Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub) is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained Self-Organized-Polymer model with side chains. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At $T_m$ Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at $T_m$, with multiple transitions between the folded and unfolded states, show a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of $\mu sec$ then Ub folding follows the diffusion-collision mechanism with intermediates many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a $P_{fold}$ analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings are not only in agreement with experiments but also provide missing details not resolvable in standard experiments

The 3-D Navier-Stokes analysis of crossing, glancing shocks/turbulent boundary layer interactions

Three dimensional viscous flow analysis is performed for a configuration where two crossing and glancing shocks interact with a turbulent boundary layer. A time marching 3-D full Navier-Stokes code, called PARC3D, is used to compute the flow field, and the solution is compared to the experimental data obtained at the NASA Lewis Research Center's 1 x 1 ft supersonic wind tunnel facility. The study is carried out as part of the continuing code assessment program in support of the generic hypersonic research at NASA Lewis. Detailed comparisons of static pressure fields and oil flow patterns are made with the corresponding solution on the wall containing the shock/boundary layer interaction in an effort to validate the code for hypersonic inlet applications

From Coherent States In Adjacent Graphene Layers Toward Low-Power Logic Circuits

Colleagues and we recently proposed a new type of transistor, a Bilayer PseudoSpin Field Effect Transistor (BiSFET), based on many-body coherent states in coupled electron and hole layers in graphene. Here we review the basic BiSFET device concept and ongoing efforts to determine how such a device, which would be far from a drop-in replacement for MOSFETs in CMOS logic, could be used for low-power logic operation, and to model the effects of engineerable device parameters on the formation and gating of interlayer coherent state.Electrical and Computer Engineerin

The design/analysis of flows through turbomachinery: A viscous/inviscid approach

The development of a design/analysis flow solver at NASA Lewis Research Center is discussed. The solver is axisymmetric and can be run inviscidly with assumed or calculated blockages, or with the viscous terms computed. The blade forces for each blade row are computed from blade-to-blade solutions, correlated data or force model, or from a full three dimensional solution. Codes currently under development can be separated into three distinct elements: the turbomachinery interactive grid generator energy distribution restart code (TIGGERC), the interactive blade element geometry generator (IBEGG), and the viscous/inviscid multi-blade-row average passage flow solver (VIADAC). Several experimental test cases were run to validate the VIADAC code. The tests, representative of typical axial turbomachinery duct axisymmetric wind tunnel body problems, were conducted on an SR7 Spinner axisymmetric body, a NASA Rotor 67 Fan test bed, and a transonic boatail body. The results show the computations to be in good agreement with test data