Mattia Gazzola

Frithjof Gressmann, Ivan Georgiev Raikov, Seung Hyun Kim et al. · stanford

Biophysical neural system simulations are among the most computationally demanding scientific applications, and their optimization requires navigating high-dimensional parameter spaces under numerous constraints that impose a binary feasible/infeasible partition with no gradient signal to guide the search. Here, we introduce DMOSOPT, a scalable optimization framework that leverages a unified, jointly learned surrogate model to capture the interplay between objectives, constraints, and parameter sensitivities. By learning a smooth approximation of both the objective landscape and the feasibility boundary, the joint surrogate provides a unified gradient that simultaneously steers the search toward improved objective values and greater constraint satisfaction, while its partial derivatives yield per-parameter sensitivity estimates that enable more targeted exploration. We validate the framework from single-cell dynamics to population-level network activity, spanning incremental stages of a neural circuit modeling workflow, and demonstrate efficient, effective optimization of highly constrained problems at supercomputing scale with substantially fewer problem evaluations. While motivated by and demonstrated in the context of computational neuroscience, the framework is general and applicable to constrained multi-objective optimization problems across scientific and engineering domains.

Tejaswin Parthasarathy, Seung Hyun Kim, Songyuan Cui et al.

Soft, slender structures are ubiquitous in natural and engineered systems, with broad application potential from biomimetic materials to soft robotics. However, there is a notable lack of computational tools that simultaneously preserve high-fidelity continuum rod mechanics, scale to large interacting ensembles, and remain flexible across diverse biophysical settings. Here we introduce Elastica++, an open-source, high-performance implementation of the Cosserat-rod model for large-scale simulations of slender-body dynamics. Elastica++ combines performance-oriented kernels with shared-memory parallelism to sustain teraflop-scale throughput despite complex discretization domains and physical interactions. The framework further interoperates with external numerical solvers, supporting efficient multiphysics workflows. We demonstrate robustness and breadth through case studies spanning passive nest-like metamaterials, collective active-matter dynamics, cilia carpets, soft magnetic microrobots, and schooling swimmers. Elastica++ thus provides a missing foundation for high-throughput studies of emergent behavior in interacting assemblies of elastic slender structures.

Seung Hyun Kim, Zhi Dou, Gaurav Upadhyay et al.

We introduce chaos-controlled Reservoir Computing (cc-RC) for living neural cultures: dynamically rich substrates of unique potential for adaptive computation. To account for intrinsic biological variability, cc-RC combines: (i) pre-training identification of each culture's dynamical signature and phase-portrait attractor; (ii) low-power optical chaos control to stabilize spontaneous and stimulus-evoked activity; (iii) readout training within this controlled regime. Across hundreds of neural samples, cc-RC enables robust learning and pattern classification, improving both accuracy and model longevity by approximately 300% over standard RC. We further propose Knowledge Transplant (KT), for which the reservoir map learned by an expert culture is transplanted to an attractor-equivalent student culture, reducing training time to minutes while improving performance. By enabling cross-substrate, reusable learned models, KT paves the way for knowledge accumulation and sharing across neural populations, transcending biological lifespan limits.

Xiaotian Zhang, Ali Albazroun, Tixian Wang et al.

Limbless terrestrial animals exhibit exceptional locomotor versatility and control, currently unmatched by engineered counterparts. Here, we introduce a computational framework that enables soft synthetic snakes to navigate unstructured, heterogeneous 3D terrains. Our approach is grounded in bio-inspired actuation and sensing models that reduce the control complexity inherent to high-degree-of-freedom, continuum bodies. These models are integrated into a reinforcement learning architecture to derive environment-traversing policies. Training first occurs in simplified, homogeneous terrains to learn locomotion primitives. These are then composed into adaptive strategies for complex landscapes. We demonstrate robustness by deploying a snake in high-fidelity 3D environments reconstructed from real-world imaging, achieving reliable navigation. Overall, this work provides a physically-realistic simulation platform and practical insights for the control of continuum systems in natural terrains.

Ugur Akcal, Seung Hyun Kim, Mikihisa Yuasa et al.

Spiking neural networks (SNNs) and biologically-inspired learning mechanisms are attractive in mobile robotics, where the size and performance of onboard neural network policies are constrained by power and computational budgets. Existing SNN approaches, such as population coding, reward modulation, and hybrid artificial neural network (ANN)-SNN architectures, have shown promising results; however, they face challenges in complex, highly stochastic environments due to SNN sensitivity to hyperparameters and inconsistent gradient signals. To address these challenges, we propose simple spiking actor (S2Act), a computationally lightweight framework that deploys an RL policy using an SNN in three steps: (1) architect an actor-critic model based on an approximated network of rate-based spiking neurons, (2) train the network with gradients using compatible activation functions, and (3) transfer the trained weights into physical parameters of rate-based leaky integrate-and-fire (LIF) neurons for inference and deployment. By globally shaping LIF neuron parameters such that their rate-based responses approximate ReLU activations, S2Act effectively mitigates the vanishing gradient problem, while pre-constraining LIF response curves reduces reliance on complex SNN-specific hyperparameter tuning. We demonstrate our method in two multi-agent stochastic environments (capture-the-flag and parking) that capture the complexity of multi-robot interactions, and deploy our trained policies on physical TurtleBot platforms using Intel's Loihi neuromorphic hardware. Our experimental results show that S2Act outperforms relevant baselines in task performance and real-time inference in nearly all considered scenarios, highlighting its potential for rapid prototyping and efficient real-world deployment of SNN-based RL policies.

Noel Naughton, Jiarui Sun, Arman Tekinalp et al.

Soft robots are notoriously hard to control. This is partly due to the scarcity of models able to capture their complex continuum mechanics, resulting in a lack of control methodologies that take full advantage of body compliance. Currently available simulation methods are either too computational demanding or overly simplistic in their physical assumptions, leading to a paucity of available simulation resources for developing such control schemes. To address this, we introduce Elastica, a free, open-source simulation environment for soft, slender rods that can bend, twist, shear and stretch. We demonstrate how Elastica can be coupled with five state-of-the-art reinforcement learning algorithms to successfully control a soft, compliant robotic arm and complete increasingly challenging tasks.

Noel Naughton, Arman Tekinalp, Keshav Shivam et al.

A long-standing engineering problem, the control of soft robots is difficult because of their highly non-linear, heterogeneous, anisotropic, and distributed nature. Here, bridging engineering and biology, a neural reservoir is employed for the dynamic control of a bio-hybrid model arm made of multiple muscle-tendon groups enveloping an elastic spine. We show how the use of reservoirs facilitates simultaneous control and self-modeling across a set of challenging tasks, outperforming classic neural network approaches. Further, by implementing a spiking reservoir on neuromorphic hardware, energy efficiency is achieved, with nearly two-orders of magnitude improvement relative to standard CPUs, with implications for the on-board control of untethered, small-scale soft robots.

Seung Hyun Kim, Heng-Sheng Chang, Chia-Hsien Shih et al.

This paper is concerned with the problem of estimating (interpolating and smoothing) the shape (pose and the six modes of deformation) of a slender flexible body from multiple camera measurements. This problem is important in both biology, where slender, soft, and elastic structures are ubiquitously encountered across species, and in engineering, particularly in the area of soft robotics. The proposed mathematical formulation for shape estimation is physics-informed, based on the use of the special Cosserat rod theory whose equations encode slender body mechanics in the presence of bending, shearing, twisting and stretching. The approach is used to derive numerical algorithms which are experimentally demonstrated for fiber reinforced and cable-driven soft robot arms. These experimental demonstrations show that the methodology is accurate (<5 mm error, three times less than the arm diameter) and robust to noise and uncertainties.

Tixian Wang, Udit Halder, Heng-Sheng Chang et al.

In this paper, we use the optimal control methodology to control a flexible, elastic Cosserat rod. An inspiration comes from stereotypical movement patterns in octopus arms, which are observed in a variety of manipulation tasks, such as reaching or fetching. To help uncover the mechanisms underlying these observed morphologies, we outline an optimal control-based framework. A single octopus arm is modeled as a Hamiltonian control system, where the continuum mechanics of the arm is modeled after the Cosserat rod theory, and internal, distributed muscle forces and couples are considered as controls. First order necessary optimality conditions are derived for an optimal control problem formulated for this infinite dimensional system. Solutions to this problem are obtained numerically by an iterative forward-backward algorithm. The state and adjoint equations are solved in a dynamic simulation environment, setting the stage for studying a broader class of optimal control problems. Trajectories that minimize control effort are demonstrated and qualitatively compared with observed behaviors.

Heng-Sheng Chang, Udit Halder, Ekaterina Gribkova et al.

This paper presents an application of the energy shaping methodology to control a flexible, elastic Cosserat rod model of a single octopus arm. The novel contributions of this work are two-fold: (i) a control-oriented modeling of the anatomically realistic internal muscular architecture of an octopus arm; and (ii) the integration of these muscle models into the energy shaping control methodology. The control-oriented modeling takes inspiration in equal parts from theories of nonlinear elasticity and energy shaping control. By introducing a stored energy function for muscles, the difficulties associated with explicitly solving the matching conditions of the energy shaping methodology are avoided. The overall control design problem is posed as a bilevel optimization problem. Its solution is obtained through iterative algorithms. The methodology is numerically implemented and demonstrated in a full-scale dynamic simulation environment Elastica. Two bio-inspired numerical experiments involving the control of octopus arms are reported.

Heng-Sheng Chang, Udit Halder, Chia-Hsien Shih et al.

This paper entails application of the energy shaping methodology to control a flexible, elastic Cosserat rod model. Recent interest in such continuum models stems from applications in soft robotics, and from the growing recognition of the role of mechanics and embodiment in biological control strategies: octopuses are often regarded as iconic examples of this interplay. Here, the dynamics of the Cosserat rod, modeling a single octopus arm, are treated as a Hamiltonian system and the internal muscle actuators are modeled as distributed forces and couples. The proposed energy shaping control design procedure involves two steps: (1) a potential energy is designed such that its minimizer is the desired equilibrium configuration; (2) an energy shaping control law is implemented to reach the desired equilibrium. By interpreting the controlled Hamiltonian as a Lyapunov function, asymptotic stability of the equilibrium configuration is deduced. The energy shaping control law is shown to require only the deformations of the equilibrium configuration. A forward-backward algorithm is proposed to compute these deformations in an online iterative manner. The overall control design methodology is implemented and demonstrated in a dynamic simulation environment. Results of several bio-inspired numerical experiments involving the control of octopus arms are reported.