Related papers: Allostery and Kinetic Proofreading
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Myosin-V is a motor protein responsible for organelle and vesicle transport in cells. Recent single-molecule experiments have shown that it is an efficient processive motor that walks along actin filaments taking steps of mean size close to…
Robust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of…
Experimental High Energy Physics has entered an era of precision measurements. However, measurements of many of the accessible processes assume that the final states' underlying kinematic distribution is the same as the Standard Model…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for…
Two headed motor proteins, such as kinesin and dynein, hidrolyze environmental ATP in order to propel unidirectionally along cytoskeletal filaments such as microtubules. In the case of kinesin, protein heads bind primarily on the alpha…
A simplified version of a classical problem in thermodynamics -- the adiabatic piston -- is discussed in the framework of kinetic theory. We consider the limit of gases whose relaxation time is extremely fast so that the gases contained on…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Contractile forces are essential for many developmental processes involving cell shape change and tissue deformation. Recent experiments on reconstituted actomyosin networks, the major component of the contractile machinery, have shown that…
Single molecular motor kinesin harnesses thermal and non-thermal fluctuations to transport various cargoes along microtubules, converting chemical energy to directed movements. To describe the non-thermal fluctuations generated by the…
Post-translational modifications of histone proteins are an important factor in epigenetic control that serve to regulate transcription, depending on the particular modification states of the histone proteins. We study the stochastic…
We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods.…
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency.…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
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…