Related papers: Physically Valid Biomolecular Interaction Modeling…
Few-Shot Medical Image Segmentation (FSMIS) aims to delineate novel anatomical targets from one or a few annotated support images, addressing the annotation scarcity in medical imaging. Notwithstanding recent advancements, current…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
We present a loosely-coupled partitioned scheme for a benchmark problem in fluid-composite structure interaction. The benchmark problem proposed here consists of an incompressible, viscous fluid interacting with a composite structure that…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
This paper is devoted to the study of a hemivariational inequality modeling the quasistatic bilateral frictional contact between a viscoelastic body and a rigid foundation. The damage effect is built into the model through a parabolic…
Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
We derive the spatial coherence and intensity profiles of beams emerging from two consecutive collimating apertures, and compare our results with data. We show how to make a Gaussian Schell-model (GSM) beam by assuming Gaussian apertures.…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
Identifying predictive world models for robots in novel environments from sparse online observations is essential for robot task planning and execution in novel environments. However, existing methods that leverage differentiable…
Atomic-scale modeling has advanced rapidly through integration of machine learning, yet a key bottleneck remains. Even with an accurate potential energy surface and a clear target material, we still lack a practical atomistic dynamics…
Large-scale linear complementarity problems (LCPs) are repeatedly solved in interactive rigid-body simulations. The projected Gauss-Seidel method is often employed for LCPs, since it has advantages in computation time, numerical robustness,…
The geometric motion of small droplets placed on an impermeable textured substrate is mainly driven by the capillary effect, the competition among surface tensions of three phases at the moving contact lines, and the impermeable substrate…
We develop a systematic projector-based Feynman diagram framework that intrinsically encodes quantum geometry for nonlinear optical responses. By explicitly incorporating geometric quantities such as the quantum geometric tensor, quantum…
Differentiable simulation of soft bodies is a foundation for system identification, trajectory optimization, and Real2Sim transfer. Yet, existing methods such as the differentiable Projective Dynamics (DiffPD) struggle when faced with…
Goal-directed molecular generation requires satisfying heterogeneous constraints such as protein--ligand compatibility and multi-objective drug-like properties, yet existing methods often optimize these constraints in isolation, failing to…
Rapid and accurate simulations of fluid dynamics around complicated geometric bodies are critical in a variety of engineering and scientific applications, including aerodynamics and biomedical flows. However, while scientific machine…