Related papers: Unfolding protein with an atomic force microscope:…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
Many biological systems are appropriately viewed as passive inclusions immersed in an active bath: from proteins on active membranes to microscopic swimmers confined by boundaries. The non-equilibrium forces exerted by the active bath on…
We characterize the fluctuation properties of a polymer chain under external tension and the fluctuation-induced forces between two ring molecules threaded around the chain. The problem is relevant in the context of fluctuation-induced…
The mechanical properties within living cells play a critical role in the adaptive regulation of their biological functions upon environmental and internal stimuli. While these properties exhibit nonequilibrium dynamics due to the thermal…
We have considered the underdamped motion of a Brownian particle in the presence of a correlated external random force. The force is modeled by an Ornstein-Uhlenbeck process. We investigate the fluctuations of the work done by the external…
We investigated the nanometer scale height fluctuations of 3T3 fibroblast cells with the atomic force microscope (AFM) under physiological conditions. Correlation between these fluctuations and lateral cellular motility can be observed.…
Earlier we showed that the fine structure of the spectrum of amplitude variations in the results of measurements of the processes of different nature (in other words, the fine structure of the dispersion of results or the pattern of the…
Autocatalytic fibril nucleation has recently been proposed to be a determining factor for the spread of neurodegenerative diseases, but the same process could also be exploited to amplify minute quantities of protein aggregates in a…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
We present direct measurements of fluctuations in the nucleus of yeast cells. While prior work has shown these fluctuations to be active and non-thermal in character, their origin and time dependence are not understood. We show that the…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
The importance of mesoscale fluctuations in flowing amorphous materials is widely accepted, without a clear understanding of their role. We propose a mean-field elastoplastic model that admits both stress and strain-rate fluctuations, and…
The free energy of inserting a protein into a membrane is determined by considering the variation in the spectrum of thermal fluctuations in response to the presence of a rigid inclusion. Both numerically and through a simple analytical…
We present an overview of possible imprints of non-extensitivity in particle and nucler physics. Special emphasis is put on the intrinsic fluctuations present in the system under consideration as the possible source of nonextensivity. The…
Active contributions to fluctuations are a direct consequence of metabolic energy consumption in living cells. Such metabolic processes continuously create active forces, which deform the membrane to control motility, proliferation as well…
It seems that a stochastic system must be a nonlinear one to observe the phenomenon, noise induced transition. But in the present paper, we have demonstrated that the phenomenon may be observed even in a linear stochastic process where both…
In stochastic thermodynamics, significant attention has been given to studying the statistical behavior of thermodynamic quantities such as heat and work. However, fluctuations in other quantities, such as kinetic energy and internal…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Mesoscopic active systems exhibit various unique behaviours - absent in passive systems - due to the forces generated by the corresponding constituents by converting their available free energies. However, estimating these forces - which…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…