Power Spectra in Spacetime Noncommutative Inflation

String/M theory inspires an uncertainty relation between space and time which deviates from general relativity. It is possible to explore this deviation from cosmological observations, in particular from the CMB fluctuation spectrum. This paper extends some previous observations to more general inflation schemes, we find that the noncommutative spacetime effects always suppress the power spectrum, of both the scalar and tensor perturbations, and may provide a large enough running of the spectral index to fit the WMAP data in the inflation model.Comment: 19 pages, 6 figures, harvmac; 2 references added; only references added; Accepted for publication in Nucl. Phys.

Reconstructing large running-index inflaton potentials

Recent fits of cosmological parameters by the first year Wilkinson Microwave Anisotropy Probe (WMAP) measurement seem to favor a primordial scalar spectrum with a large varying index from blue to red. We use the inflationary flow equations to reconstruct large running-index inflaton potentials and comment on current status on the inflationary flow. We find previous negligence of higher order slow rolling contributions when using the flow equations would lead to unprecise results.Comment: Final version to appear in Class. Quant. Grav. References adde

Protein Design Using Continuous Rotamers

Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein flexibility to occur during this optimization, or they may fail to find the best sequence with the lowest energy. Most design algorithms implement side-chain flexibility by allowing the side chains to move between a small set of discrete, low-energy states, which we call rigid rotamers. In this work we show that allowing continuous side-chain flexibility (which we call continuous rotamers) greatly improves protein flexibility modeling. We present a large-scale study that compares the sequences and best energy conformations in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model. We show that in nearly all of our redesigns the sequence found by the continuous-rotamer model is different and has a lower energy than the one found by the rigid-rotamer model. Moreover, the sequences found by the continuous-rotamer model are more similar to the native sequences. We then show that the seemingly easy solution of sampling more rigid rotamers within the continuous region is not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer model and almost always resulted in higher energies. Finally, we present a new protein design algorithm based on the dead-end elimination (DEE) algorithm, which we call iMinDEE, that makes the use of continuous rotamers feasible in larger systems. iMinDEE guarantees finding the optimal answer while pruning the search space with close to the same efficiency of DEE. Availability: Software is available under the Lesser GNU Public License v3. Contact the authors for source code

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis (CF). The most prevalent CFTR mutation, ΔF508, blocks folding in the endoplasmic reticulum. Recent work has shown that some ΔF508-CFTR channel activity can be recovered by pharmaceutical modulators (“potentiators” and “correctors”), but ΔF508-CFTR can still be rapidly degraded via a lysosomal pathway involving the CFTR-associated ligand (CAL), which binds CFTR via a PDZ interaction domain. We present a study that goes from theory, to new structure-based computational design algorithms, to computational predictions, to biochemical testing and ultimately to epithelial-cell validation of novel, effective CAL PDZ inhibitors (called “stabilizers”) that rescue ΔF508-CFTR activity. To design the “stabilizers”, we extended our structural ensemble-based computational protein redesign algorithm to encompass protein-protein and protein-peptide interactions. The computational predictions achieved high accuracy: all of the top-predicted peptide inhibitors bound well to CAL. Furthermore, when compared to state-of-the-art CAL inhibitors, our design methodology achieved higher affinity and increased binding efficiency. The designed inhibitor with the highest affinity for CAL (kCAL01) binds six-fold more tightly than the previous best hexamer (iCAL35), and 170-fold more tightly than the CFTR C-terminus. We show that kCAL01 has physiological activity and can rescue chloride efflux in CF patient-derived airway epithelial cells. Since stabilizers address a different cellular CF defect from potentiators and correctors, our inhibitors provide an additional therapeutic pathway that can be used in conjunction with current methods

Review of in-situ process monitoring and in-situ metrology for metal additive manufacturing

Lack of assurance of quality with additively manufactured (AM) parts is a key technological barrier that prevents manufacturers from adopting AM technologies, especially for high-value applications where component failure cannot be tolerated. Developments in process control have allowed significant enhancement of AM techniques and marked improvements in surface roughness and material properties, along with a reduction in inter-build variation and the occurrence of embedded material discontinuities. As a result, the exploitation of AM processes continues to accelerate. Unlike established subtractive processes, where in-process monitoring is now commonplace, factory-ready AM processes have not yet incorporated monitoring technologies that allow discontinuities to be detected in process. Researchers have investigated new forms of instrumentation and adaptive approaches which, when integrated, will allow further enhancement to the assurance that can be offered when producing AM components. The state-of-the-art with respect to inspection methodologies compatible with AM processes is explored here. Their suitability for the inspection and identification of typical material discontinuities and failure modes is discussed with the intention of identifying new avenues for research and proposing approaches to integration into future generations of AM systems

Simulation based energy-resource efficient manufacturing integrated with in-process virtual management

Supported by the EU 7th Framework ICT Programme under EuroEnergest Project (Contract No. 288102)

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion