Related papers: Force-dependent switch in protein unfolding pathwa…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
Reversed von K\'arm\'an streets are responsible for a velocity surplus in the wake of flapping foils, indicating the onset of thrust generation. However, the wake pattern cannot be predicted based solely on the flapping peak-to-peak…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
Reversible control of the topological invariants from nontrivial to trivial states has fundamental implications for quantum information processors and spintronics, by realizing of an on/off switch for robust and dissipationless…
Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main…
We report inelastic x-ray scattering experiments on the lattice dynamics in SmFeAsO and superconducting SmFeAsO$_{0.6}$F$_{0.35}$ single crystals. Particular attention was paid to the dispersions along the [100] direction of three optical…
A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for…
The ability of biomolecules to exert forces on their surroundings or resist compression from the environment is essential in a variety of biologically relevant contexts. As has been understood for centuries, slender rods can only be…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
We study the mechanical unfolding pathways of the $FnIII_{10}$ domain of fibronectin by means of an Ising--like model, using both constant force and constant velocity protocols. At high forces and high velocities our results are consistent…
We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of propagating front of…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
High-energy physics experiments rely heavily on precise measurements of energy and momentum, yet face significant challenges due to detector limitations, calibration errors, and the intrinsic nature of particle interactions. Traditional…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find…