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Over the past decade, reflection matrix microscopy (RMM) and advanced image reconstruction algorithms have emerged to address the fundamental imaging depth limitations of optical microscopy in thick biological tissues and complex media. In…
The abundance of data has given machine learning considerable momentum in natural sciences and engineering, though modeling of physical processes is often difficult. A particularly tough problem is the efficient representation of geometric…
Several authors have employed Finite Element Analysis (FEA) for stress and strain analysis in orthopaedic biomechanics. Unfortunately, the use of three-dimensional models is time consuming and consequently the number of analysis to be…
Modern computing systems are capable of exascale calculations, which are revolutionizing the development and application of high-fidelity numerical models in computational science and engineering. While these systems continue to grow in…
Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of…
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…
Polygon meshes are an efficient representation of 3D geometry, and are of central importance in computer graphics, robotics and games development. Existing learning-based approaches have avoided the challenges of working with 3D meshes,…
The recent advances in text and image synthesis show a great promise for the future of generative models in creative fields. However, a less explored area is the one of 3D model generation, with a lot of potential applications to game…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…
We present an administration technique for the bookkeeping of adaptive mesh refinement on (hyper-)rectangular meshes. Our technique is a unified approach for h-refinement on 1-, 2- and 3D domains, which is easy to use and avoids traversing…
Facial expression editing methods can be mainly categorized into two types based on their architectures: 2D-based and 3D-based methods. The former lacks 3D face modeling capabilities, making it difficult to edit 3D factors effectively. The…
Creating tetrahedral meshes with anatomically accurate surfaces is critically important for a wide range of model-based neuroimaging modalities. However, computationally efficient brain meshing algorithms and software are greatly lacking.…
We equip dynamic geometry software (DGS) with a user-friendly method that enables massively parallel calculations on the graphics processing unit (GPU). This interplay of DGS and GPU opens up various applications in education and…
For modeling the 3D world behind 2D images, which 3D representation is most appropriate? A polygon mesh is a promising candidate for its compactness and geometric properties. However, it is not straightforward to model a polygon mesh from…
Transforming planar mesoscale devices into precise 3-D architectures is vital for next-generation flexible electronics, implants, and adaptive optics, yet wafer-based manufacturing to free-standing 3-D structures remain elusive. We…
Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…
3D printing has revolutionized numerous scientific fields and industries, with printing in biological systems emerging as a rapidly advancing area of research. However, its application to the subcellular level remains largely unexplored.…
Lightsheet microscopy is a powerful 3-D imaging technique that addresses limitations of traditional optical and confocal microscopy but suffers from a low penetration depth and reduced image quality at greater depths. Multiview lightsheet…