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Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Axial piston pumps are indispensable power sources in high-stakes fluid power systems, including aerospace, marine, and heavy machinery applications. Their operational reliability is frequently compromised by compound faults that…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…
Background: Coronary angiography (CAG) is a cornerstone imaging modality for assessing coronary artery disease and guiding interventional treatment decisions. However, in real-world clinical settings, angiographic images are often…
Bone structure is generally hierarchically organized into organic (collagen, proteins,...), inorganic (hydroxyapatite (HAP)) components. However, many fundamental mechanisms of the biomineralization processes such as HAP formation, the…
Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
The simplified Lennard-Jones (LJ) potential minimization problem is $f(x)=4\sum_{i=1}^N \sum_{j=1,j<i}^N (\frac{1}{\tau_{ij}^6} -\frac{1}{\tau_{ij}^3}) {subject to} x\in \mathbb{R}^n,$ where $\tau_{ij}=(x_{3i-2}-x_{3j-2})^2…
Accurate fovea localization is essential for analyzing retinal diseases to prevent irreversible vision loss. While current deep learning-based methods outperform traditional ones, they still face challenges such as the lack of local…
AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are…
We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…
Prion diseases cover a large range of neurodegenerative diseases in humans and animals, which are invariably fatal and highly infectious. By now there have not been some effective therapeutic approaches or medications to treat all prion…
Automatic Medical Imaging Narrative generation aims to alleviate the workload of radiologists by producing accurate clinical descriptions directly from radiological images. However, the subtle visual nuances and domain-specific terminology…
Prion-like proteins play crucial parts in biological processes in organisms ranging from yeast to humans. For instance, many neurodegenerative diseases are believed to be caused by the production of prion-like proteins in neural tissue. As…
The prion-forming C-terminal domain of the fungal prion HET-s forms infectious amyloid fibrils at physiological pH. The conformational switch from the non-prion soluble form to the prion fibrillar form is believed to have a functional role,…
Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar…
The mechanical properties of collagen fibrils depend on the amount and the distribution of water molecules within the fibrils. Here, we use atomic force microscopy (AFM) to study the effect of hydration on the viscoelastic properties of…
Twinning is an important deformation mode in plastically deformed hexagonal close-packed materials. The extremely high twin growth rates at the nanoscale make atomistic simulations an attractive method for investigating the role of…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…