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Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Precise control of particle positioning is desirable in many optical propulsion and sorting applications. Here, we develop an integrated platform for particle manipulation consisting of a combined optical nanofibre and optical tweezers…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
We have developed a light scattering technique based on differential measurement and polarization (differential light scattering, DLS) capable in principle of retrieving timing information with picosecond resolution without the need for…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
Determination of protein concentration in often an absolute pre-requisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are…
Learning to sample from complex unnormalized distributions over discrete domains emerged as a promising research direction with applications in statistical physics, variational inference, and combinatorial optimization. Recent work has…
Protein rotational kinetics are essential for understanding macromolecular behavior in crowded environments, yet measuring these dynamics at solid-liquid interfaces remains a significant challenge due to low signal strengths. Here, we…
We present a simplified model for dynamical diffraction of particles through a periodic thick perfect crystal based on repeated application of a coherent beam splitting unitary at coarse-grained lattice sites. By demanding translational…
In order to relate nanoparticle properties to function, fast and detailed particle characterization, is needed. The ability to characterize nanoparticle samples using optical microscopy techniques has drastically improved over the past few…
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Diffusing-Wave Spectroscopy (DWS) treats the transport of photons through turbid samples as a diffusion process, thereby making it possible to extract the dynamics of scatterers from measured correlation functions. The analysis of DWS data…
Protein flexibility is crucial for understanding protein structures, functions, and dynamics, and it can be measured through experimental methods such as X-ray crystallography. Theoretical approaches have also been developed to predict…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
Super-resolution microscopy overcomes the diffraction limit of conventional light microscopy in spatial resolution. By providing novel spatial or spatio-temporal information on biological processes at nanometer resolution with molecular…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The use of an extra SDS separation in a different buffer system provide a technique for deconvoluting 2D gel spots made of several proteins (Colignon et al. Proteomics, 2013, 13, 2077-2082). This technique keeps the quantitative analysis of…