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A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
The existence of a very special ratcheting regime has recently been reported in a granular packing subjected to cyclic loading \cite{alonso04}. In this state, the system accumulates a small permanent deformation after each cycle. After a…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
We introduce a model of fracture which includes the out-of-plane degrees of freedom necessary to describe buckling in a thin-sheet material. The model is a regular square lattice of elastic beams, rigidly connected at the nodes so as to…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and…
Changes in the dynamics of supported polymer films in comparison to bulk materials involve a complex convolution of effects, such as substrate interactions, roughness and compliance, in addition to film thickness. We consider molecular…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Deviations from linearity in the dependence of the logarithm of protein unfolding rates, $\log k_u(f)$, as a function of mechanical force, $f$, measurable in single molecule experiments, can arise for many reasons. In particular, upward…
Understanding mechanosensitivity, i.e. how cells sense the stiffness of their environment is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of…
Dislocation slip is a general deformation mode and governs the strength of metals. Via discrete dislocation dynamics and molecular dynamics simulations, we investigate the strain rate and dislocation density dependence of the strength of…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
The suppression of friction between sliding objects, modulated or enhanced by mechanical vibrations, is well established. However, the precise conditions of occurrence of these phenomena is not well understood. Here we address these…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…