Classical MD Simulation and Ab-initio Mixed-basis Band Calculation of C_<60> Adsorbed on Si(100) Surface

Constant temperature classical molecular dynamics(MD) simulation and ab-initio mixed-basis band calculation are carried out to provide a theoretical understanding of for the results of the recent STM experiment concerning the epitaxial growth of C_ monolayer film deposited on the Si(100) surface. While performing the classical MD simulation, we often observe c(4×3) and c(4×4) structures of C_ molecules on the Si(100) substrate, and their rotational motions are suppressed by the strong interaction between carbon and silicon atoms. The present theoretical results closely agree with the experimental results of the STM observations of this system. An ab-initio band structure calculation using mixed-basis is also performed for the same system. According to this band structure calculation, Fermi surface is concluded to be relatively small around Γ point suggesting electron conduction. The spacial distribution of the partial charge densities calculated for HOMO and LUMO band agrees with the "stripes" observed by STM experiment with negative bias condition

Visualisation Reveals Model Defect

Abstract not availabl

Different Aspects of Ultra-weak Photon Emissions: A Review Article

All biological samples emit ultra-low intensity light without any external stimulation. Recently, scientific communities have paid particular attention to this phenomenon, known as ultra-weak photon emission (UPE). UPE has been introduced in the literature as an alternative for biophoton, low-level chemiluminescence and ultra-weak bioluminescence, while it differs from ordinary bioluminescence, fluorescence and phosphorescence. Some UPE parameters including spectrum and intensity have been already recognized, while other features such as the main origin(s), statistical distribution and fractality of UPE are partially understood. Ultra-weak photon detection has a broad range of potential applications in different industries such as agriculture and medicine. The correlation between UPE and physiological state of a system facilitates the use of UPE as a completely non-invasive diagnostic method in cases such as cancer detection. In this review article, we aimed to provide useful information on specific characteristics, possible origin(s) and potential applications of UPE. Moreover, we introduced some physical models for UPE and presented several controversial hypotheses in this context

A multi-scale atomistic-continuum modelling of crack propagation in a two-dimensional macroscopic plate

A novel multi-scale seamless model of brittle-crack propagation is proposed and applied to the simulation of fracture growth in a two-dimensional Ag plate with macroscopic dimensions. The model represents the crack propagation at the macroscopic scale as the drift-diffusion motion of the crack tip alone. The diffusive motion is associated with the crack-tip coordinates in the position space, and reflects the oscillations observed in the crack velocity following its critical value. The model couples the crack dynamics at the macroscales and nanoscales via an intermediate mesoscale continuum. The finite-element method is employed to make the transition from the macroscale to the nanoscale by computing the continuum-based displacements of the atoms at the boundary of an atomic lattice embedded within the plate and surrounding the tip. Molecular dynamics (MD) simulation then drives the crack tip forward, producing the tip critical velocity and its diffusion constant. These are then used in the Ito stochastic calculus to make the reverse transition from the nanoscale back to the macroscale. The MD-level modelling is based on the use of a many-body potential. The model successfully reproduces the crack-velocity oscillations, roughening transitions of the crack surfaces, as well as the macroscopic crack trajectory. The implications for a 3-D modelling are discussed

Interaction of low frequency external electric fields and pancreatic β-cell: a mathematical modeling approach to identify the influence of excitation parameters

<p><b>Purpose:</b> Although the effect of electromagnetic fields on biological systems has attracted attraction in recent years, there has not been any conclusive result concerning the effects of interaction and the underlying mechanisms involved. Besides the complexity of biological systems, the parameters of the applied electromagnetic field have not been estimated in most of the experiments.</p> <p><b>Materials and Methods:</b> In this study, we have used computational approach in order to find the excitation parameters of an external electric field which produces sensible effects in the function of insulin secretory machinery, whose failure triggers the diabetes disease. A mathematical model of the human β-cell has been used and the effects of external electric fields with different amplitudes, frequencies and wave shapes have been studied.</p> <p><b>Results:</b> The results from our simulations show that the external electric field can influence the membrane electrical activity and perhaps the insulin secretion when its amplitude exceeds a threshold value. Furthermore, our simulations reveal that different waveforms have distinct effects on the β-cell membrane electrical activity and the characteristic features of the excitation like frequency would change the interaction mechanism.</p> <p><b>Conclusion:</b> The results could help the researchers to investigate the possible role of the environmental electromagnetic fields on the promotion of diabetes disease.</p

Structural and functional effect of an oscillating electric field on the dopamine-D3 receptor: A molecular dynamics simulation study

Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along the z-direction, on the dopamine-D3R complex. The simulations showed that at some frequencies, the application of an external oscillating electric field along the z-direction has a considerable effect on the dopamine-D3R. However, there is no enough evidence for prediction of changes in specific frequency, implying that there is no order in changes. Computing the correlation coefficient parameter showed that increasing the field frequency can weaken the interaction between dopamine and D3R and may decrease the Arg128{3.50}-Glu324{6.30} distance. Because of high stability of α helices along the z-direction, applying an oscillating electric field in this direction with an amplitude 10-time higher did not have a considerable effect. However, applying the oscillating field at the frequency of 0.6 GHz along other directions, such as X-Y and Y-Z planes, could change the energy between the dopamine and the D3R, and the number of internal hydrogen bonds of the protein. This can be due to the effect of the direction of the electric field vis-à-vis the ligands orientation and the interaction of the oscillating electric field with the dipole moment of the protein

Structural and Functional Effect of an Oscillating Electric Field on the Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study

<div><p>Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along the z-direction, on the dopamine-D3R complex. The simulations showed that at some frequencies, the application of an external oscillating electric field along the z-direction has a considerable effect on the dopamine-D3R. However, there is no enough evidence for prediction of changes in specific frequency, implying that there is no order in changes. Computing the correlation coefficient parameter showed that increasing the field frequency can weaken the interaction between dopamine and D3R and may decrease the Arg128{3.50}-Glu324{6.30} distance. Because of high stability of α helices along the z-direction, applying an oscillating electric field in this direction with an amplitude 10-time higher did not have a considerable effect. However, applying the oscillating field at the frequency of 0.6 GHz along other directions, such as X-Y and Y-Z planes, could change the energy between the dopamine and the D3R, and the number of internal hydrogen bonds of the protein. This can be due to the effect of the direction of the electric field vis-à-vis the ligands orientation and the interaction of the oscillating electric field with the dipole moment of the protein.</p></div

A cross-sectional view of the D3R in membrane.

<p>A cross-sectional view of the D3R in membrane.</p