@misc{22852,
  abstract     = {This Research Data contains supplemental videos for Chapter 4 "Designing bistable nanostructures for target behavior" of my PhD Thesis "Biological functionality without biochemistry: designing nanomachines for target behavior".
Supplemental video 1: Video showing the transition pathway of a bistable nanostructure with sphere-based arms, corresponding to the Machine in Scenario 4.
Supplemental video 2: Video showing the transition pathway of the Source in Scenario 1. The arm tips change sides during the transition, demonstrating that the arms pass through each other.
Supplemental video 3: Video showing the transition pathway of a fully polyhedral hinge structure with unconstrained arms. Note that we only show the ends of the arms.
Supplemental video 4: Video showing the transition pathway of the coupled energy-delivery reaction of a Machine (gray) and a Source (blue) nanostructure for the optimized parameters in Scenario 3. Note that we only show the ends of the arms.},
  author       = {Ehrmann, Andreas},
  keywords     = {functional nanostructures, bistability, target behavior, transition pathway},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Supplemental videos for Designing bistable nanostructures for target behavior}},
  doi          = {10.15479/AT-ISTA-22852},
  year         = {2026},
}

@phdthesis{22873,
  author       = {Ehrmann, Andreas},
  isbn         = {978-3-99078-092-3},
  issn         = {2663-337X},
  keywords     = {PhD Thesis, functional nanomachines, biological functionality, nanotechnology, energy delivery, target behavior, dynamics, design principles, optimization, differentiable statistical physics, machine learning},
  pages        = {168},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Biological functionality without biochemistry: Designing nanomachines for target behavior}},
  doi          = {10.15479/AT-ISTA-22873},
  year         = {2026},
}

@unpublished{22893,
  abstract     = {Many biological machines function through controlled conformational transitions, yet designing synthetic nanostructures with prescribed dynamical behavior remains a major challenge. Here, we develop a modular inverse-design framework for bistable nanostructures whose function is controlled by an energy profile along a geometric reaction coordinate. Inspired by proteins with rigid domains connected by flexible hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls the energetics of a conformational transition, while rigid arms map this transition onto the separation between external binding sites. Specifically, we ask which features of a target energy profile can be programmed under different design constraints. We find that the energy barriers and the binding-site separations in the two metastable states can be readily designed, while controlling the location of the transition state or the full shape of the energy profile requires additional design freedom. Using a differentiable design framework, we find that some optimized solutions are numerically inexact but still display the functional behavior for which the target profile was selected, emphasizing the importance of function-based evaluation criteria. These results establish a practical hierarchy of designability for bistable nanostructures and provide a route toward synthetic nanomachines that couple conformational transitions to target behavior.},
  author       = {Ehrmann, Andreas and Krstić, Marija and Samadzadeh, Sahar and Goodrich, Carl Peter},
  booktitle    = {arXiv},
  title        = {{Designing bistable nanostructures for target behavior}},
  doi          = {10.48550/arXiv.2606.31620},
  year         = {2026},
}

@unpublished{22892,
  abstract     = {Countless biological processes are fueled by energy-rich molecules like ATP and GTP that supply energy with extreme efficiency. However, designing similar energy-delivery schemes from the bottom up, essential for the development of powered nanostructures and other \emph{de novo} machinery, presents a significant challenge: how can an energy-rich structure be stable in solution yet still deliver this energy at precisely the right time? In this paper, we present a purely physical mechanism that solves this challenge, facilitating energy transfer akin to ATP hydrolysis, yet occurring between synthetic nanostructures without any biochemical interactions. This targeted energy delivery is achieved by exploiting a differentiable state-based model to balance the energy profiles that govern the structural transitions in the two nanostructures, creating a coupled relaxation pathway with minimal barriers that facilitates energy delivery. We verify the effectiveness and robustness of this mechanism through Langevin Dynamics simulations, demonstrating that a bath of the high-energy structures can systematically and repeatedly drive the target structure out of equilibrium, enabling it to perform tasks. As the mechanism operates only through explicit physical forces without any biochemistry or internal state variables, our results present generic and far-reaching design principles, setting the stage for the next generation of synthetic nanomachines.},
  author       = {Ehrmann, Andreas and Goodrich, Carl Peter},
  booktitle    = {arXiv},
  title        = {{Controlling energy delivery with bistable nanostructures}},
  doi          = {10.48550/arXiv.2506.14266},
  year         = {2026},
}