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DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Cellular membranes are a heterogeneous mix of lipids, proteins and small molecules. Special groupings of saturated lipids and cholesterol form a liquid-ordered phase, known as `lipid rafts,' serving as platforms for signaling, trafficking…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…
Multilayer networks provide a powerful framework for modeling complex systems that capture different types of interactions between the same set of entities across multiple layers. Core-periphery detection involves partitioning the nodes of…
Functional MRI (fMRI) and diffusion MRI (dMRI) are non-invasive imaging modalities that allow in-vivo analysis of a patient's brain network (known as a connectome). Use of these technologies has enabled faster and better diagnoses and…
The architecture of the network of protein-protein physical interactions in Saccharomyces cerevisiae is exposed through the combination of two complementary theoretical network measures, betweenness centrality and `Q-modularity'. The yeast…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…
We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a…
A cell membrane can be simply regarded as composite material consisting of lipid bilayer, membrane cytoskeleton beneath lipid bilayer, and proteins embedded in lipid bilayer and linked with membrane cytoskeleton if one only concerns its…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…
We discuss the hydrodynamic collective effects due to active protein molecules that are immersed in lipid bilayer membranes and modeled as stochastic force dipoles. We specifically take into account the presence of the bulk solvent which…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Accurate and robust recording and decoding from the central nervous system (CNS) is essential for advances in human-machine interfacing. However, technologies used to directly measure CNS activity are limited by their resolution,…
It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamic simulations the competitive protein…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
A study is made of how active membrane proteins can modify the long wavelength mechanics of fluid membranes. The activity of the proteins is modelled as disturbing the protein surroundings through non-local force distributions of which a…