunderstanding and incorrect configurations of cryptographic primitives have exposed severe security vulnerabilities to attackers. Due to the pervasiveness and diversity of cryptographic misuses, a comprehensive and accurate understanding of how cryptographic misuses can undermine the security of an Android app is critical to the subsequent mitigation strategies but also challenging. Although various approaches have been proposed to detect cryptographic misuse in Android apps, studies have yet to focus on estimating the security risks of cryptographic misuse. To address this problem, we present an extensible framework for deciding the threat level of cryptographic misuse in Android apps. Firstly, we propose a general and unified specification for representing cryptographic misuses to make our framework extensible and develop adapters to unify the detection results of the state-of-the-art cryptographic misuse detectors, resulting in an adapter-based detection tool chain for a more comprehensive list of cryptographic misuses. Secondly, we employ a misuse-originating data-flow analysis to connect each cryptographic misuse to a set of data-flow sinks in an app, based on which we propose a quantitative data-flow-driven metric for assessing the overall risk of the app introduced by cryptographic misuses. To make the per-app assessment more useful for app vetting at the app-store level, we apply unsupervised learning to predict and classify the top risky threats to guide more efficient subsequent mitigation. In the experiments on an instantiated implementation of the framework, we evaluate the accuracy of our detection and the effect of data-flow-driven risk assessment of our framework. Our empirical study on over 40,000 apps and the analysis of popular apps reveal important security observations on the real threats of cryptographic misuse in Android apps.

cs.CR↗

arXiv2023

Dynamics of flexible fibers in confined shear flows at finite Reynolds numbers

We carry out a numerical study on the dynamics of a single non-Brownian flexible fiber in two-dimensional Couette flows at finite Reynolds numbers. We employ the bead-spring model of flexible fibers to extend the fluid particle dynamics (FPD) method that is originally developed for rigid particles in viscous liquids. We implement the extended FPD method using a multiple-relaxation-time (MRT) scheme of the lattice Boltzmann method (LBM). The numerical scheme is validated firstly by a series of benchmark simulations that involve liquid-solid coupling. The method is then used to study the dynamics of flexible fibers in Couette flows. We only consider the highly symmetric case where the fibers are placed on the symmetry center of Couette flows and we focus on the effects of the fiber stiffness, the confinement strength, and the finite Reynolds number (from 1 to 10). A diagram of the fiber shape is obtained. For fibers under weak confinement and a small Reynolds number, three distinct tumbling orbits have been identified. (1) Jeffery orbits of rigid fibers. The fibers behave like rigid rods and tumble periodically without any visible deformation. (2) S-turn orbits of slightly flexible fibers. The fiber is bent to an S-shape and is straightened again when it orients to an angle of around 45 degrees relative to the positive x direction. (3) S-coiled orbits of fairly flexible fibers. The fiber is folded to an S-shape and tumbles periodically and steadily without being straightened anymore during its rotation. Moreover, the fiber tumbling is found to be hindered by increasing either the Reynolds number or the confinement strength, or both.

cond-mat.soft↗

arXiv2022

Activity-assisted barrier-crossing of self-propelled colloids over parallel microgrooves

We report a systematic study of the dynamics of self-propelled particles (SPPs) over a one-dimensional periodic potential landscape, which is fabricated on a microgroove-patterned polydimethylsiloxane (PDMS) substrate. From the measured non-equilibrium probability density function of the SPPs, we find that the escape dynamics of the slow-rotating SPPs across the potential landscape can be described by an effective potential, once the self-propulsion force is included into the potential under the fixed angle approximation. This work demonstrates that the parallel microgrooves provide a versatile platform for a quantitative understanding of the interplay among the self-propulsion force, spatial confinement by the potential landscape, and thermal noise, as well as its effects on activity-assisted escape dynamics and transport of the SPPs.

cond-mat.soft↗

arXiv2022

Spontaneous Bending of Hydra Tissue Fragments Driven by Supracellular Actomyosin Bundles

Hydra tissue fragments excised freshly from Hydra body bend spontaneously to some quasi-stable shape in several minutes. We propose that the spontaneous bending is driven mechanically by supracellular actomyosin bundles inherited from parent Hydra. An active-laminated-plate model is constructed, from which we predict that the fragment shape characterized by spontaneous curvature is determined by its anisotropy in contractility and elasticity. The inward bending to endoderm side is ensured by the presence of a soft intermediate matrix (mesoglea) layer. The bending process starts diffusively from the edges and relaxes exponentially to the final quasi-stable shape. Two characteristic time scales are identified from the dissipation due to viscous drag and interlayer frictional sliding, respectively. The former is about 0.01 seconds, but the latter is much larger, about several minutes, consistent with experiments.

physics.bio-ph↗

arXiv2022

Variational methods and deep Ritz method for active elastic solids

Variational methods have been widely used in soft matter physics for both static and dynamic problems. These methods are mostly based on two variational principles: the variational principle of minimum free energy (MFEVP) and Onsager's variational principle (OVP). Our interests lie in the applications of these variational methods to active matter physics. In our former work [Soft Matter, 2021, 17, 3634], we have explored the applications of OVP-based variational methods for the modeling of active matter dynamics. In the present work, we explore variational (or energy) methods that are based on MFEVP for static problems in active elastic solids. We show that MFEVP can be used not only to derive equilibrium equations, but also to develop approximate solution methods, such as Ritz method, for active solid statics. Moreover, the power of Ritz-type method can be further enhanced using deep learning methods if we use deep neural networks to construct the trial solutions of the variational problems. We then apply these variational methods and the deep Ritz method to study the spontaneous bending and contraction of a thin active circular plate that is induced by internal asymmetric active contraction. The circular plate is found to be bent towards its contracting side. The study of such a simple toy system gives implications for understanding the morphogenesis of solid-like confluent cell monolayers. In addition, we introduce a so-called activogravity length to characterize the importance of gravitational forces relative to internal active contraction in driving the bending of the active plate. When the lateral plate dimension is larger than the activogravity length (about 100 micron), gravitational forces become important. Such gravitaxis behaviors at multicellular scales may play significant roles in the morphogenesis and in the up-down symmetry broken during tissue development.

cond-mat.soft↗

arXiv2022

Variational approximation method for the long-range force transmission in biopolymer gels

The variational principle of minimum free energy (MFEVP) has been widely used in the study of soft matter statics. MFEVP can be used not only to derive equilibrium equations (including both bulk equations and boundary conditions), but also to develop direct variational methods (such as Ritz method) to find approximate solutions to these equilibrium equations. In this work, we applied these variational methods to study long-range force transmission in nonlinear elastic biopolymer gels. We showed that the slow decay of cell-induced displacements measured experimentally for fibroblast spheroids in three-dimensional fibrin gels can be well explained by variational approximations based on the three-chain model of biopolymer gels.

cond-mat.soft↗

arXiv2021

The origin of the soft X-ray excess in the narrow-line Seyfert 1 galaxy SBS 1353+564

We present for the first time the timing and spectral analyses for a narrow-line Seyfert 1 galaxy, SBS 1353+564, using \it{XMM-Newton} and \it{Swift} multi-band observations from 2007 to 2019. Our main results are as follows: 1) The temporal variability of SBS 1353+564 is random, while the hardness ratio is relatively constant over a time span of 13 years; 2) We find a prominent soft X-ray excess feature below 2 keV, which cannot be well described by a simple blackbody component; 3) After comparing the two most prevailing models for interpreting the origin of the soft X-ray excess, we find that the relativistically smeared reflection model is unable to fit the data above 5 keV well and the X-ray spectra do not show any reflection features, such as the Fe Kαemission line. However, the warm corona model can obtain a good fitting result. For the warm corona model, we try to use three different sets of spin values to fit the data and derive different best-fitting parameter sets; 4) We compare the UV/optical spectral data with the extrapolated values of the warm corona model to determine which spin value is more appropriate for this source, and we find that the warm corona model with non-spin can sufficiently account for the soft X-ray excess in SBS 1353+564.

astro-ph.HE↗

arXiv2020

Onsager's variational principle in active soft matter

Onsager's variational principle (OVP) was originally proposed by Lars Onsager in 1931 [L. Onsager, $Phys. Rev.$, 1931, $37$, 405]. This fundamental principle provides a very powerful tool for formulating thermodynamically consistent models. It can also be employed to find approximate solutions, especially in the study of soft matter dynamics. In this work, OVP is extended and applied to the dynamic modeling of active soft matter such as suspensions of bacteria and aggregates of animal cells. We first extend the general formulation of OVP to active matter dynamics where active forces are included as external non-conservative forces. We then use OVP to analyze the directional motion of individual active units: a molecular motor walking on a stiff biofilament and a toy two-sphere microswimmer. Next, we use OVP to formulate a diffuse-interface model for an active polar droplet on a solid substrate. In addition to the generalized hydrodynamic equations for active polar fluids in the bulk region, we have also derived thermodynamically consistent boundary conditions. Finally, we consider the dynamics of a thin active polar droplet under the lubrication approximation. We use OVP to derive a generalized thin film equation and then employ OVP as an approximation tool to find the spreading laws for the thin active polar droplet. By incorporating the activity of biological systems into OVP, we develop a general approach to construct thermodynamically consistent models for better understanding the emergent behaviors of individual animal cells and cell aggregates or tissues.

cond-mat.soft↗

arXiv2020

Continuum elastic models for force transmissions in biopolymer gels

We review continuum elastic models for the transmission of both external forces and internal active cellular forces in biopolymer gels, and relate them to recent experiments. Rather than being exhaustive, we focus on continuum elastic models for small affine deformations and intend to provide a systematic continuum method and some analytical perspectives to the study of force transmissions in biopolymer gels. We start from a very brief review of the nonlinear mechanics of individual biopolymers and a summary of constitutive models for the nonlinear elasticity of biopolymer gels. We next show that the simple 3-chain model can give predictions that well fit the shear experiments of some biopolymer gels, including the effects of strain-stiffening and negative normal stress. We then review continuum models for the transmission of internal active forces that are induced by a spherically contracting cell embedded in a three-dimensional biopolymer gel. Various scaling regimes for the decay of cell-induced displacements are identified for linear isotropic and anisotropic materials, and for biopolymer gels with nonlinear compressive-softening and strain-stiffening elasticity, respectively. After that, we present (using an energetic approach) the generic and unified continuum theory proposed in [Ben-Yaakov, Soft Matter, 2015, 11, 1412] about how the transmission of forces in the biogel matrix can mediate long-range interactions between cells with mechanical homeostasis. We show the predictions of the theory in a special hexagonal multicellular array, and relate them to recent experiments. Finally, we conclude this paper with comments on the limitations and outlook of continuum modeling, and highlight the needs of complementary theoretical approaches such as discrete network simulations to force transmissions in biopolymer gels and phenomenological active gel theories for multicellular systems.

cond-mat.soft↗