Growth and consumption rates of the phase layers during interdiffusion in a diffusion couple with finite end member

The relations for the growth and consumption rates of a layer with finite thickness as an end member and the product phases in the interdiffusion zone are developed. We have used two different methodologies, the diffusion based and the physico-chemical approach to develop the same relations. We have shown that the diffusion based approach is rather straightforward; however, the physico-chemical approach is much more versatile than the other method. It was found that the position of the marker plane becomes vague in the second stage of the interdiffusion process in pure A thin layer/B couple, where two phases grow simultaneously.

Passive vibration isolation of reaction wheel disturbances using a low frequency flexible space platform

Reaction wheel assemblies (RWAs) are momentum exchange devices used in fine pointing control of spacecrafts. Even though the spinning rotor of the reaction wheel is precisely balanced to minimize emitted vibration due to static and dynamic imbalances, precision instrument payloads placed in the neighborhood can always be severely impacted by residual vibration forces emitted by reaction wheel assemblies. The reduction of the vibration level at sensitive payloads can be achieved by placing the RWA on appropriate mountings. A low frequency flexible space platform consisting of folded continuous beams has been designed to serve as a mount for isolating a disturbance source in precision payloads equipped spacecrafts. Analytical and experimental investigations have been carried out to test the usefulness of the low frequency flexible platform as a vibration isolator for RWAs. Measurements and tests have been conducted at varying wheel speeds, to quantify and characterize the amount of isolation obtained from the reaction wheel generated vibration. These tests are further extended to other variants of similar design in order to bring out the best isolation for given disturbance loads. Both time and frequency domain analysis of test data show that the flexible beam platform as a mount for reaction wheels is quite effective and can be used in spacecrafts for passive vibration control. (C) 2011 Elsevier Ltd. All rights reserved.

Validation of a Modified Eddy Dissipation Concept Model for Stationary and Nonstationary Turbulent Diffusion Flames

A transient flame simulation tool based on unsteady Reynolds average Navier Stokes (RANS) is characterized for stationary and nonstationary flame applications with a motivation of performing computationally affordable flame stability studies. Specifically, the KIVA-3V code is utilized with incorporation of a recently proposed modified eddy dissipation concept for simulating turbulence-chemistry interaction along with a model for radiation loss. Detailed comparison of velocities, turbulent kinetic energies, temperature, and species are made with the experimental data of the turbulent, non-premixed DLR_A CH4/H-2/N-2 jet flame. The comparison shows that the model is able to predict flame structure very well. The effect of some of the modeling assumptions is assessed, and strategies to model a stationary diffusion flame are recommended. Unsteady flame simulation capabilities of the numerical model are assessed by simulating an acoustically excited, experimental, oscillatory H-2-air diffusion flame. Comparisons are made with oscillatory velocity field and OH plots, and the numerical code is observed to predict transient flame structure well.

Growth mechanism of the Nb(X)Si-2 and [Nb(X)](5)Si-3 phases by reactive diffusion in Nb (X = Ti, Mo, or Zr)-Si systems

The effects of Mo, Ti, and Zr on the diffusion and growth of the Nb(X)Si-2 and Nb(X)(5)Si-3 phases in an Nb(X)-Si system are analyzed. The integrated diffusion coefficients are determined from diffusion couple experiments and compared with the data previously calculated in a binary Nb-Si system. The growth rates of both phases are affected by the addition of Mo and Zr, whereas the addition of Ti has no effect. The atomic mechanism of diffusion is also discussed based on the crystal structure and the possible changes in the defect concentrations due to alloying. Finally, the growth mechanism of the phases is discussed on the basis of a physico-chemical approach. (C) 2011 Elsevier Ltd. All rights reserved.

Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

Mechanistic insights into type III restriction enzymes

Type III restriction-modification (R-M) enzymes need to interact with two separate unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient cleavage to occur at a defined location next to only one of the two sites. However, cleavage of sites that are not in head-to-head orientation have been observed to occur under certain reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod that form a homodimeric Mod(2) and a heterotetrameric Res(2)Mod(2) complex. The Mod subunit in M-2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I and EcoP15I. Divergent opinions about how the long-distance interaction between the recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or 3D-DNA looping have been proposed.

Decoupling of diffusion from viscosity: Difference scenario for translational and rotational motions

Recent experiments have indicated a dramatically different viscosity dependence of the translational and the rotational diffusion coefficients in a supercooled liquid as the glass transition temperature is approached from above. While the translational motion seems to be decoupled from the rising viscosity (eta), the rotational motion seems to remain firmly coupled to eta. In order to understand the microscopic origin of this behavior, we have carried nut detailed theoretical calculations of both the quantities by using a self-consistent mode-coupling theory (MCT). it is found that when the size of the solute is same as that of the solvent molecules, the conventional MCT fails to predict the observed decoupling. The solvent inhomogeneity is found to play a decisive role in determining the decoupling. The difference in the viscosity dependence between rotation and translational diffusion coefficient is discussed.

Self-diffusion of colloids at freezing

This is an introduction to the theory of interacting Brownian particles, as applied to charge-stabilised colloidal suspensions near their equilibrium liquid-solid transition. The density functional approach to the statics of the transition is reviewed briefly, and the generalised Langevin equation method for the dynamics presented in detail. Work with A.V. Indrani [1] on a self-consistent approach for calculating the excess single-particle friction is presented, which explains the observed [2] ''universal'' suppression of self-diffusion at freezing as a consequence of the universal structure-factor height at this transition. Criticisms, open questions, and challenges to theory are discussed.

Shear-enhanced diffusion in charge-stabilised colloids

The generalised Langevin equation method for the dynamics of interacting colloids presented in my previous lecture is extended here to the case of a sheared suspension. A calculation of shear-dependent diffusivities using these methods is found to account for puzzling observations in experiments and simulations. The limitations of the method are discussed, and important unresolved questions presented. This lecture summarises work done in collaboration with A.V. Indrani [1].

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.