Related papers: Phenomenological and microscopic theories for catc…
The shape of materials is often subject to a number of geometric constraints that limit the size of the system or fix the structure of its boundary. In soft and biological materials, however, these constraints are not always hard, but are…
Collective dynamics and force generation by cytoskeletal filaments are crucial in many cellular processes. Investigating growth dynamics of a bundle of N independent cytoskeletal filaments pushing against a wall, we show that chemical…
We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance the…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
Biological systems are among the most challenging subjects for theoretical physicists, as well as experimentalists or simulationists. Physical principles should have been both constraints and guide-lines for the evolution of living systems…
Theoretical quest of flat-band tight-binding models usually relies on lattice structures on which electrons reside. Typical examples of candidate lattice structures include the Lieb-type lattices and the line graphs. Meanwhile, there can be…
We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the…
Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the…
We consider a dynamic system of nonlinear partial differential equations modeling the motions of a suspension bridge. This fish-bone model captures the flexural displacements of the bridge deck's mid-line, and each chordal filament's…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Various adhesion mechanisms that have been understood in the field of synthetic adhesives are described and these are linked with situations relevant to fouling issues. The review mainly deals with mechanical aspects of adhesion phenomena,…
We present atomistic molecular dynamics simulations of two Polyethylene systems where all entanglements are trapped: a perfect network, and a melt with grafted chain ends. We examine microscopically at what level topological constraints can…
The mean-field theory of Kinetically-Constrained-Models is developed by considering the Fredrickson-Andersen model on the Bethe lattice. Using certain properties of the dynamics observed in actual numerical experiments we derive asymptotic…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…
A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activity data from about 40000 such sequences. The discrepancy…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…