Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer

Important questions exist regarding the quality of force fields used in molecular dynamics (MD) simulations and their interoperable use with other available MD implementations. NAMD is one of the most efficient and scalable parallel molecular dynamics codes for large-scale biomolecular simulations in the open source domain. It is the aim of this article to analyze and compare the dynamics of a benchmark DNA dodecamer d(CTTTTGCAAAAG)2 system, including its binding to a specific drug molecule arising from the use of various simulation protocols in NAMD using Amber98, with the dynamics arising from simulations of the same dodecamer using Amber98 in the AMBER package, one of the most well-established simulation codes for nucleic acids. Based upon a set of validation benchmarks, the details of which are discussed, we find that nucleic acid simulations using NAMD give meaningful results and that the essential features of the resulting dynamics are similar to those arising from the AMBER package. This sets the stage for reliable large-scale simulations of nucleic acids using NAMD.     

Structure of the products of condensation of hydroxylamine with trifluoromethyl-beta-diketones: assignments of the diastereotopic protons of the 4-methylene group in 5-hydroxy-5-trifluoromethyl-delta2-isoxazolines

The combined use of 1H NMR spectroscopy with theoretical calculations of chemical shifts (GIAO) and coupling constants (B3LYP/6-311 ++G**) of a 5-hydroxy-5-trifluoromethyl-Delta2-isoxazoline has enabled solving the problem of the assignments of the diastereotopic protons in this compound. This result has been extended to 5-hydroxy-5-trifluoromethyl-Delta2-pyrazolines and the corresponding 5-trichloromethyl derivatives.     

Polarographic study of mixed ligand complex stability constants and kinetic parameters of reduction of zinc(II)-tartrate—Thiocyanate system

The Zn-tartrate-thiocyanate system has been investigated polarographically and the composition and stability constants of mixed complexes formed have been determined.     

Envelope-soliton propagation for three interacting coherent excitations in a dispersive medium

An initial value problem is set up to describe propagation of a low-frequency wave-field interacting with two almost transparent wave-fields in a dispersive medium. With no linear loss, perfect phase-matching, and equal group velocities for the two high-frequency wave-packets, it is shown how the solution of the above problem can evolve to well-known soliton solutions of the sine-Gordon equation. Other attempts for solving the more general problem in which all the group velocities are different are also discussed.     

Dusty effects on pulsating viscous flow of two immiscible fluids between two parallel plates

The flow of two immiscible incompressible dusty viscous fluids between two parallel plates generated by a pulsating pressure gradient is investigated. Velocity fields for the fluid-particle system along with the expressions for the skin friction drag at the plates are obtained and studied graphically. It is found that there is an immediate response to pressure fluctuations in the first stream at low frequency range 0<σ≤4 being maximum at σ=4. On the contrary, the second stream is more responsive to fluctuations at relatively higher frequencies. The maximum response in this case is shifted to σ=16.     

Enhancement of Cooling Rate for a Hot Steel Plate using Air-Atomized Spray with Surfactant-Added Water

The objective of the current research deals with the experimental study of an air-atomized spray with surfactant-added water, cooling a 12-mm-thick AISI-1020 stationary steel plate at three different initial surface temperatures (400°C, 600°C, and 900°C). Furthermore, the effects of surfactant concentration and airflow rate on the cooling rate have been investigated. The surface heat flux and surface temperature show a significant improvement in cooling for all three cases of initial surface temperatures when the air-atomized spray was used with surfactant-added water.     

Structural asymmetry in liquid Fe–Si alloys

The thermodynamic properties and microscopic structure of liquid Fe–Si alloys at 1873 K were studied by using the regular associated solution model. The model was utilized to determine the complex concentration in a regular associated solution of Fe, Si and Fe₂Si. The complex concentration was then used to calculate the integral excess free energy of mixing, activity, concentration fluctuations in the long-wavelength limit, S_CC (0), and the Warren–Cowley short-range parameter α ₁. The analysis suggests that heterocoordination leading to the formation of complex Fe₂Si is likely to exist in the liquid and is of a strongly interacting nature. The theoretical analysis reveals that the alloy is more ordered towards the Fe-rich region. The observed asymmetry in the properties of mixing of Fe–Si alloys in the molten state is successfully explained on the basis of the regular associated solution model.     

Pressure-induced structural phase transition and electronic properties of RESb (RE = Ho,Er and Tm) compounds: ab initio calculations

The structural phase transition and electronic properties at ambient (B ₁-phase) and high pressure (B ₂-phase) of heavy rare earth monoantimonides (RESb; RE?=?Ho, Er, and Tm) have been studied theoretically using the self-consistent tight binding linear muffin tin orbital method. These compounds show metallic behavior under ambient condition and undergo a structural phase transition to the B ₂ phase at high pressure. We predict a structural phase transition from the B ₁ to B ₂ phase in the pressure range 30.0–35.0?GPa. Apart from this, the ground state properties, such as lattice parameter and bulk modulus are calculated and compared with the available theoretical and experimental results.     

Unsteady MHD two-phase Couette flow of fluid–particle suspension

The problem of two-phase unsteady MHD Couette flow between two parallel infinite plates has been studied taking the viscosity effect of the two phases into consideration. Unified closed form expressions are obtained for the velocities and the skin frictions for both cases of the applied magnetic field being fixed to either the fluid or the moving plate. The novelty of this study is that we have obtained the solution of the unsteady flow using the Laplace transform technique, D’Alemberts method and the Riemann-sum approximation method. The solution obtained is validated by assenting comparisons with the closed form solutions obtained for the steady states which have been derived separately and also by the implicit finite difference method. Graphical result for the velocity of both phases based on the semi-analytical solutions are presented and discussed. A parametric study of some of the physical parameters involved in the problem is conducted. The skin friction for both the fluid and the particle phases decreases with time on both plates until a steady state is reached, it is also observed to decrease with increase in the particle viscosity on the moving plate while an opposite behaviour has been noticed on the stationary plate.