We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein's surface in 3D and time. Our method utilizes the zero-level set of signed distance functions (SDFs) to represent protein surfaces, enabling temporally and spatially continuous representations of protein dynamics. Our experimental results demonstrate that our model accurately captures protein dynamic trajectories and can interpolate and extrapolate in 3D and time. Importantly, this is the first study to introduce this method and successfully model large-scale protein dynamics. This approach offers a promising alternative to current methods, overcoming the limitations of first-principles-based and deep learning methods, and provides a more scalable and efficient approach to modeling protein dynamics. Additionally, our surface representation approach simplifies calculations and allows identifying movement trends and amplitudes of protein domains, making it a useful tool for protein dynamics research. Codes are available at https://github.com/Sundw-818/DSR,

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein's surface in 3D and time.

Machine learning interatomic potentials (MLIPs) enable efficient molecular dynamics (MD) simulations with ab initio accuracy and have been applied across various domains in physical science. However, their performance often relies on large-scale labeled training data. While existing pretraining strategies can improve model performance, they often suffer from a mismatch between the objectives of pretraining and downstream tasks or rely on extensive labeled datasets and increasingly complex architectures to achieve broad generalization. To address these challenges, we propose Iterative Pretraining for Interatomic Potentials (IPIP), a framework designed to iteratively improve the predictive performance of MLIP models. IPIP incorporates a forgetting mechanism to prevent iterative training from converging to suboptimal local minima. Unlike general-purpose foundation models, which frequently underperform on specialized tasks due to a trade-off between generality and system-specific accuracy, IPIP achieves higher accuracy and efficiency using lightweight architectures. Compared to general-purpose force fields, this approach achieves over 80% reduction in prediction error and up to 4x speedup in the challenging Mo-S-O system, enabling fast and accurate simulations.

Robotic simulators play a crucial role in the development and testing of autonomous systems, particularly in the realm of Uncrewed Aerial Vehicles (UAV). However, existing simulators often lack high-level autonomy, hindering their immediate applicability to complex tasks such as autonomous navigation in unknown environments. This limitation stems from the challenge of integrating realistic physics, photorealistic rendering, and diverse sensor modalities into a single simulation environment. At the same time, the existing photorealistic UAV simulators use mostly hand-crafted environments with limited environment sizes, which prevents the testing of long-range missions. This restricts the usage of existing simulators to only low-level tasks such as control and collision avoidance. To this end, we propose the novel FlightForge UAV open-source simulator. FlightForge offers advanced rendering capabilities, diverse control modalities, and, foremost, procedural generation of environments. Moreover, the simulator is already integrated with a fully autonomous UAV system capable of long-range flights in cluttered unknown environments. The key innovation lies in novel procedural environment generation and seamless integration of high-level autonomy into the simulation environment. Experimental results demonstrate superior sensor rendering capability compared to existing simulators, and also the ability of autonomous navigation in almost infinite environments.

An echo state network (ESN) is a type of reservoir computer that uses a recurrent neural network with a sparsely connected hidden layer. Compared with other recurrent neural networks, one great advantage of ESN is the simplicity of its training process. Yet, despite the seemingly restricted learnable parameters, ESN has been shown to successfully capture the spatial-temporal dynamics of complex patterns. Here we build an ESN to model the coarsening dynamics of charge-density waves (CDW) in a semi-classical Holstein model, which exhibits a checkerboard electron density modulation at half-filling stabilized by a commensurate lattice distortion. The inputs to the ESN are local CDW order-parameters in a finite neighborhood centered around a given site, while the output is the predicted CDW order of the center site at the next time step. Special care is taken in the design of couplings between hidden layer and input nodes to ensure lattice symmetries are properly incorporated into the ESN model. Since the model predictions depend only on CDW configurations of a finite domain, the ESN is scalable and transferrable in the sense that a model trained on dataset from a small system can be directly applied to dynamical simulations on larger lattices. Our work opens a new avenue for efficient dynamical modeling of pattern formations in functional electron materials.

Estimating physical properties for visual data is a crucial task in computer vision, graphics, and robotics, underpinning applications such as augmented reality, physical simulation, and robotic grasping. However, this area remains under-explored due to the inherent ambiguities in physical property estimation. To address these challenges, we introduce GaussianProperty, a training-free framework that assigns physical properties of materials to 3D Gaussians. Specifically, we integrate the segmentation capability of SAM with the recognition capability of GPT-4V(ision) to formulate a global-local physical property reasoning module for 2D images. Then we project the physical properties from multi-view 2D images to 3D Gaussians using a voting strategy. We demonstrate that 3D Gaussians with physical property annotations enable applications in physics-based dynamic simulation and robotic grasping. For physics-based dynamic simulation, we leverage the Material Point Method (MPM) for realistic dynamic simulation. For robot grasping, we develop a grasping force prediction strategy that estimates a safe force range required for object grasping based on the estimated physical properties. Extensive experiments on material segmentation, physics-based dynamic simulation, and robotic grasping validate the effectiveness of our proposed method, highlighting its crucial role in understanding physical properties from visual data. Online demo, code, more cases and annotated datasets are available on \href{https://Gaussian-Property.github.io}{this https URL}.

Recently, deep learning models have increasingly been used in cognitive modelling of language. This study asks whether deep learning can help us to better understand the learning problem that needs to be solved by speakers, above and beyond linear methods. We utilise the Discriminative Lexicon Model (DLM, Baayen et al., 2019), which models comprehension and production with mappings between numeric form and meaning vectors. While so far, these mappings have been linear (Linear Discriminative Learning, LDL), in the present study we replace them with deep dense neural networks (Deep Discriminative Learning, DDL). We find that DDL affords more accurate mappings for large and diverse datasets from English and Dutch, but not necessarily for Estonian and Taiwan Mandarin. DDL outperforms LDL in particular for words with pseudo-morphological structure such as slend+er. Applied to average reaction times, we find that DDL is outperformed by frequency-informed linear mappings (FIL). However, DDL trained in a frequency-informed way ('frequency-informed' deep learning, FIDDL) substantially outperforms FIL. Finally, while linear mappings can very effectively be updated from trial-to-trial to model incremental lexical learning (Heitmeier et al., 2023), deep mappings cannot do so as effectively. At present, both linear and deep mappings are informative for understanding language.

Quadratic Programs (QPs) have become a mature technology for the control of robots of all kinds, including humanoid robots. One aspect has been largely overlooked, however, which is the accuracy with which these QPs should be solved. Typical QP solvers aim at providing solutions accurate up to floating point precision ($\approx10^{-8}$). Considering physical quantities expressed in SI or similar units (meters, radians, etc.), such precision seems completely unrelated to both task requirements and hardware capacity. Typically, humanoid robots never achieve, nor are capable of achieving sub-millimeter precision in manipulation tasks. With this observation in mind, our objectives in this paper are two-fold: first examine how the QP solution accuracy impacts the resulting robot motion accuracy, then evaluate how a reduced solution accuracy requirement can be leveraged to reduce the corresponding computational effort. Numerical experiments with a dynamic simulation of a HRP-4 robot indicate that computational effort can be divided by more than 20 while maintaining the desired motion accuracy.