- Award ID(s):
- 1608628
- PAR ID:
- 10120674
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Chemistry – A European Journal
- Volume:
- 25
- Issue:
- 62
- ISSN:
- 0947-6539
- Page Range / eLocation ID:
- p. 14140-14147
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Intelligent biological systems are characterized by their embodiment in a complex environment and the intimate interplay between their nervous systems and the nonlinear mechanical properties of their bodies. This coordination, in which the dynamics of the motor system co-evolved to reduce the computational burden on the brain, is referred to as "mechanical intelligence" or "morphological computation". In this work, we seek to develop machine learning analogs of this process, in which we jointly learn the morphology of complex nonlinear elastic solids along with a deep neural network to control it. By using a specialized differentiable simulator of elastic mechanics coupled to conventional deep learning architectures---which we refer to as neuromechanical autoencoders---we are able to learn to perform morphological computation via gradient descent. Key to our approach is the use of mechanical metamaterials---cellular solids, in particular---as the morphological substrate. Just as deep neural networks provide flexible and massively-parametric function approximators for perceptual and control tasks, cellular solid metamaterials are promising as a rich and learnable space for approximating a variety of actuation tasks. In this work we take advantage of these complementary computational concepts to co-design materials and neural network controls to achieve nonintuitive mechanical behavior. We demonstrate in simulation how it is possible to achieve translation, rotation, and shape matching, as well as a "digital MNIST" task. We additionally manufacture and evaluate one of the designs to verify its real-world behavior.more » « less
-
Predator
– prey interactions are fundamental to ecological and evolutionary dynamics. Yet, predicting the outcome of such interactions—whether predators intercept prey or fail to do so—remains a challenge. An emerging hypothesis holds that interception trajectories of diverse predator species can be described by simple feedback control laws that map sensory inputs to motor outputs. This form of feedback control is widely used in engineered systems but suffers from degraded performance in the presence of processing delays such as those found in biological brains. We tested whether delay-uncompensated feedback control could explain predator pursuit manoeuvres using a novel experimental system to present hunting fish with virtual targets that manoeuvred in ways that push the limits of this type of control. We found that predator behaviour cannot be explained by delay-uncompensated feedback control, but is instead consistent with a pursuit algorithm that combines short-term forecasting of self-motion and prey motion with feedback control. This model predicts both predator interception trajectories and whether predators capture or fail to capture prey on a trial-by-trial basis. Our results demonstrate how animals can combine short-term forecasting with feedback control to generate robust flexible behaviours in the face of significant processing delays. -
Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.