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Correction to “Site-Dependent Fluctuations Optimize Electronic Energy Transfer in the Fenna–Matthews–Olson Protein”
Revised Table 1 is provided. (Table Presented). The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpcb.9b11080. Revised Table S1 of exciton energies and eigenfunctions (PDF).
Absence of Selection for Quantum Coherence in the Fenna–Matthews–Olson Complex: A Combined Evolutionary and Excitonic Study
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The Fate of the Triplet Excitations in the Fenna-Matthews-Olson Complex
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Coherent wavepackets in the Fenna–Matthews–Olson complex are robust to excitonic-structure perturbations caused by mutagenesis
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Diversity and Physiology of Siderophilic Cyanobacteria: Implication for the Bioenergetics
Prior to 2.4 Ga, global oceans were likely significantly enriched in soluble iron (Rouxel, Bekker, Edwards, 2005), a condition that is not conducive to the growth of most contemporary mesophilic cyanobacteria (CB). Recent studies of the mechanisms of iron-deficiency stress in CB suggest that contemporary mesophilic freshwater and marine B underwent long-term adaptation to a permanent decrease in soluble iron in the ocean environment (Boyer, et al., 1987; Braun, Hantke, and Koster, 1998). Of all extant environments, iron-depositing hot springs may constitute the most appropriate natural models for analysis of the transition of ancestral cyanobacteria (CB) or protocyanobacteria (PCB) (Olson, 2001) from anoxygenic photosynthesis to oxygenic one and biogeochemical processes in the late Archean and early Paleoproterozoic eras. In particular, Olson (2001) proposed the definition for PCB and postulated that the common ancestor of PCB and CB might well have used Fe(OH)+ as the principal electron donor for CO2 fixation (Widdel, et al., 1993; Ehrenreich and Widdel, 1994; Pierson and Olson, 1989; Olson, 2006). Olson (2001) proposed that the driving force for the evolution of RC2, in addition to RC1, was the necessity to use Fe(OH)+ effectively for CO2 fixation in the absence of reduced sulfur compounds. The global decrease of dissolved environmental reduced iron could have been the driving force for the transition from anoxygenic to oxygenic photosynthesis (Brown et al., 2007). Despite the insights into the ecology, evolutionary biology, paleogeobiochemistry, and astrobiology the examination of iron depositing hot springs (IDHS) could potentially provide, very few studies dedicated to the diversity and physiology of cyanobacteria inhabiting IDHS have been conducted. Here we describe the phylogeny, physiology and ultrastructure and biogeochemical activity of several recent CB isolates from two different greater Yellowstone area IDHS, e.g. LaDuke and Chocolate Pots. Phylogenetic analysis of 16S rRNA genes indicated that 6 of 12 new isolates examined could not be placed within established CB genera. Some of the isolates exhibited pronounced requirements for elevated iron concentrations, with maximum growth rates observed when 0.4-1 mM Fe(3+) was present in the media. However, the pronounced effect of iron limitation on the proliferation of siderophilic CB can be observed only after several passages through iron "free" media. TEM studies of several species of siderophilic CB revealed that the cultures JSC-3 and -11 are probably capable of some sort of pinocytosis of precipitated iron. This phenomenon may explain high tolerance of siderophilic CB to iron deficit. We also found that the stimulation of the growth of siderophilic CB by oxidized iron is accompanied by the decrease of O2 evolution by some species after addition Fe(2+) in iron "free" medium.
PyAMG: Algebraic Multigrid Solvers in Python
PyAMG is a Python package of algebraic multigrid (AMG) solvers and supporting tools for approximating the solution to large, sparse linear systems of algebraic equations, Ax = b, where A is an n × n sparse matrix. Sparse linear systems arise in a range of problems in science, from fluid flows to solid mechanics to data analysis. While the direct solvers available in SciPy’s sparse linear algebra package (scipy.sparse.linalg) are highly efficient, in many cases iterative methods are preferred due to overall complexity. However, the iterative methods in SciPy, such as CG and GMRES, often require an efficient preconditioner in order to achieve a lower complexity. Preconditioning is a powerful tool whereby the conditioning of the linear system and convergence rate of the iterative method are both dramatically improved. PyAMG constructs multigrid solvers for use as a preconditioner in this setting. A summary of multigrid and algebraic multigrid solvers can be found in Olson (2015a), in Olson (2015b), and in Falgout (2006); a detailed description can be found in Briggs et al. (2000) and Trottenberg et al. (2001).
Theoretical estimates of flammability bounds for thin condensed fuel diffusion flames in microgravity using detailed models of chemistry and radiation
Recently, U-shape flammability maps have been constructed showing minimal oxygen vs. flame strain for opposed flame spread in micro-gravity by Olson and Ferkul. The U-shape defines the limiting flammability bounds from radiative extinction and flame blow-off. Here, the minimum of the U corresponds to the minimum possible oxidizer concentration where burning can occur, and is an important quantity of interest for fire safety. While high strain extinction bounds have been well analyzed, low strain radiative extinction has not. To estimate low strain extinction, in this study an analytical theory is developed based on thin flame theory coupled with a heat and mass transfer model for solid fuels. A reaction progress variable based on the Damköhler number is adapted in the theory to account for incomplete combustion at high strain rates and enable the capturing of the full flammability map. The analytical model is compared to a one dimensional numerical model w/ detailed chemical kinetics and coupled radiation heat transfer in planar and spherical geometries. The flammability maps are then qualitatively compared to experimental extinguishment data compiled by Olson and Ferkul for cylindrical rods of PMMA showing similar trends. The results show the newly developed analytics capture the radiative extinction bound compared to the numerical model and qualitatively agrees with microgravity data.
Inhomogeneous dephasing masks coherence lifetimes in ensemble measurements
An open question at the forefront of modern physical sciences is what role, if any, quantum effects may play in biological sensing and energy transport mechanisms. One area of such research concerns the possibility of coherent energy transport in photosynthetic systems. Spectroscopic evidence of long-lived quantum coherence in photosynthetic light-harvesting pigment protein complexes (PPCs), along with theoretical modeling of PPCs, has indicated that coherent energy transport might boost efficiency of energy transport in photosynthesis. Accurate assessment of coherence lifetimes is crucial for modeling the extent to which quantum effects participate in this energy transfer, because such quantum effects can only contribute to mechanisms proceeding on timescales over which the coherences persist. While spectroscopy is a useful way to measure coherence lifetimes, inhomogeneity in the transition energies across the measured ensemble may lead to underestimation of coherence lifetimes from spectroscopic experiments. Theoretical models of antenna complexes generally model a single system, and direct comparison of single system models to ensemble averaged experimental data may lead to systematic underestimation of coherence lifetimes, distorting much of the current discussion. In this study, we use simulations of the Fenna-Matthews-Olson complex to model single complexes as well as averaged ensembles to demonstrate and roughly quantify the effect of averaging over an inhomogeneous ensemble on measured coherence lifetimes. We choose to model the Fenna-Matthews-Olson complex because that system has been a focus for much of the recent discussion of quantum effects in biology, and use an early version of the well known environment-assisted quantum transport model to facilitate straightforward comparison between the current model and past work. Although ensemble inhomogeneity is known to lead to shorter lifetimes of observed oscillations (simply inhomogeneous spectral broadening in the time domain), this important fact has been left out of recent discussions of spectroscopic measurements of energy transport in photosynthesis. In general, these discussions have compared single-system theoretical models to whole-ensemble laboratory measurements without addressing the effect of inhomogeneous dephasing. Our work addresses this distinction between single system and ensemble averaged observations, and shows that the ensemble averaging inherent in many experiments leads to an underestimation of coherence lifetimes in individual systems.
NREL Scientists Spurred the Success of Multijunction Solar Cells (Fact Sheet)
Before 1984, many scientists believed that high-quality gallium indium phosphide (GaInP) alloys could not be grown for use as semiconductors because the alloys would separate. One researcher at the Solar Energy Research Institute (SERI) thought differently. His name was Jerry Olson, and his innovative thinking changed solar history. Olson identified a material combination that allowed themultijunction cell to flourish. It is now the workhorse that powers satellites and the catalyst for renewed interest in concentrator photovoltaic (CPV) products.
Electric Power Generation from Low to Intermediate Temperature Resourcces
The UND-CLR Binary Geothermal Power Plant was a collaborative effort of the U.S. Department of Energy (DOE), Continental Resources, Inc. (CRL), Slope Electric Cooperative (SEC), Access Energy, LLC (AE), Basin Electric Cooperative (BEC), Olson Construction, the North Dakota Industrial Commission Renewable Energy Council (NDIC-REC), the North Dakota Department of Commerce Centers of Excellence Program (NDDC-COE), and the University of North Dakota (UND). The primary objective of project was to demonstrate/test the technical and economic feasibility of generating electricity from non-conventional, low-temperature (90 ºC to 150 °C) geothermal resources using binary technology. CLR provided the access to 98 ºC water flowing at 51 l s-1 at the Davis Water Injection Plan in Bowman County, ND. Funding for the project was from DOE –GTO, NDIC-REC, NDD-COE, and BEC. Logistics, on-site construction, and power grid access were facilitated by Slope Electric Cooperative and Olson Construction. Access Energy supplied prototype organic Rankine Cycle engines for the project. The potential power output from this project is 250 kW at a cost of $3,400 per kW. A key factor in the economics of this project is a significant advance in binary power technology by Access Energy, LLC. Other commercially available ORC engines have efficiencies 8 to 10 percent and produce 50 to 250 kW per unit. The AE ORC units are designed to generate 125 kW with efficiencies up to 14 percent and they can be installed in arrays of tens of units to produce several MW of power where geothermal waters are available. This demonstration project is small but the potential for large-scale development in deeper, hotter formations is promising. The UND team’s analysis of the entire Williston Basin using data on porosity, formation thicknesses, and fluid temperatures reveals that 4.0 x 1019 Joules of energy is available and that 1.36 x 109 MWh of power could be produced using ORC binary power plants. Much of the infrastructure necessary to develop extensive geothermal power in the Williston Basin exists as abandoned oil and gas wells. Re-completing wells for water production could provide local power throughout the basin thus reducing power loss through transmission over long distances. Water production in normal oil and gas operations is relatively low by design, but it could be one to two orders of magnitude greater in wells completed and pumped for water production. A promising method for geothermal power production recognized in this project is drilling horizontal open-hole wells in the permeable carbonate aquifers. Horizontal drilling in the aquifers increases borehole exposure to the resource and consequently increases the capacity for fluid production by up to an order of magnitude.
Regimes of Kinetic Magnetic Reconnection in the Laboratory (Final Technical Report)
The DOE award No. DE-SC0019153, supported in part one graduate student (J. Olson) and material expenses, enabling the student to prepare a basic plasma physics experiment on magnetic reconnection (which we now call the Terrestrial Reconnection Experiment, TREX) within at the Wisconsin Plasma Physics Laboratory (WiPPL). The study of the collisionless magnetic reconnection constituted the primary research carried out under this grant and lead to new observations of unexpected shock formation below the TREX reconnection layer. The shock formation was found fundamental to regulating the normalized rate of reconnection, and the results were part of our experimental observations detailed in a paper first authored by Dr. J. Olson and now published in the Journal of Plasma Physics. In this Report we review the general motivation of this work and provide an overview of our experimental results enabled by the support through the award.
Variable convergence liquid layer implosions on the National Ignition Facility
Liquid layer implosions using the “wetted foam” technique, where the liquid fuel is wicked into a supporting foam, have been recently conducted on the National Ignition Facility for the first time [Olson et al., Phys. Rev. Lett. 117, 245001 (2016)]. In this paper, we report on a series of wetted foam implosions where the convergence ratio was varied between 12 and 20. Reduced nuclear performance is observed as convergence ratio increases. 2-D radiation-hydrodynamics simulations accurately capture the performance at convergence ratios (CR) ~ 12, but we observe a significant discrepancy at CR ~ 20. Finally, this may be due to suppressed hot-spot formation or an anomalous energy loss mechanism.
A windowed mean trajectory approximation for condensed phase dynamics
We propose a trajectory-based quasi-classical method for approximating dynamics in condensed phase systems. Building upon the previously developed optimized mean trajectory approximation that has been used to compute linear and nonlinear spectra, we borrow some ideas from filtering trajectory methods to obtain a novel semiclassical method for the dynamical propagation of density matrices. This new approximation is tested rigorously against standard multistate electronic models, spin-boson models, and models of the Fenna–Matthews–Olson complex. For dissipative systems, the current method is significantly better or as good as many other semiclassical methods available, especially at low temperatures and for off-diagonal density matrix elements, whereas for scattering models, the current method bears similar limitations as mean-field propagation schemes. All results are tested against the numerically exact hierarchical equations of motion method. In conclusion, the new method shows excellent agreement across various parameter regimes with numerically exact results, highlighting the robustness and accuracy of our approach.
Comparison between explicit and implicit discretization strategies for a dissipative thermal environment
We investigate strategies for simulating open quantum systems coupled to dissipative baths by comparing explicit wave function-based discretization [via multi-layer multi-configuration time-dependent Hartree (ML-MCTDH)] and the implicit density matrix-based master equation method [via tree tensor network hierarchical equations of motion (TTN-HEOM)]. For dissipative baths characterized by exponentially decaying bath correlation functions, the implicit discretization approach of HEOM—rooted in bath correlation function decompositions—proves significantly more efficient than explicit discretization of the bath into discrete harmonic modes. Explicit methods, like ML-MCTDH, require extensive mode discretization to approximate continuum baths, leading to computational bottlenecks. Case studies for two-level systems and a Fenna–Matthews–Olson complex model highlight TTN-HEOM’s superiority in capturing dissipative dynamics with relaxations with a minimal number of auxiliary modes, while the explicit methods are as exact as the HEOM in pure dephasing regimes. This comparison is enabled by the TENSO package, which has both ML-MCTDH and TTN-HEOM implemented using the same computational structure and propagation strategy.
Assessment of Large Scale Artifacts Associated with Idaho National Laboratory's Nuclear Reactor Testing Historic Context
INL Archives and Special Collections Assessment of Large-Scale Artifacts Associated with Idaho National Laboratory’s Nuclear Reactor Testing Historic Context PREPARED BY: Christina Olson Idaho National Laboratory Cultural Resource Management Office FOR: Idaho State Archives Idaho State Historical Museum