Related papers: Peeling and Sliding in Nucleosome Repositioning
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
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…
Large-scale atomistic calculations, using empirical potentials for modeling semiconductors, have been performed on a stressed system with linear surface defects like steps. Although the elastic limits of systems with surface defects remain…
In this work, we analyse the stick-slip motion of a soft elastomeric block on a smooth, hard surface under the application of shear, which is induced by a puller moving at a steady velocity. The frictional stress is generated by make-break…
The classical motion of gliding dislocation lines in slip planes of crystalline solid helium leads to plastic deformation even at temperatures far below the Debye temperature and can affect elastic properties. In this work we argue that the…
Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
Histone variants regulate replication, transcription, DNA damage repair, and chromosome segregation. Though widely accepted as a paradigm, it has not been rigorously demonstrated that histone variants encode unique mechanical properties.…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
The propulsion of mammalian spermatozoa relies on the spontaneous periodic oscillation of their flagella. These oscillations are driven internally by the coordinated action of ATP-powered dynein motors that exert sliding forces between…
We formulate and study a stochastic model for the thermally-driven motion of interacting straight screw dislocations in a cylindrical domain with a convex polygonal cross-section. Motion is modelled as a Markov jump process, where waiting…
Tribological loading of metals induces microstructural changes by dislocation-mediated plastic deformation. During continued sliding, combined shear and lattice rotation result in the formation of crystallographic textures which influence…
The wear-driven structural evolution of nanocrystalline Cu was simulated with molecular dynamics under constant normal loads, followed by a quantitative analysis. While the microstructure far away from the sliding contact remains unchanged,…
Cellular cargo can be bound to cytoskeletal filaments by one or multiple active or passive molecular motors. Recent experiments have shown that the presence of auxiliary, nondriving motors, results in an enhanced processivity of the cargo,…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…