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The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
This study uses a combination of stochastic optimization, statistical mechanical theory, and molecular simulation to test the extent to which the long-time dynamics of a single tracer particle can be enhanced by rationally modifying its…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
This paper constructs dynamical models and estimation algorithms for the concentration of target molecules in a fluid flow using an array of novel biosensors. Each biosensor is constructed out of protein molecules embedded in a synthetic…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…
Many biological materials must couple mechanical strength with the ability to rapidly self-assemble at a specific location. In particular, biomolecular condensates readily self-assemble via phase separation, but may also need to resist…
We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ~25 nm^2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic…
We present a novel Monte Carlo simulation of the phase separation dynamics of a model fluid membrane. Such a phase segregation induces shape changes of the membrane and results in local `budding' under favourable conditions. We present a…
Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112,…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
In this article, we study in details the fluid dynamics system proposed in Clarelli et al (2013) to model the formation of cyanobacteria biofilms. After analyzing the linear stability of the unique non trivial equilibrium of the system, we…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Lipid vesicles composed of a mixture of two types of lipids are studied by intensive Monte-Carlo numerical simulations. The coupling between the local composition and the membrane shape is induced by two different spontaneous curvatures of…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
We study colloidal particle dynamics of a model glass system using confocal and fluorescence microscopy as the sample evolves from a hard-sphere glass to a liquid with attractive interparticle interactions. The transition from hard-sphere…
Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated…