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At least 577 records · Page 32

Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Abstract The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano‐ and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein‐protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.

Chemistry↗

Nonequilibrium Aspects of Integrable Models

Driven by breakthroughs in experimental and theoretical techniques, the study of nonequilibrium quantum physics is a rapidly expanding field with many exciting new developments. Among the manifold ways the topic can be investigated, one-dimensional systems provide a particularly fine platform. The trifecta of strongly correlated physics, powerful theoretical techniques, and experimental viability have resulted in a flurry of research activity over the past decade or so. In this review, we explore the nonequilibrium aspects of one-dimensional systems that are integrable. Through a number of illustrative examples, we discuss nonequilibrium phenomena that arise in such models, the role played by integrability, and the consequences these have for more generic systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA Tech Briefs, November 2011

The topics include: 1) Flight Test Results from the Rake Airflow Gage Experiment on the F-15B; 2) Telemetry and Science Data Software System; 3) CropEx Web-Based Agricultural Monitoring and Decision Support; 4) High-Performance Data Analysis Tools for Sun-Earth Connection Missions; 5) Experiment in Onboard Synthetic Aperture Radar Data Processing; 6) Microfabrication of a High-Throughput Nanochannel Delivery/Filtration System; 7) Improved Design and Fabrication of Hydrated-Salt Pills; 8) Monolithic Flexure Pre-Stressed Ultrasonic Horns; 9) Cryogenic Quenching Process for Electronic Part Screening; 10) Broadband Via-Less Microwave Crossover Using Microstrip-CPW Transitions; 11) Wheel-Based Ice Sensors for Road Vehicles; 12) G-DYN Multibody Dynamics Engine; 13) Multibody Simulation Software Testbed for Small-Body Exploration and Sampling; 14) Propulsive Reaction Control System Model; 15) Licklider Transmission Protocol Implementation; 16) Core Recursive Hierarchical Image Segmentation; 17) Two-Stage Centrifugal Fan; 18) Combined Structural and Trajectory Control of Variable-Geometry Planetary Entry Systems; 19) Pressure Regulator With Internal Ejector Circulation Pump, Flow and Pressure Measurement Porting, and Fuel Cell System Integration Options; 20) Temperature-Sensitive Coating Sensor Based on Hematite; 21) Standardization of a Volumetric Displacement Measurement for Two-Body Abrasion Scratch Test Data Analysis; 22) Detection of Carbon Monoxide Using Polymer-Carbon Composite Films; 23) Substituted Quaternary Ammonium Salts Improve Low-Temperature Performance of Double-Layer Capacitors; 24) Sustainably Sourced, Thermally Resistant, Radiation Hard Biopolymer; 25) Integrated Lens Antennas for Multi-Pixel Receivers; 26) 180-GHz Interferometric Imager; 27) Maturation of Structural Health Management Systems for Solid Rocket Motors; 28) Validating Phasing and Geometry of Large Focal Plane Arrays; 29) Transverse Pupil Shifts for Adaptive Optics Non-Common Path Calibration; 30) Qualification of Fiber Optic Cables for Martian Extreme Temperature Environments; 31) Solid-State Spectral Light Source System; 32) Multiple-Event, Single-Photon Counting Imaging Sensor; 33) Surface Modeling to Support Small-Body Spacecraft Exploration and Proximity Operations; and 34) Achieving Exact and Constant Turnaround Ratio in a DDS-Based Coherent Transponder.

Source record↗

Nuclear Fuel and Pu Redox Studies from The Glenn T. Seaborg Institute at Idaho National Laboratory

The Glenn T. Seaborg Institute at Idaho National Laboratory (INL-GTSI) focuses on advancing fundamental research in the actinide sciences by providing unique opportunities to early career scientists and engineers to gain experience studying the actinide elements and their associated systems. The INL-GTSI is built from three focus areas that are based on the expertise and supporting infrastructure at INL and include solid state chemistry and physics, solution phase chemistry and physics, and forensic and isotope science. INL is the lead Laboratory for nuclear energy research and development in the U. S. and the research on nuclear fuels performed under the INL-GTSI gives good examples of solid state studies. Uranium-Molybdenum (U-Mo) alloys are leading fuel candidates for conversion of high performance research and test reactors to low-enriched fuels. During irradiation, generated fission gas accumulates into bubbles and self-organizes into a gas bubble superlattice (GBS) that effectively stores fission gases and inhibits fuel swelling. A study on the early self- organizing behavior of the GBS shows that not only grain boundaries but the interfaces between the U-Mo matrix and uranium carbide (UC) impurities are important to GBS formation.[1] In solution, understanding the complex redox behavior of plutonium in aqueous environments is critical for establishing optimized nuclear waste reprocessing solvent systems and storage tank environments. INL-GTSI researchers have produced an experimentally validated multi-scale model of the gamma radiation induced behavior of plutonium ions in concentrated aqueous HNO3 solutions.[2] Here, gamma radiation effected only minimal steady state changes in the redox distribution of the plutonium oxidation states. The redox cycling between Pu(IV) and Pu(III) is demonstrated to be mediated by the •OH/NO3• radical oxidation of Pu(III) and the H2O2/HNO3 driven reduction of Pu(IV). The INL-GTSI offers young researchers the unique chance to work directly with actinide bearing materials in a U. S. National Laboratory environment. Further topical areas of interest to the INL-GTSI include, but are not limited to, fundamental actinide properties, structure/property (electronic, magnetic, thermal) relations, actinide quantum criticality, f- electron interactions, electron correlations, computational studies, new phases, defect effects, interface interactions, isotope production and separation, forensic analytical chemistry, structure and dynamic properties of actinides in non-aqueous media, separations chemistry and kinetics for advanced nuclear fuel cycles, radiation effects, and innovative and advanced ligand design for complexation of the actinides.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Effects of electron-phonon interaction on thermal and electrical transport through molecular nano-conductors

The topic of this review is the effects of electron-phonon interaction (EPI) on the transport properties of molecular nano-conductors. A nano-conductor connects to two electron leads and two phonon leads, possibly at different temperatures or chemical potentials. The EPI appears only in the nano-conductor. We focus on its effects on charge and energy transport. We introduce three approaches. For weak EPI, we use the nonequilibrium Green’s function method to treat it perturbatively. We derive the expressions for the charge and heat currents. For weak system-lead couplings, we use the quantum master equation approach. In both cases, we use a simple single level model to study the effects of EPI on the system’s thermoelectric transport properties. It is also interesting to look at the effect of currents on the dynamics of the phonon system. For this, we derive a semi-classical generalized Langevin equation to describe the nano-conductor’s atomic dynamics, taking the nonequilibrium electron system, as well as the rest of the atomic degrees of freedom as effective baths. We show simple applications of this approach to the problem of energy transfer between electrons and phonons.

36 MATERIALS SCIENCE↗

Strain-controlled thermal conductivity in ferroic twinned films

Large reversible changes of thermal conductivity are induced by mechanical stress, and the corresponding device is a key element for phononics applications. We show that the thermal conductivity k of ferroic twinned thin films can be reversibly controlled by strain. Nonequilibrium molecular dynamics simulations reveal that thermal conductivity decreases linearly with the number of twin boundaries perpendicular to the direction of heat flow. Our demonstration of large and reversible changes in thermal conductivity driven by strain may inspire the design of controllable thermal switches for thermal logic gates and all-solid-state cooling devices.

SURFACES, INTERFACES AND THIN FILMS↗

De novo design of drug-binding proteins with predictable binding energy and specificity

The de novo design of small molecule–binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase–1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule–binding proteins with tuned interaction energies is feasible entirely from computation.

Science & Technology - Other Topics↗

Collective neural network behavior in a dynamically driven disordered system of superconducting loops

Collective properties of complex systems composed of many interacting components such as neurons in our brain can be modeled by artificial networks based on disordered systems. We show that a disordered neural network of superconducting loops with Josephson junctions can exhibit computational properties like categorization and associative memory in the time evolution of its state in response to information from external excitations. Superconducting loops can trap multiples of fluxons in many discrete memory configurations defined by the local free energy minima in the configuration space of all possible states. A memory state can be updated by exciting the Josephson junctions to fire or allow the movement of fluxons through the network as the current through them surpasses their critical current thresholds. Simulations performed with a lumped element circuit model of a 4-loop network show that information written through excitations is translated into stable states of trapped flux and their time evolution. Experimental implementation on a high-Tc superconductor YBCO-based 4-loop network shows dynamically stable flux flow in each pathway characterized by the correlations between junction firing statistics. Neural network behavior is observed as energy barriers separating state categories in simulations in response to multiple excitations, and experimentally as junction responses characterizing different flux flow patterns in the network. The state categories that produce these patterns have different temporal stabilities relative to each other and the excitations. This provides strong evidence for time-dependent (short-to-long-term) memories, that are dependent on the geometrical and junction parameters of the loops, as described with a network model.

Josephson junctions↗

Hamiltonian engineering of spin-orbit–coupled fermions in a Wannier-Stark optical lattice clock

Engineering a Hamiltonian system with tunable interactions provides opportunities to optimize performance for quantum sensing and explore emerging phenomena of many-body systems. An optical lattice clock based on partially delocalized Wannier-Stark states in a gravity-tilted shallow lattice supports superior quantum coherence and adjustable interactions via spin-orbit coupling, thus presenting a powerful spin model realization. The relative strength of the on-site and off-site interactions can be tuned to achieve a zero density shift at a “magic” lattice depth. This mechanism, together with a large number of atoms, enables the demonstration of the most stable atomic clock while minimizing a key systematic uncertainty related to atomic density. Interactions can also be maximized by driving off-site Wannier-Stark transitions, realizing a ferromagnetic to paramagnetic dynamical phase transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 34th and AIAA/ASME Adaptive Structures Forum, La Jolla, CA, Apr. 19-22, 1993, Technical Papers. Pts. 1-6

Topics addressed include the prediction of helicopter component loads using neural networks, spacecraft on-orbit coupled loads analysis, hypersonic flutter of a curved shallow panel with aerodynamic heating, thermal-acoustic fatigue of ceramic matrix composite materials, transition elements based on transfinite interpolation, damage progression in stiffened composite panels, a direct treatment of min-max dynamic response optimization problems, and sources of helicopter rotor hub inplane shears. Also discussed are dynamics of a layered elastic system, confidence bounds on structural reliability, mixed triangular space-time finite elements, advanced transparency development for USAF aircraft, a low-velocity impact on a graphite/PEEK, an automated mode-tracking strategy, transonic flutter suppression by a passive flap, a nonlinear response of composite panels to random excitation, an optimal placement of elastic supports on a simply supported plate, a probabilistic assessment of composite structures, a model for mode I failure of laminated composites, a residual flexibility approach to multibody dynamics,and multilayer piezoelectric actuators.

Source record↗

Modeling the Influence of Correlated Molecular Disorder on the Dynamics of Excitons in Organic Molecular Semiconductors

In this paper, we investigate the role of correlated molecular disorder on the dynamics of excitons in oligothiophene-based organic semiconductors. We simulate exciton dynamics using the Frenkel exciton model and derive parameters for this model so that they reflect the specific characteristics of all-atom molecular systems. By systematically modifying the parameters of the Frenkel exciton model, we isolate the influence of spatial and temporal molecular correlations on the dynamics of excitons in these systems. For the oligothiophene systems considered here, we find that the molecular fluctuations exhibit long-lived memory effects, but these effects do not significantly influence the dynamic properties of excitons. We also find that excitons can be sensitive to the molecular-scale spatial correlations, and that this sensitivity grows with the amount of energetic disorder within the material. We conclude that control over spatial correlations can mitigate the negative influence of disorder on exciton transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Screening Diffusion of Small Molecules in Flexible Zeolitic Imidazolate Frameworks Using a DFT-Parameterized Force Field

Quantitatively modeling adsorbate diffusion through zeolitic imidazolate frameworks (ZIFs) must account for the inherent flexibility of these materials. Here, the lack of a transferable intramolecular ZIF force field (FF) for use in classical simulations has previously made an accurate simulation of adsorbate diffusion in many ZIFs impossible. We resolve this problem by introducing a density functional theory parameterized force field (FF) for ZIFs named the intraZIF-FF, which includes perturbations to the class I force fields previously used to model ZIFs. This FF outperforms ad hoc force fields at predicting ab initio relative energies and atomic forces taken from fully periodic ab initio molecular dynamics simulations of SALEM-2, ZIF-7, ZIF-8, and ZIF-90. We use the intraZIF-FF to predict the infinite dilution self-diffusion coefficients of 30 adsorbates with molecular diameters ranging from 2.66 to 7.0 Å in these 4 ZIFs. These results greatly increase the number of adsorbates for which accurate information about molecular diffusion in ZIFs is available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the Elevated Temperature Thermal Stability of Nanoscale Mn-Ni-Si Precipitates Formed at Lower Temperature in Highly Irradiated Reactor Pressure Vessel Steels

Atom probe tomography (APT) and scanning transmission electron microscopy (STEM) techniques were used to probe the long-time thermal stability of nm-scale Mn-Ni-Si precipitates (MNSPs) formed in intermediate and high Ni reactor pressure vessel steels under high fluence neutron irradiation at ≈320 °C. Post irradiation annealing (PIA) at 425 °C for up to 57 weeks was used to determine if the MNSPs are: (a) non-equilibrium solute clusters formed and sustained by radiation induced segregation (RIS); or, (b) equilibrium G or Γ 2 phases, that precipitate at accelerated rates due to radiation enhanced diffusion (RED). Note the latter is consistent with both thermodynamic models and x-ray diffraction (XRD) measurements. Both the experimental and an independently calibrated cluster dynamics (CD) model results show that the stability of the MNSPs is very sensitive to the alloy Ni and, to a lesser extent, Mn content. Thus, a small fraction of the largest MNSPs in the high Ni steel persist, and begin to coarsen at long times. These results suggest that the MNSPs remain a stable phase, even at 105 °C higher than they formed at, thus are most certainly equilibrium phases at much lower service relevant temperatures of ≈290 °C.

36 MATERIALS SCIENCE↗

Magnetic Microspheres and Tissue Model Studies for Therapeutical Applications

Hyperthermia is a well known cancer therapy and consists of heating a tumor region to the elevated temperatures in the range of 40-45 C for an extended period of time (2-8 hours). This leads to thermal inactivation of cell regulatory and growth processes with resulting widespread necrosis, carbonization and coagulation. Moreover, heat boosts the tumor response to other treatments such as radiation, chemotherapy or immunotherapy. Of particular importance is careful control of generated heat in the treated region and keeping it localized. Higher heating, to about 56 C can lead to tissue thermo-ablation. With accurate temperature control, hyperthermia has the advantage of having minimal side effects. Several heating techniques are utilized for this purpose, such as whole body hyperthermia, radio-frequency (RF) hyperthermia, ultrasound technique, inductive microwave antenna hyperthermia, inductive needles (thermoseeds), and magnetic fluid hyperthermia (MFH).MFH offers many advantages as targeting capability by applying magnets. However, this technology still suffers significant inefficiencies due to lack of thermal control. This paper will provide a review of the topic and outline the ongoing work in this area. The main emphasis is in devising ways to overcome the technical difficulty in hyperthermia breast therapy of achieving a uniform therapeutic temperature over the required region of the body and holding it steady for an extended period (2-3 hours). The basic shortcomings of the presently utilized heating methods stem from the non-uniform thermal properties of the tissue and the point heating characteristics of the techniques without any thermal control. Our approach is to develop a novel class of magnetic fluids, which have inherent thermoregulating properties. We have identified a few magnetic alloys which can serve as suitable nano to micron-size particle material. The objective is to synthesize, characterize and evaluate the efficacy of Thermo Regulating Magnetic Fluids (TRMF) for hyperthermia therapy. The development of a tissue model and testing the fluid dynamics of particle motion, settling, distribution in the tissue matrix and heat generation will be discussed.

Ramachandran, N.↗

CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline

In silico prediction of a protein’s tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three ‘assisted’ protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Pore Length on Hydrogenolysis of Polyethylene within a Mesoporous Support Architecture

Due to the plastic waste crisis, selective chemical upcycling of polyolefins into value-added products is a topic of intense interest, demanding polymer deconstruction processes that afford control over the product chain lengths. Recently, a catalytic architecture was synthesized in which a polyolefin melt infiltrates a porous support, and its chains are cleaved by a metal nanoparticle catalyst at the bottom of the pores, yielding a narrow distribution of alkane products. Although the influence of various parameters of these catalytic materials, including the effects of the nanoparticle size and pore diameter on product chain length, has been examined before, here, we investigate the role of the pore length in the cleavage process through the first study that combines catalytic hydrogenolysis and coarse-grained modeling to gain insights not available by experiment alone. We show that the pore length can permit control over the average product length with qualitative agreement between experiment and simulation. In conclusion, we go beyond this observation to uncover the dynamic phenomenon responsible for the pore-length dependence of the cleavage products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling

In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein–protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On uncorrelated inter-monomer Förster energy transfer in Fenna–Matthews–Olson complexes

The Fenna–Matthews–Olson (FMO) light-harvesting antenna protein of green sulfur bacteria is a long-studied pigment–protein complex which funnels energy from the chlorosome to the reaction centre where photochemistry takes place. The structure of the FMO protein from Chlorobaculum tepidum is known as a homotrimeric complex containing eight bacteriochlorophyll a per monomer. Owing to this structure FMO has strong intra-monomer and weak inter-monomer electronic coupling constants. While long-lived (sub-picosecond) coherences within a monomer have been a prevalent topic of study over the past decade, various experimental evidence supports the presence of subsequent inter-monomer energy transfer on a picosecond time scale. The latter has been neglected by most authors in recent years by considering only sub-picosecond time scales or assuming that the inter-monomer coupling between low-energy states is too weak to warrant consideration of the entire trimer. However, Förster theory predicts that energy transfer of the order of picoseconds is possible even for very weak (less than 5 c m-1 ) electronic coupling between chromophores. This work reviews experimental data (with a focus on emission and hole-burned spectra) and simulations of exciton dynamics which demonstrate inter-monomer energy transfer. It is shown that the lowest energy 825 nm absorbance band cannot be properly described by a single excitonic state. The energy transfer through FMO is modelled by generalized Förster theory using a non-Markovian, reduced density matrix approach to describe the electronic structure. The disorder-averaged inter-monomer transfer time across the 825 nm band is about 27 ps. While only isolated FMO proteins are presented, the presence of inter-monomer energy transfer in the context of the overall photosystem is also briefly discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗