Toovercome this bottleneck, data are collected via biased simulations that explore the state space more rapidly. Wepropose aframeworkforlearning frombiased simulations rooted in the infinitesimal generator of the process and the associated resolvent operator. Wecontrast our approach to more common ones based on the transfer operator, showing thatitcanprovably learn thespectral properties oftheunbiased system frombiaseddata.

MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution.

We propose a deep generative Markov State Model (DeepGenMSM) learningframework for inference of metastable dynamical systems and prediction of tra-jectories.

The generation of equilibrium samples of molecular systems has been a longstanding problem in statistical physics.

We propose a deep generative Markov State Model (DeepGenMSM) learning framework for inference of metastable dynamical systems and prediction of trajectories. After unsupervised training on time series data, the model contains (i) a probabilistic encoder that maps from high-dimensional configuration space to a small-sized vector indicating the membership to metastable (long-lived) states, (ii) a Markov chain that governs the transitions between metastable states and facilitates analysis of the long-time dynamics, and (iii) a generative part that samples the conditional distribution of configurations in the next time step. The model can be operated in a recursive fashion to generate trajectories to predict the system evolution from a defined starting state and propose new configurations. The DeepGenMSM is demonstrated to provide accurate estimates of the long-time kinetics and generate valid distributions for molecular dynamics (MD) benchmark systems. Remarkably, we show that DeepGenMSMs are able to make long time-steps in molecular configuration space and generate physically realistic structures in regions that were not seen in training data.

MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution.

Deployable structures inspired by origami have provided lightweight, compact, and reconfigurable solutions for various robotic and architectural applications. However, creating an integrated structural system that can effectively balance the competing requirements of high packing efficiency, simple deployment, and precise morphing into multiple load-bearing configurations remains a significant challenge. This study introduces a new class of hyper-Yoshimura origami, which exhibits a wide range of kinematically admissible and locally metastable states, including newly discovered symmetric "self-packing" and asymmetric "pop-out" states. This metastability is achieved by breaking a design rule of Yoshimura origami that has been in place for many decades. To this end, this study derives a new set of mathematically rigorous design rules and geometric formulations. Based on this, forward and inverse kinematic strategies are developed to stack hyper-Yoshimura modules into deployable booms that can approximate complex 3D shapes. Finally, this study showcases the potential of hyper-Yoshimura with a meter-scale pop-up cellphone charging station deployed at our university's bus transit station, along with a 3D-printed, scaled prototype of a space crane that can function as an object manipulator, solar tracking device, or high-load-bearing structure. These results establish hyper-Yoshimura as a promising platform for deployable and adaptable robotic systems in both terrestrial and space environments.

Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms. Projecting these distributions onto meaningful low-dimensional representations enables interpretability and downstream analysis. Recent advances in generative AI, particularly flow models such as Normalizing Flows (NFs), have shown promise in modeling such distributions, but their scope is limited without tailored representation learning. In this work, we introduce Latent Thermodynamic Flows (LaTF), an end-to-end framework that tightly integrates representation learning and generative modeling. LaTF unifies the State Predictive Information Bottleneck (SPIB) with NFs to simultaneously learn low-dimensional latent representations, referred to as Collective Variables (CVs), classify metastable states, and generate equilibrium distributions across temperatures beyond the training data. The two components of representation learning and generative modeling are optimized jointly, ensuring that the learned latent features capture the system's slow, important degrees of freedom while the generative model accurately reproduces the system's equilibrium behavior. We demonstrate LaTF's effectiveness across diverse systems, including a model potential, the Chignolin protein, and cluster of Lennard Jones particles, with thorough evaluations and benchmarking using multiple metrics and extensive simulations. Finally, we apply LaTF to a RNA tetraloop system, where despite using simulation data from only two temperatures, LaTF reconstructs the temperature-dependent structural ensemble and melting behavior, consistent with experimental and prior extensive computational results.

Physically motivated stochastic dynamics are often used to sample from high-dimensional distributions. However such dynamics often get stuck in specific regions of their state space and mix very slowly to the desired stationary state. This causes such systems to approximately sample from a metastable distribution which is usually quite different from the desired, stationary distribution of the dynamic. We rigorously show that, in the case of multi-variable discrete distributions, the true model describing the stationary distribution can be recovered from samples produced from a metastable distribution under minimal assumptions about the system. This follows from a fundamental observation that the single-variable conditionals of metastable distributions that satisfy a strong metastability condition are on average close to those of the stationary distribution. This holds even when the metastable distribution differs considerably from the true model in terms of global metrics like Kullback-Leibler divergence or total variation distance. This property allows us to learn the true model using a conditional likelihood based estimator, even when the samples come from a metastable distribution concentrated in a small region of the state space. Explicit examples of such metastable states can be constructed from regions that effectively bottleneck the probability flow and cause poor mixing of the Markov chain. For specific cases of binary pairwise undirected graphical models (i.e. Ising models), we extend our results to further rigorously show that data coming from metastable states can be used to learn the parameters of the energy function and recover the structure of the model.

Content-addressable memories such as Modern Hopfield Networks (MHN) have been studied as mathematical models of auto-association and storage/retrieval in the human declarative memory, yet their practical use for large-scale content storage faces challenges. Chief among them is the occurrence of meta-stable states, particularly when handling large amounts of high dimensional content. This paper introduces Hopfield Encoding Networks (HEN), a framework that integrates encoded neural representations into MHNs to improve pattern separability and reduce meta-stable states. We show that HEN can also be used for retrieval in the context of hetero association of images with natural language queries, thus removing the limitation of requiring access to partial content in the same domain. Experimental results demonstrate substantial reduction in meta-stable states and increased storage capacity while still enabling perfect recall of a significantly larger number of inputs advancing the practical utility of associative memory networks for real-world tasks.