相关论文: The effect of undulations on Spontaneous Braid for…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
We consider a one-dimensional elastic membrane, which is pushed by growing filaments. The filaments tend to grow by creating local protrusions in the membrane and this process has surface energy and bending energy costs. Although it is…
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…
We propose an elasticity theory for one and two dimensional arrays of globular proteins for which the free energy is affected by relative position and relative rotation between neighboring molecules. The kinematics of such assemblies is…
We study the emergence of helical structures subjected to a stretching force, demonstrating that the force transforms disk-shaped colloidal membranes into twisted chiral ribbons of predetermined handedness. Using an experimental technique…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Conical inclusions in a lipid bilayer generate an overall spontaneous curvature of the membrane that depends on concentration and geometry of the inclusions. Examples are integral and attached membrane proteins, viruses, and lipid domains.…
Hydra tissue fragments excised freshly from Hydra body bend spontaneously to some quasi-stable shape in several minutes. We propose that the spontaneous bending is driven mechanically by supracellular actomyosin bundles inherited from…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We study a physical model for the formation of bud-like invaginations on fluid membranes under tension, and apply this model to caveolae formation. We demonstrate that budding can be driven by membrane-bound inclusions (proteins) provided…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…