Related papers: Role of Loading Device on Single-Molecule Mechanic…
Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling…
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring,…
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…
In dynamic force spectroscopy, a (bio-)molecular complex is subjected to a steadily increasing force until the chemical bond breaks. Repeating the same experiment many times results in a broad distribution of rupture forces, whose…
The strength of a simple soft bond under constant loading rate is studied theoretically. We find a scaling regime where rebinding is negligible and the rupture force of the bond scales as $const. + (\ln (kv))^{2/3}$, where $kv$ is the…
Mechanical reliability plays an outsized role in determining the durability of flexible electronic devices because of the significant mechanical stresses they can experience during manufacturing and operation. These devices are typically…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
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…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
Crumpling of a thin film leads to a unique stiff yet lightweight structure. The stiffness has been attributed to a complex interplay between four basic elements - smooth bends, sharp folds, localized points (developable cones), and…
The mechanical properties of biological materials are spatially heterogeneous. Typical tissues are made up of a spanning fibrous extracellular matrix in which various inclusions, such as living cells, are embedded. While the influence of…
Conventional kinesin is a homodimeric motor protein that is capable of walking unidirectionally along a cytoskeletal filament. While previous experiments indicated unyielding unidirectionality against an opposing load up to the so-called…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
A three-dimensional simulation model is proposed here to study the erosive wear of structure caused by solid particles, which accounts for the accumulation of surface deformation and degradation during the erosion process. Although there…
We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…
Particulate matter in a fluid injected into a porous reservoir impairs its permeability spatio-temporally due to pore clogging. As particle volume fraction increases near the pore throats, inter-particle contact mechanics determine their…
We generalize the robotics equation describing the dynamics of open kinematic chains by including the effect of time-dependent change of inertial parameters as well as the effects of causative mass-density redistribution, triggered by…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…