Related papers: SMART: Spatial Modeling Algorithms for Reaction an…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically…
Parametric 3D models have formed a fundamental role in modeling deformable objects, such as human bodies, faces, and hands; however, the construction of such parametric models requires significant manual intervention and domain expertise.…
This paper presents SMART-3D, an extension of the SMART algorithm to 3D environments. SMART-3D is a tree-based adaptive replanning algorithm for dynamic environments with fast moving obstacles. SMART-3D morphs the underlying tree to find a…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize…
We present a novel finite element analysis of inelastic structures containing Shape Memory Alloys (SMAs). Phenomenological constitutive models for SMAs lead to material nonlinearities, that require substantial computational effort to…
We propose a new method for spatio-temporal forecasting on arbitrarily distributed points. Assuming that the observed system follows an unknown partial differential equation, we derive a continuous-time model for the dynamics of the data…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…
Numerical approximations of partial differential equations (PDEs) are routinely employed to formulate the solution of physics, engineering, and mathematical problems involving functions of several variables, such as the propagation of heat…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
Robotic and animal mapping systems share many challenges and characteristics: they must function in a wide variety of environmental conditions, enable the robot or animal to navigate effectively to find food or shelter, and be…
Simulation of stochastic spatially-extended systems is a challenging problem. The fundamental quantities in these models are individual entities such as molecules, cells, or animals, which move and react in a random manner. In big systems,…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
We present an elastic simulator for domains defined as evolving implicit functions, which is efficient, robust, and differentiable with respect to both shape and material. This simulator is motivated by applications in 3D reconstruction: it…
The paper presents an algorithm, called Self-Morphing Adaptive Replanning Tree (SMART), that facilitates fast replanning in dynamic environments. SMART performs risk based tree-pruning if the current path is obstructed by nearby moving…
The motivation of this work is to produce an integrated formulation for material response due to detonation wave loading. Here, we focus on elastoplastic structural response. In particular, we are interested to capture miscible and…
Sparse autoencoders (SAEs) have become a central tool for interpreting language models. However, two key SAE analyses that remain difficult to scale are (1) matching semantically similar features across multi-layers and (2) compressing…
Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…