Related papers: Velocity and processivity of helicase unwinding of…
It is suggested that there is an interesting transition in double helices. The transition is between a helix, which has maximal torsion for the constituting helical strands, and a double helix which is nearly optimally packed illustrated by…
We numerically study the multi-scale properties of a 2d active gel to address the energy transfer mechanism. We find that activity is able to excite long-ranged distortions of the nematic pattern giving rise to spontaneous laminar flows and…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Point defects such as interstitial atoms are known to be attracted to screw dislocations. Understanding these interaction mechanisms is key to predicting the plasticity of real materials. Using a new machine learning interatomic potential…
We study helical structures in spin-spiral single crystals. In the continuum approach for the helicity potential energy the simple electronic band splits into two non-parabolic bands. For the Fermi energy greater than the splitting between…
Directional locking occurs when a particle moving over a periodic substrate becomes constrained to travel along certain substrate symmetry directions. Such locking effects arise for colloids and superconducting vortices moving over ordered…
We study the spontaneous ''sliding'' of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
We present a dynamical system that naturally exhibits two unstable attractors that are completely enclosed by each others basin volume. This counter-intuitive phenomenon occurs in networks of pulse-coupled oscillators with delayed…
Hagfish slime is a unique predator defense material containing a network of long fibrous threads each ~ 10 cm in length. Hagfish release the threads in a condensed coiled state known as thread cells, or skeins (~ 100 microns), which must…
Effective control and prediction of dynamical systems often require appropriate handling of continuous-time and discrete, event-triggered processes. Stochastic hybrid systems (SHSs), common across engineering domains, provide a formalism…
The paper presents a theoretical study of the dynamics of the H + HCl system on the potential energy surface (PES) of Bian and Werner (Bian, W.; Werner, H. -J., J. Chem. Phys. 2000, 112, 220). A time-dependent wave packet approach was…
Many elastic structures have two possible equilibrium states: from umbrellas that become inverted in a sudden gust of wind, to nano-electromechanical switches, origami patterns and the hopper popper, which jumps after being turned…
We study dynamical phase transitions in a model supercooled liquid. These transitions occur in ensembles of trajectories that are biased towards low (or high) dynamical activity. We compare two different measures of activity that were…
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…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
When investigating the mode of hydrogen activation by [Fe] hydrogenases, not only the chemical reactivity at the active site is of importance but also the large-scale conformational change between the so-called open and closed…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…