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At least 325 records · Page 18

Complexity Phase Diagram for Interacting and Long-Range Bosonic Hamiltonians

Here, we classify phases of a bosonic lattice model based on the computational complexity of classically simulating the system. We show that the system transitions from being classically simulable to classically hard to simulate as it evolves in time, extending previous results to include on-site number-conserving interactions and long-range hopping. Specifically, we construct a complexity phase diagram with easy and hard “phases” and derive analytic bounds on the location of the phase boundary with respect to the evolution time and the degree of locality. We find that the location of the phase transition is intimately related to upper bounds on the spread of quantum correlations and protocols to transfer quantum information. Remarkably, although the location of the transition point is unchanged by on-site interactions, the nature of the transition point does change. Specifically, we find that there are two kinds of transitions, sharp and coarse, broadly corresponding to interacting and noninteracting bosons, respectively. Our Letter motivates future studies of complexity in many-body systems and its interplay with the associated physical phenomena.

97 MATHEMATICS AND COMPUTING↗

Resilience Modeling in Complex Engineered Systems with Human-Machine Interactions

In recent times, there has been a growing interest in resilience-based design. Resilience-based design operates on the concept that failures and unexpected events will happen, and when they occur, complex engineered systems should be able to operate within acceptable bounds and recover reasonably. Humans can contribute to the resilience of a system by quickly detecting unforeseen events and taking corrective measures. To this effect, researchers have proposed guidelines and design approaches that can help promote human-system resilience. However, there is no early design stage tool to validate if a system is indeed resilient after applying these guidelines and design methods. In this research, we integrate the Human Error and Functional Failure Reasoning (HEFFR) framework into the fmdtools toolkit to enable designers to model the combined (machine, human, and joint) failures, including their propagation and dynamic effects, during early design stages. This integrated tool also allows designers to model the effects of performance shaping factors, team dynamics, and human-machine interactions in systems of systems. A demonstrative example of a remotely operated rover is explored to demonstrate how this approach can be applied to understand resilience in complex engineered systems with human interactions.

Lukman Irshad↗

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.

60 APPLIED LIFE SCIENCES↗

The complex momentum representation approach and its application to low-lying resonances in ${^{17}}$O and ${^{29,31}}$F

Approaches for predicting low-lying resonances, uniformly treating bound, and resonant levels have been a long-standing goal in nuclear theory. Accordingly, we explored the viability of the complex momentum representation (CMR) approach coupled with new potentials. We focus on predicting the energy of the low-lying 2p 3/2 resonance in 17 O, which is critical for s-process nucleosynthesis and missing in previous theoretical research. Here, using a Woods-Saxon potential based on the Koning-Delaroche optical model and constrained by the experimental one-neutron separation energy, we successfully predicted the resonant energy of this level for the first time. Our predictions of the bound levels and 1d 3/2 resonance agree well with the measurement results. Additionally, we utilize this approach to study the near-threshold resonances that play a role when forming a two-neutron halo in 29,31 F. We found that the CMR-based predictions of the bound-level energies and unbound 1f 7/2 level agree well with the results obtained using the scattering phase shift method. Subsequently, we successfully found a solution for the 2p 3/2 resonance with energy just above the threshold, which is decisive for halo formation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Space in Space: Designing for Privacy in the Workplace

Privacy is cultural, socially embedded in the spatial, temporal, and material aspects of the lived experience. Definitions of privacy are as varied among scholars as they are among those who fight for their personal rights in the home and the workplace. Privacy in the workplace has become a topic of interest in recent years, as evident in discussions on Big Data as well as the shrinking office spaces in which people work. An article in The New York Times published in February of this year noted that "many companies are looking to cut costs, and one way to do that is by trimming personal space". Increasingly, organizations ranging from tech start-ups to large corporations are downsizing square footage and opting for open-office floorplans hoping to trim the budget and spark creative, productive communication among their employees. The question of how much is too much to trim when it comes to privacy, is one that is being actively addressed by the National Aeronautics and Space Administration (NASA) as they explore habitat designs for future space missions. NASA recognizes privacy as a design-related stressor impacting human health and performance. Given the challenges of sustaining life in an isolated, confined, and extreme environment such as Mars, NASA deems it necessary to determine the acceptable minimal amount for habitable volume for activities requiring at least some level of privacy in order to support optimal crew performance. Ethnographic research was conducted in 2013 to explore perceptions of privacy and privacy needs among astronauts living and working in space as part of a long-distance, long-duration mission. The allocation of space, or habitable volume, becomes an increasingly complex issue in outer space due to the costs associated with maintaining an artificial, confined environment bounded by limitations of mass while located in an extreme environment. Privacy in space, or space in space, provides a unique case study of the complex notions of privacy, the impact of design and others on achieving it, and the sensemaking that occurs when privacy is less than expected. The findings show that privacy is not just a personal, individual need but is also a need that is shared among teams and groups. Moreover, the case of space in space reveals the influence the design of the built and social environments have on privacy needs and on achieving privacy. When the level of privacy is less than expected, sensemaking occurs and the lack of privacy is dealt with by means of absencing the present. creating new social norms, and "making space" by manipulating the spatial, temporal, material aspects of the lived experience. Although the Mars habitat study represents an extreme case of privacy in the workplace, lessons learned from outer space are applicable to life in the Earth-bound workplace. A mini-case study was conducted to evaluate office space at the headquarters of a major American airline that illustrates the usefulness of building unexpected bridges between the unknown, unfamiliar Mars habitat and the everyday workplace. The comparative studies reveal insight into the interconnected, social nature of the spatial, temporal, and material aspects of the lived experience and how users of the habitat and office workspace view privacy, self, and others through an embodied, design interaction.

Akin, Jonie↗

Data for Simultaneous Suppression of Lignin, Tricin and Wall-Bound Phenolic Biosynthesis via the Expression of Monolignol 4- O -Methyltransferases in Rice

Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross-link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro-industrial applications. In the present study, we assess the applications of two engineered monolignol 4- O -methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para-methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan-bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol-extractable 4- O -methylated ferulic acid and 5–7 μmol/g 4- O -methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de-starched rice straw biomass after diluted acid-pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar-based production of biofuel and bio-chemicals.

Biomass Analytics↗

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗

Implications of the Upper Bound on h → μ + μ - on the Baryon Asymmetry of the Universe

The upper bounds from the ATLAS and CMS experiments on the decay rate of the Higgs boson to two muons provide the strongest constraint on an imaginary part of the muon Yukawa coupling. This bound is more than an order of magnitude stronger than bounds from $\mathcal{CP}$-violating observables, specifically the electric dipole moment of the electron. It excludes a scenario $-$ which had been viable prior to these measurements $-$ that a complex muon Yukawa coupling is the dominant source of the baryon asymmetry. Even with this bound, the muon source can still contribute ${\cal O}(16\%)$ of the asymmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Analytic continuation of the relativistic three-particle scattering amplitudes

We investigate the relativistic scattering of three identical scalar bosons interacting via pair-wise interactions. Extending techniques from the nonrelativistic three-body scattering theory, we provide a detailed and general prescription for solving and analytically continuing integral equations describing the three-body reactions. We use these techniques to study a system with zero angular momenta described by a single scattering length leading to a bound state in a two-body subchannel. We obtain bound-state-particle and three-particle amplitudes in the previously unexplored kinematical regime; in particular, for real energies below elastic thresholds and complex energies in the physical and unphysical Riemann sheets. We extract positions of three-particle bound-states that agree with previous finite-volume studies, providing further evidence for the consistency of the relativistic finite-volume three-body quantization conditions. We also determine previously unobserved virtual bound states in this theory. Lastly, we find numerical evidence of the breakdown of the two-body finite-volume formalism in the vicinity of the left-hand cuts and argue for the generalization of the existing formalism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Polyamine binding to proteins in oat and Petunia protoplasts

Previous work (A Apelbaum et al. [1988] Plant Physiol 88: 996-998) has demonstrated binding of labeled spermidine (Spd) to a developmentally regulated 18 kilodalton protein in tobacco tissue cultures derived from thin surface layer explants. To assess the general importance of such Spd-protein complexes, we attempted bulk isolation from protoplasts of Petunia and oat (Avena sativa). In Petunia, as in tobacco, fed radioactive Spd is bound to protein, but in oat, Spd is first converted to 1,3,-diaminopropane (DAP), probably by polyamine oxidase action. In oat, binding of DAP to protein depends on age of donor leaf and conditions of illumination and temperature, and the extraction of the DAP-protein complex depends upon buffer and pH. The yield of the DAP-protein complex was maximized by extraction of frozen-thawed protoplasts with a pH 8.8 carbonate buffer containing SDS. Its molecular size, based on Sephacryl column fractionation of ammonium sulfate precipitated material, exceeded 45 kilodaltons. Bound Spd or DAP can be released from their complexes by the action of Pronase, but not DNAse, RNAse, or strong salt solutions, indicating covalent attachment to protein.

NASA Discipline Plant Biology↗

Homoleptic 1,2-benzenedithiolate complexes of thorium and uranium

Reaction of 4 equiv. of [Li(TMEDA)] 2 [1,2-S 2 C 6 H 4 ] with [ThCl 4 (DME) 2 ] or [UCl 4 (THF) 3 ] in THF results in formation of [Li(THF) 2 ] 4 [An(1,2-S 2 C 6 H 4 ) 4 ] (An = Th, 1; An = U, 2), whereas reaction of 4 equiv. of [Li(TMEDA)] 2 [1,2-S 2 C 6 H 4 ] with UCl 4 in Et 2 O results in formation of [Li(TMEDA)] 4 [U(1,2-S 2 C 6 H 4 ) 4 ] (3). Complexes 1–3 represent the first reported benzenedithiolate complexes of the actinides. Here, they were characterized by NMR spectroscopy and X-ray crystallography. In the solid state, complexes 1–3 exhibit triangular dodecahedral geometries about their actinide centers. Additionally, their Li + cations are bound by two sulfur atoms of adjacent [1,2-S 2 C 6 H 4 ] 2− ligands, in addition to two solvent donor atoms. In solution, complexes 2 and 3 exhibit spectral data consistent with S 4 symmetry (and non-exchanging Li + sites), whereas complex 1 exhibits spectral properties consistent with labile Li + cations.

X-ray↗

Theory of Trotter Error with Commutator Scaling

The Lie-Trotter formula, together with its higher-order generalizations, provides a simple approach to decomposing the exponential of a sum of operators. Despite significant effort, the error scaling of such product formulas remains poorly understood. We develop a theory of Trotter error that overcomes the limitations of truncating the Baker-Campbell-Hausdorff expansion. Our analysis directly exploits the commutativity of operator summands, producing tighter error bounds for both real- and imaginary-time evolutions. Whereas previous work achieves similar goals for systems with geometric locality or Lie-algebraic structure, our approach holds in general. We give a host of improved algorithms for digital quantum simulation and quantum Monte Carlo methods, nearly matching or even outperforming the best previous results. Our applications include: (i) a simulation of second-quantized plane-wave electronic structure, nearly matching the interaction-picture algorithm of Low and Wiebe; (ii) a simulation of $k$-local Hamiltonians almost with induced one-norm scaling, faster than the qubitization algorithm of Low and Chuang; (iii) a simulation of rapidly decaying power-law interactions, outperforming the Lieb-Robinson-based approach of Tran et al.; (iv) a hybrid simulation of clustered Hamiltonians, dramatically improving the result of Peng, Harrow, Ozols, and Wu; and (v) quantum Monte Carlo simulations of the transverse field Ising model and quantum ferromagnets, tightening previous analyses of Bravyi and Gosset. We obtain further speedups using the fact that product formulas can preserve the locality of the simulated system. Specifically, we show that local observables can be simulated with complexity independent of the system size for power-law interacting systems, which implies a Lieb-Robinson bound nearly matching a recent result of Tran et al. Our analysis reproduces known tight bounds for first- and second-order formulas. We further investigate the tightness of our bounds for higher-order formulas. For quantum simulation of a one-dimensional Heisenberg model with an even-odd ordering of terms, our result overestimates the complexity by only a factor of $5$. Our bound is also close to tight for power-law interactions and other orderings of terms. This suggests that our theory can accurately characterize Trotter error in terms of both the asymptotic scaling and the constant prefactor.

quantum computing, numerical analysis↗

Mercury Removal from Contaminated Water by Wood-Based Biochar Depends on Natural Organic Matter and Ionic Composition

Biochars can remove potentially toxic elements, such as inorganic mercury [Hg(II)] from contaminated waters. However, their performance in complex water matrices is rarely investigated, and the combined roles of natural organic matter (NOM) and ionic composition in the removal of Hg(II) by biochar remain unclear. Here, we investigate the influence of NOM and major ions such as chloride (Cl – ), nitrate (NO 3 – ), calcium (Ca 2+ ), and sodium (Na + ) on Hg(II) removal by a wood-based biochar (SWP700). Multiple sorption sites containing sulfur (S) were located within the porous SWP700. In the absence of NOM, Hg(II) removal was driven by these sites. Ca 2+ bridging was important in enhancing removal of negatively charged Hg(II)-chloro complexes. In the presence of NOM, formation of soluble Hg-NOM complexes (as seen from speciation calculations), which have limited access to biochar pores, suppressed Hg(II) removal, but Cl – and Ca 2+ could still facilitate it. The ability of Ca 2+ to aggregate NOM, including Hg-NOM complexes, promoted Hg(II) removal from the dissolved fraction (<0.45 μm). Hg(II) removal in the presence of Cl – followed a stepwise mechanism. Weakly bound oxygen functional groups in NOM were outcompeted by Cl – , forming smaller-sized Hg(II)-chloro complexes, which could access additional intraparticle sorption sites. Therein, Cl – was outcompeted by S, which finally immobilized Hg(II) in SWP700 as confirmed by extended X-ray absorption fine structure spectroscopy. We conclude that in NOM containing oxic waters, with relatively high molar ratios of Cl – : NOM and Ca 2+ : NOM, Hg(II) removal can still be effective with SWP700.

54 ENVIRONMENTAL SCIENCES↗

An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ

The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.

59 BASIC BIOLOGICAL SCIENCES↗

Simultaneous suppression of lignin, tricin and wall‐bound phenolic biosynthesis via the expression of monolignol 4‐ O ‐methyltransferases in rice

Summary Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross‐link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro‐industrial applications. In the present study, we assess the applications of two engineered monolignol 4‐ O ‐methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para ‐methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan‐bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol‐extractable 4‐ O ‐methylated ferulic acid and 5–7 μmol/g 4‐ O ‐methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de‐starched rice straw biomass after diluted acid‐pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar‐based production of biofuel and bio‐chemicals.

4-O-methylated↗

Revealing the nature of electron correlation in transition metal complexes with symmetry breaking and chemical intuition

Here, in this work, we provide a nuanced view of electron correlation in the context of transition metal complexes, reconciling computational characterization via spin and spatial symmetry breaking in single-reference methods with qualitative concepts from ligand-field and molecular orbital theories. These insights provide the tools to reliably diagnose the multi-reference character, and our analysis reveals that while strong (i.e., static) correlation can be found in linear molecules (e.g., diatomics) and weakly bound and antiferromagnetically coupled (monometal-noninnocent ligand or multi-metal) complexes, it is rarely found in the ground-states of mono-transition-metal complexes. This leads to a picture of static correlation that is no more complex for transition metals than it is, e.g., for organic biradicaloids. In contrast, the ability of organometallic species to form more complex interactions, involving both ligand-to-metal σ-donation and metal-to-ligand π-backdonation, places a larger burden on a theory's treatment of dynamic correlation. We hypothesize that chemical bonds in which inter-electron pair correlation is non-negligible cannot be adequately described by theories using MP2 correlation energies and indeed find large errors vs experiment for carbonyl-dissociation energies from double-hybrid density functionals. A theory's description of dynamic correlation (and to a less important extent, delocalization error), which affects relative spin-state energetics and thus spin symmetry breaking, is found to govern the efficacy of its use to diagnose static correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single‐Site Carbon‐Supported Metal‐Oxo Complexes in Heterogeneous Catalysis: Structure, Reactivity, and Mechanism

Abstract When early transition metal complexes are molecularly grafted onto catalyst supports, well‐defined, surface‐bound species are created, which are highly active and selective single‐site heterogeneous catalysts (SSHCs) for diverse chemical transformations. In this minireview, we analyze and summarize a less conventional type of SSHC in which molybdenum dioxo species are grafted onto unusual carbon‐unsaturated scaffolds, such as activated carbon, reduced graphene oxide, and carbon nanohorns. The choice of earth‐abundant, low‐toxicity, versatile metal constituents, and various carbon supports illustrates “catalyst by design” principles and yields insights into new catalytic systems of both academic and technological interest. Here, we summarize experimental and computational investigations of the bonding, electronic structure, reaction scope, and mechanistic pathways of these unusual catalysts.

Liu, Yiqi↗