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In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
We have prepared a homologous series of filamentous viruses with varying contour length using molecular cloning techniques. These viruses are monodisperse enough to form a stable smectic phase. Two systems are studied. The first system…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Left-right axis specification establishes embryonic laterality through asymmetric signaling cascades originating at the cellular scale. We previously reported the presence of a directionality bias in confined pairs of endothelial (and…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and…
Blebs are cell protrusions generated by local membrane-cortex detachments followed by expansion of the plasma membrane. Blebs are formed by some migrating cells, for example primordial germ cells of the zebrafish. While blebs occur randomly…
We study a model of rolling particles subject to stochastic fluctuations, which may be relevant in systems of nano- or micro-scale particles where rolling is an approximation for strong static friction. We consider the simplest possible…
Motor proteins drive persistent motion and self-organisation of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modelling approaches focus on large length and time scales. Here, we perform…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…
In a general stochastic multistate promoter model of dynamic mRNA/protein interactions, we identify the stationary joint distribution of the promoter state, mRNA, and protein levels through an explicit `stick-breaking' construction of…
For the first time, we carry out molecular dynamics (MD) simulation of shear-induced martensitic phase transitions between the orthorhombic and non-orthorhombic (triclinic and monoclinic) phases of crystalline polyethylene (PE) in the…
A stochastic model of electric field-driven polarization reversal in orthorhombic ferroelectrics is advanced, providing a description of their temporal electromechanical response. The theory accounts for all possible parallel and sequential…
Hydrodynamics and confinement dominate bacterial mobility near solid or air-water boundaries, causing flagellated bacteria to move in circular trajectories. This phenomenon results from the counter-rotation between the bacterial body and…
Near-field hydrodynamic interactions between bacteria and no-slip solid surfaces are the main mechanism underlying surface entrapment of bacteria. In this study, we employ a chiral two-body model to simulate bacterial dynamics near the…
We study the structure and the dynamics in the formation of irreversible gels by means of molecular dynamics simulation of a model system where the gelation transition is due to the random percolation of permanent bonds between neighboring…