A functional study of AUXILIN-LIKE1 and 2, two putative clathrin uncoating factors in Arabidopsis

Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterized compared with that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing tandem affinity purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologs of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in Arabidopsis caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like1/2 loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the ongoing characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in Arabidopsis

Atomistically enabled nonsingular anisotropic elastic representation of near-core dislocation stress fields in α\alpha-iron

The stress fields of dislocations predicted by classical elasticity are known to be unrealistically large approaching the dislocation core, due to the singular nature of the theory. While in many cases this is remedied with the approximation of an effective core radius, inside which ad hoc regularizations are implemented, such approximations lead to a compromise in the accuracy of the calculations. In this work, an anisotropic non-singular elastic representation of dislocation fields is developed to accurately represent the near-core stresses of dislocations in $\alpha$-iron. The regularized stress field is enabled through the use of a non-singular Green's tensor function of Helmholtz-type gradient anisotropic elasticity, which requires only a single characteristic length parameter in addition to the material's elastic constants. Using a novel magnetic bond-order potential to model atomic interactions in iron, molecular statics calculations are performed, and an optimization procedure is developed to extract the required length parameter. Results show the method can accurately replicate the magnitude and decay of the near-core dislocation stresses even for atoms belonging to the core itself. Comparisons with the singular isotropic and anisotropic theories show the non-singular anisotropic theory leads to a substantially more accurate representation of the stresses of both screw and edge dislocations near the core, in some cases showing improvements in accuracy of up to an order of magnitude. The spatial extent of the region in which the singular and non-singular stress differ substantially is also discussed. The general procedure we describe may in principle be applied to accurately model the near-core dislocation stresses of any arbitrarily shaped dislocation in anisotropic cubic media.Comment: Appearing in Phys. Rev.

*Interactive Earthquake Visualization with Open Data

Because earthquakes claim thousands of lives and billions of dollars yearly, there is a great need to recognize patterns in seismic data. While some tools for analysis exist, most geological software is expensive and open earthquake visualizations are limited. In this project, we provide accessible earthquake visualizations aimed to encourage geologists, and science enthusiasts in general, to explore open data using accessible, yet powerful, tools

Cooperative Control of Formations of Underwater Vehicles

This thesis investigates various control algorithms for marine vehicles. Most of the algorithms proposed in the thesis address the formation path-following problem for a fleet of underactuated autonomous underwater vehicles, although other types of vehicles, such as autonomous surface vehicles and differential drive robots, and other types of control problems, such as collision avoidance, trajectory tracking, and path following, are also considered. The thesis is divided into three parts. In the first part, we develop a collision avoidance algorithm for overactuated vehicles. The vehicles must reach a desired position while maintaining some minimum safety distance from each other. To solve this problem, we propose an optimizationbased control allocation scheme augmented with control barrier functions. Control allocation is a collection of methods for finding an actuator configuration that satisfies a given goal (e.g., reaching a desired position), while control barrier functions allow us to enforce constraints on dynamical systems (e.g., keeping a minimum safety distance). By combining control allocation with control barrier functions, we can create a controller that satisfies a given goal while avoiding collisions. The proposed controller is tested in numerical simulations on two types of autonomous surface vehicles: the milliAmpere ferry, and the Inocean Cat I drillship. The second part addresses the formation path-following problem. We propose to solve the problem using the null-space-behavioral method. This method allows us to decompose the problem into several tasks. Then, by combining these tasks in a hierarchic manner, we can achieve the desired behavior. To solve the formation path-following problem, we define three tasks: collision avoidance, formation keeping, and path following. In this thesis, we develop and analyze three different null-space-behavioral algorithms for the formation path-following problem. The first algorithm uses a model of an autonomous underwater vehicle with five degrees of freedom. Using Lyapunov analysis, we show that the path-following task is uniformly semiglobally exponentially stable. Numerical simulations then validate this result. The second algorithm uses a six-degree-of-freedom model. Compared to the previous method, this algorithm does not suffer from numerical singularities. This algorithm also contains additional tasks, namely obstacle avoidance and depth limiting. Moreover, we prove that both the path-following and the formation-keeping tasks are uniformly semiglobally exponentially stable. These theoretical results are then validated in numerical simulations. One issue with null-space-behavioral algorithms is that they are centralized. In many applications, centralized algorithms are difficult to implement, as they require a central node or an agent that can communicate and coordinate with other agents in real-time. To solve this issue, the third algorithm combines the null-space-behavioral method with consensus, resulting in a fully distributed controller. We propose two types of consensus algorithms. First, we propose a continuous-time consensus algorithm and prove its stability using Lyapunov analysis. Then, we present a modified discrete-time version of the algorithm based on event-triggered control. The effectiveness of both the continuous- and discrete-time algorithms is demonstrated in numerical simulations. Furthermore, the discrete-time version is also tested in field experiments. The third part of the thesis extends the hand position approach to underactuated underwater vehicles moving in three dimensions. This approach was originally developed to stabilize nonholonomic vehicles. By treating the hand position of the vehicle as the output of the system, we can use input-output feedback linearization to transform the underactuated highly nonlinear vehicle model into a system with linear external dynamics and nonlinear internal dynamics. We analyze the closed-loop behavior of a generic hand position-based controller and present four applications of the hand position approach. First, we use this approach to solve the trajectory-tracking and path-following problems. We propose simple PID-based controllers to solve these problems and show that using these controllers renders the external states globally exponentially stable, while the internal states remain bounded. The theoretical results are validated in numerical simulations as well as field experiments. Next, we present a spline-based model predictive control method for solving the formation path-following problem. The proposed method is not restricted to the hand position approach only. In fact, the method is applicable to any vehicle with a differentially flat model. To demonstrate this, we present two case studies: underwater vehicles with the hand position controller, and differential drive robots. Next, we use the hand position concept to solve the tracking-in-formation problem for a fleet of autonomous underwater vehicles. The proposed method combines consensus with barrier Lyapunov functions, allowing the fleet to reach the desired formation while avoiding collisions and maintaining connectivity. We show that the closed-loop system is almost-everywhere uniformly asymptotically stable and that the output error dynamics converge to the origin exponentially fast while satisfying the constraints. The theoretical results are verified in numerical simulations. Finally, we combine the hand position approach with null-space-behavioral control. Specifically, we extend the null-spacebehavioral algorithm, which was originally developed for first-order kinematic systems, to second-order systems. Similarly to our previous work, we then design the path-following, formation-keeping, and collision-avoidance tasks, so that the fleet can follow a given path in a formation while avoiding collisions. We prove the stability of the control scheme using Lyapunov analysis and verify its effectiveness in simulations