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Highlights

Molecular simulation

Repository Description Stats
WHAM Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches. Stars Forks
postmetad Python package for post-processing PLUMED metadynamics and OPES simulations. Stars Forks
stringmethod Python implementation of the string method to compute the minimum energy path between two points on any 2-dimensional energy landscape. Stars Forks
pyves Python package to perform variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables, using OpenMM + PyTorch. Stars Forks
INDUSAnalysis Python package to analyze molecular simulation data generated using GROMACS-INDUS. Stars Forks
bootstrapping_tutorial Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data. Stars Forks
gcmc C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble. Stars Forks

Literature search

Repository Description Stats
paperfetcher Python package to automate handsearching and citation searching for systematic reviews. PyPI version fury.io Stars Forks
paperfetcher-web-app Streamlit web-app for paperfetcher. Stars Forks
paperfetcheR-Notebooks R-Notebooks demonstrating how to use paperfetcher in R. Stars Forks
paperfetcheR-starter R scripts to help you quickly get started with handsearching and citation searching using paperfetcher. Stars Forks

Miscellaneous

Repository Description Stats
gemini_penn Unofficial fork of the Gemini beamerposter theme with the University of Pennsylvania logo, colors, and fonts. Stars Forks
GameOfLife Conway's Game of Life on a rectangular 2D grid with OpenMP parallelization. Stars Forks
multiagent_timetable_scheduling Netlogo implementation of a multi-agent based algorithm for solving a simplified version of the University Timetabling Problem, using Simulated Annealing. Stars Forks
keras_sklearn_models tf2/keras deep learning models on image data and sklearn machine learning models on tabular data. Stars Forks
torch_models Deep learning models in PyTorch. Stars Forks

Akash Pallath's Projects

amalthea16 icon amalthea16

Beta version of Official Website for Amalthea 2016 (Technical Summit of Indian Institute of Technology Gandhinagar)

bootstrapping_tutorial icon bootstrapping_tutorial

Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data.

chemical_process_calculations icon chemical_process_calculations

The course titled "Chemical Process Calculations" to be offered at IIT Gandhinagar during the Semester I of the year 2016. Course code: CL 201

clipcross icon clipcross

Simple Python-Based Clipboard-Sharing Application

comp icon comp

Solutions to Programming Contest/Practice Problems

gameoflife icon gameoflife

Conway's Game of Life on a rectangular 2D grid with OpenMP parallelization.

gcmc icon gcmc

C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble.

gemini_penn icon gemini_penn

gemini_penn is an (unofficial) fork of the Gemini beamerposter theme with the University of Pennsylvania logo, colors, and fonts

hexagdly icon hexagdly

Process hexagonally sampled data with PyTorch

indusanalysis icon indusanalysis

Python package to analyze molecular simulation data generated using GROMACS-INDUS.

keras_sklearn_models icon keras_sklearn_models

Basic tf2/keras deep learning models on image data and sklearn machine learning models on tabular data.

multiagent_timetable_scheduling icon 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

network_flow icon network_flow

Implementation of selected flow algorithms and programming contest problems (TopCoder and ACM-ICPC)

paperfetcher-starter icon paperfetcher-starter

R script templates to help you get started with handsearching and citation searching using paperfetcher.

parallel_algos icon parallel_algos

Implementations of high performance shared and distributed memory parallel algorithms using OpenMP and MPI in C [work in progress].

pgcc icon pgcc

Website for Penn Graduate Consulting Club

postmetad icon postmetad

Python package for post-processing PLUMED metadynamics and OPES simulations.

pyib icon pyib

PyTorch & OpenMM implementations of information bottleneck based approaches for learning and biasing reaction coordinates in molecular simulations.

pyves icon 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 icon sl-correlation-scripts

MATLAB scripts for calculating correlations for fluctuations at solid-liquid interface, using LAMMPS MD simulation datta

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