Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “neuron”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways

Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP’s enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP’s role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery

Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Impact of Nutrition on the Gut Microbiota: Implications for Parkinson’s Disease

Abstract Parkinson’s disease (PD) is a multifactorial neurodegenerative disease that is characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta and by the anomalous accumulation of α-synuclein aggregates into Lewy bodies and Lewy neurites. Research suggests 2 distinct subtypes of PD: the brain-first subtype if the pathology arises from the brain and then spreads to the peripheral nervous system (PNS) and the body-first subtype, where the pathological process begins in the PNS and then spreads to the central nervous system. This review primarily focuses on the body-first subtype. The influence of the gut microbiota on the development of PD has been the subject of growing interest among researchers. It has been suggested that gut inflammation may be closely associated with pathogenesis in PD, therefore leading to the hypothesis that gut microbiota modulation could play a significant role in this process. Nutrition can influence gut health and alter the risk and progression of PD by altering inflammatory markers. This review provides an overview of recent research that correlates variations in gut microbiota composition between patients with PD and healthy individuals with the impact of certain nutrients and dietary patterns, including the Mediterranean diet, the Western diet, and the ketogenic diet. It explores how these diets influence gut microbiota composition and, consequently, the risk of PD. Last, it examines fecal transplantation and the use of prebiotics, probiotics, or synbiotics as potential therapeutic strategies to balance the gut microbiome, aiming to reduce the risk or delay the progression of PD.

Sobral, Joana (ORCID:0009000334922337)↗
DOE OSTI2025

From disorganized data to emergent dynamic models: Questionnaires to partial differential equations

Starting with sets of disorganized observations of spatially varying and temporally evolving systems, obtained at different (also disorganized) sets of parameters, we demonstrate the data-driven derivation of parameter dependent, evolutionary partial differential equation (PDE) models capable of generating the data. This tensor type of data is reminiscent of shuffled (multidimensional) puzzle tiles. The independent variables for the evolution equations (their “space” and “time”) as well as their effective parameters are all emergent , i.e. determined in a data-driven way from our disorganized observations of behavior in them. We use a diffusion map based questionnaire approach to build a smooth parametrization of our emergent space/time/parameter space for the data. This approach iteratively processes the data by successively observing them on the “space,” the “time” and the “parameter” axes of a tensor. Once the data become organized, we use machine learning (here, neural networks) to approximate the operators governing the evolution equations in this emergent space. Our illustrative examples are based (i) on a simple advection–diffusion model; (ii) on a previously developed vertex-plus-signaling model of Drosophila embryonic development; and (iii) on two complex dynamic network models (one neuronal and one coupled oscillator model) for which no obvious smooth embedding geometry is known a priori. This allows us to discuss features of the process like symmetry breaking, translational invariance, and autonomousness of the emergent PDE model, as well as its interpretability.

generative models↗
DOE OSTI2022

Integrating Data From In Vitro New Approach Methodologies for Developmental Neurotoxicity

Abstract In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array neuronal network formation assay; and high-content imaging to evaluate proliferation, apoptosis, neurite outgrowth, and synaptogenesis. This work addresses 3 hypotheses: (1) a broad screening battery provides a sensitive marker of DNT bioactivity; (2) selective bioactivity (occurring at noncytotoxic concentrations) may indicate functional processes disrupted; and, (3) a subset of endpoints may optimally classify chemicals with in vivo evidence for DNT. The dataset was comprised of 92 chemicals screened in all 57 assay endpoints sourced from publicly available data, including a set of DNT NAM evaluation chemicals with putative positives (53) and negatives (13). The DNT NAM battery provides a sensitive marker of DNT bioactivity, particularly in cytotoxicity and network connectivity parameters. Hierarchical clustering suggested potency (including cytotoxicity) was important for classifying positive chemicals with high sensitivity (93%) but failed to distinguish patterns of disrupted functional processes. In contrast, clustering of selective values revealed informative patterns of differential activity but demonstrated lower sensitivity (74%). The false negatives were associated with several limitations, such as the maximal concentration tested or gaps in the biology captured by the current battery. This work demonstrates that this multi-dimensional assay suite provides a sensitive biomarker for DNT bioactivity, with selective activity providing possible insight into specific functional processes affected by chemical exposure and a basis for further research.

Carstens, Kelly E.↗
DOE OSTI2018

Correlation between Toluene Exposure and Toxicity Effects of Toluene on Drosophila Melanogaster Fecundity and Offspring Survivability

Toluene is a volatile organic compound that is a common indoor contaminant. According to the U.S. Department of Health and Human Services, chronic toluene exposure negatively affects organ systems, such as nervous and respiratory, and acts as a fetotoxic agent in the development of humans. Toluene exposure causes damage to human myelin sheaths, thus we propose that damage to the fly nervous system will be similar to that seen in humans exposed to toluene. Our ultimate goal is to determine the effects of toluene exposure on developmental and neuronal processes in D. melanogaster . In this first phase, we hypothesize that toluene‐exposed adults, at the interpolated Lethal Exposure (LE 50 ), will demonstrate decreased fecundity and that offspring from toluene‐exposed females will have decreased survivability from the egg to adult stage. We developed a continuous flow system that delivers known concentrations of gaseous toluene to populations of D. melanogaster . Ten to twenty adult female flies per trial were exposed for 24 hours to known concentrations of toluene. Surviving females were collected, counted and mated to non‐exposed adult males. The toluene‐exposed females were placed on a colored agar plate to lay eggs for 24 hours. Eggs were counted to determine fecundity (number of eggs produced by a single female fly). Survivability of eggs to later life stages, was measured by counting number of larvae, pupae, and adults divided by number eggs, larvae, and pupae respectively. The interpolated LE 50 of gaseous toluene was between 1000 and 1500 ppm after 24‐hour exposure. Fecundity of toluene‐exposed females decreased by approximately 50% when compared to airexposed females. The survivability of offspring of air‐exposed flies from egg to larval stages was 84% higher than published studies. We observed that larval eclosure from eggs laid by toluene‐exposed females was 35–50% higher on days 1 and 2 when compared to larval eclosure from eggs of air‐exposed exposed females. On days 3–6 the eclosure rate was relatively similar. These data showed toluene's effects on fecundity and survivability were measurable, however, additional replicates are in progress to fully assess the life table characteristics of offspring of toluene‐exposed female flies. Further studies will focus on toluene's effect on nervous and reproductive organs of fruit flies, along with a study on the mutagenic effects of toluene on fly DNA. Support or Funding Information U.S. DOE, Hispanic‐Serving Institutions, STEM Articulation Grant P031C110128 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

MacGregor, Michael Charles↗
DOE OSTI2019

Efficacy of Midazolam and Ketamine Combination Therapy over Midazolam Monotherapy against Soman Exposure in Carboxylesterase Knockout Mice

Introduction Chemical warfare nerve agents (CWNAs) inhibit acetylcholinesterase (AChE), which leads to status epilepticus (SE), spontaneous recurrent seizures (SRS) and severe neuropathology when treatment is delayed. In addition to binding to AChE, some organophosphorus (OP) CWNAs such as soman (GD) also inhibit carboxylesterase (CaE), which acts as a bioscavenger and can thus reduce the severity of the toxicity of OP agent exposure. Unlike humans, rodents have plasma CaE activity. The CaE knockout (ES1−/−) mouse specifically lacks plasma CaE and might better model human GD exposure compared to wildtype rodents. Delayed treatment of CWNA‐induced SE with midazolam leads to benzodiazepine‐refractory SE. We evaluated combination therapy of midazolam and the NMDA antagonist ketamine in male and female mice for efficacy against soman‐induced lethality, SE and epileptogenesis. Methods Mice implanted with telemetry transmitters for electroencephalography (EEG) seizure identification were exposed to 82 μg/kg GD (~4LD 50 ) and treated with an admix (ip) of atropine sulfate (4 mg/kg) and HI‐6 (50 mg/kg) 1 min after exposure, and with midazolam (3 mg/kg; ip) alone or in combination with ketamine (30 mg/kg, ip) at 40 min after seizure onset. Mice were continuously recorded to evaluate initial seizure duration and SRS and then euthanized 2 weeks after exposure for neuropathology assessment. Results Delayed treatment with midazolam resulted in poor survival, was unable to rapidly terminate behavioral or EEG seizure activity and did not prevent the development of SRS or neuronal loss following GD exposure. Combination therapy of midazolam and ketamine resulted in improved outcome, including an increase in survival from 30% to 78% in female and from 57% to 77% in males compared to midazolam monotherapy. In addition, the incidence of epileptogenesis was lower in mice treated with ketamine and midazolam dual therapy compared to midazolam monotherapy. Conclusions This study demonstrates that delayed treatment of SE with midazolam is not fully protective against the GD‐induced epileptogenesis and neuropathology, exemplifying the need for adjunct treatment to midazolam to prevent or reduce effects of GD‐induced SE. Ketamine combination with midazolam improves outcome. Support or Funding Information Research was supported by the CounterACT Program, NIH OD, and the NINDS (Grant 1R21NS103820‐01 to LA Lumley‐Lange) and by DTRA‐JSTO. Erica Kundrick, Katie Walker, and Sean O'Brien were supported in part by an appointment to the Research Participation Program for the U.S. Army Medical Research and Materiel Command administered by the Oak Ridge Institute for Science and Education through an agreement between the U.S. Department of Energy and U.S. Army Medical Research and Materiel Command. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Marrero‐Rosado, Brenda↗
DOE OSTI2018

PIP4Kγ as a potential target for Huntington's disease

Phosphoinositide lipids provide spatial and temporal regulation of cell signaling and membrane traffic. The PI5P‐4‐kinase family is one of the less studied phosphoinositide lipid kinases. These enzymes catalyze the conversion of phosphatidylinositol 5‐phosphate to phosphatidylinositol 4,5‐bis phosphate. A recent study by Vicinanza et al., a suggested that depletion of the PI5P‐4‐kinase, PIP4Kγ promotes a non‐canonical autophagy pathway. Moreover, this depletion reduced the presence of huntingtin‐exon1‐polyglutamine aggregates. Expression of exon1 of huntingtin with an extended polyglutamine tract is a model for huntingtin protein aggregates. To further test the hypothesis that PIP4Kγ is a potential target to reduce huntingtin aggregates, we tested the depletion of PIP4Kγ in cell culture models that express full length mutant huntingtin (mHtt). We determined that depletion of PIP4Kγ, but not PIP4Kα or PIP4Kβ, lowers the levels of mHtt in patient fibroblasts and in immortalized Hdh Q111 mouse striatal neurons. We show that PIP4Kγ‐dependent depletion of mHtt requires lysosomal function because the depletion is blocked by the lysosomal inhibitor, bafilomycin A1. Moreover, we show that depletion of PIP4Kγ increases autophagic flux, as measured by an increase in LC3‐II levels by western blot analysis and an increase in LC3‐II puncta by microscopy. Our studies suggest that PIP4kγ should be further pursued as a target for Huntington's disease. Support or Funding Information This work was supported by AHA postdoctoral fellowship 14POST20480137 (Sai Srinivas Panapakkam Giridharan), NIH grants R01GM050403 and NS064015 (Lois S Weisman) and by HSS funding 1R03MH084839 (Juan Marugan)

Giridharan, Sai Srinivas Panapakkam↗
DOE OSTI2022

Investigation of the photoluminescent properties, scintillation behaviour and toxicological profile of various magnesium tungstate nanoscale motifs

We have synthesized several morphologies and crystal structures of MgWO 4 using a one-pot hydrothermal method, producing not only monoclinic stars and large nanoparticles but also triclinic wool balls and sub-10 nm nanoparticles. Herein we describe the importance of reaction parameters in demonstrating morphology control of as-prepared MgWO 4 . Moreover, we correlate structure and composition with the resulting photoluminescence and radioluminescence properties. Specifically, triclinic-phase samples yielded a photoluminescence emission of 421 nm, whereas monoclinic-phase materials gave rise to an emission maximum of 515 nm. The corresponding radioluminescence data were characterized by a broad emission peak, located at 500 nm for all samples. Annealing the wool balls and sub-10 nm particles to transform the crystal structure from a triclinic to a monoclinic phase yielded a radioluminescence (RL) emission signal that was two orders of magnitude greater than that of their unannealed counterparts. Finally, to confirm the practical utility of these materials for biomedical applications, a series of sub-10 nm particles, including as-prepared and annealed samples, were functionalized with biocompatible PEG molecules, and subsequently were found to be readily taken up by various cell lines as well as primary cultured hippocampal neurons with low levels of toxicity, thereby highlighting for the first time the potential of this particular class of metal oxides as viable and readily generated platforms for a range of biomedical applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly

In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U) 4–6 G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. Here, we further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m 7 G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m 7 G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Comprehensive identification and analysis of human accelerated regulatory DNA

It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Intrinsic and Extrinsic Factors Influencing the Dynamics of VO 2 Mott Oscillators

Oscillatory devices have gained significant interest recently as key components of computing systems based on biomimetic neuronal spiking. An understanding of the time scales underlying the spiking is essential for engineering fast, controllable, low energy devices. However, we find that the intrinsic dynamics of these devices are difficult to properly characterize, as they can be heavily influenced by the external circuitry used to measure them. Here we demonstrate these challenges using a VO 2 Mott oscillator with a sub-100 nm effective size, achieved using a nanogap cut in a metallic carbon nanotube electrode. Given the nanoscale thermal volume of this device, it would be expected to exhibit rapid oscillations. However, due to external parasitics present within commonly used current sources, we see orders of magnitude slower dynamics. Here, we outline methods for determining when measurements are dominated by extrinsic factors and discuss the operating conditions under which intrinsic oscillation frequencies may be observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Compensation of Anisotropy in Spin Hall Devices for Neuromorphic Applications

Spintronic nano-oscillators and diodes with reduced nonlinearity benefit from low phase noise and improved device properties. Moreover, they could offer key advantages for realizing neuromorphic applications, such as spike-based neurons and frequency multiplexing in neural networks. Here, in this work, we experimentally demonstrate the reduction in nonlinearity of a spin Hall nano-oscillator (SHNO) by compensation of its effective magnetic anisotropy. The study involves optimization of Co/Ni multilayer growth to achieve the compensation, followed by spin-diode measurements on patterned microstrips to quantify their anisotropy. The relationship between the second- (H k 2 = 0.47 mT) and first-order ($H^{eff}_{k_1}$ = -0.8 mT) anisotropy fields reveals the existence of an easy cone, thereby validating the presence of compensation. Furthermore, we demonstrate a compensated spin diode that has a fixed frequency when the input power is varied. We then study the current-induced auto-oscillation properties of SHNOs on compensated films by patterning nanoconstrictions of 200 and 100 nm wide. The invariance of the resonance frequency and linewidth of the compensated SHNO with applied dc current indicates the absence of nonlinearity. This independence is maintained irrespective of the applied external fields and their orientations. The compensated SHNO obtained has a linewidth of 1.1 MHz and a peak output power of up to 1 pW/MHz.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Phase-field model of coupled insulator-metal transitions and oxygen vacancy redox reactions

A predominant ubiquitous feature of strongly correlated oxides is the possible presence of oxygen vacancies, which has recently been shown to have profound effects on their electronic phase transitions. Here, we formulate a comprehensive phase-field model of intercoupled insulator-metal transitions and oxygen vacancy redox reactions, taking into account the valence electron state of oxygen vacancies. We use the model to study the voltage self-oscillation phenomenon in a prototypical strongly correlated oxide, VO 2 , and discover the mutual activation of the insulator-metal transition and oxygen vacancy redox reactions leading to systematic enhancement of the oscillation frequency. Furthermore, the established methodology and the mutual activation mechanism are generally applicable to understanding any insulator-metal transition dynamics in oxygen-deficient correlated oxides and improving the performance of voltage self-oscillation-based artificial neurons.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Spin frustration and an exotic critical point in ferromagnets from nonuniform opposite g factors

Here, it is demonstrated that novel spin frustration can be induced in ferromagnets with nonuniform opposite Landé g-factors. The frustrated state is characterized by a mutual interplay of typical ferromagnetic (FM) and antiferromagnetic (AF) features, such as the zero-field susceptibility being FM-like at low temperatures but AF-like at high temperatures. It is also found to contain an exotic zero-temperature 'half fire, half ice' critical point at which the spins on one sublattice are fully disordered and on the other one are fully ordered. We suggest that such frustration may occur in a number of copper-iridium oxides such as Sr 3 CuIrO 6 . We also anticipate a realization of the frustration and 'partial fire, partial ice' states in certain antiferromagnets, lattice gas, and neuron systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Active elastohydrodynamics of vesicles in narrow blind constrictions

Fluid-resistance limited transport of vesicles through narrow constrictions is a recurring theme in many biological and engineering applications. Inspired by the motor-driven movement of soft membrane-bound vesicles into closed neuronal dendritic spines, here we study this problem using a combination of passive three-dimensional simulations and a simplified semianalytical theory for the active transport of vesicles forced through constrictions by molecular motors. We show that the motion of these objects is characterized by two dimensionless quantities related to the geometry and to the strength of forcing relative to the vesicle elasticity. We use numerical simulations to characterize the transit time for a vesicle forced by fluid pressure through a constriction in a channel and find that relative to an open channel, transport into a blind end leads to the formation of a smaller forward-flowing lubrication layer that strongly impedes motion. When the fluid pressure forcing is complemented by forces due to molecular motors that are responsible for vesicle trafficking into dendritic spines, we find that the competition between motor forcing and fluid drag results in multistable dynamics reminiscent of the real system. Our study highlights the role of nonlocal hydrodynamic effects in determining the kinetics of vesicular transport in constricted geometries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Exact block encoding of imaginary time evolution with universal quantum neural networks

We develop a constructive approach to generate quantum neural networks capable of representing the exact thermal states of all many-body qubit Hamiltonians. The Trotter expansion of the imaginary time propagator is implemented through an exact block encoding by means of a unitary, restricted Boltzmann machine architecture. Marginalization over the hidden-layer neurons (auxiliary qubits) creates the nonunitary action on the visible layer. Then, we introduce a unitary deep Boltzmann machine architecture in which the hidden-layer qubits are allowed to couple laterally to other hidden qubits. We prove that this wave-function is closed under the action of the imaginary time propagator and, more generally, can represent the action of a universal set of quantum gate operations. We provide analytic expressions for the coefficients for both architectures, thus enabling exact network representations of thermal states without stochastic optimization of the network parameters. In the limit of large imaginary time, the yields the ground state of the system. The number of qubits grows linearly with the number of interactions and total imaginary time for a fixed interaction order. Both networks can be readily implemented on quantum hardware via midcircuit measurements of auxiliary qubits. If only one auxiliary qubit is measured and reset, the circuit depth scales linearly with imaginary time and number of interactions, while the width is constant. Alternatively, one can employ a number of auxiliary qubits linearly proportional to the number of interactions, and circuit depth grows linearly with imaginary time only. Every midcircuit measurement has a postselection success probability, and the overall success probability is equal to the product of the probabilities of the midcircuit measurements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder

Crystals of human CRMP-4 showed severe lattice-translocation disorder. Intensities were demodulated using the so-called lattice-alignment method and a new more general method with simplified parameterization, and the structure is presented. Collapsin response mediator proteins (CRMPs) are cytosolic phosphoproteins that are mainly involved in neuronal cell development. In humans, the CRMP family comprises five members. Here, crystal structures of human CRMP-4 in a truncated and a full-length version are presented. The latter was determined from two types of crystals, which were either twinned or partially disordered. The crystal disorder was coupled with translational NCS in ordered domains and manifested itself with a rather sophisticated modulation of intensities. The data were demodulated using either the two-lattice treatment of lattice-translocation effects or a novel method in which demodulation was achieved by independent scaling of several groups of intensities. This iterative protocol does not rely on any particular parameterization of the modulation coefficients, but uses the current refined structure as a reference. The best results in terms of R factors and map correlation coefficients were obtained using this new method. The determined structures of CRMP-4 are similar to those of other CRMPs. Structural comparison allowed the confirmation of known residues, as well as the identification of new residues, that are important for the homo- and hetero-oligomerization of these proteins, which are critical to nerve-cell development. The structures provide further insight into the effects of medically relevant mutations of the DPYSL-3 gene encoding CRMP-4 and the putative enzymatic activities of CRMPs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗