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Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary…
We present a computational framework for simulating filaments interacting with rigid bodies through contact. Filaments are challenging to simulate due to their codimensionality, i.e., they are one-dimensional structures embedded in…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
Adhesive contact between a thin elastic sheet and a substrate in a liquid environment arises in a range of biological, physical and technological applications. By considering the dynamics of this process that naturally couples fluid flow,…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that…
Thin cylindrical tethers are common lipid bilayer membrane structures, arising in situations ranging from micromanipulation experiments on artificial vesicles to the dynamic structure of the Golgi apparatus. We study the shape and formation…
In experiments on model membranes, a formation of large domains of different lipid composition is readily observed. However, no such phase separation is observed in the membranes of intact cells. Instead, a structure of small transient…
Plasma membranes appear as deformable systems wherein molecules are free to move and diffuse giving rise to condensed microdomains (composed of ordered lipids, transmembrane proteins and cholesterol) surrounded by disordered lipid…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
Tuning cell rearrangements is essential in collective cell movement that underlies cancer progression, wound repair, and embryonic development. A key question is how tissue material properties and morphology emerge from cellular factors…
The study of the interactions of living adherent cells with mechanically stable (visco)elastic materials enables understanding and exploiting physiological phenomena mediated by cell-extracellular communication. However, insight on the…
Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the enzyme can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is…
For optimal application, pressure-sensitive adhesives must have rheological properties in between those of a viscoplastic solid and those of a viscoelastic liquid. Such adhesives can be produced by emulsion polymerisation, resulting in…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…