apallath
PhD candidate @patellab511, University of Pennsylvania // dev of @paperfetcher // scientific software // comp chem & bio
University of PennsylvaniaUnited States
Pinned Repositories
gcmc
C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble.
INDUSAnalysis
Python package to analyze molecular simulation data generated using GROMACS-INDUS.
postmetad
Python package for post-processing PLUMED metadynamics and OPES simulations.
pyves
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
sl-correlation-scripts
MATLAB scripts for calculating correlations for fluctuations at solid-liquid interface, using LAMMPS MD simulation datta
stringmethod
Python implementation of the string method to compute the minimum energy path between two points on any 2-dimensional energy landscape.
torch_models
Basic deep learning models in PyTorch.
WHAM
Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches.
paperfetcher
Pip-installable Python package to automate handsearching and citation searching for systematic reviews.
paperfetcher-web-app
Automate handsearching and citation searching for your systematic reviews.
apallath's Repositories
apallath/WHAM
Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches.
apallath/torch_models
Basic deep learning models in PyTorch.
apallath/stringmethod
Python implementation of the string method to compute the minimum energy path between two points on any 2-dimensional energy landscape.
apallath/gcmc
C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble.
apallath/postmetad
Python package for post-processing PLUMED metadynamics and OPES simulations.
apallath/sl-correlation-scripts
MATLAB scripts for calculating correlations for fluctuations at solid-liquid interface, using LAMMPS MD simulation datta
apallath/parallel_algos
Implementations of high performance shared and distributed memory parallel algorithms using OpenMP and MPI in C [work in progress].
apallath/crossref_miner
A simple tool to fetch citations using the Crossref REST API.
apallath/INDUSAnalysis
Python package to analyze molecular simulation data generated using GROMACS-INDUS.
apallath/keras_sklearn_models
Basic tf2/keras deep learning models on image data and sklearn machine learning models on tabular data.
apallath/pyves
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
apallath/acad-council-website
Website for IITGN Academic Council 2017-18
apallath/apallath
apallath/apallath.github.io
apallath/autoencoders_project
apallath/bootstrapping_tutorial
Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data.
apallath/comp
Solutions to Programming Contest/Practice Problems
apallath/ENM531
apallath/GameOfLife
Conway's Game of Life on a rectangular 2D grid with OpenMP parallelization.
apallath/gemini_penn
gemini_penn is an (unofficial) fork of the Gemini beamerposter theme with the University of Pennsylvania logo, colors, and fonts
apallath/hexagdly
Process hexagonally sampled data with PyTorch
apallath/multiagent_timetable_scheduling
Implementation of a multi-agent based algorithm for solving a simplified version of the University Timetabling Problem, using Simulated Annealing, in NetLogo
apallath/network_flow
Implementation of selected flow algorithms and programming contest problems (TopCoder and ACM-ICPC)
apallath/paperfetcher
apallath/paperfetcheR-Notebooks
R-Notebooks demonstrating how to use paperfetcher in R through reticulate.
apallath/paperfetcheR-starter
R script templates to help you get started with handsearching and citation searching using paperfetcher.
apallath/paperfetcher-web-app
apallath/pgcc
Website for Penn Graduate Consulting Club
apallath/prog_practices_demo
Repository accompanying the Patel Group tutorial on good programming practices.
apallath/pyib
PyTorch & OpenMM implementations of information bottleneck based approaches for learning and biasing reaction coordinates in molecular simulations.