Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Experimental Studies on Drop Formation at the Tip of Melting Rods

Drop formation at the conical tips of melting rods has been experimentally studied using the transparent wax-alcohol/acetonitrile system. The effects of cone angle, rod diameter, immersion depth, and bath temperature on the detached drop mass have been studied over a wide range, besides recording useful qualitative information based on visual observation. The experimental results suggest that the phenomenon of drop formation at the tip of melting rods has a close parallel with the drop formation at conical tips, at least on a qualitative basis. However, the results could not be quantified owing to difficulties in characterizing the physical properties of the system, despite efforts to minimize them.

Experimental studies on a two stage pulse tube cryocooler reaching 2.5K

A two stage Pulse Tube Cryocooler (PTC) is designed and fabricated which reaches a no-load temperature of 2.5K in the second stage and similar to 60 K in the first stage respectively. The system provides a cooling power of similar to 250 mW at 5K in the second stage. Stainless steel meshes (size 200) and lead (Pb) granules are used as the first stage regenerator materials and combination of Pb with Er3Ni / HoCu2 are used as the second stage regenerator materials. The system operates at 1.6 Hz using a 6 kW water cooled helium compressor. Studies conducted by varying the dimensions of Pulse Tubes and regenerators show that the dimensions of the Pulse Tubes are more critical to the performance of the Cryocooler than those of the regenerators. Experimental studies show that the optimum volume ratios of Er3Ni to Pb and HoCu2 to Pb in the second stage regenerator should be 3:2 and 2:3 respectively for the best performance. Further, systems with HoCu2 performed better than those with Er3Ni. The theoretical analysis of the system has been carried out using a simple isothermal model. The experimentally measured cooling powers are in good agreement with the theoretical predictions.

Experimental studies on the wear of engine components

Wear studies of engine components of high-speed diesel engines running under various operating conditions are presented. Tests were conducted under controlled conditions over long periods. The results of the various tests are discussed and attempts have been made to examine the effects of engine operating variables and the quality of the lubricating oil on the wear of engine components.

Theoretical and Experimental Studies on an Ammonia-Based Loop Heat Pipe With a Flat Evaporator

An ammonia loop heat pipe (LHP) with a flat plate evaporator is developed and tested. The device uses a nickel wick encased in an aluminum-stainless steel casing. The loop is tested for various heat loads and different sink temperatures, and it demonstrated reliable startup characteristics. Results with the analysis of the experimental observation indicate that the conductance between the compensation chamber and the heater plate can significantly influence the operating temperatures of the LHP. A mathematical model is also presented which is validated against the experimental observations.

Experimental studies and phase field modeling of microstructure evolution during solidification with electromagnetic stirring

Thixocasting requires manufacturing of billets with non-dendritic microstructure. Aluminum alloy A356 billets were produced by rheocasting in a mould placed inside a linear electromagnetic stirrer. Subsequent heat treatment was used to produce a transition from rosette to globular microstructure. The current and the duration of stirring were explored as control parameters. Simultaneous induction heating of the billet during stirring was quantified using experimentally determined thermal profiles. The effect of processing parameters on the dendrite fragmentation was discussed. Corresponding computational modeling of the process was performed using phase-field modeling of alloy solidification in order to gain insight into the process of morphological changes of a solid during this process. A non-isothermal alloy solidification model was used for simulations. The morphological evolution under such imposed thermal cycles was simulated and compared with experimentally determined one. Suitable scaling using the thermosolutal diffusion distances was used to overcome computational difficulties in quantitative comparison at system scale. The results were interpreted in the light of existing theories of microstructure refinement and globularisation.

Stereochemically constrained peptides. Theoretical and experimental studies on the conformations of peptides containing 1-aminocyclohexane carboxylic acid

Conformational energy calculations on the model system N-acetyl- 1 -aminocyclohexanecarboxylic acid N'methylamide (Ac-Acc6-NHMe), using an average geometry derived from 13 crystallographic observations, establish that the Acc6 residue is constrained to adopt conformations in the helical regions of In contrast, the a,a-dialkylated residue with linear hydrocarbon side chains, a,a-di-n-propylglycine favors fully extended backbone structures (6 1= $ = 180'). The crystal structures of two model peptides, Boc-(Acc6),-OMe (type 111 @-turn at -Acc6(1)-Acc6(2)-) and Boc-Pro-Acc6-Ala-OMe (type I1 P-turn at -Pro-Acc6-), establish that Acc6 residues can occupy either position of type 111 P-turns and the i + 2 position of type I1 @-turns. The stereochemical rigidity of these peptides is demonstrated in solution by NMR studies, which establish the presence of one intramolecular hydrogen bond in each peptide in CDCI, and (CDJ2S0. Nuclear Overhauser effects permit characterization of the @-turn conformations in solution and establish their similarity to the solid-state structures. The implications for the use of Acc6 residues in conformational design are considered.

Experimental studies of a distorted turbulent spot in a three-dimensional flow

We report here on the results of a series of experiments carried out on a turbulent spot in a distorted duct to study the effects of a divergence with straight streamlines preceded by a short stretch of transverse streamline curvature, both in the absence of any pressure gradient. It is found that the distortion produces substantial asymmetry in the spot: the angles at which the spot cuts across the local streamlines are altered dramatically (in contradiction of a hypothesis commonly made in transition zone modelling), and the Tollmien-Schlichting waves that accompany the wing tips of the spot are much stronger on the outside of the bend than on the inside. However there is no strong effect on the internal structure of the spot and the eddies therein, or on such propagation characteristics as overall spread rate and the celerities of the leading and trailing edges. Both lateral streamline curvature and non-homogeneity of the laminar boundary layer into which the spot propagates are shown to be strong factors responsible for the observed asymmetry. It is concluded that these factors produce chiefly a geometric distortion of the coherent structure in the spot, but do not otherwise affect its dynamics in any significant way.

Grain Floatation During Equiaxed Solidification of an Al-Cu Alloy in a Side-Cooled Cavity: Part I-Experimental Studies

Experimental studies were performed to investigate the role and influence of grain movement on macrosegregation and microstructure evolution during equiaxed solidification. Casting experiments were performed with a grain-refined Al-Cu alloy in a rectangular sand mold. For the aluminum alloy studied, the equiaxed grains are lighter than the bulk melt and thus float up. Experiments were designed to investigate floatation phenomena of equiaxed grains in the presence of thermosolutal convection. Cooling curves were recorded at key locations in both the casting and the chill. Quantitative image analysis and spatial chemical analysis were performed on the solidified casting to observe the chemical and microstructural inhomogeneity created by the melt convection and solid floatation. Several notable features that can be attributed to grain movement were observed in temperature histories, macrosegregation patterns, and microstructures. In our experiments, the floatation of grains influences the thermal conditions and the overall flow direction in the casting cavity. In some cases, the induced flow resulting from the grain movement caused a flow reversal. This in turn influences the solidification direction, microstructure evolution, and the overall macrosegregation behavior.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

Computational and experimental studies of fluid flow and heat transfer in a Calandria based reactor

CFD investigations are carried out to study the heat flux and temperature distribution in the calandria using a 3–Dimensional RANS code. Internal flow computations and experimental studies are carried out for a calandria embedded with a matrix of tubes working together as a reactor. Numerical investigations are carried on the Calandria reactor vessel with horizontal inlets and outlets located on top and the bottom to study the flow pattern and the associated temperature distribution. The computations have been carried out to simulate fluid flow and convective heat transfer for assigned near–to working conditions with different moderator injection rates and reacting heat fluxes. The results of computations provide an estimate of the tolerance bands for safe working limits for the heat dissipation at different working conditions by virtue of prediction of the hot spots in the calandria. The isothermal CFD results are validated by a set of experiments on a specially designed scaled model conducted over a range of flows and simulation parameters. The comparison of CFD results with experiments show good agreement.