Papers & Write-ups
Published work, preprints, and polished research notes. Also on Google Scholar.
Published & Preprints
Virus-Like Particles as a CRISPR-Cas9 Delivery Tool
A review of virus-like particles as delivery vehicles for CRISPR-Cas9 genome editing components, covering clinical context, advantages and limitations of VLPs, and key studies that couple the two technologies.
Comparing the Performance of Leading VQE Algorithms for Computing Ground-State Energies of Amino Acids
An integrated benchmarking repository for variational quantum eigensolver ansatzes and truncation methods, applied to amino-acid Hamiltonians from the QMProt dataset across noise resilience, trainability, adaptive growth, and accuracy–expressivity tradeoffs.
White Papers & Polished Notes
Investigating LLMs’ Understanding of Causality in Measurements Using OpenADMET Experiments
Uses paired PXR primary and counter-screen assays as a causal identification testbed to ask whether LLMs distinguish assay activity from evidence of target engagement — probing selectivity representations, counter-screen fragility, activation patching across equivalent notations, and whether models request the missing scientific control.
Varying Random Unitary Circuits in a Classically-Modelled Quantum Neural Network
Explores how circuit choice affects predictive accuracy when a classical layer in a 3D/SGCNN fusion model for protein–ligand binding affinity is replaced with parameterized random G3 unitary circuits.
Modelling Antibody Therapy Dynamics with Applications to Glofitamab
A summary of modelling experiments on antibody therapy dynamics, with applications to Glofitamab.
pflotran-py: A Python Wrapper for Generating PFLOTRAN Input Files and Processing Simulation Results
A Python package that generates experiment-specific PFLOTRAN input files, supports custom sandbox reactions (including water-activity inhibition of methanogenesis), and post-processes simulation outputs for bio-based carbon sequestration modeling.
