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At least 613 records · Page 34

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.

36 MATERIALS SCIENCE↗

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

97 MATHEMATICS AND COMPUTING↗

Impact of network topology on synchrony of oscillatory power grids

Replacing conventional power sources by renewable sources in current power grids drastically alters their structure and functionality. In particular, power generation in the resulting grid will be far more decentralized, with a distinctly different topology. Here, we analyze the impact of grid topologies on spontaneous synchronization, considering regular, random, and small-world topologies and focusing on the influence of decentralization. We model the consumers and sources of the power grid as second order oscillators. First, we analyze the global dynamics of the simplest non-trivial (two-node) network that exhibit a synchronous (normal operation) state, a limit cycle (power outage), and coexistence of both. Second, we estimate stability thresholds for the collective dynamics of small network motifs, in particular, star-like networks and regular grid motifs. For larger networks, we numerically investigate decentralization scenarios finding that decentralization itself may support power grids in exhibiting a stable state for lower transmission line capacities. Decentralization may thus be beneficial for power grids, regardless of the details of their resulting topology. Regular grids show a specific sharper transition not found for random or small-world grids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accuracy of AFM force distance curves via direct solution of the Euler-Bernoulli equation

In an effort to improve the accuracy of force-separation curves obtained from atomic force microscope data, we compare force-separation curves computed using two methods to solve the Euler-Bernoulli equation. A recently introduced method using a direct sequential forward solution, Causal Time-Domain Analysis, is compared against a previously introduced Tikhonov Regularization method. Using the direct solution as a benchmark, it is found that the regularization technique is unable to reproduce accurate curve shapes. Using L-curve analysis and adjusting the regularization parameter, λ, to match either the depth or the full width at half maximum of the force curves, the two techniques are contrasted. Matched depths result in full width at half maxima that are off by an average of 27% and matched full width at half maxima produce depths that are off by an average of 109%.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Transitional properties of supersolitons in a two electron temperature warm multi-ion plasma

The existence domain of an ion acoustic supersoliton and its transition to a regular kind of solitary wave have been explored in detail using Sagdeev pseudopotential technique for a two electron temperature warm multi-ion plasma having two species of ions. It was found that both the cold to hot electron temperature ratio and their respective ambient densities play a deterministic role for the existence of a supersoliton, as well as its transitional processes to a regular solitary wave. Analogous to a double layer solution, which often marks the boundary of the existence domain of a regular solitary wave, a “curve of inflection” determines the boundary of the existence domain of a supersoliton. The characteristics of the “curve of inflection,” in turn, depend on the respective concentrations of the two ion species. It is observed that the supersolitons are actually a subset of a more general kind of solutions which are characterized by a fluctuation in the corresponding charge separation which precedes their maximum amplitude. It is also observed that these novel kinds of solitary structures, including supersolitons, occur only for a very narrow range of parameters near constant amplitude beyond which the wave breaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Studying excited-state-specific perturbation theory on the Thiel set

Here, we explore the performance of a recently introduced N 5 -scaling excited-state-specific second order perturbation theory (ESMP2) on the singlet excitations of the Thiel benchmarking set. We find that, without regularization, ESMP2 is quite sensitive to π system size, performing well in molecules with small π systems but poorly in those with larger π systems. With regularization, ESMP2 is far less sensitive to π system size and shows a higher overall accuracy on the Thiel set than CC2, equation of motion-coupled cluster with singles and doubles, CC3, and a wide variety of time-dependent density functional approaches. Unsurprisingly, even regularized ESMP2 is less accurate than multi-reference perturbation theory on this test set, which can, in part, be explained by the set’s inclusion of some doubly excited states but none of the strong charge transfer states that often pose challenges for state-averaging. Beyond energetics, we find that the ESMP2 doubles norm offers a relatively low-cost way to test for doubly excited character without the need to define an active space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On finite-dimensional smoothed-particle Hamiltonian reductions of the Vlasov equation

The inclusion of spatial smoothing in finite-dimensional particle-based Hamiltonian reductions of the Vlasov equation and related models is considered. Here, this work investigates the underlying Hamiltonian structure of such smoothed particle-based methods for Hamiltonian systems and the small-scale regularization such methods implicitly make in approximating the continuum theory. In the context of the Vlasov–Poisson equation and other mean-field Lie–Poisson systems, of which Vlasov–Poisson is a special case, smoothing amounts to a convolutive regularization of the Hamiltonian. This regularization may be interpreted as a change of the inner product structure used to identify the dual space in the Lie–Poisson Hamiltonian formulation. In particular, the shape function used for spatial smoothing may be identified as the kernel function of a reproducing kernel Hilbert space whose inner product is used to define the Lie–Poisson Hamiltonian structure. It is likewise possible to introduce smoothing in the Vlasov–Maxwell system, but in this case the Poisson bracket must be modified rather than the Hamiltonian. The smoothing applied to the Vlasov–Maxwell system is incorporated by inserting smoothing in the map from canonical to kinematic coordinates. In the filtered system, the Lorentz force law and the current, the two terms coupling the Vlasov equation with Maxwell’s equations, are spatially smoothed.

Hamiltonian mechanics↗

PHOTOEVAPORATION AS A TRUNCATION MECHANISM FOR CIRCUMPLANETARY DISKS

We investigate the conditions under which the regular satellites of Jupiter and Saturn formed. The final stage of giant planet accretion is thought to occur slowly over a relatively long, 10 Myr, timescale. Gas accretion during this stage, through a completely or partially opened gap in the solar nebula, occurs slowly, allowing for the condensation of ices and incomplete differentiation seen in the regular satellites of the giant planets. Furthermore, the dichotomy seen in the Jovian and Saturnian systems may be explained as this infall wanes or is completely shutoff as a result of gaps opening or global depletion of gas in the solar nebula. We present one-dimensional simulations of circumplanetary disks that couple the viscous transport of material with the loss of mass at the disk outer edge by ultraviolet photoevaporation as well as the infall of material from the solar nebula. We find that the circumplanetary disks of these protoplanets are truncated as a result of photoevaporation at a range of values with the mean corresponding to Almost-Equal-To 0.16 Hill radii. These truncation radii are broadly consistent with the current locations of the regular satellite systems of Jupiter and Saturn. We also find that photoevaporation can successfully act as a clearing mechanism for circumplanetary nebulae on the potentially short timescales, 10{sup 2}-10{sup 4} yr, over which mass accretion from the solar nebula wanes as a result of a gap opening. Such a rapid clearing of the circum-Jovian disk may be required to explain the survival of the Galilean satellites.

79 ASTRONOMY AND ASTROPHYSICS↗

ACTIVE AND PASSIVE GALAXIES AT z {approx} 2: REST-FRAME OPTICAL MORPHOLOGIES WITH WFC3

We use the high angular resolution in the near-infrared of the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope to determine YHVz color-color-selection criteria to identify and characterize 1.5 < z < 3.5 galaxies in the Hubble Ultra Deep Field 2009 (HUDF09) and Early Release Science (GOODS-South) fields. The WFC3 NIR images reveal galaxies at these redshifts that were undetected in the rest-frame UV HUDF/GOODS images, as well as true centers and regular disks in galaxies classified as highly irregular in rest-frame UV light. Across the 1.5 < z < 2.15 redshift range, regular disks are unveiled in the WFC3 images of {approx}25% of both intermediate and high mass galaxies, i.e., above 10{sup 10} M{sub Sun }. Meanwhile, galaxies maintaining diffuse and/or irregular morphologies in the rest-frame optical light-i.e., not yet dynamically settled-at these epochs are almost entirely restricted to masses below 10{sup 11} M{sub Sun }. In contrast at 2.25 < z < 3.5 these diffuse and/or irregular structures overwhelmingly dominate the morphological mix in both the intermediate and high mass regimes, while no regular disks, and only a small fraction ({approx}25%) of smooth spheroids, are evident above 10{sup 11} M{sub Sun }. Strikingly, by 1.5 < z < 2.25 roughly two out of every three galaxies at the highest masses are spheroids. In our small sample, the fraction of star-forming galaxies at these mass scales decreases concurrently from {approx}60% to {approx}5%. If confirmed, this indicates that z {approx} 2 is the epoch of both the morphological transformation and quenching of star formation which assemble the first substantial population of massive ellipticals.

79 ASTRONOMY AND ASTROPHYSICS↗

Non-ideal magnetohydrodynamic simulations of the two-stage fragmentation model for cluster formation

We model molecular cloud fragmentation with thin-disk, non-ideal magnetohydrodynamic simulations that include ambipolar diffusion and partial ionization that transitions from primarily ultraviolet-dominated to cosmic-ray-dominated regimes. These simulations are used to determine the conditions required for star clusters to form through a two-stage fragmentation scenario. Recent linear analyses have shown that the fragmentation length scales and timescales can undergo a dramatic drop across the column density boundary that separates the ultraviolet- and cosmic-ray-dominated ionization regimes. As found in earlier studies, the absence of an ionization drop and regular perturbations leads to a single-stage fragmentation on pc scales in transcritical clouds, so that the nonlinear evolution yields the same fragment sizes as predicted by linear theory. However, we find that a combination of initial transcritical mass-to-flux ratio, evolution through a column density regime in which the ionization drop takes place, and regular small perturbations to the mass-to-flux ratio is sufficient to cause a second stage of fragmentation during the nonlinear evolution. Cores of size ∼0.1 pc are formed within an initial fragment of ∼pc size. Regular perturbations to the mass-to-flux ratio also accelerate the onset of runaway collapse.

79 ASTRONOMY AND ASTROPHYSICS↗

Inducing chaos by breaking axial symmetry in a black hole magnetosphere

While the motion of particles near a rotating, electrically neutral (Kerr), and charged (Kerr-Newman) black hole is always strictly regular, a perturbation in the gravitational or the electromagnetic field generally leads to chaos. The transition from regular to chaotic dynamics is relatively gradual if the system preserves axial symmetry, whereas non-axisymmetry induces chaos more efficiently. Here we study the development of chaos in an oblique (electro-vacuum) magnetosphere of a magnetized black hole. Besides the strong gravity of the massive source represented by the Kerr metric, we consider the presence of a weak, ordered, large-scale magnetic field. An axially symmetric model consisting of a rotating black hole embedded in an aligned magnetic field is generalized by allowing an oblique direction of the field having a general inclination with respect to the rotation axis of the system. The inclination of the field acts as an additional perturbation to the motion of charged particles as it breaks the axial symmetry of the system and cancels the related integral of motion. The axial component of angular momentum is no longer conserved and the resulting system thus has three degrees of freedom. Our primary concern within this contribution is to find out how sensitive the system of bound particles is to the inclination of the field. We employ the method of the maximal Lyapunov exponent to distinguish between regular and chaotic orbits and to quantify their chaoticity. We find that even a small misalignment induces chaotic motion.

79 ASTRONOMY AND ASTROPHYSICS↗

Where did the tumor start? An inverse solver with sparse localization for tumor growth models

In this work, we present a numerical scheme for solving an inverse problem for parameter estimation in tumor growth models for glioblastomas, a form of aggressive primary brain tumor. The growth model is a reaction–diffusion partial differential equation (PDE) for the tumor concentration. We use a PDE-constrained optimization formulation for the inverse problem. The unknown parameters are the reaction coefficient (proliferation), the diffusion coefficient (infiltration), and the initial condition field for the tumor PDE. Segmentation of magnetic resonance imaging (MRI) scans drive the inverse problem where segmented tumor regions serve as partial observations of the tumor concentration. Like most cases in clinical practice, we use data from a single time snapshot. Moreover, the precise time relative to the initiation of the tumor is unknown, which poses an additional difficulty for inversion. We perform a frozen-coefficient spectral analysis and show that the inverse problem is severely ill-posed. We introduce a biophysically motivated regularization on the structure and magnitude of the tumor initial condition. In particular, we assume that the tumor starts at a few locations (enforced with a sparsity constraint on the initial condition of the tumor) and that the initial condition magnitude in the maximum norm is equal to one. We solve the resulting optimization problem using an inexact quasi-Newton method combined with a compressive sampling algorithm for the sparsity constraint. Our implementation uses PETSc and AccFFT libraries. We conduct numerical experiments on synthetic and clinical images to highlight the improved performance of our solver over a previously existing solver that uses standard two-norm regularization for the calibration parameters. The existing solver is unable to localize the initial condition. Our new solver can localize the initial condition and recover infiltration and proliferation. In clinical datasets (for which the ground truth is unknown), our solver results in qualitatively different solutions compared to the two-norm regularized solver.

97 MATHEMATICS AND COMPUTING↗

An improved current potential method for fast computation of stellarator coil shapes

Several fast methods for computing stellarator coil shapes are compared, including the classical NESCOIL procedure, its generalization using truncated singular value decomposition, and a Tikhonov regularization approach we call REGCOIL in which the squared current density is included in the objective function. Considering W7-X and NCSX geometries, and for any desired level of regularization, we find the REGCOIL approach simultaneously achieves lower surface-averaged and maximum values of both current density (on the coil winding surface) and normal magnetic field (on the desired plasma surface). This approach therefore can simultaneously improve the free-boundary reconstruction of the target plasma shape while substantially increasing the minimum distances between coils, preventing collisions between coils while improving access for ports and maintenance. The REGCOIL method also allows finer control over the level of regularization, it preserves convexity to ensure the local optimum found is the global optimum, and it eliminates two pathologies of NESCOIL: the resulting coil shapes become independent of the arbitrary choice of angles used to parameterize the coil surface, and the resulting coil shapes converge rather than diverge as Fourier resolution is increased. We therefore contend that REGCOIL should be used instead of NESCOIL for applications in which a fast and robust method for coil calculation is needed, such as when targeting coil complexity in fixed-boundary plasma optimization, or for scoping new stellarator geometries.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Electron interference in atomic ionization by two crossing polarized ultrashort pulses

Formation of geometrically regular interference patterns in the photoelectron momentum distributions (PMDs) corresponding to the photoionization of atoms by two single-color, crossing ultrashort pulses is investigated both analytically and numerically. It is shown that, in contrast to the photoionization by monochromatic pulses, PMDs for the ionization by crossing and co-propagating broadband pulses are essentially different (unless both pulses are linearly polarized), namely, when one pulse is linearly polarized along the propagation direction, ˆk, of the circularly polarized (CP) pulse, then interference maxima (minima) of the ionization probability have the form of three-dimensional single-arm regular spirals which are wound along ˆk. Next, the interference maxima (minima) of the ionization probability by a pair of crossing elliptically polarized pulses have the form of either Newton's rings or two-arm Fermat's spirals, depending on the position of a detection plane. Remarkably, these regular patterns occur only for certain values of the pulse ellipticities, and they become distorted for CP pulses. For both above-mentioned pulse configurations, the features of interference patterns depend on the time delay between pulses, their relative electric field amplitude, and relative carrier-envelope phase. Our predictions, illustrated by the numerical results for the ionization of H and He atoms by two orthogonal pulses, are quite general and we expect them to be valid for the ionization of any randomly oriented atomic or molecular target.

74 ATOMIC AND MOLECULAR PHYSICS↗

Obstacles to quantum annealing in a planar embedding of XORSAT

We introduce a planar embedding of the k-regular k-XORSAT problem, in which solutions are encoded in the ground state of a classical statistical mechanics model of reversible logic gates arranged on a square grid and acting on bits that represent the Boolean variables of the problem. The special feature of this embedding is that the resulting model lacks a finite-temperature phase transition, thus bypassing the first-order thermodynamic transition known to occur in the random graph representation of XORSAT. In spite of this attractive feature, the thermal relaxation into the ground state displays remarkably slow glassy behavior. The question addressed in this paper is whether this planar embedding can afford an efficient path to solution of k-regular k-XORSAT via quantum adiabatic annealing. We first show that our model bypasses an avoided level crossing and consequent exponentially small gap in the limit of small transverse fields. We then present quantum Monte Carlo results for our embedding of the k-regular k-XORSAT that strongly support a picture in which second-order and first-order transitions develop at a finite transverse field for k = 2 and k = 3, respectively. Furthermore, this translates into power-law and exponential dependences in the scaling of energy gaps with system size, corresponding to times-to-solution which are, respectively, polynomial and exponential in the number of variables. We conclude that neither classical nor quantum annealing can efficiently solve our reformulation of XORSAT, even though the original problem can be solved in polynomial time by Gaussian elimination.

2-dimensional systems↗

Degeneracy engineering for classical and quantum annealing: A case study of sparse linear regression in collider physics

Classical and quantum annealing are computing paradigms that have been proposed to solve a wide range of optimization problems. In this paper, we aim to enhance the performance of annealing algorithms by introducing the technique of degeneracy engineering, through which the relative degeneracy of the ground state is increased by modifying a subset of terms in the objective Hamiltonian. We illustrate this novel approach by applying it to the example of ℓ 0 -norm regularization for sparse linear regression, which is, in general, an NP-hard optimization problem. Specifically, we show how to cast ℓ 0 -norm regularization as a quadratic unconstrained binary optimization (QUBO) problem, suitable for implementation on annealing platforms. As a case study, we apply this QUBO formulation to energy flow polynomials in high-energy collider physics, finding that degeneracy engineering substantially improves the annealing performance. Furthermore, our results motivate the application of degeneracy engineering to a variety of regularized optimization problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The inverse problem of bimorph mirror tuning on a beamline

One of the challenges of tuning bimorph mirrors with many electrodes is that the calculated focusing voltages can be different by more than the safety limit (such as 500 V for the mirrors used at 17-ID at the Advanced Photon Source) between adjacent electrodes. A study of this problem at 17-ID revealed that the inverse problem of the tuning in situ, using X-rays, became ill-conditioned when the number of electrodes was large and the calculated focusing voltages were contaminated with measurement errors. Increasing the number of beamlets during the tuning could reduce the matrix condition number in the problem, but obtaining voltages with variation below the safety limit was still not always guaranteed and multiple iterations of tuning were often required. Applying Tikhonov regularization and using the L-curve criterion for the determination of the regularization parameter made it straightforward to obtain focusing voltages with well behaved variations. Some characteristics of the tuning results obtained using Tikhonov regularization are given in this paper.

43 PARTICLE ACCELERATORS↗