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At least 19 records

Better, Cheaper, Faster Molecular Dynamics

Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

Pohorille, Andrew↗

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗

Reactive phosphine combinatorial co-sputtering of cation disordered ZnGeP2 films

The discovery of new materials by coupling high-throughput synthesis with computational screening is being increasingly adopted. However, thus far, phosphides have been largely overlooked for both computational screening and high-throughput synthesis. In this paper, we report on the use of a high-throughput synthesis technique, reactive combinatorial co-sputtering with PH 3 , to deposit ZnGeP 2 thin films. We grew amorphous films over a wide range of compositions and found an upper limit in growth temperature determined by Zn and P volatility. We found that depositing in a Ge-limited regime could be utilized to slow the growth rate to compensate for the desorption of the Zn and P. Crystalline films were achieved by depositing films at higher temperatures in this Ge-limited regime with a reduced deposition rate. X-ray diffraction revealed that the films had crystallized in the zinc blende, cation-disordered structure. The crystalline films exhibited optical absorption energy threshold values ranging from 0.8 to 1.3 eV. Increased Ge content was found in films that exhibited a decreased absorption onset energy. Native defect calculations were used to gain an understanding of the off-stoichiometry seen in these films. This work provides the first high-throughput investigation of ZnGeP 2 , demonstrating the ability to grow amorphous and cation disordered ZnGeP 2 over a wide range of compositions with varying optical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sicangu Village Solar Project

The Sicangu Village Solar Project, spearheaded by the Rosebud Sioux Tribe in partnership with GRID Alternatives, aimed to enhance energy sustainability within the community through the installation of a 149 kW community solar Photovoltaic (PV) array and 13 residential rooftop solar PV systems. Located in Todd County, South Dakota, the project addresses longstanding challenges of rising electricity costs and economic disparities faced by the Tribe. By leveraging solar energy production, the project not only reduces electricity expenses for the community, but also serves as a pivotal step towards achieving the Tribe's energy sovereignty goals. Despite encountering interconnection challenges and delays, particularly exacerbated by regulatory and infrastructure complexities, the project has successfully demonstrated the feasibility of solar energy deployment within the community.

14 SOLAR ENERGY↗

Energetic considerations for engineering novel biochemistries in photosynthetic organisms

Humans have been harnessing biology to make valuable compounds for generations. From beer and biofuels to pharmaceuticals, biology provides an efficient alternative to industrial processes. With the continuing advancement of molecular tools to genetically modify organisms, biotechnology is poised to solve urgent global problems related to environment, increasing population, and public health. However, the light dependent reactions of photosynthesis are constrained to produce a fixed stoichiometry of ATP and reducing equivalents that may not match the newly introduced synthetic metabolism, leading to inefficiency or damage. While photosynthetic organisms have evolved several ways to modify the ATP/NADPH output from their thylakoid electron transport chain, it is unknown if the native energy balancing mechanisms grant enough flexibility to match the demands of the synthetic metabolism. In this review we discuss the role of photosynthesis in the biotech industry, and the energetic considerations of using photosynthesis to power synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Pueblo of Laguna Village Community Solar

The project was to install approximately 11.44 kilowatts (kW) rooftop solar photovoltaic (PV) system on the Mesita Village Community Center, an approximately 9.24 kW rooftop solar PV system on the Paguate Village Community Center, an approximately 21.56 kW rooftop solar PV system on the Paraje Village Community Center, and an approximately 11.00 kW rooftop solar PV system on the Seama Community Center, for a total of about 53.24 kW on four village community centers. The systems were expected to generate approximately 93,329 kWh annually. Installing solar PV systems on the four village community centers would have helped achieve the Pueblo of Laguna’s six energy objectives: community development (decreased utility bills, funds for other needs), economic development (training and participation in the renewable energy economy), energy reliability (future storage), community resilience (alternative sources), relationship to people and the natural world (reducing fossil fuel use), and energy sovereignty (Pueblo decision-making). Installing solar PV systems would have also met specific project goals to offset not less than 85% of each selected building’s annual electricity use, ranging from 87% to 103% of demand; save a minimum of 70% of the cost of utility bills per year for each building, ranging from 75% to 77% percent (including service charges); and would have had payback periods shorter than the estimated useful life of the project

14 SOLAR ENERGY↗

Native and radiation induced point defects in AlN and Sc-doped AlN

Herein, we have performed first-principles calculations to investigate the electronic structure, configurations, formation, and binding energies of native and radiation induced point defects in pristine and Sc-doped wurtzite AlN. For the native defects, the nitrogen vacancy has the lowest formation energy in p-type material while the aluminum vacancy has the lowest formation energy in n-type material which is consistent with the previous studies. Several interstitial defect structures were modeled for Al, N, and Sc atoms. The effects of charge state on their relative stability were investigated. The binding energy of Sc with point defects was calculated and found to be dependent strongly on the defect type and charge state. The results obtained are discussed in light of the possible Sc effects on the radiation damage evolution in AlN. Thus the attraction of Sc atom to N vacancy and both Al and N interstitials reduces their mobility and increases Frenkel pair recombination distance.

36 MATERIALS SCIENCE↗

Controlling thermoelectric transport via native defects in the diamond-like semiconductors Cu 2 HgGeTe 4 and Hg 2 GeTe 4

Diamond like semiconductors (DLS) have emerged as candidates for thermoelectric energy conversion. Towards understanding and optimizing performance, we present a comprehensive investigation of the electronic properties of two DLS phases, quaternary Cu 2 HgGeTe 4 and related ordered vacancy compound Hg 2 GeTe 4 , including thermodynamic stability, defect chemistry, and transport properties. To establish the thermodynamic link between the related but distinct phases, the stability region for both is visualized in chemical potential space. In spite of their similar structure and bonding, we show that the two materials exhibit reciprocal behaviors for dopability. Cu 2 HgGeTe 4 is degenerately p-type in all environments despite its wide stability region, due to the presence of low-energy acceptor defects V Cu and Cu Hg and is resistant to extrinsic n-type doping. Meanwhile Hg 2 GeTe 4 has a narrow stability region and intrinsic behavior due to the relatively high formation energy of native defects, but presents an opportunity for bi-polar doping. While these two compounds have similar structure, bonding, and chemical constituents, the reciprocal nature of their dopability emerges from significant differences in band edge positions. A Brouwer band diagram approach is utilized to visualize the role of native defects on carrier concentrations, dopability, and transport properties. Here this study elucidates the doping asymmetry between two solid-solution forming DLS phases Cu 2 HgGeTe 4 and Hg 2 GeTe 4 by revealing the defect chemistry of each compound, and suggests design strategies for defect engineering of DLS phases.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

First principles investigation of dopants and defect complexes in CdSe$_x$Te$_{1-x}$

Se alloying is a common approach to improve the performance of CdTe solar cells by tuning the bandgap, defect levels, and carrier density. A fundamental understanding of these improvements, specifically the effect of Se alloying on the behavior of defects and dopants in CdTe, remains unclear. Here, in this work, we present a density functional theory (DFT) study of point defect energetics in CdTe and CdSe x Te 1-x with x = 0.25, leading to a comparison of how native defects, dopants (As and Cu), impurities (Cl and O), and related defect complexes behave in CdTe vs CdSe x Te 1-x . Our calculations, performed by combining semi-local and nonlocal hybrid functionals, show a general lowering of the formation energies of native defects as well as substitutional defects formed by As and Cl upon Se addition. For successful p-type doping with As, destabilizing Cl-based defects in the CdSeTe lattice would be essential. We find evidence for some low-energy defect complexes of As, Cl, and O in CdSe 0.25 Te 0.75 . The computed defect formation energies further enable estimates of temperature-dependent defect concentrations and self-consistent Fermi levels. A comparison of defect energetics with the energies of impurity phases reveals that As, Cu, Cl, and O overwhelmingly prefer being segregated to unwanted As 2 O 5 , AsCl 3 , Cd 2 AsCl 2 , and CuO x phases rather than remain at defect sites, but such segregation is less likely to happen in CdSe 0.25 Te 0.75 than in CdTe. Overall, our work presents a list of likely defects and complexes in CdTe and Se-incorporated CdTe, paving the way to explain and mitigate limited dopant activation in experimental observations.

CdTe↗

Multi-Sector Solar Career Training for Native Americans and Veterans

The “Multi-Sector Solar Career Training for Native Americans and Veterans” program (DE-EE0008575; Blue Lake Rancheria Tribe, with GRID Alternatives), was a job training and capacity-building project for Native American people and tribal communities. The project adds to understanding by identifying potential solutions to barriers that individuals and tribes may face as they seek to build 1) individual skillsets as solar technicians, and 2) staff capacity to develop solar energy projects.

14 SOLAR ENERGY↗

Concept Developed for an Implanted Stimulated Muscle-Powered Piezoelectric Generator

Implanted electronic devices are typically powered by batteries or transcutaneous power transmission. Batteries must be replaced or recharged, and transcutaneous power sources burden the patient or subject with external equipment prone to failure. A completely self-sustaining implanted power source would alleviate these limitations. Skeletal muscle provides an available autologous power source containing native chemical energy that produces power in excess of the requirements for muscle activation by motor nerve stimulation. A concept has been developed to convert stimulated skeletal muscle power into electrical energy (see the preceding illustration). We propose to connect a piezoelectric generator between a muscle tendon and bone. Electrically stimulated muscle contractions would exert force on the piezoelectric generator, charging a storage circuit that would be used to power the stimulator and other devices.

Lewandowski, Beth↗

Aniak Energy Efficiency Retrofit Project

The Native Village of Aniak (NVA), a federally recognized Yup'ik Tribe, undertook this energy efficiency initiative to enhance energy performance in key community buildings, including the Tribal Office, Community Center, Duplex, and Association of Village Council Presidents (AVCP) Office. Through energy audits and upgrades, the project focused on high-impact improvements like air sealing, LED lighting, and programmable thermostats, primarily in the Tribal Office due to funding constraints. The initiative aimed to reduce energy waste, lower heating and electricity costs, and improve facility comfort and longevity while achieving long-term savings for further improvements by decreasing reliance on imported fuel oil. Despite scope limitations exacerbated by budget constraints, this project achieved an approximately 52% reduction in EUI. Reducing operational costs emphasizes economic and environmental benefits, aligning closely with Aniak's broader energy sustainability objectives. This initiative aligned with the Tribe's vision for responsible energy use, addressing the challenges of high fuel prices in a remote community; it could serve as a model for similar efforts in Aniak and other Alaska Native villages pursuing energy self-reliance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Variation in energy balance components from six sites in a native prairie for three years

Six automatic stations were used to evaluate the surface energy and radiation balances on a native prairie near Manhattan, Kansas, using the Bowen ratio technique for a total of 300 days. Data were taken during the periods from May 26 to October 16, 1987, May 10 to September 18, 1988, and July 21 to August 13, 1989. The station site locations were selected to represent burned and unburned treatments on ridges, valley bottoms, and slopes with various aspects. The measured variables were (1) air and wet bulb temperatures at two heights, (2) net radiation, (3) solar radiation (up and down), (4) total hemispherical radiation (up and down), (5) diffuse radiation, (6) soil heat flow and soil temperature, (7) wind speed, (8) wind direction, and (9) precipitation. Energy balance components at the sites were compared for the 3 years. The variation between sites and years was small, even though some sites were as much as 10 km apart and the years had different rainfall amounts. The average values for the four summer intensive field campaigns (IFCs) were as follows: albedo, 0.2; ratio of net radiation to solar radiation, 62 percent; evaporation equivalent, 4 mm/d; Bowen ratio, 0.32; evaporation fraction, 70 percent; and the ratio of evaporation to solar energy, 40 percent. These values were different for the fall IFC. The latent and sensible heat fluxes were more variable than the radiation terms reflecting soil moisture differences between IFCs.

Fritschen, Leo J.↗

Defect Stability in CdTe Based on Formation Energies and Migration Barriers

Native point defects are thought to play a key role in CdTe, either as compensation centers in intentionally doped material, as a source of conductivity in nominally undoped material, or as electron–hole recombination centers. Here, the discussion of their concentration and impact has often centered only on formation energies and transition levels. Using hybrid density functional calculations, including the effects of spin–orbit coupling (SOC), we discuss the stability of native point defects in CdTe based on their formation energies and migration barriers. We show that although Cd interstitials are the lowest energy donor defects, they are unstable at room temperature due to a low migration barrier. They are important for maintaining charge neutrality during growth or annealing at high temperatures, but once the material is brought to room temperature, they are not frozen in as often assumed and are expected to anneal out, leaving the other more stable defects to determine the conductivity. Taking this into account in the solution of the charge neutrality equation, we are able to predict the conductivity type and carrier concentrations that are in good agreement with experimental observations.

14 SOLAR ENERGY↗

Akiachak Energy Efficiency Retrofit Project

The goal of the project is to reduce the overall energy use of the Akiachak Native Community (ANC) by implementing energy efficiency measures in five high-use Tribal buildings. This project will have the following outcomes: Projected annual energy savings of $17,369; projected annual reduction in fuel oil #1 of 1,200 gallons and electricity of 17,751 kWh; annual reduction in carbon dioxide emissions of approximately 60,340 pounds/year. ANC will install energy efficiency measures in the Laundry, Tribal Indian Reorganization Act (IRA) Office, Clinic, Daycare, and Police Station. ANC obtained energy audits on these buildings in 2018, and this project will implement high-payback recommendations such as replacing lighting with LEDs, installing setback thermostats and occupancy sensors, replacing furnaces with more efficient models, replacing the circulation pumps with variable speed ones, air tightening, and adding insulation. Buildings will see energy cost reductions from 15% to 40%. These retrofits will help build ANC’s long-term vision for sustainable energy usage and address the first goal of the Tribal IRA Council’s Energy Efficiency and Conservation Strategy, to “create and maintain functionally appropriate, sustainable, accessible, high quality tribal infrastructure and facilities.” ANC intends to replicate this project by using the resulting energy savings to address audit recommendations in other buildings as well as to demonstrate the value of energy efficiency to community members. Other outcomes will include an increase in community resiliency, reduced dependence on outside shipments of fuel oil, training for maintenance staff, and no-touch control of building appliances to reduce transmission of diseases such as COVID-19.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Akiachak Energy Efficiency Retrofit Project (Final Technical Report)

The Akiachak Native Community (ANC), a federally recognized Yup'ik Tribe, undertook this energy efficiency initiative to enhance energy performance in key community buildings, including the Tribal IRA Office, Laundry, Police Station, Clinic, and Daycare. Through energy audits and upgrades, the project focused on high-impact improvements like air sealing, LED lighting, and programmable thermostats, primarily in the Tribal Office due to funding constraints. The initiative aims to reduce energy waste, lower heating and electricity costs, and improve facility comfort and longevity. The project aims to generate long-term savings for further improvements by decreasing reliance on imported fuel oil. This initiative aligns with the Tribe's vision for responsible energy use, addressing the challenges of high fuel prices in a remote community, and serves as a model for similar efforts in Akiachak and other Alaska Native villages pursuing energy self-reliance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Aniak Energy Efficiency Retrofit Project

The Native Village of Aniak (NVA) is a remote Yup’ik community in western Alaska. NVA is proposing to install energy efficiency measures in the Tribal Office, Community Center, Association of Village Council Presidents (AVCP) Office, and Duplex. The goal of the project is to reduce the overall energy use of the NVA by implementing energy efficiency measures in four high-use tribal buildings. This project expects to have the following outcomes: projected annual energy savings of approximately $24,238; projected annual reduction in fuel oil of roughly 1,802 gallons and electricity of around 24,537 kWh; and annual reduction in carbon dioxide emissions of approximately 84,594 pounds/year.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗