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Researcher Evidence Record

John D. Chodera

This bounded record lists 22 Pith paper rows and 0 imported work rows attributed to this corpus identity. The enumerated, non-disputed paper rows include cond-mat.stat-mech, physics.chem-ph, q-bio.BM work dated 2009 to 2024. The record describes sources and coverage; it makes no judgment about the person.

Compiled coverage vector

Measured lane counts only. Not a trust score or person verdict.

Identity 2 canonical identity row plus typed public identifiers Pith papers 22 attributed paper rows in the Pith corpus, itemized below Imported works 0 imported works beyond the paper ledger Current reviews 0 of 22 papers carrying a current Pith review; presence, not outcome Sourced citations 1 of 22 works with a source-named citation count Coauthors 50 distinct coauthors across shared paper rows
Enumerated paper scope: 6 fields (cond-mat.stat-mech, physics.chem-ph, q-bio.BM, +3 more) · 2009-2024 sources: authors, author_identifiers · paper_authors · author_works · current_verdicts · cited_works

A sourced case file for attributed work. It is neither a profile score nor a verdict about this researcher.

Attributed works

A bounded ledger from the Pith paper and imported-work queries. Counts and source confidence stay with each work.

  1. 2024 Pith paper

    Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning

    physics.chem-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    3
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  2. 2024 Pith paper

    Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials

    physics.chem-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    4
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  3. 2023 Pith paper

    OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

    physics.chem-ph provisional measured, no current review

    paper citation record paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    23
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    • 1 pith inbound references from cited_work_pith_inbound_counts
  4. 2023 Pith paper

    Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

    physics.chem-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    13
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  5. 2023 Pith paper

    EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment

    cs.LG provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    7
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  6. 2023 Pith paper

    Spatial Attention Kinetic Networks with E(n)-Equivariance

    cs.LG provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  7. 2022 Pith paper

    SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

    physics.chem-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    8
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  8. 2022 Pith paper

    NNP/MM: Accelerating molecular dynamics simulations with machine learning potentials and molecular mechanic

    q-bio.BM provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    7
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  9. 2021 Pith paper

    Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks

    q-bio.BM provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    4
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  10. 2020 Pith paper

    End-to-End Differentiable Molecular Mechanics Force Field Construction

    physics.comp-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    9
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  11. 2020 Pith paper

    Best Practices for Alchemical Free Energy Calculations

    q-bio.BM provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    4
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  12. 2015 Pith paper

    Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    physics.chem-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    6
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  13. 2013 Pith paper

    Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems

    physics.comp-ph provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  14. 2012 Pith paper

    Spectral rate theory for projected two-state kinetics

    physics.data-an provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  15. 2011 Pith paper

    A robust approach to estimating rates from time-correlation functions

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    1
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  16. 2011 Pith paper

    Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertainty

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    1
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  17. 2011 Pith paper

    Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  18. 2011 Pith paper

    Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    1
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  19. 2011 Pith paper

    Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    4
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  20. 2011 Pith paper

    Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    1
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  21. 2010 Pith paper

    Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.
  22. 2009 Pith paper

    Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

    cond-mat.stat-mech provisional measured, no current review

    paper paper evidence challenge this paper

    Sources and evidence
    Authorship source
    arxiv_oai
    Printed name
    John D. Chodera
    Author position
    2
    Identity state
    provisional
    Source confidence
    0.7
    Review coverage
    Measured: no current Pith review exists.
    Citation counts
    No source count is attached to this work row.

Evidence apparatus

The machinery behind this record. Every lane states whether Pith measured it, did not query it, could not reach it, or withheld it.

LaneStateObservedBoundary and source
identity Measured 2 Canonical identity row plus public typed identifiers.
source=authors, author_identifiers
papers Measured 22 of 22 bounded rows Rows attributed to this author UUID in the Pith corpus.
source=paper_authors
works Measured zero 0 of 0 bounded rows Imported works not duplicated by the paper ledger.
source=author_works
reviews Measured zero 0 of 22 bounded rows Coverage count only. No review outcome is projected onto the person.
source=current_verdicts
citations Measured 1 of 22 bounded rows Counts remain itemized by work and source.
source=cited_works
coauthors Measured 50 of 22 bounded rows Shared-work edges from admitted paper rows.
source=paper_authors
account Unavailable No public count of 1 bounded rows Account metadata is separate from corpus evidence.
source=users.author_id
Public identity sources
  • name variant
    John D. Chodera     backfill
    confidence 0.6

identity history

Enumerated research scope

Fields and dates come only from enumerated, non-disputed Pith paper rows. They do not claim career completeness.

  • cond-mat.stat-mech8 rows
  • physics.chem-ph6 rows
  • q-bio.BM3 rows
  • cs.LG2 rows
  • physics.comp-ph2 rows
  • physics.data-an1 rows
  • 20091 rows
  • 20101 rows
  • 20116 rows
  • 20121 rows
  • 20131 rows
  • 20151 rows
  • 20202 rows
  • 20211 rows
  • 20222 rows
  • 20234 rows
  • 20242 rows
Shared-work index
Record scope

The work queries are bounded. Missing rows may mean measured zero, an unavailable source, a query that did not run, or private data that Pith withheld. The lane table keeps those cases separate.

Paper findings remain attached to papers. They do not become findings about this researcher.