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Resonant Energy Transfer (RET) from an optically excited donor molecule (D) to a non-excited acceptor molecule (A) residing nearby is widely used to detect molecular interactions in living cells. Stoichiometric information, such as the…
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through…
Functionalizing colloids with reactive DNA linkers is a versatile way of programming self-assembly. DNA selectivity provides direct control over colloid-colloid interactions allowing the engineering of structures such as complex crystals or…
Nanophotonic devices excel at confining light into intense hot spots of the electromagnetic near fields, creating unprecedented opportunities for light-matter coupling and surface-enhanced sensing. Recently, all-dielectric metasurfaces with…
Cell detection in microscopy images is important to study how cells move and interact with their environment. Most recent deep learning-based methods for cell detection use convolutional neural networks (CNNs). However, inspired by the…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
Machine learning (ML) strategies are opening the door to faster computer simulations, allowing us to simulate more realistic colloidal systems. Since the interactions in colloidal systems are often highly many-body, stemming from e.g.…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
From viruses to nanoparticles, constructs functionalized with multiple ligands display peculiar binding properties that only arise from multivalent effects. Using statistical mechanical modelling, we describe here how multivalency can be…
Proteins are fundamental biological entities mediating key roles in cellular function and disease. This paper introduces a multi-scale graph construction of a protein -- HoloProt -- connecting surface to structure and sequence. The surface…
Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…
Protein adsorption at the solid-liquid interface is an important phenomenon that often can be observed as a first step in biological processes. Despite its inherent importance, still relatively little is known about the underlying…
Molecular Communications (MC) uses molecules as information carriers between nanomachines. MC channel in practice can be crowded with different types of molecules, i.e., ligands, which can have similar binding properties causing severe…
Colloidal particles with DNA `legs' that can bind reversibly to receptors on a surface can be made to `walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
In this paper, we consider bidirectional relaying between two diffusion-based molecular transceivers (bio-nodes). As opposed to existing literature, we incorporate the effect of direct diffusion links between the nodes and leverage it to…
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…
Using video-microscopy imaging we demonstrate the existence of a short-ranged equilibrium attraction between heavy silica colloids diffusing on soft surfaces of cross-linked polymer gels. The inter-colloid potential can be tuned by changing…