Kim Sneppen ( Niels Bohr Institute, Copenhagen)
Oct 2013

This visit was instrumental in the completion of an existing project, studying protein roadblocking of DNA transcription in bacteria. Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. We have been combining systematic experiments (in Ian Dodd’s laboratory) and mathematical modelling (a collaboration between Kim Sneppen and Sandeep Krishna) to analyse how roadblocking by the lac repressor (LacI) in E. coli cells is affected by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein Mfd, and promoter-roadblock spacing. In this visit we were able to build models of RNAP traffic and LacI roadblocking, and combine them with experiments to make specific predictions that will lead to further experiments. In the spring of 2014 we submitted a manuscript on this work to Nucelic Acids Research where it is currently under a second round of reviewing after revisions

Mahesh Bandi (Okinawa Institute of Science and Technology.)
Aug 2013

Mahesh Bandi and Madhu Venkadesan are co-investigators on a project funded by the Human Frontier Science Program to study the biomechanical function and evolution of the human foot. As part of this project, we are working on problems ranging from creating new force measurement devices to building robotic feet. Mahesh also has overlapping research interest with Madan Rao. Mahesh's interests lie the mechanical response and dynamical behaviour of granular media,] amorphous solids such as bubble rafts, solid-fluid interfaces etc. His experimental program coincides with Madan Rao's interests in the theories of no affine deformations in crystalline, amorphous and network solids. For instance, Madan Rao's group has recently shown the existence of a hidden
mechanical critical point in a model crystalline solid subject to pure shear. This work was part of the PhD thesis of Tamoghna Das, who is now a post-doc with Mahesh. It would be fascinating to test some of these ideas in the bubble raft set up. As a result of Prof. Bandi's visit to NCBS, we now share a postdoc who does experimental work in Japan, and a combination of human subject experiments
and control theoretic work in my lab.

Shreyas Mandre (Brown University)
Aug 2013

Shreyas Mandre and Madhu Venkadesan are co-investigators on a project funded by the Human Frontier Science Program to study the biomechanical function and evolution of the human foot. As part of this project, we are working on problems ranging from measurement of elasticity of the foot from human subject experiments to understanding the limits of foot function by extending MV’s work on optimal control to spatially extended elastic bodies such as the foot. Shreyas Mandre also has overlapping research interests with Madan Rao. Following Shreyas' recent work on the near field capillary attraction between objects of different shapes floating on a fluid surface, Madan has been iscussing how local deformations of the fluid membrane can induce attraction between two proteins or protein aggregates of different shapes. Madan Rao's group has been working on phase segregation and dynamics of clustering of molecules induced by active stresses and currents. One way to approach this problem is via boundary layer theory. They have been discussing many aspects of this problem with Shreyas Mandre. Madan and Shreyas share a common interest in the mechanics of solids and fluids at low Reynolds numbers, and its fascinating applications to problems of biological interest. As a result of Prof. Mandre's visit to NCBS, we have submitted two conference abstracts, and are in the process of working on at least two collaborative journal articles.

Mogens Jensen (Niels Bohr Institute, Copenhagen)
Jul 2013

This visit was an extension of a long-standing collaboration on various aspects of oscillatory behaviour in biological systems. Recently we have been studying entrainment and synchronization in
coupled oscillators involved in vertebrate somitogenesis. During the visit we initiated a new collaboration with Sanjay Sane (NCBS) on coupled oscillators in insect wings. Our plan is to formulate a model based on Lagrangian dynamics in order to describe the coupling between the large wings on the insect and the smaller wings on the back, called halteres. Halteres are thought to be
important in stabilizing flight, but their precise role in this is not understood. We are interested in the synchronization between the two oscillating system under change of the frequency of the larger wings, obtained by cutting the length of the wings. We have recently obtained funding from The Danish Research Council for a PhD working on this project.

Rob Phillips (Caltech )
May 2013

Rob Phillips’s first visit to NCBS was prior to the official launch of the Simons Centre. Along with Jane Kondev, Rob ran a week-long workshop at NCBS on the Physical Biology of the Cell, targeted at our more theoretically minded PhD students but also at experimental biologists who were interested in developing a more quantitative understanding of their work. During his visit in December 2013 Rob participated in the launch of the Simons Centre, during which he led a discussion on the role of theory in biology. Potential future collaborations between Mukund Thattai’s group and the Phillips group include questions in evolutionary cell biology, particularly on whether physical constraints on cellular organization have evolutionary implications. These questions were explored during a longterm program evolutionary cell biology program organized by Mukund Thattai at the Kavli Insitute for Theoretical Physics in 2010. Rob Phillips is one of the organizers of a follow-up program at KITP on the same topic, in the fall of 2015.

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