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Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
We solve the analysis sparse coding problem considering a combination of convex and non-convex sparsity promoting penalties. The multi-penalty formulation results in an iterative algorithm involving proximal-averaging. We then unfold the…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct…
Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps…
Column chromatography is an important process in downstream biopharmaceutical manufacturing that enables high-selectivity separation of proteins through various modalities, such as affinity, ion exchange, hydrophobic interactions, or a…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
We present a tool for resolution recovery in multimodal clinical magnetic resonance imaging (MRI). Such images exhibit great variability, both biological and instrumental. This variability makes automated processing with neuroimaging…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Flow-Imaging Microscopy (FIM) is commonly used in both academia and industry to characterize subvisible particles (those $\le 25 \mu m$ in size) in protein therapeutics. Pharmaceutical companies are required to record vast volumes of FIM…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
Given a set of inelastic material models, a microstructure, a macroscopic structural geometry, and a set of boundary conditions, one can in principle always solve the governing equations to determine the system's mechanical response.…
In this paper we address the problem of protein classification starting from a multi-view 2D representation of proteins. From each 3D protein structure, a large set of 2D projections is generated using the protein visualization software…