In the present work, we explored the diameter selectivity of dynamic self-assembly for the single-strand DNA (ssDNA) encapsulation in double-walled nanotubes (DWNTs) via molecular dynamics simulation method. Moreover, the pulling out process was carried out by steered molecular dynamics simulations. Considering p–p stacking and solvent accessibility together, base–CNT binding should be stronges...

Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin I27, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to stretch-induced unfolding of I27, the rupture of hydrogen bonds bridging beta-strands A and B, and those bridging beta-strands A' and G, the latter rupture occurring at an extension...

The estimation of ion channel permeability poses a considerable challenge for computer simulations because of the significant free energy barriers involved, but also offers valuable molecular information on the ion permeation process not directly available from experiments. In this article we determine the equilibrium free energy barrier for potassium ion permeability in Gramicidin A in an effi...

A theoretical analysis of the unfolding pathway of simple modular proteins in lengthcontrolled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the ranges of pulling speeds in which we expect our theory to hold. These theoretical predictions are checked by means of steered molecular dynamics of a simple c...

This review is focused on reactions that gate (control) the electron transfer between the primary quinone Q(A) and secondary quinone Q(B) in the photosynthetic reaction centre of Rhodobacter sphaeroides. The results on electron and proton transfer are discussed in relation to structural information and to the steered molecular dynamics simulations of the Q(B) ring flip in its binding pocket. De...

We have synthesized epitaxial Au, Pd, and AuPd nanowire arrays in vertical or horizontal alignment on a c-cut sapphire substrate. We show that the vertical and horizontal nanowire arrays grow from half-octahedral seeds by the correlations of the geometry and orientation of seed crystals with those of as-grown nanowires. The alignment of nanowires can be steered by changing the atom flux. At low...

the accurate mechanism of how EIIC transports a sugar has not been clearly demonstrated yet. To investigate more detailed and accurate transportation mechanisms, we performed collective variable-based steered molecular dynamics (CVSMD) simulations. Our simulation shows the spontaneous transportation of the sugar toward the opposite side of the membrane with the preserved H-bonding interactions,...