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HelixMC documentation

HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model. It provides a powerful tool to understand the flexibility of DNA/RNA helices through numerical simualtions.

The base-pair level model, first developed by Olson and collegues, bridges between the simple elastic rod model and the full-atom representation, providing a reasonably sophiscated and yet computationally tractable way to model long DNA/RNA helices up to thousands of base-pairs and to evalute their mechanical properties. HelixMC has the utility of applying external stetching forces and torques to the helix, and measuring the helix extension and the rotation of the helix (known as the linking number) during the process. This properly emulate the setup of recent single-molecule tweezers experiments, making HelixMC a useful tool for direct simulations of these experiments.

HelixMC is coded in Python in an object-oriented fashion. Rate-limiting core computations are speeded up using Cython. Therefore HelixMC provides a framework that is easy to use and to extend, as well as being reasonably fast when it comes to large-scale computations.

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