Path Of Molecules Research Articles

Simulating fullerene polyhedral formation from planar precursors.

The synthesis path of the C60-Buckyball fullerene from a planar precursor developed by Scott et al. [Science, 2002, 295, 5559] is investigated with density functional theory (DFT) methods. Various theoretically possible closing paths are analysed with respect to structural and energetic properties. The initial geometries were obtained by geometric interpolation of a cardboard-like model comprising rigid rings connected by hinges, which were then fully optimized with a selection of DFT-functionals. Analysis of the fully optimised geometries shows remarkable stability of face planarity, bond lengths and bond angles for all studied geometries, indicating soundness of the "cardboard with hinges"-model for approximating reaction paths for molecules of this type. This raises hope for development of a force field description of fullerene precursor molecules that can aid in discovery and analysis of good precursor candidates for rational synthesis of new fullerenes.

Structure‐Independent Conductance of Thiophene‐Based Single‐Stacking Junctions

AbstractThe experimental investigation of intermolecular charge transport in π‐conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single‐molecule and single‐stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single‐stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single‐molecule junctions with the same building blocks, and the dominant charge‐transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.

Simulation of the generation of turbulence motion in edge wakes

The process of generating turbulence in edge wakes has been simulated and the results of the simulation are presented. The proposed mathematical model follows from a special procedure, which aims to average the flow parameters on scales comparable with the free path of molecules. The examined mechanism of generating turbulence is described by an expended set of Euler and Navier-Stokes nonstationary equations, with additional dispersive summands of the third order, which are obtained, if one uses the averaging procedure. The basic hydrodynamic equations are integrated by means of the well-known Godunov procedure of the second order. The calculated averaged performances of the turbulent flows agree with the experimental data.

Electric field mediated DNA motion model

Understanding the motion and the governing equations of a molecule's path in tissue is an ultimate requirement for the repeatable, site specific delivery of molecules [Joseph D. Hickey. Modelling the Motion of Ions and Molecules in Electroporation and Electrophoresis Field Conditions. University of South Florida, College of Arts and Sciences, Department of Physics, Tampa, Florida, 2003., Joseph D. Hickey and Richard Gilbert. Modeling the electromobility of ions in a target tissue. DNA and Cell Biology, 22 (12) (2003) 823–828.]. This paper describes a computationally efficient mathematical model and simulation technique for the examination of DNA fragments in a 1% agarose gel. The speed of the individual DNA fragments through the agarose gel was described through two parts. The maximum velocity was calculated using the Coulombic force divided by Stoke's law and that value was retarded by an exponential rate equation. The simulation utilizes previously published techniques modified for this specific application [Joseph D. Hickey and Richard Gilbert. Fluid flow electrophoresis model. Bioelectrochemistry, 63 (2) (2004) 365–367., Joseph D. Hickey and Richard Gilbert. Modeling the electromobility of ions in a target tissue. DNA and Cell Biology, 22 (12) (2003) 823–828.]. Five representative DNA fragment sizes that span the resolution of a 1% agarose gel were chosen for this analysis. The speeds corresponding to these five DNA fragment sizes were converted into discrete values and used in a 50 step simulation. The resultant error comparing the simulation with experimental distance was 7.76%. Through a 1-D optimization procedure, this error was reduced to 3.02% for a 52 step simulation.

Molecular reorientation in assembled CO structures and contrast inversion in STM

Recent scanning tunneling microscopy experiments [S. Zöphel, J. Repp, G. Meyer, K.-H. Rieder, Chem. Phys. Lett. 310 (1999) 145; A.J. Heinrich, C.P. Lutz, J.A. Gupta, D.M. Eigler, Science 298 (2002) 1381] for CO on Cu(1 1 1) and Cu(2 1 1) surfaces show CO monomers as dark depressions, whereas dimers and trimers appear as bright patterns. The dark image of a monomer has been shown to result from a destructive interference between two tunneling paths [J. Nieminen, E. Niemi, K.-H. Rieder, Surf. Sci. 552 (2004) L47]. In this Letter, we show how switching between tunneling channels within the through molecule path can be induced by reorientation of a molecule. Hence, a destructive interference between through vacuum and through molecule paths can be reversed into constructive interference by manipulating the adsorbate geometry.

Vaporization of Small Spherical Drops in a Gas

The process of vaporization of a small (compared to the free path of molecules in the medium) spherical liquid drop in an infinite nonabsorbing gaseous medium is considered. Analytical expressions for the time dependence of the drop radius are derived under assumption that vaporized molecules escape from the drop in the asymptotic diffusion regime, and the thermal energy flux toward the vaporizing drop is formed as a result of collisions of vaporized and gas molecules. It is demonstrated that consideration of unsaturated vapor at the surface of the evaporating drop increases the estimated vaporization time of submicron drops by several orders of magnitude compared to the Maxwell classical model.

Intense evaporation of molecular gas from a spherical particle into vacuum

In this paper, we solve the kinetic problem of intense evaporation of molecular gas from a spherical particle into vacuum. We explicitly find the hydrodynamic boundary conditions for intense evaporation of diatomic and triatomic gases and demonstrate their strong dependence on the Knudsen number in the range 0 < Kn ≤ 0.1 (Kn = λ/r0, λ is the mean free path of molecules near the evaporating surface and r0 is the particle radius). This problem was not discussed in earlier papers [1–3]. We show that internal degrees of freedom lead to an appreciable decrease in the temperature jump and only slightly affect the gas concentration at the boundary of the Knudsen layer.

Study on the Deposition Profile Characteristics in the Micron-Scale Trench Using Direct Simulation Monte Carlo Method

As integrated circuits are advancing toward smaller device features, step-coverage in submicron trenches and holes in thin film deposition are becoming of concern. Deposition consists of gas flow in the vapor phase and film growth in the solid phase. A deposition profile simulator using the direct simulation Monte Carlo method has been developed to investigate deposition profile characteristics on small trenches which have nearly the same dimension as the mean free path of molecules. This simulator can be applied to several deposition processes such as sputter deposition, and atmospheric- or low-pressure chemical vapor deposition. In the case of low-pressure processes such as sputter deposition, upstream boundary conditions of the trenches can be calculated by means of rarefied gas flow analysis in the reactor. The effects of upstream boundary conditions, molecular collisions, sticking coefficients, and surface migration on deposition profiles in the trenches were clarified.

Ultrathin N 2 O ‐Oxide with Atomically Flat Interfaces

Silicon oxide has been grown in a low pressure furnace using . An atomically flat interface, as determined by high resolution transmission electron microscopy, has been achieved by desorbing the native oxide in situ tor oxide thicknesses 11 to 38 Å. The thickness variation of a 20 Å ‐oxide, grown on a 4 in. substrate <1 Å. The excellent uniformity is attributed to the increased mean‐free path of molecules in the low pressure environment. Since only one Si plane was distorted beneath the ‐oxide/Si interface, this suggests that thermal stress is not the limiting factor for obtaining an atomically smooth interface.

1H magnetic cross-relaxation between multiple solvent components and rotationally immobilized protein.

Magnetic cross-relaxation spectra or Z-spectra are presented for water, acetone, methanol, dimethylsulfoxide, and acetonitrile in cross-linked bovine serum albumin gels. Each solvent studied, reports the same Z-spectrum linewidth and shape for the solid component that follows from solutions of the coupled relaxation equations. The Z-spectra demonstrate competition among solvents for specific protein binding sites. The rate of magnetization transfer in the rotationally immobilized protein environment is approximated by 1/T2 for the solid component, which is shown to account for the observed magnetization transfer rates in the systems studied. The temperature dependence of the Z-spectra are different for water compared with the organic solvents. The cross-relaxation efficiency in the organic solvents decreases with increasing temperature because molecules bind less well at high temperature. For water, the hydrogen exchange path becomes increasingly important relative to the whole molecule path with increasing temperature, which improves the net cross-relaxation efficiency.

Decoration technique and surface physics

Besides the atomic surface structure, diverging in special cases with respect to the bulk structure, the real structure of a surface Is determined by the step structure. Using the decoration technique /1/ it is possible to image step structures having step heights down to a single lattice plane distance electron-microscopically. For a number of problems the knowledge of the monatomic step structures is important, because numerous problems of surface physics are directly connected with processes taking place at these steps, e.g. crystal growth or evaporation, sorption and nucleatlon as initial stage of overgrowth of thin films.To demonstrate the decoration technique by means of evaporation of heavy metals Fig. 1 from our former investigations shows the monatomic step structure of an evaporated NaCI crystal. of special Importance Is the detection of the movement of steps during the growth or evaporation of a crystal. From the velocity of a step fundamental quantities for the molecular processes can be determined, e.g. the mean free diffusion path of molecules.

Motion equations for a discrete structure fluid

The Maxwell method allows us to carry out a transition to the equations of hydrodynamics at any function of a molecule distribution with respect to velocities. This is the advantage of the above method. However, that the Navier-Stokes equations be obtained, Maxwell had to assume that in a physically small volume, over which the averaging is made, the transport velocities of two impinging molecules are equal. So Maxwell identified a hydrodynamic velocity with a mean velocity of atoms or molecules. — This Maxwell hypothesis may appear to be doubtful in a rarefied gas where the mean free path of molecules is commensurable with the dimensions of a physically small volume and a body in a flow and in eddy flows.

Thermal and diffusive relaxation of an evaporating drop with internal heat liberation

The problem of nonsteady-state evaporation or growth of a radiating drop with uniformly distributed internal heat sources is considered. The Reynolds R=ua/v ≪1 and Peclet PD= ua/D ≪1 numbers are assumed to be small (a is the radius of the drop, u the velocity of its relative motion, andv, D, χ the coefficients of viscosity, diffusion and thermal diffusivity of the vapor-gas medium). This enables the convective transfer of vapor and heat to be neglected, and the concentration and temperature fields to be regarded as spherically symmetric [1]. In view of the fact that the density of saturated vapor is less than the density of liquid the convective flow caused by the change in radius of the drop is not taken into account [2]. It has already been shown [3,4], that for χ≪χr (χ, χr are the coefficients of molecular and radiative thermal conductivity) there exists a bounded region ryo (1/α) √χ/χr (α is the absorption coefficient for radiation in the gas), in which the effect of radiation on the temperature relaxation of the vapor-gas medium is negligible. If the conditiona ≪ (1/α) √χ/χr is satisfied, then the temperature at the outer boundary of this region will be practically the same as the temperature at infinity T=T∞. This means that terms in the energy equation connected with energy transferred by radiation can be neglected. It is assumed that the free path of molecules in the gas is less than the radius of the drop, and so concentration and temperature discontinuities close to the surface of the drop can be neglected [2].