Nanopore Translocation and Nanochannel Confined Biopolymers: bridging theory and experiments
Notice from the organizers:
Due to ongoing COVID-19 travel and gathering restrictions, the workshop on "Nanopore Translocation and Nanochannel Confined Biopolymers” is postponed to 2021.
Most likely it will be held at the end of August or beginning of September 2021; the exact dates will be communicated in Autumn 2020.
We therefore ask perspective participants to check this webpage again at that time before applying.
MOTIVATION AND SIGNIFICANCE
In this workshop, we propose to bring together researchers from a diverse discipline of physics, chemistry, molecular biology, and engineering to discuss topics central to the behavior of biopolymers driven through nanopores or confined in nanochannels.
These research avenues that have witnessed spectacular growth in the last 5 years, as reflected in the order of magnitude increase in number of publications, largely due to the advancement of single-molecule manipulation techniques that have provided unprecedented quantitative insight into the ubiquity of various forms of pore translocation or channel-like confinement in biological contexts, such as, during RNA transcription, mRNA translation and degradation of ubiquinated proteins by the proteasome [1-7]. The wealth of available experimental data has, in turn, spurred much activity on the theoretical and modeling side aimed at understanding the general physical mechanisms that underpin the observed phenomenology, as well as understanding their biological implications [8-13]. For these reasons we will seek a good balance between theorists involved in modelling and simulations of the aforementioned systems and experimentalists.
The two pivotal topics of the workshop, pore translocation and channel confinement, were selected for their general relevance and broader implications. For the former, we recall that by capturing and pulling DNAs and proteins through nanopores, and straightening them in nanochannels, it is now possible to sequence a single human genome without amplification . It is believed that nano-pore and nano-channel based technologies will have major impact in human health and disease, such as cancer, with accurate, albeit cheaper and faster routine desktop analyses of human genome. For instance, the emerging field of protein sequencing by nanopore open the possibility to profile gene expression at single molecule level .
For the second, instead, we note the ongoing debate in the community of polymer theorists regarding the existence of previously unforeseen metric scaling regimes that bridge between the two classic ones named after de Gennes and Odijk . The richer than expected theoretical background poses more challenges for interpreting experimental data and begs to address by simulations large segments of channel-confined genomic DNA for further numerical expediency and new outlook on coarse graining. Recent developments in self consistent field theories of confined polymers may provide clues for bridging experimental and simulation length and time scales . Deviations from ideal conditions in experiments, such as, presence of fluorescent dyes, charges at the channel surfaces, etc. need to be incorporated in theory and modeling.
The proposed flagship CECAM workshop has three aims: map out the current challenges in nanopore translocation and channel-confinement of biopolymers, compare the methodological approaches that are currently being used and finally shape future research directions especially those bridging theory and experiments. To this end we plan to organize in 2020 a three-day dedicated workshop at the local CECAM node in Trieste, Italy, to bring together those scientists working in theory, numerical simulation, and experiments that, over the past few years, have significantly and systematically contributed to the advancement of the field. Among them, we have singled out the scientists listed below as invited speakers and have already secured the commitment of most of them to take part to this planned node activity. Having already secured the support of the local CECAM node, and a pledge of the Statistical and Biological Physics group to support it too, we are applying for having the Flagship status because we believe it would benefit the community in at least two ways.
First, the CECAM scientific endorsement would further boost the scientific impact of the topics that, to our knowledge, have not been previously covered as CECAM thematic workshops. Secondly, by providing a broader visibility to the workshop, it would facilitate the participation of young scientists which would benefit by interacting personally with the leaders in the field. Precisely to help establishing young researchers we note that, besides the scheduled invited talk, are planning to have poster sessions and the best posters, selected by an independent jury, will be prized with an oral presentation.
Fabien Montel Montel (CNRS / ENS de Lyon) - Organiser
Matteo Ceccarelli (University of Cagliari) - Organiser
Cristian Micheletti (SISSA) - Organiser
Matteo Dal Peraro (Swiss Federal Institute of Technology Lausanne (EPFL) ) - Organiser
Aleksandra Radenovic (École polytechnique fédérale de Lausanne) - Organiser
Aniket Bhattacharya (University of Central Florida) - Organiser