Art 0.1.0

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data/examples/config.yaml

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+# Example user/config.yaml. Copy to user/config.yaml and edit; anything here
+# overrides the code repository's config.yaml (nested keys override, lists
+# replace).
+
+contact:
+  email: you@example.edu      # sent to arXiv and Crossref (polite pool)
+
+arxiv:
+  categories:                 # rss.arxiv.org category names
+    - cond-mat.soft
+    - physics.flu-dyn
+
+screen:
+  thresholds:                 # re-ranker score for a highlight, per profile id
+    default: 0.2
+    # suspension-rheology: 0.3
+  calibrated: null

data/examples/interest_profile.md

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+# Research Interest Profile (example)
+
+Replace this file with your own: copy it to user/interest_profile.md. It is a
+prose version of your interests, read only by the LLM-as-classifier baseline
+(art/baselines/llm_score.py); the screen itself uses user/profiles.yaml.
+
+## Research focus
+
+The structure, dynamics, and rheology of soft matter, with emphasis on
+concentrated suspensions and the microscopic origins of bulk rheological
+behavior.
+
+## Priority topics
+
+- **Suspension rheology**: viscosity, shear thickening and thinning, normal
+  stresses, and viscoelasticity of concentrated suspensions
+- **Microrheology**: passive and active probe techniques and their connection
+  to bulk rheology
+
+## Not of primary interest
+
+- Polymer processing (extrusion, injection molding)
+- Computational fluid dynamics without rheological content

data/examples/profiles.yaml

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+# Example interest profiles for bingham. Copy to user/profiles.yaml and edit,
+# or draft one from your own papers with `bingham init` (see README).
+#
+# Each profile:
+#   description  2-3 sentences in the field's vocabulary; the query for
+#                embedding and re-ranking
+#   keywords     technical terms and abbreviations for BM25 (see data/vocabulary.md)
+#   exemplars    papers that typify the topic, as `doi:` or `arxiv:`. A paper's
+#                embedding score is its maximum similarity over the description
+#                and the exemplars. Abstracts are fetched once; paste one under
+#                `abstract:` if no source has it.
+#
+# A profile's version is a hash of its content, so editing a profile re-screens
+# against that profile only.
+
+# Papers with a tracked author always reach the re-ranker and the digest.
+# Match on full names; initials are ambiguous across arXiv.
+tracked_authors: []
+  # - name: Jane Q. Researcher
+  #   match: [Jane Q. Researcher, Jane Researcher]
+
+profiles:
+  - id: suspension-rheology
+    name: Suspension rheology
+    description: >
+      Rheology of suspensions of solid particles in Newtonian and viscoelastic
+      liquids: viscosity as a function of volume fraction, shear thinning and
+      shear thickening, normal stress differences, yield stress, and
+      viscoelasticity of concentrated hard-sphere, charged, attractive, and
+      non-Brownian suspensions.
+    keywords: [suspension, non-Brownian, volume fraction, jamming, Peclet number,
+      hydrodynamic interactions, lubrication force, Stokesian dynamics,
+      normal stress difference, shear thickening, DST, yield stress, SAOS, LAOS]
+    exemplars:
+      - doi: 10.1146/annurev-chembioeng-060713-040221   # Denn & Morris 2014, review
+
+  - id: microrheology
+    name: Microrheology
+    description: >
+      Passive and active microrheology of soft materials: tracer particle
+      tracking and the mean squared displacement, the generalized
+      Stokes-Einstein relation, one- and two-point microrheology, optical and
+      magnetic tweezers, and diffusing wave spectroscopy.
+    keywords: [microrheology, mean squared displacement, MSD, GSER,
+      two-point microrheology, particle tracking, optical tweezers,
+      magnetic tweezers, DWS]
+    exemplars: []

data/feeds.yaml

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+# Journal RSS feeds for rheology literature (read with fetch_rss).
+#
+# arXiv categories are in config.yaml (arxiv.categories); the daily run reads
+# rss.arxiv.org for each. J. Rheol. is also queried through Crossref by ISSN
+# (config.yaml jor), because these AIP feeds carry no authors and only the
+# issue in progress. Items from both are merged by DOI.
+#
+# source: the name shown in the digest; feeds with the same source are merged.
+# Journal RSS URLs are known to change. Verify each before enabling.
+
+feeds:
+  - name: Journal of Rheology - current issue
+    source: J. Rheol.
+    url: https://pubs.aip.org/rss/site_1000105/1000055.xml
+    enabled: true          # verified 2026-09-27: full abstracts, DOIs, no authors
+
+  - name: Journal of Rheology - open issues
+    source: J. Rheol.
+    url: https://pubs.aip.org/rss/site_1000105/LatestOpenIssueArticles_1000055.xml
+    enabled: true          # verified 2026-09-27: subset of current issue
+
+  - name: Rheologica Acta
+    source: Rheol. Acta
+    url: https://link.springer.com/search.rss?query=&search-within=Journal&facet-journal-id=397
+    enabled: false
+
+  - name: Soft Matter
+    source: Soft Matter
+    url: https://feeds.rsc.org/rss/sm
+    enabled: false
+
+  - name: Journal of Non-Newtonian Fluid Mechanics
+    source: JNNFM
+    url: https://rss.sciencedirect.com/publication/science/03770257
+    enabled: false
+
+  - name: Macromolecules
+    source: Macromolecules
+    url: https://pubs.acs.org/action/showFeed?type=axatoc&feed=rss&jc=mamobx
+    enabled: false

data/vocabulary.md

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+# Rheology Vocabulary
+
+Maintained term list. Feeds BM25 keyword expansion (v0.5) and prompt context.
+
+## Core rheological quantities
+
+- viscosity, dynamic viscosity, kinematic viscosity
+- shear rate, shear stress, normal stress, normal stress difference
+- storage modulus G', loss modulus G'', complex modulus G*
+- loss tangent tan(delta), phase angle
+- viscoelasticity, linear viscoelastic regime (LVR)
+- creep, creep compliance, stress relaxation
+- relaxation time, relaxation spectrum, retardation time
+- yield stress, static yield stress, dynamic yield stress
+- flow curve, Newtonian plateau, non-Newtonian
+
+## Flow behavior
+
+- shear thinning, shear thickening
+- discontinuous shear thickening (DST), continuous shear thickening (CST)
+- thixotropy, rheopexy, anti-thixotropy
+- jamming, jamming transition
+- plug flow, slip, wall slip
+- steady-state flow, transient flow, startup flow, cessation of flow
+
+## Constitutive models
+
+- Maxwell model, Kelvin-Voigt model, Jeffreys model
+- Oldroyd-B, Giesekus, FENE-P
+- Bingham model, Herschel-Bulkley, Casson model
+- Cross model, Carreau model, Bird-Carreau
+- Doi-Edwards, reptation
+
+## Suspension and colloidal systems
+
+- hard-sphere suspension, charged colloid
+- volume fraction phi, packing fraction
+- Peclet number (Pe), Stokes number
+- hydrodynamic interactions, lubrication force
+- frictional contact, frictionless contact
+- microstructure, pair distribution function g(r)
+- colloidal gel, arrested state, percolation
+- depletion interaction, depletion flocculation
+- DLVO theory, electrostatic double layer
+- Hamaker constant, van der Waals force
+
+## Microrheology
+
+- passive microrheology, active microrheology
+- mean squared displacement (MSD)
+- generalized Stokes-Einstein relation (GSER)
+- one-point microrheology, two-point microrheology
+- optical tweezers, magnetic tweezers
+- diffusing wave spectroscopy (DWS), dynamic light scattering (DLS)
+- tracer particle, probe particle
+
+## Experimental techniques
+
+- rotational rheometer, cone-and-plate, parallel plate
+- Couette geometry, Taylor-Couette flow
+- capillary rheometer, slit rheometer
+- small-amplitude oscillatory shear (SAOS), large-amplitude oscillatory shear (LAOS)
+- strain sweep, frequency sweep, temperature sweep
+- rheo-NMR, rheo-SANS, rheo-SAXS, rheo-microscopy
+- particle image velocimetry (PIV), confocal microscopy
+
+## Polymer rheology
+
+- entanglement, entanglement molecular weight Me
+- Rouse model, Zimm model, reptation, tube model
+- plateau modulus GN0, terminal relaxation
+- polydispersity, molecular weight distribution
+- star polymer, ring polymer, branched polymer
+
+## Interfacial and emulsion rheology
+
+- interfacial rheology, surface viscosity, surface elasticity
+- Marangoni effect, surfactant
+- emulsion, droplet size distribution, coalescence
+- Pickering emulsion, particle-stabilized emulsion
+- foam, foam drainage, bubble coarsening
+
+## Active and biological matter
+
+- active matter, self-propulsion, motility
+- active gel, cytoskeletal network
+- biopolymer, actin, microtubule, collagen
+- cell mechanics, extracellular matrix (ECM)
+
+## Friction and contact mechanics
+
+- lubrication-to-friction transition, shear jamming, Wyart-Cates model
+- sliding friction, rolling friction, sticky friction, dynamic bonds
+- surface roughness, asperity, contact mechanics
+- tribology, nanotribology, lateral force microscopy, colloidal probe
+
+## Data-driven rheology
+
+- machine learning, neural network, physics-informed neural network (PINN)
+- rheology-informed neural network (RhINN), symbolic regression
+- constitutive model discovery, surrogate model, Gaussian process
+- graph neural network, Bayesian inference
+
+## LLMs and retrieval
+
+- large language model (LLM), small language model, open-weight model, local model
+- Ollama, quantization, context window, num_ctx
+- retrieval-augmented generation (RAG), dense retrieval, BM25, hybrid retrieval
+- cross-encoder, re-ranking, embedding, semantic search
+- structured output, JSON schema, schema drift, hallucination, grounding, citation
+- AI tutor, chatbot, generative AI, physics education, engineering education