The study of transcription remains one the centerpieces modern biology with implications in settings from development to metabolism evolution disease. Precision measurements using a host different techniques including fluorescence and sequencing readouts have raised bar for what it means quantitatively understand transcriptional regulation. In particular our understanding simplest genetic circu...

A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include ...

Thermodynamic properties of several lattice hard-sphere models were obtained from grand canonical histogram- reweighting Monte Carlo simulations. Sphere centers occupy positions on a simple cubic lattice of unit spacing and exclude neighboring sites up to a distance sigma. The nearestneighbor exclusion model, sigma = radical2, was previously found to have a second-order transition. Models with ...