Related papers: Undulations in a weakly interacting mechanically g…
This is an archival document; the work contains theoretical development to be used in new publications and to stimulate further development. Here, we develop a statistical mechanical treatment of a braid formed of two molecules subject to…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
This paper extends on a recent work where it was shown that forces dependent on the helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et Al, Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of DNA…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
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…
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the…
This is a technical document that outlines a calculation of an electrostatic interaction energy between two rods, with charge helices on them, forming a braid. We deal here with screened electrostatics. A general braid geometry is…
The friction and adhesion between elastic bodies are strongly influenced by the roughness of the surfaces in contact. Here we develop a multiscale molecular dynamics approach to contact mechanics, which can be used also when the surfaces…
Curvature in biological membranes can be generated by a variety of different molecular mechanisms such as protein scaffolding, lipid or protein asymmetry, cytoskeletal forces, etc. These mechanisms have the net effect of generating stresses…
Dual mechanical braiding experiments provide a useful tool with which investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an…
In this paper we present an individual-based mechanical model that describes the dynamics of two contiguous cell populations with different proliferative and mechanical characteristics. An off-lattice modelling approach is considered…
When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
We study a material modeled as a network of nodes connected by edges. Using a discrete approach, we build a nonlinear algebraic system that connects applied forces to internal forces and node positions. The model can describe elasticity,…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…