ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations.

Gradient-based Design of Computational Granular Crystals

There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computations. Granular metamaterials are one such substrate that has emerged as a promising platform for building wave-based information processing devices with the potential to integrate sensing, actuation, and computation. Their high-dimensional and nonlinear dynamics result in nontrivial and sometimes counter-intuitive wave responses that can be shaped by the material properties, geometry, and configuration of individual grains. Such highly tunable rich dynamics can be utilized for mechanical computing in special-purpose applications. However, there are currently no general frameworks for the inverse design of large-scale granular materials. Here, we build upon the similarity between the spatiotemporal dynamics of wave propagation in material and the computational dynamics of Recurrent Neural Networks to develop a gradient-based optimization framework for harmonically driven granular crystals. We showcase how our framework can be utilized to design basic logic gates where mechanical vibrations carry the information at predetermined frequencies. We compare our design methodology with classic gradient-free methods and find that our approach discovers higher-performing configurations with less computational effort. Our findings show that a gradient-based optimization method can greatly expand the design space of metamaterials and provide the opportunity to systematically traverse the parameter space to find materials with the desired functionalities.

Universal Mechanical Polycomputation in Granular Matter

Unconventional computing devices are increasingly of interest as they can operate in environments hostile to silicon-based electronics, or compute in ways that traditional electronics cannot. Mechanical computers, wherein information processing is a material property emerging from the interaction of components with the environment, are one such class of devices. This information processing can be manifested in various physical substrates, one of which is granular matter. In a granular assembly, vibration can be treated as the information-bearing mode. This can be exploited to realize "polycomputing": materials can be evolved such that a single grain within them can report the result of multiple logical operations simultaneously at different frequencies, without recourse to quantum effects. Here, we demonstrate the evolution of a material in which one grain acts simultaneously as two different NAND gates at two different frequencies. NAND gates are of interest as any logical operations can be built from them. Moreover, they are nonlinear thus demonstrating a step toward general-purpose, computationally dense mechanical computers. Polycomputation was found to be distributed across each evolved material, suggesting the material's robustness. With recent advances in material sciences, hardware realization of these materials may eventually provide devices that challenge the computational density of traditional computers.

Evolving Programmable Computational Metamaterials

Granular metamaterials are a promising choice for the realization of mechanical computing devices. As preliminary evidence of this, we demonstrate here how to embed Boolean logic gates (AND and XOR) into a granular metamaterial by evolving where particular grains are placed in the material. Our results confirm the existence of gradients of increasing "AND-ness" and "XOR-ness" within the space of possible materials that can be followed by evolutionary search. We measure the computational functionality of a material by probing how it transforms bits encoded as vibrations with zero or non-zero amplitude. We compared the evolution of materials built from mass-contrasting particles and materials built from stiffness-contrasting particles, and found that the latter were more evolvable. We believe this work may pave the way toward evolutionary design of increasingly sophisticated, programmable, and computationally dense metamaterials with certain advantages over more traditional computational substrates.