Related papers: Mode-coupling points to functionally important res…
We discuss the dynamic behavior of a tagged particle close to a classical localization transition in the framework of the mode-coupling theory of the glass transition. Asymptotic results are derived for the order parameter as well as the…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
A data fitting procedure is devised and thoroughly tested to provide self-consistent estimates of the relevant mechanokinetic parameters involved in a plausible scheme underpinning the output of an ensemble of myosin II molecular motors…
In the standard picture of structure formation, initially random-phase fluctuations are amplified by non-linear gravitational instability to produce a final distribution of mass which is highly non-Gaussian and has highly coupled Fourier…
We analyse the connections between structure and dynamics in two model glass-formers, using the mutual information between an initial configuration and the ensuing dynamics to compare the predictive value of different structural…
Networks of interacting, communicating subsystems are common in many fields, from ecology, biology, epidemiology to engineering and robotics. In the presence of noise and uncertainty, inter- actions between the individual components can…
We elucidate how the strong coupling phases of a coupled driven model, originally proposed in S. Mukherjee, Phys. Rev. E 108, 024219 (2023), are affected by noise cross correlations in general dimensions $d$. This model has two dynamical…
We exactly calculate two-point spatial correlation functions in steady state in a broad class of conserved-mass transport processes, which are governed by chipping, diffusion and coalescence of masses. We find that the spatial correlations…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce…
The rheology of biological cells is not only determined by their cytoskeletal networks, but also by the molecular motors that crosslink and contract them. Recently it has been found that the assemblies of myosin II molecular motors in…
Nanomechanical and other mesoscopic vibrational systems typically have several nonlinearly coupled modes with different frequencies and with long lifetime. We consider the power spectrum of one of these modes. Thermal fluctuations of the…
With reference to the experimental observations by T. Yanagida and his co-workers on actomyosin interaction, a Brownian motor of fluctuating ratchet kind is designed with the aim to describe the interaction between a Myosin II head and a…
We report the results of molecular dynamics simulations of the protein myosin carried out with an elastic network model. Quenching the system, we observe glassy behavior of a density correlation function and a density response function that…
We address the controversial hot question concerning the validity of the loose-coupling versus the lever-arm models in the actomyosin dynamics by re-interpreting and extending the washboard potential model proposed by some of us in a…
The intracellular environment is a dynamic space filled with various organelles moving in all directions. Included in this diverse group of organelles are vesicles, which are involved in transport of molecular cargo throughout the cell.…
Having established the fact that interacting classical kicked rotor systems exhibit long-lived prethermal phase with quasi-conserved average Hamiltonian before entering into chaotic heating regime, we use spatio-temporal fluctuation…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…