Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulatio...

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive...

We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four c...

MOTIVATION One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activi...

has been studied extensively by many researchers, where 2 < p < 6. This system has been first introduced in [5] as a physical model describing a charged wave interacting with its own electrostatic field in quantum mechanic. The unknowns u and Φ represent the wave functions associated to the particle and electric potential, and functions V and K are respectively an external potential and nonnega...

In this paper, by using a quantum hydrodynamic plasma model which incorporates the important quantum statistical pressure and electron diffraction force, we present the corrected plasmon dispersion relation for graphene which includes a k quantum term arising from the collective electron density wave interference effects (which  is integer and constant and k is wave vector). The longitudinal ...

The human–computer interaction (HCI) design of educational technologies influences cognitive behaviour, so it is imperative to assess how different HCI strategies support intended behaviour. We developed a neuroscience-inspired game that trains children's use “stopping-and-thinking” (S&amp;T)—an inhibitory control-related behaviour—in the context counterintuitive science problems. tested effica...

the effect of geometry and material of the micro/nano particle on contact mechanic for manipulation was studied in this work based on atomic force microscopy. hertz contact model simulation for eph biological micro particle with spherical, cylindrical, and circular crowned roller shape was used to investigate the effect of geometry on contact simulation process in manipulation. then, to validat...

In this paper, we investigate variation of the wavelength, intensity and polarization of the self-assembled InAs/GaAs quantum dots emission by microphotoluminescence spectroscopy at the liquid helium temperature. The microcavity wafer sample is grown by molecular beam epitaxy (MBE) and chemically etched into the micropillar structure (with elliptical cross section - long and short axis 2µm×1.5µ...

In this paper, we investigate variation of the wavelength, intensity and polarization of the self-assembled InAs/GaAs quantum dots emission by microphotoluminescence spectroscopy at the liquid helium temperature. The microcavity wafer sample is grown by molecular beam epitaxy (MBE) and chemically etched into the micropillar structure (with elliptical cross section - long and short axis 2µm×1.5µ...