Related papers: Peeling and Sliding in Nucleosome Repositioning
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Sliding is one of the fundamental mechanical movements in machinery. In macroscopic systems, double-rack pinion machines employ gears to slide two linear tracks along opposite directions. In microscopic systems, kinesin-5 proteins crosslink…
Dislocation climb mobilities, assuming vacancy bulk diffusion, are derived and implemented in dislocation dynamics simulations to study the coarsening of vacancy prismatic loops in fcc metals. When loops cannot glide, the comparison of the…
We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We present our recent study on rough adhesive contacts of viscoelastic materials in steady-state sliding, focusing on the interplay between adhesion and viscoelasticity by means of a novel energy approach. We investigate tribological…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
We discuss the stick-slip motion of an elastic block sliding along a rigid substrate. We argue that for a given external shear stress this system shows a discontinuous nonequilibrium transition from a uniform stick state to uniform sliding…
Peeling is one of the most common detachment mechanisms adopted in industrial applications. However, although several experimental investigations have proven the possible occurrence of relative sliding at the interface close to the peeling…
Active adaptive matter has attracted considerable interest due to its rich, largely unexplained dynamics and its relevance to a wide range of synthetic and biological materials. An important subclass of such systems consists of active…
The transport by molecular motors along cytoskeletal filaments is studied theoretically in the presence of static defects. The movements of single motors are described as biased random walks along the filament as well as binding to and…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
Hypersonic leading-edge separation is studied towards understanding the varying shock-related unsteadiness with freestream Reynolds number ($1.66 \times 10^5 \leq Re_D \leq 5.85 \times 10^5$) in the newly constructed hypersonic Ludwieg…
We report a surprising hysteretic behavior in the dynamics of a simple one-dimensional nonlinear model inspired by the tribological problem of two sliding surfaces with a thin solid lubricant layer in between. In particular, we consider the…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale…