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Speaker: Enrico Carlon Title: Tension propagation/release mechanisms in single polymer dynamics Abstract: We review recent work on dynamical properties of single polymers with examples ranging from DNA hairpin formation and polymer unwinding. The aim of the talk is to show how the dynamics of these processes can be understood by means of mechanisms of tension propagation (or tension release) and by blob arguments. The predictions from these theories match well the results of Langevin dynamics simulations. J-C Walter et al. "Unwinding Relaxation Dynamics of Polymers", Phys. Rev. Lett. 110, 068301 (2013) J-C Walter et al. "Unwinding dynamics of helically wrapped polymers", Macromol. 47, 4840 (2014) R Frederickx et al. "Anomalous Dynamics of DNA hairpin folding", Phys. Rev. Lett. 112, 198102 (2014) M. Laleman et al. "Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning", Macromol. (2015) Speaker: Mohammad Reza Ejtehadi Title: Just before polymer finds the pore Abstract: Transloocations of DNA and other polyelectrolytes through nanopores, which are driven by an external electric field, have attracted a great interest in the recent decades. With the hope to find a fast method of the sequencing, many of the studies have focused on characterizing the signals during translocation when the chain or part of it is inside the pore. Also, distribution of dwell time and its relation with the chain length have been invetigated. But there are some questions left with regards to capturing process of the polymer by the pore. Here we show, when the polymer approaches the pore, both non-uniform electrostatic field and hydrodynamic interactions align the chain in vicinity of the pore and help terminal monomers find the orifice. Speaker: Alexander Y. Grosberg Title: Tight knots and how they go through a nanopore Abstract: The idea that knots in polymers self-tighten for topological reasons is pretty old, and received recently a boost from nanopore experiments. In the talk, both theoretical and experimental aspects will be discussed. Also, time permitting, other topics related to electrophoresis at the pore entrance, may be mentioned. Speaker: Riku Linna Title: Polymer ejection from strong spherical confinement Abstract: I will present our work where we have examined the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We used molecular dynamics for unprecedentedly high initial monomer densities and shown that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we showed this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We showed that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids. Time permitting I will also make a brief note on the surprisingly precise description of driven translocation by a quasi-static (geometric) model. References: 1. J. Piili and R.P. Linna, "Polymer ejection from strong spherical confinement", Phys. Rev. E 92, 062715 (2015). 2. P.M. Suhonen, K. Kaski, and R.P. Linna, "Criteria for minimal model of driven polymer translocation", Phys. Rev. E 90, 042702 (2014). Speaker: Cristian Micheletti Title: Pore translocation of knotted polymer chains: how friction depends on knot complexity Abstract: Knots can affect the capability of polymers to translocate through narrow pores in complex and counter-intuitive ways that are still relatively unexplored. We report here on a systematic theoretical and computational investigation of the driven translocation of flexible chains accommodating a large repertoire of knots trapped at the pore entrance. These include composites knots, which are the most common form of spontaneous entanglement in long polymers. Two unexpected results emerge from this study. First, the high force translocation compliance does not decrease systematically with knot complexity. Secondly, the response of composite knots is so dependent on the order of their factor knots, that their hindrance can even be lower than some of their prime components. We show that the resulting rich and seemingly disparate phenomenology can be captured in a seamless framework based on the mechanism by which tension is propagated along and past the knots. The quantitative scheme can be viably used for predictive purposes and hence ought to be useful in applicative contexts, too. Speaker: Murugappan Muthukumar Title: ... Abstract: ... Speaker: Takahiro Sakaue Title: Dynamics of translocation in complex medium Abstract: Extensive studies in the last decade have clarified several important features on how the polymer is sucked into a pore in the translocation process. The (moderate) driving force acting at the pore site propagates along the chain with time, which results in a characteristic non-equilibrium dynamics. In the presentation, I will think about the translocation dynamics in complex medium, and ask how the basic features established so far in a simple fluid may be altered. Speaker: Gary W. Slater Title: Reducing the initial conformational phase space of the polymer chain as a way to narrowing the distribution of translocation times Abstract: The width of the distribution of translocation times is partly due to the large range of initial polymer conformations present in a typical population of chain molecules. In order to better understand this, we first examine driven translocation out of an open tube. As the tube diameter is decreased and the polymer is squeezed into a long series of blobs, the translocation time is observed to increase while the width of the distribution of translocation times is reduced. We derive a theoretical explanation in terms based of the Tension-Propagation model in the strongly driven limit and good agreement is obtained. Reducing the lateral degrees of freedom of the initial conformation thus lead to a more deterministic translocation process. We then cap the injection tube to create a cylindrical cavity and limit the axial degree of freedom of the chain in the tube. In this case, we can play with both the tube diameter and its aspect ratio. Our results show that there are both an optimal cavity size and an optimal cavity shape that can reduce further the width of the distribution of translocation times. Speaker: Meni Wanunu Title: Voltage-driven transport of spheres and semiflexible chains through nanopores: Some experiments Abstract: In the context of this talk, a nanopore is a single nanoscale hole through an ultrathin insulating membrane. The membrane is immersed in electrolyte solution such that the only fluid contact between both membrane sides is at the nanopore. When voltage is applied across the membrane, a nonlinear electric field profile centered at the nanopore develops. Voltage-driven transport measurements reveal distribution shapes that are in good agreement with first-passage time distributions obtained from a 1D diffusion with drift model. The output parameters in this simple model, D and v, are useful experimentally for characterizing pore behavior and biomolecular transport kinetics. However, given the thin pore geometry and the broad range of biopolymer geometries tested with this model, the model's underlying physical significance is in question. In this talk, I will begin by demonstrating a mesoscopic system of bead transport that tests the validity of the model for voltage-driven transport. Then, I will show that sampling small populations of various protein molecules accurately reveals their size when the experimental system is carefully optimized. Finally, I will touch on coil entanglement issues during transport of long DNA molecules through pores, and on how to resolve entanglement by considering the electric field profile outside and pore and the pore geometry. |