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Protein flotation is a process in which protein molecules are enriched by adsorption at rising bubbles. The bubbles then form a foam above the solution, where the liquid drains down and the dried foam, which is concentrated in protein, is…
Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while…
Biological membranes are able to exhibit various morphology due to the fluidity of the lipid molecules within the monolayers. The shape transformation of membranes has been well described by the classical Helfrich theory, which consists…
Innovative membrane technologies optimally integrated into large separation process plants are essential for economical water treatment and disposal. However, the mass transport through membranes is commonly described by nonlinear…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
In recent years dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However it is often computationally unfeasible to apply exact statistical methodologies in the context of large…
Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…
Permeability is a central concept in the macroscopic description of flow through porous media, with applications spanning from oil recovery to hydrology. Traditional methods for determining the permeability tensor involving flow simulations…
This paper presents a general and robust method for the fluid-structure interaction of membranes and shells undergoing large displacement and large added-mass effects by coupling an immersed-boundary method with a shell finite-element…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…
Undersampling is a common method in Magnetic Resonance Imaging (MRI) to subsample the number of data points in k-space, reducing acquisition times at the cost of decreased image quality. A popular approach is to employ undersampling…
Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
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…