Characteristics investigation on heat transfer growth of sonochemically synthesized ZnO-DW based nanofluids inside square heat exchanger

Journal of Thermal Analysis and Calorimetry - In recent decades, the growth of heat transfer using nanomaterials in the conventional base fluid has caught the attention of researchers...     

The effect of rapid rotation on a vertical bridgman furnace at large Rayleigh number

In quasi-steady operation, convection currents in a Bridgmandevice, used for producing a semi-conductor crystal, createinhomogeneities that may make the crystal unusable. It has oftenbeen suggested that additional forces due to rotation or magnetismmight be efficacious in reducing the segregation of the elementsof the alloy. It has been found that, over a wide range of rotationrates, there is no improvement in performance due to rotationabout the vertical axis. However, numerical results that havebeen obtained previously (Lee & Pearlstein, J. Crys. Growth240, 2002) indicate that, when effects of centrifugal buoyancyare introduced, a substantial reduction in segregation is achieved.In the work reported here, by contrast, in which we extend previouslarge-Rayleigh-number asymptotic analysis to include centrifugalbuoyancy, we find no improvement in radial segregation, butrather increasing segregation with increasing rotation rate.     

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

We present a method to identify small molecule ligand binding sites and poses within a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand to an unphysical end state where the ligand does not interact with the protein. As replicas explore the space of Hamiltonians interpolating between these states, the ligand can rapidly escape local minima and explore potential binding sites. Geometric restraints keep the ligands from leaving the vicinity of the protein and an alchemical pathway designed to increase phase space overlap between intermediates ensures good mixing. Because of the rigorous statistical mechanical nature of the Hamiltonian exchange framework, we can also extract binding free energy estimates for all putative binding sites. We present results of this methodology applied to the T4 lysozyme L99A model system for three known ligands and one non-binder as a control, using an implicit solvent. We find that our methodology identifies known crystallographic binding sites consistently and accurately for the small number of ligands considered here and gives free energies consistent with experiment. We are also able to analyze the contribution of individual binding sites to the overall binding affinity. Our methodology points to near term potential applications in early-stage structure-guided drug discovery.     

Controlled hydrothermal growth of ZnO nanostructures by sequestering the Zn metal ions with the chelating agent EDTA

In the present work, a controlled growth of ZnO nanostructures by manipulating Zn metal ion concentration by the chelating action of ethylene diaminetetra acetic acid in hydrothermal method is studied. EDTA produces metal–chelate complex by the formation of bidentate ligand with Zn²⁺ in the solution and diminishes the reactivity of Zn metal cations. Concentration of EDTA in the mother solution was varied in different ranges like 3, 5 and 10 mM while retaining the zinc metal salt and the NaOH concentration the same. Three different morphologies of wurtzite structured ZnO nanostructures such as nanorods-bunch, separate/discrete uniformly sized hexagonal nanorods and tapered flower petals like shapes are achieved by 3, 5 and 10 mM strengths of EDTA, respectively. The medium concentration 5 mM of EDTA is found to have moderate control over producing ZnO nanostructures of uniform diameter and a high aspect (length to diameter) ratio. An array of vertically aligned free standing ZnO nanorods with uniform spacing is successfully achieved by the addition of 5 mM of EDTA in the mother solution and the same is studied for its fluorescence property at an excitation of 325 nm and it has exhibited a characteristic UV emission of ZnO around 383 nm.     

Guidelines for the analysis of free energy calculations

Journal of Computer-Aided Molecular Design - Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of...     

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods. The method does not require a priori knowledge of the binding pose as long as the docking technique used can generate reasonable binding modes. We demonstrate the method on the protein FKBP12 and eight of its inhibitors.     

Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase

We estimate the global minimum variance path for computing the free energy insertion into or deletion of small molecules from a dense fluid. We perform this optimization over all pair potentials, irrespective of functional form, using functional optimization with a two-body approximation for the radial distribution function. Surprisingly, the optimal pairwise path obtained via this method is almost identical to the path obtained using a optimized generalized "soft core" potential reported by Pham and Shirts [J. Chem. Phys. 135, 034114 (2011)]. We also derive the lowest variance non-pairwise potential path for molecular insertion or deletion and compare its efficiency to the pairwise path. Under certain conditions, non-pairwise pathways can reduce the total variance by up to 60% compared to optimal pairwise pathways. However, optimal non-pairwise pathways do not appear generally feasible for practical free energy calculations because an accurate estimate of the free energy, the parameter that is itself is desired, is required for constructing this non-pairwise path. Additionally, simulations at most intermediate states of these non-pairwise paths have significantly longer correlation times, often exceeding standard simulation lengths for solvation of bulky molecules. The findings suggest that the previously obtained soft core pathway is the lowest variance pathway for molecular insertion or deletion in practice. The findings also demonstrate the utility of functional optimization for determining the efficiency of thermodynamic processes performed with molecular simulation.