Search for: All records

Using fluorescence microscopy and single-particle tracking, we have directly observed the dynamics of λ-DNA trapped inside poly(acrylamide-co-acrylate) hydrogels under an externally applied electric field. Congruent with the recent discovery of the nondiffusive topologically frustrated dynamical state (TFDS) that emerges at intermediate confinements between the traditional entropic barrier and reptation regimes, we observe the immobility of λ-DNA in the absence of an electric field. The electrophoretic mobility of the molecule is triggered upon application of an electric field with strength above a threshold value Ec. The existence of the threshold value to elicit mobility is attributed to a large entropic barrier, arising from many entropic traps acting simultaneously on a single molecule. Using the measured Ec which depends on the extent of confinement, we have determined the net entropic barrier of up to 130 kBT, which is responsible for the long-lived metastable TFDS. The net entropic barrier from multiple entropic traps is nonmonotonic with the extent of confinement and tends to vanish at the boundaries of the TFDS with the single-entropic barrier regime at lower confinements and the reptation regime at higher confinements. We present an estimate of the mesh size of the hydrogel that switches off the nondiffusive TFDS and releases chin diffusion in the heavily entangled state. 

The ubiquitin-binding NBR1 autophagy receptor plays a prominent role in recognizing ubiquitylated protein aggregates for vacuolar degradation by macroautophagy. Here, we show that upon exposing Arabidopsis plants to intense light, NBR1 associates with photodamaged chloroplasts independently of ATG7, a core component of the canonical autophagy machinery. NBR1 coats both the surface and interior of chloroplasts, which is then followed by direct engulfment of the organelles into the central vacuole via a microautophagy-type process. The relocalization of NBR1 into chloroplasts does not require the chloroplast translocon complexes embedded in the envelope but is instead greatly enhanced by removing the self-oligomerization mPB1 domain of NBR1. The delivery of NBR1-decorated chloroplasts into vacuoles depends on the ubiquitin-binding UBA2 domain of NBR1 but is independent of the ubiquitin E3 ligases SP1 and PUB4, known to direct the ubiquitylation of chloroplast surface proteins. Compared to wild-type plants, nbr1 mutants have altered levels of a subset of chloroplast proteins and display abnormal chloroplast density and sizes upon high light exposure. We postulate that, as photodamaged chloroplasts lose envelope integrity, cytosolic ligases reach the chloroplast interior to ubiquitylate thylakoid and stroma proteins which are then recognized by NBR1 for autophagic clearance. This study uncovers a new function of NBR1 in the degradation of damaged chloroplasts by microautophagy. 

The single most intrinsic property of nonrigid polymer chains is their ability to adopt enormous numbers of chain conformations, resulting in huge conformational entropy. When such macromolecules move in media with restrictive spatial constraints, their trajectories are subjected to reductions in their conformational entropy. The corresponding free energy landscapes are interrupted by entropic barriers separating consecutive spatial domains which function as entropic traps where macromolecules can adopt their conformations more favorably. Movement of macromolecules by negotiating a sequence of entropic barriers is a common paradigm for polymer dynamics in restrictive media. However, if a single chain is simultaneously trapped by many entropic traps, it has recently been suggested that the macromolecule does not undergo diffusion and is localized into a topologically frustrated dynamical state, in apparent violation of Einstein’s theorem. Using fluorescently labeled λ-DNA as the guest macromolecule embedded inside a similarly charged hydrogel with more than 95% water content, we present direct evidence for this new state of polymer dynamics at intermediate confinements. Furthermore, using a combination of theory and experiments, we measure the entropic barrier for a single macromolecule as several tens of thermal energy, which is responsible for the extraordinarily long extreme metastability. The combined theory–experiment protocol presented here is a determination of single-molecule entropic barriers in polymer dynamics. Furthermore, this method offers a convenient general procedure to quantify the underlying free energy landscapes behind the ubiquitous phenomenon of movement of single charged macromolecules in crowded environments. 

Abstract Foot slip is one of the major causes of falls in human locomotion. Analytical bipedal models provide an insight into the complex slip dynamics and reactive control strategies for slip-induced fall prevention. Most of the existing bipedal dynamics models are built on no foot slip assumption and cannot be used directly for such analysis. We relax the no-slip assumption and present a new bipedal model to capture and predict human walking locomotion under slip. We first validate the proposed slip walking dynamic model by tuning and optimizing the model parameters to match the experimental results. The results demonstrate that the model successfully predicts both the human walking and recovery gaits with slip. Then, we extend the hybrid zero dynamics (HZD) model and properties to capture human walking with slip. We present the closed-form of the HZD for human walking and discuss the transition between the nonslip and slip states through slip recovery control design. The analysis and design are illustrated through human walking experiments. The models and analysis can be further used to design and control wearable robotic assistive devices to prevent slip-and-fall.