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arXiv 2025年

作者： Ruangkriengsin, Tachin Brandão, Rodolfo Wu, Katie Hwang, Jonghyun Boyko, Evgeniy Stone, Howard A. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States School of Mathematics University of Bristol Fry Building Woodland Road BristolBS8 1UG United Kingdom Department of Mechanical and Aerospace Engineering Princeton University PrincetonNJ08544 United States Faculty of Mechanical Engineering Technion – Israel Institute of Technology Haifa3200003 Israel

The Weissenberg effect, or rod-climbing phenomenon, occurs in non-Newtonian fluids where the fluid interface ascends along a rotating rod. Despite its prominence, theoretical insights into this phenomenon remain limited. In earlier work, Joseph & Fosdick (Arch. Rat. Mech. Anal., vol. 49, 1973, pp. 321–380) employed domain perturbation methods for second-order fluids to determine the equilibrium interface height by expanding solutions based on the rotation speed. In this work, we investigate the time-dependent interface height through asymptotic analysis with dimensionless variables and equations using the Oldroyd-B model. We begin by neglecting surface tension and inertia to focus on the interaction between gravity and viscoelasticity. In the small-deformation scenario, the governing equations indicate the presence of a boundary layer in time, where the interface rises rapidly over a short time scale before gradually approaching a steady state. By employing a stretched time variable, we derive the transient velocity field and corresponding interface profile on this short time scale and recover the steady-state profile on a longer time scale. Subsequently, we reintroduce small but finite inertial effects to investigate their interplay with viscoelasticity and propose a criterion for determining the conditions under which rod-climbing occurs. © 2025, CC BY.

关键词： Non Newtonian liquids

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Nordgren Physics-Informed Neural Networks to Variational Quantum Eigensolver: Advancing Hydraulic Fracturing Simulations in Shale Reservoirs

Research Square

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Research Square 2025年

作者： Wayo, Dennis Delali Kwesi Irawan, Sonny Noor, Mohd Zulkifli Bin Mohamad Zafar, Mudasar Juziyeva, Shynar Saporetti, Camila Martins Goliatt, Leonardo Hazlett, Randy Department of Petroleum Engineering School of Mining and Geosciences Nazarbayev University Astana010000 Kazakhstan Faculty of Chemical and Process Engineering Technology Universiti Malaysia Pahang Al-Sultan Abdullah Kuantan26300 Malaysia School of Mathematics Actuarial and Quantitative Studies Asia Pacific University of Technology and Innovation Kuala Lumpur0000 Malaysia Department of Computational Modeling Polytechnic Institute Rio de Janeiro State University Nova Friburgo28625-570 Brazil Department of Computational and Applied Mechanics Federal University of Juiz de Fora Juiz de Fora36036-900 Brazil

This study advances hydraulic fracturing simulations in shale reservoirs using two computational paradigms, Physics-Informed Neural Networks (PINNs) and the Variational Quantum Eigensolver (VQE). PINNs are employed to solve Nordgren’s equation, which governs fracture width evolution, by embedding physical laws into the neural network architecture. Using TensorFlow on Google Colab, the PINN training process incorporates Adam, L-BFGS, and Newton-CG optimizers, achieving an accuracy of 1.23x10−9 for fluid viscosity µ = 8.0 Pa.s, fracture height H = 2.0m, and leak-off coefficient CL = 1.0. However, this approach demands significant computational resources, with training times exceeding 1454 seconds and memory usage of 1136 MB in some cases. Conversely, the VQE framework leverages Qiskit on Qbraid to optimize the Hamiltonian representing the fracture system. With qubit-based ansatz circuits and classical optimizers (SPSA, COBYLA, and L-BFGS), VQE achieves rapid energy minimization, converging to approximately -0.583+0j in under 2 seconds with negligible memory requirements. Spatiotemporal fracture width predictions from VQE align well with expected trends but exhibit slight oscillations due to quantum noise. This comparative study highlights the trade-offs where PINNs excel in accuracy and physical adherence, while VQE offers unparalleled efficiency for rapid computations. The hybrid application of PINN precision and VQE speed provides a robust toolkit for optimizing hydrocarbon recovery. Future research will explore integrating these paradigms for scalable, high-fidelity simulations across complex geological settings. © 2025, CC BY.

关键词： Hamiltonians

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THE BREAK-UP OF A HETEROCLINIC CONNECTION IN A VOLUME PRESERVING MAPPING

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PHYSICA D 1993年第1-4期62卷 51-65页

作者： ROMKEDAR, V KADANOFF, LP CHING, ESC AMICK, C Computational and Applied Mathematics Program The Department of Mathematics The University of Chicago Chicago IL 60637 USA

We consider a family of three-dimensional, volume preserving maps depending on a small parameter epsilon. As epsilon --> 0+ these maps asymptote to flows which attain a heteroclinic connection. We show that for small epsilon the heteroclinic connection breaks up and that the splitting between its components scales with epsilon like epsilon(gamma) exp(-beta/epsilon). We estimate beta using the singularities of the epsilon --> 0+ heteroclinic orbit in the complex plane. We then estimate gamma using linearization about orbits in the complex plane. While these estimates are not proven, they are well supported by our numerical calculations. The work described here is a special case of the theory derived by Amick et al. which applies to q-dimensional volume preserving mappings.

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Deuteration removes quantum dipolar defects from KDP crystals

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npj computational Materials 2024年第1期10卷 684-693页

作者： Bingjia Yang Pinchen Xie Roberto Car Department of Chemistry Princeton UniversityPrincetonNJ 08544USA Program in Applied and Computational Mathematics Princeton UniversityPrincetonNJ 08544USA Department of Chemistry Department of PhysicsProgram in Applied and Computational MathematicsPrinceton Materials InstitutePrinceton UniversityPrincetonNJ 08544USA

Dielectric properties of the hydrogen-bonded ferroelectric crystal KH_(2)PO_(4)(KDP)differ significantly from those of KD_(2)PO_(4)(DKDP).It is well established that deuteration affects the interplay of hydrogenbond switches and heavy ion displacements that underlie the emergence of macroscopic polarization,but a detailed microscopic model is *** show that all-atompath integral molecular dynamics simulations can predict the isotope effects,revealing the microscopic mechanism that differentiates KDP and *** tunneling generates phosphate configurations that do not contribute to the *** low temperatures,these quantum dipolar defects are substantial in KDP but negligible in *** intrinsic defects explain why KDP has lower spontaneous polarization and transition entropy than *** prominent role of quantum fluctuations in KDP is related to the unusual strength of the hydrogen bonds and should be equally important in other crystals of the KDP family,which exhibit similar isotope effects.

关键词： quantum KDP remove

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Structural properties of hyperuniform Voronoi networks

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Physical Review E 2025年第3期111卷 034123-034123页

作者： Eli Newby Wenlong Shi Yang Jiao Reka Albert Salvatore Torquato Department of Physics Pennsylvania State University University Park Pennsylvania 16802 USA Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Department of Physics Arizona State University Tempe Arizona 85287 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered hyperuniform many-particle systems are recently discovered exotic states of matter, characterized by the complete suppression of normalized infinite-wavelength density fluctuations, as in perfect crystals, while lacking conventional long-range order, as in liquids and glasses. In this work, we begin a program to quantify the structural properties of nonhyperuniform and hyperuniform networks. In particular, large two-dimensional (2D) Voronoi networks (graphs) containing approximately 10,000 nodes are created from a variety of different point configurations, including the antihyperuniform hyperplane intersection process (HIP), nonhyperuniform Poisson process, nonhyperuniform random sequential addition (RSA) saturated packing, and both non-stealthy and stealthy hyperuniform point processes. We carry out an extensive study of the Voronoi-cell area distribution of each of the networks by determining multiple metrics that characterize the distribution, including their average areas and corresponding variances as well as higher-order cumulants (i.e., skewness γ1 and excess kurtosis γ2). We show that the HIP distribution is far from Gaussian, as evidenced by a high skewness (γ1=3.16) and large positive excess kurtosis (γ2=16.2). The Poisson (with γ1=1.07 and γ2=1.79) and non-stealthy hyperuniform (with γ1=0.257 and γ2=0.0217) distributions are Gaussian-like distributions, since they exhibit a small but positive skewness and excess kurtosis. The RSA (with γ1=0.450 and γ2=−0.0384) and the highest stealthy hyperuniform distributions (with γ1=0.0272 and γ2=−0.0626) are also non-Gaussian because of their low skewness and negative excess kurtosis, which is diametrically opposite of the non-Gaussian behavior of the HIP. The fact that the cell-area distributions of large, finite-sized RSA and stealthy hyperuniform networks (e.g., with N≈10,000 nodes) are narrower, have larger peaks, and smaller tails than a Gaussian distribution implies that in the thermodynamic limit th

关键词： Gaussian distribution

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Asymptotic Analysis of Quantum Dynamics in Crystals: the Bloch-Wigner Transform, Bloch Dynamics and Berry Phase

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Acta Mathematicae Applicatae Sinica 2013年第3期29卷 465-476页

作者： Weinan E Jian-feng LU Xu YANG Department of Mathematics Princeton University Program in Applied and Computational Mathematics Princeton University School of Mathematical Sciences Peking University

We study the semi-classical limit of the Schro¨dinger equation in a crystal in the presence of an external potential and magnetic field. We first introduce the Bloch-Wigner transform and derive the asymptotic equations governing this transform in the semi-classical setting. For the second part, we focus on the appearance of the Berry curvature terms in the asymptotic equations. These terms play a crucial role in many important physical phenomena such as the quantum Hall effect. We give a simple derivation of these terms in different settings using asymptotic analysis.

关键词： semiclassical limit Bloch-Wigner transform Bloch dynamics Berry phase asymptotic analysis

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4D seismic monitoring of CO2 sequestration based upon spectral-element and adjoint methods: Comparison of acoustic, elastic and poroelastic theories 80

4D seismic monitoring of CO2 sequestration based upon spectr...

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Society of Exploration Geophysicists International Exposition and 80th Annual Meeting 2010, SEG 2010

作者： Morency, Christina Luo, Yang Tromp, Jeroen Department of Geosciences Princeton University United States Department of Geosciences and Program in Applied and Computational Mathematics Princeton University United States

ISBN: (纸本)9781617389801

The key issues in CO2 sequestration monitoring involve accurate monitoring, from the injection stage to prediction & verification, of CO2 movement over time for environmental considerations. A natural non-intrusive monitoring technique is referred to as "4D seismics", which involves 3D time-lapse seismic surveys. The success of monitoring the CO2 movement is subject to a proper description of the physical properties of the structure. We realize time-lapse migrations comparing acoustic, elastic, and poroelastic simulations of 4D seismic imaging to characterize the storage zone, based solely upon the first arrival traveltime anomaly arising from the injection of CO2. This approach highlights the influence of using different physical theories on interpreting seismic data, and, more importantly, on extracting the CO2 signature from the seismic wave field. Simulations are performed using a spectral-element method, which allows for highly accurate results. Biot? Equations are implemented to account for poroelastic effects. The sensitivity of observables to the model parameters is quantified based upon finite-frequency sensitivity kernels calculated using an adjoint method. © 2010 SEG.

关键词： Carbon dioxide

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The complex interplay between risk tolerance and the spread of infectious diseases

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Journal of the Royal Society Interface 2025年第225期22卷 20240486页

作者： Nguyen, Maximilian M. Freedman, Ari S. Cheung, Matthew A. Saad-Roy, Chadi M. Espinoza, Baltazar Grenfell, Bryan T. Levin, Simon A. Lewis-Sigler Institute Princeton University PrincetonNJ United States Department of Ecology and Evolutionary Biology Princeton University PrincetonNJ United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Miller Institute for Basic Research in Science University of California Berkeley BerkeleyCA United States Department of Integrative Biology University of California BerkeleyCA United States Biocomplexity Institute University of Virginia CharlottesvilleVA United States

Risk-driven behaviour provides a feedback mechanism through which individuals both shape and are collectively affected by an epidemic. We introduce a general and flexible compartmental model to study the effect of heterogeneity in the population with regard to risk tolerance. The interplay between behaviour and epidemiology leads to a rich set of possible epidemic dynamics. Depending on the behavioural composition of the population, we find that increasing heterogeneity in risk tolerance can either increase or decrease the epidemic size. We find that multiple waves of infection can arise due to the interplay between transmission and behaviour, even without the replenishment of susceptibles. We find that increasing protective mechanisms such as the effectiveness of interventions, the fraction of risk-averse people in the population and the duration of intervention usage reduce the epidemic overshoot. When the protection is pushed past a critical threshold, the epidemic dynamics enter an underdamped regime where the epidemic size exactly equals the herd immunity threshold and overshoot is eliminated. Finally, we can find regimes where epidemic size does not monotonically decrease with a population that becomes increasingly risk-averse. © 2025 The Author(s).

关键词： epidemic size heterogeneous behaviour intervention adoption and usage risk tolerance

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Integrating Chain-of-Thought and Retrieval Augmented Generation Enhances Rare Disease Diagnosis from Clinical Notes

arXiv

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arXiv 2025年

作者： Wu, Da Wang, Zhanliang Nguyen, Quan Wang, Kai Raymond G. Perelman Center for Cellular and Molecular Therapeutics Children's Hospital of Philadelphia PhiladelphiaPA19104 United States Applied Mathematics and Computational Science Graduate Program University of Pennsylvania PhiladelphiaPA19104 United States Bioengineering Graduate Program University of Pennsylvania PhiladelphiaPA19104 United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104 United States

Background: Several studies show that large language models (LLMs) struggle with phenotype-driven gene prioritization for rare diseases. These studies typically use Human Phenotype Ontology (HPO) terms to prompt foundation models like GPT and LLaMA to predict candidate genes. However, in real-world settings, foundation models are not optimized for domain-specific tasks like clinical diagnosis, yet inputs are unstructured clinical notes rather than standardized terms. How LLMs can be instructed to predict candidate genes or disease diagnosis from unstructured clinical notes remains a major challenge. Methods: We introduce RAG-driven CoT and CoT-driven RAG, two methods that combine Chain-of-Thought (CoT) and Retrieval Augmented Generation (RAG) to analyze clinical notes. A five-question CoT protocol mimics expert reasoning, while RAG retrieves data from sources like HPO and OMIM (Online Mendelian Inheritance in Man). We evaluated these approaches on rare disease datasets, including 5,980 Phenopacket-derived notes, 255 literature-based narratives, and 220 in-house clinical notes from Children’s Hospital of Philadelphia. Results: We found that recent foundations models, including Llama 3.3-70B-Instruct and DeepSeek-R1-Distill-Llama-70B, outperformed earlier versions such as Llama 2 and GPT-3.5. We also showed that RAG-driven CoT and CoT-driven RAG both outperform foundation models in candidate gene prioritization from clinical notes;in particular, both methods with DeepSeek backbone resulted in a top-10 gene accuracy of over 40% on Phenopacket-derived clinical notes. RAG-driven CoT works better for high-quality notes, where early retrieval can anchor the subsequent reasoning steps in domain-specific evidence, while CoT-driven RAG has advantage when processing lengthy and noisy notes. Conclusions: Integrating CoT and RAG enhances LLMs’ understanding of clinical notes in the context of rare disease diagnosis, and can facilitate various downstream medical tasks. © 2025, CC

关键词： Chains

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Optimization-Based String Method for Finding Minimum Energy Path

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Communications in computational Physics 2013年第7期14卷 265-275页

作者： Amit Samanta Weinan E Program in Applied and Computational Mathematics Princeton UniversityPrincetonNew JerseyUSA Department of Mathematics and Program in Applied and Computational Mathematics Princeton UniversityPrincetonNew JerseyUSA Beijing International Center for Mathematical Research Peking UniversityBeijingChina

We present an efficient algorithm for calculating the minimum energy path(MEP)and energy barriers between local minima on a multidimensional potential energy surface(PES).Such paths play a central role in the understanding of transition pathways between metastable *** method relies on the original formulation of the string method[***.B,66,052301(2002)],*** evolve a smooth curve along a direction normal to the *** algorithm works by performing minimization steps on hyperplanes normal to the *** the problem of finding MEP on the PES is remodeled as a set of constrained minimization *** provides the flexibility of using minimization algorithms faster than the steepest descent method used in the simplified string method[***.,126(16),164103(2007)].At the same time,it provides a more direct analog of the finite temperature string *** applicability of the algorithm is demonstrated using various examples.

关键词： Rare events string method minimum energy path dislocation nucleation

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