Related papers: Coherent X-rays reveal anomalous molecular diffusi…
A topic of intense current investigation pursues the question how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of…
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
Intracellular transport of vesicular cargos, organelles, and other macromolecules is an essential process to move large items through a crowded, and inhomogeneous cellular environment. In an effort to dissect the fundamental effects of…
Normal diffusion in corrugated potentials with spatially uncorrelated Gaussian energy disorder famously explains the origin of non-Arrhenius $\exp[-\sigma^2/(k_BT^2)]$ temperature-dependence in disordered systems. Here we show that unbiased…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Cell membranes phase separate into ordered ${\rm L_o}$ and disordered ${\rm L_d}$ domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to…
The advent of ultrafast pulsed X-ray free-electron lasers with very high brightness has enabled the determination of transient molecular structures of small and medium-sized organic molecules in excited states and undergoing chemical…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
Sub-angstrom spatial resolution of electron density coupled with sub-femtosecond temporal resolution is required to directly observe the dynamics of the electronic structure of a molecule after photoinitiation or some other ultrafast…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
Advances in our ability to understand and utilize the world around us have always relied on the development of advanced tools for probing and manipulating materials properties. X-ray matter interactions played a critical role in the…
The transport equation of active motion is generalised to consider time-fractional dynamics for describing the anomalous diffusion of self-propelled particles observed in many different systems. In the present study, we consider an…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
A vertically shaken granular medium hosts a blade rotating around a fixed vertical axis, which acts as a mesorheological probe. At high densities, independently from the shaking intensity, the blade's dynamics show strong caging effects,…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…