Together with our colleagues from the Babraham institute (Dr. Peter Fraser), Cambridge, we are working on developing a platform to simulate and analyze transcription dynamics in a nucleus. At moment, we have a simple model (treat each gene as a point) to study the transcription dynamics . We are developing more realistic models (polymer as chromosome) and eventually we hope to have a virtual nucleus.
Figure: Chromosomes in a nucleus, from (Dekker J. 2009, Science).
 Jing Kang, Bing Xu, Conor Hennessy, Peter Fraser, Jianfeng Feng: A dynamical model reveals gene colocalizations in nucleus (in preparation).