相关论文: Velocity and processivity of helicase unwinding of…

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…

Dynamic resistance occurs in a superconducting tape carrying a dc transport current while being exposed to an alternating magnetic field. This effect is caused by flux movements interacting with the transport current. The dynamic resistance…

We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…

The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…

Active motion of molecules along filamentous structures is a crucial feature of cell biology and is often modeled with the paradigmatic asymmetric simple exclusion process. Motivated by recent experimental studies that have addressed the…

Combining simulations and theory I study the interplay between bundle elastic degrees of freedom and crosslink binding propensity. By slowly driving bundles into a deformed configuration, and depending on the mechanical stiffness of the…

This Chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full…

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,…

A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…

The motion of metastable helium atoms travelling through a standing light wave is investigated with a semi-classical numerical model. The results of a calculation including the velocity dependence of the dipole force are compared with those…

Plasticity in body-centered cubic (BCC) nanocrystals is often associated with twin nucleation phenomena under extreme loading conditions. Here, we reveal unconventional twinning pathways that operate at the intersection of crystal…

Using numerical simulations, we examine a simple model of two or more coupled one-dimensional channels of driven particles with repulsive interactions in the presence of quenched disorder. We find that this model exhibits a remarkably rich…

We examine the influence of bidirectional anchoring on the unwinding of a planar cholesteric liquid crystal induced by the application of a magnetic field. We consider a liquid crystal layer confined between two plates with the helical axis…

Hierarchical dynamics in glass-forming systems span multiple timescales, from fast vibrations to slow structural rearrangements, appearing in both supercooled fluids and glassy states. Understanding how these diverse processes interact…

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand…

Helical molecules have been identified as potential candidates for investigating electronic transport, spin filtering, or even piezoelectricity. However, the description of the transport mechanism is not straightforward in single molecular…

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…

Using molecular dynamics simulations we study the static and dynamic properties of spherical nanoparticles (NPs) embedded in a disordered and polydisperse polymer network. Purely repulsive (RNP) as well as weakly attractive (ANP) polymer-NP…

Gravitational falling in AdS has two characteristic properties \cite{ohsin}: i) A thick shell becomes a thin shell. ii) Any shape become spherical. Such focusing character of AdS, for the collapse of dusts, leads to the rapid thermalization…

DDX3X is a human DEAD-box RNA helicase implicated in many cancers and in viral progression. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. Here, we investigate the substrate and protein requirements…