There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best ac...

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biologica...

Optoelectronic applications of colloidal quantum dots demand a high emission efficiency, stability in time, and narrow spectral bandwidth. Electronic trap states interfere with the above properties but understanding of their origin remains lacking, inhibiting the development of robust passivation techniques. Here we show that surface vacancies improve the fluorescence yield compared to vacancy-...

This paper investigates the conditions under which dominant airlines internalize self-imposed delays in a deterministic bottleneck model of airport pricing, complementing the similar analysis of Brueckner and Van Dender (BVD, 2008) for the standard congestion-pricing model. A unified model of bottleneck tolling includes untolled, uniform-, coarse-, multi-step-, and continuous-toll equilibria as...

One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quan...

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META ...

We present a general strategy for generating full atomistic models of nanopolycrystalline materials including bulk and thin film. In particular, models for oxide nanoparticles were constructed using simulated amorphisation and crystallisation and used to populate a library of oxide nanoparticles (amorphous and crystalline) with different radii. Nanoparticles were then taken from this library an...

Connexins are plasma membrane proteins that associate in hexameric complexes to form channels named connexons. Two connexons in neighboring cells may dock to form a "gap junction" channel, i.e. an intercellular conduit that permits the direct exchange of solutes between the cytoplasm of adjacent cells and thus mediate cell-cell ion and metabolic signaling. The lack of high resolution data for c...

We develop an empirical interatomic potential model for the gold-silicon binary system that is fitted to the experimental phase diagram. The model is constructed on the basis of the modified embedded-atom-method formalism and its binary phase diagram is computed by efficient free energy methods. The eutectic temperature and eutectic composition of the model match well with the experimental valu...

A 3D statistical ‘atomistic’ simulation technique has been developed to study the effect of the random dopant induced parameter fluctuations in aggressively scaled MOSFETs. Efficient implementation of the ‘atomistic’ simulation approach has been used to investigate the threshold voltage standard deviation and lowering in the case of uniformly doped MOSFETs, and in fluctuation-resistant architec...