2019.05.13 Energetic funnel facilitates facilitated diffusion

2019-07-07 01:02:06 9




    目:Energetic funnel facilitates facilitated diffusion

报告人:Simone Pigolotti, Ph.D.

Associate Professor, Okinawa Institute of Science and Technology (OIST)


    点:北京大学吕志和楼B101报告厅Rm. B101, Lui Che Woo Building

主持人:Dr. Lucas Carey


Transcription factors find their target on DNA by facilitated diffusion, i.e. by alternating 3D diffusion and 1D sliding along the DNA. This suggest that the genetic context, i.e. the DNA energy landscape around a specific target sequence can play an important role for the transcription factor kinetics. By analyzing DNA sequences from E.coli, I will show how the genetic context can be exploited to speed-up target search. Predictions are tested by an extensive computational study of a stochastic model of protein sliding events. I will conclude by discussing possible evolutionary implications of this finding and implications for understanding TF specificity in eukaryotes.


Reference: M. Cencini and S. Pigolotti, Nucleic Acid Research 46(2), 558-567 (2018).



  Simone Pigolotti received a degree in Physics at University of Rome “La Sapienza”. He later moved to SISSA/ISAS (Trieste, Italy), where he obtained his Ph.D. in Statistical and Biological Physics in 2004 under the supervision of Prof. Amos Maritan.

  He then worked his postdoc at the Niels Bohr International Academy (Copenhagen, Denmark). After that, he moved to the Universitat Politecnica de Catalunya (UPC) in Barcelona, Spain in 2011 as an independent Ramon y Cajal researcher.

  Since 2017, he is Associate Professor at the Okinawa Institute of Science and Technology Graduate University (OIST), where he leads the Biological Complexity Unit.

  Simone Pigolotti’s research focuses on the stochastic dynamics of biophysical systems. By means of a combination of theoretical and computational approaches, he seeks to understand how such systems can function despite the effect of random fluctuations. He authored more than 50 publications in major physics, biology, and interdisciplinary journals. He was recently appointed member of the Editorial Board of Physical Biology.