DNA electrophoresis in designed channels

We present a simple description on the electrophoretic dynamics of polyelectrolytes going through designed channels with narrow constrictions of slit geometry. By analyzing rheological behaviours of the stuck chain, which is coupled to the effect of solvent flow, three critical electric fields (permeation field $E^{(per)} \sim N^{-1}$, deformation field $E^{(def)} \sim N^{-3/5}$ and injection field $E^{(inj)} \simeq N^0$, with $N$ polymerization index) are clarified. Between $E^{(per)}$ and $E^{(inj)}$, the chain migration is dictated by the driven activation process. In particular, at $E>E^{(def)}$, the stuck chain at the slit entrance is strongly deformed, which enhances the rate of the permeation. From these observations, electrophoretic mobility at a given electric field is deduced, which shows non-monotonic dependence on $N$. For long enough chains, mobility increases with $N$, in good agreement with experiments. An abrupt change in the electrophoretic flow at a threshold electric field is formally regarded as a nonequilibrium phase transition.Comment: 11 pages, 8 figure

Hydrodynamics of Suspensions of Passive and Active Rigid Particles: A Rigid Multiblob Approach

We develop a rigid multiblob method for numerically solving the mobility problem for suspensions of passive and active rigid particles of complex shape in Stokes flow in unconfined, partially confined, and fully confined geometries. As in a number of existing methods, we discretize rigid bodies using a collection of minimally-resolved spherical blobs constrained to move as a rigid body, to arrive at a potentially large linear system of equations for the unknown Lagrange multipliers and rigid-body motions. Here we develop a block-diagonal preconditioner for this linear system and show that a standard Krylov solver converges in a modest number of iterations that is essentially independent of the number of particles. For unbounded suspensions and suspensions sedimented against a single no-slip boundary, we rely on existing analytical expressions for the Rotne-Prager tensor combined with a fast multipole method or a direct summation on a Graphical Processing Unit to obtain an simple yet efficient and scalable implementation. For fully confined domains, such as periodic suspensions or suspensions confined in slit and square channels, we extend a recently-developed rigid-body immersed boundary method to suspensions of freely-moving passive or active rigid particles at zero Reynolds number. We demonstrate that the iterative solver for the coupled fluid and rigid body equations converges in a bounded number of iterations regardless of the system size. We optimize a number of parameters in the iterative solvers and apply our method to a variety of benchmark problems to carefully assess the accuracy of the rigid multiblob approach as a function of the resolution. We also model the dynamics of colloidal particles studied in recent experiments, such as passive boomerangs in a slit channel, as well as a pair of non-Brownian active nanorods sedimented against a wall.Comment: Under revision in CAMCOS, Nov 201

Hiking networks generation from elevation maps

In this project we propose a highly controllable automatic method to synthesize plausible hiking networks connecting the different points of interest on a real or synthetic terrain. Our approach relies on a geometry graph generation algorithm based on a non-Euclidean metric combined with a path finding algorithm to generate a hiking network containing trails with different grades of difficulty. Unlike previous work, our method does not require a specific path merging stage, instead, each path generated takes into account the existing paths and merges with them if the conditions allow it. The trajectory of the trails is based on the different parameters of the scene, including the slope of the terrain, the exposure to falling, the natural obstacles such as lakes or snowy regions and the already existing trails

Coarse-graining polymer solutions: a critical appraisal of single- and multi-site models

We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density and density-dependent pair potentials. We highlight advantages and limitations of each option in reproducing the thermodynamic behavior and the large-scale structure of the underlying reference model. As a case study we consider solutions of linear homopolymers in a solvent of variable quality. Secondly, we extend the discussion to multi-component systems presenting, as a test case, results for mixtures of colloids and polymers. Specifically, we found the CG model with zero-density potentials to be unable to predict fluid-fluid demixing in a reasonable range of densities for mixtures of colloids and polymers of equal size. For larger colloids, the polymer volume fractions at which phase separation occurs are largely overestimated. CG models with density-dependent potentials are somewhat less accurate than models with zero-density potentials in reproducing the thermodynamics of the system and, although they presents a phase separation, they significantly underestimate the polymer volume fractions along the binodal. Finally, we discuss a general multi-site strategy, which is thermodynamically consistent and fully transferable with the number of sites, and that allows us to overcome most of the limitations discussed for single-site models.Comment: 23 pages, 9 figures, 4 table

Aerial-Ground collaborative sensing: Third-Person view for teleoperation

Rapid deployment and operation are key requirements in time critical application, such as Search and Rescue (SaR). Efficiently teleoperated ground robots can support first-responders in such situations. However, first-person view teleoperation is sub-optimal in difficult terrains, while a third-person perspective can drastically increase teleoperation performance. Here, we propose a Micro Aerial Vehicle (MAV)-based system that can autonomously provide third-person perspective to ground robots. While our approach is based on local visual servoing, it further leverages the global localization of several ground robots to seamlessly transfer between these ground robots in GPS-denied environments. Therewith one MAV can support multiple ground robots on a demand basis. Furthermore, our system enables different visual detection regimes, and enhanced operability, and return-home functionality. We evaluate our system in real-world SaR scenarios.Comment: Accepted for publication in 2018 IEEE International Symposium on Safety, Security and Rescue Robotics (SSRR