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At least 343 records · Page 19

The emergence of Zipf's law - Spontaneous encoding optimization by users of a command language

The distribution of commands issued by experienced users of a computer operating system allowing command customization tends to conform to Zipf's law. This result documents the emergence of a statistical property of natural language as users master an artificial language. Analysis of Zipf's law by Mandelbrot and Cherry shows that its emergence in the computer interaction of experienced users may be interpreted as evidence that these users optimize their encoding of commands. Accordingly, the extent to which users of a command language exhibit Zipf's law can provide a metric of the naturalness and efficiency with which that language is used.

Ellis, S. R.↗

The specification-based validation of reliable multicast protocol: Problem Report

Reliable Multicast Protocol (RMP) is a communication protocol that provides an atomic, totally ordered, reliable multicast service on top of unreliable IP multicasting. In this report, we develop formal models for RMP using existing automated verification systems, and perform validation on the formal RMP specifications. The validation analysis help identifies some minor specification and design problems. We also use the formal models of RMP to generate a test suite for conformance testing of the implementation. Throughout the process of RMP development, we follow an iterative, interactive approach that emphasizes concurrent and parallel progress of implementation and verification processes. Through this approach, we incorporate formal techniques into our development process, promote a common understanding for the protocol, increase the reliability of our software, and maintain high fidelity between the specifications of RMP and its implementation.

Wu, Yunqing↗

The Specification-Based Validation of Reliable Multicast Protocol

Reliable Multicast Protocol (RMP) is a communication protocol that provides an atomic, totally ordered, reliable multicast service on top of unreliable IP multicasting. In this report, we develop formal models for RMP using existing automated verification systems, and perform validation on the formal RMP specifications. The validation analysis help identifies some minor specification and design problems. We also use the formal models of RMP to generate a test suite for conformance testing of the implementation. Throughout the process of RMP development, we follow an iterative, interactive approach that emphasizes concurrent and parallel progress of the implementation and verification processes. Through this approach, we incorporate formal techniques into our development process, promote a common understanding for the protocol, increase the reliability of our software, and maintain high fidelity between the specifications of RMP and its implementation.

Wu, Yunqing↗

Optimization of Car Body under Constraints of Noise, Vibration, and Harshness (NVH), and Crash

To be competitive on the today's market, cars have to be as light as possible while meeting the Noise, Vibration, and Harshness (NVH) requirements and conforming to Government-man dated crash survival regulations. The latter are difficult to meet because they involve very compute-intensive, nonlinear analysis, e.g., the code RADIOSS capable of simulation of the dynamics, and the geometrical and material nonlinearities of a thin-walled car structure in crash, would require over 12 days of elapsed time for a single design of a 390K elastic degrees of freedom model, if executed on a single processor of the state-of-the-art SGI Origin2000 computer. Of course, in optimization that crash analysis would have to be invoked many times. Needless to say, that has rendered such optimization intractable until now. The car finite element model is shown. The advent of computers that comprise large numbers of concurrently operating processors has created a new environment wherein the above optimization, and other engineering problems heretofore regarded as intractable may be solved. The procedure, shown, is a piecewise approximation based method and involves using a sensitivity based Taylor series approximation model for NVH and a polynomial response surface model for Crash. In that method the NVH constraints are evaluated using a finite element code (MSC/NASTRAN) that yields the constraint values and their derivatives with respect to design variables. The crash constraints are evaluated using the explicit code RADIOSS on the Origin 2000 operating on 256 processors simultaneously to generate data for a polynomial response surface in the design variable domain. The NVH constraints and their derivatives combined with the response surface for the crash constraints form an approximation to the system analysis (surrogate analysis) that enables a cycle of multidisciplinary optimization within move limits. In the inner loop, the NVH sensitivities are recomputed to update the NVH approximation model while keeping the Crash response surface constant. In every outer loop, the Crash response surface approximation is updated, including a gradual increase in the order of the response surface and the response surface extension in the direction of the search. In this optimization task, the NVH discipline has 30 design variables while the crash discipline has 20 design variables. A subset of these design variables (10) are common to both the NVH and crash disciplines. In order to construct a linear response surface for the Crash discipline constraints, a minimum of 21 design points would have to be analyzed using the RADIOSS code. On a single processor in Origin 2000 that amount of computing would require over 9 months! In this work, these runs were carried out concurrently on the Origin 2000 using multiple processors, ranging from 8 to 16, for each crash (RADIOSS) analysis. Another figure shows the wall time required for a single RADIOSS analysis using varying number of processors, as well as provides a comparison of 2 different common data placement procedures within the allotted memories for each analysis. The initial design is an infeasible design with NVH discipline Static Torsion constraint violations of over 10%. The final optimized design is a feasible design with a weight reduction of 15 kg compared to the initial design. This work demonstrates how advanced methodology for optimization combined with the technology of concurrent processing enables applications that until now were out of reach because of very long time-to-solution.

Kodiyalam, Srinivas↗

Symmetric Mass Generation with Four SU(2) Doublet Fermions

We study a single exactly massless staggered fermion in the fundamental representation of an SU(2) gauge group. We utilize an nHYP-smeared fermion action supplemented with additional heavy Pauli-Villars fields that serve to decrease lattice artifacts. The phase diagram exhibits a clear two-phase structure with a conformal phase at weak coupling and a novel new phase, the symmetric mass generation (SMG) phase, appearing at strong coupling. The SMG phase is confining with all states gapped and chiral symmetry unbroken. Our finite size scaling analysis provides strong evidence that the phase transition between these two phases is continuous, which would allow for the existence of a continuum SMG phase. Furthermore, the renormalization group flows are consistent with a 𝛽 function that vanishes quadratically at the new fixed point, suggesting that the 𝑁 𝑓 = 4 flavor SU(2) gauge theory lies at the opening of the conformal window.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗

X-Ray Diffraction Analysis of NLO Crystals: Traditional Applications and More New Opportunities

Single crystal X-ray diffraction analysis is one of the more important methods for the molecular and crystal structure determination of matter and therefore it has a great importance in material science including design and engineering of different compounds with non-linear optical (NLO) properties. It was shown in our previous publications that this method provides unique information about molecular structure of NLO compounds, their crystal symmetry and crystal packing arrays, molecular conformation and geometries and many other structural and electronic characteristics that are important for understanding the nature of NLO properties of solids. A very new application of the X-ray diffraction method is related to analysis of the electron density distribution p(r) in crystals and some of its characteristics (atomic and group charges, dipole and higher multipole moments, etc.), that may be obtained directly form the diffraction measurements. In the present work, we will discuss our preliminary low temperature high-resolution X-ray data for the m-nitroaniline (mNA) single crystal (VI). This is one of the "classical" organic NLO materials and electron density distribution analysis in this simple compound has a great scientific interest.

Antipin, Mikhail Yu.↗

How Do Ionic Liquids “Fold” Ionenes? Computational and Experimental Analysis of Imidazolium Polymers Based on Ether and Alkyl Chain Variations Dissolved in an Ionic Liquid

Molecular dynamics (MD) simulations and complementary experiments are used here to understand the inter- and intramolecular structure and conformational properties of ionenes (i.e., cationic polymers formed from condensation reactions) dissolved in an ionic liquid (IL), 1-ethyl-3-methylimidazolium bistriflimide [C 2 mim + ][Tf 2 N - ]. The simulated structural properties are benchmarked against experimental analyses of these same polymers, mainly using dynamic light scattering (DLS) experiments. Four different imidazolium ionenes are considered, corresponding to variations in the chemistry and structure of the repeat units including: (1) poly (decylimidazolium) (PD 10 ); (2) poly (tetraethyleneglycolimidazolium) (PE 10 ); (3) alternating copolymer (P(ED) 5 ); and (4) a block copolymer (PE 5 D 5 ). Detailed computational analyses of the polymer structure and conformational properties were performed, including the radius of gyration, end-to-end distance, torsional distributions, and site-site and spatial distribution functions. Overall, there is a competition between intramolecular associations between the imidazolium groups and the ether sites in the polymers versus the intermolecular interactions of the polymer imidazolium groups with the surrounding anion molecules. The polymer with only ether linkages (PE 10 ) results in the most intramolecular interactions, leading to significant coiling behavior and chain contraction. These strong interactions reduce chain flexibility, but they also result in much more linear chain configurations and alignment of the imidazolium groups. The polymer structure is strongly affected as the concentration of alkyl groups is increased, and we find that the polymer architecture (alternating versus block copolymer) also has an important influence. Furthermore, these detailed observations are important for understanding the connection between the molecular design of imidazolium polymers and their emergent structural properties, which could lead to unique opportunities for creating polymer composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A one-loop test of the near-AdS 2 /near-CFT 1 correspondence

We analyze quantum fluctuations around black hole solutions to the Jackiw-Teitelboim model. We use harmonic analysis on Euclidean AdS 2 to show that the logarithmic corrections to the partition function are determined entirely by quadratic holomorphic differentials, even when conformal symmetry is broken and harmonic modes are no longer true zero modes. Our quantum-corrected partition function agrees precisely with the SYK result. We argue that our effective quantum field theory methods and results generalize to other theories of two-dimensional dilaton gravity.

2D Gravity↗

Structural determinants for pH-dependent activation of a plant metacaspase

Arabidopsis thaliana metacaspase 9 (AtMC9) plays roles in clearing dead cells, forming xylem vessels, and regulating immunity and programmed cell death in plants. The protease's activation is controlled by pH levels, but the exact structural mechanism behind this has not been elucidated. In this work, high-resolution crystal structures for AtMC9 at active (pH 5.5 and pH 4.2) and inactive (pH 7.5) conditions are reported. The three structures are similar except for local conformations where their hydrogen bonding interactions with solvents are mediated through the protonation of specific titratable amino acid residues' side chains. By combining structural analysis, molecular dynamics simulations under constant pHs, and biochemical assays coupled with site-directed mutagenesis, we show that the regulation of AtMC9 activation involves multiple titratable glutamate and histidine residues across the three domains of p20, linker, and p10. Specifically, deprotonated Glu112, His193, and His208 can suppress AtMC9 proteolytic activity, while protonation of Glu255 and His307 at acidic pH may promote it. This study provides valuable insights into the pH-dependent activation of AtMC9 and could potentially lead to improving crops with enhanced immunity and controlled cell death, ultimately increasing agricultural productivity.

59 BASIC BIOLOGICAL SCIENCES↗

The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase

TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitive detection of structural dynamics using a statistical framework for comparative crystallography

Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differences that are subtle or arise in only a subset of molecules. Direct comparison of crystallographic datasets is, in principle, more powerful, but systematic errors (“scales”) often mask changes in the crystallographic observables (“structure factors”). Machine learning algorithms that jointly estimate scales and structure factors can address this limitation. Here, we augment this approach with multivariate, structured priors derived from crystallographic theory, implemented in the variational deep learning framework Careless. Doing so strongly improves the detection of protein dynamics, element-specific anomalous signals, and the binding of drug candidates, offering a robust approach to comparative crystallography and, potentially, to detection of protein dynamics by other structure determination methods.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗

The divergence characteristics of constrained-sheath optics systems for use with 5-eV atomic oxygen sources

The potential usefulness of the constrained sheath optics concept as a means of controlling the divergence of low energy, high current density ion beams is examined numerically and experimentally. Numerical results demonstrate that some control of the divergence of typical ion beamlets can be achieved at perveance levels of interest by contouring the surface of the constrained sheath properly. Experimental results demonstrate that a sheath can be constrained by a wire mesh attached to the screen plate of the ion optics system. The numerically predicted beamlet divergence characteristics are shown to depart from those measured experimentally, and additional numerical analysis is used to demonstrate that this departure is probably due to distortions of the sheath caused by the fact that it attempts to conform to the individual wires that make up the sheath constraining mesh. The concept is considered potentially useful in controlling the divergence of ion beamlets in applications where low divergence, low energy, high current density beamlets are being sought, but more work is required to demonstrate this for net beam ion energies as low as 5 eV.

Anderson, John R.↗

A test of a vortex method for the computation of flap side edge noise

Upon approach to landing, a major source location of airframe noise occurs at the side edges of the part span, trailing edge flaps. In the vicinity of these flaps, a complex arrangement of spanwise flow with primary and secondary tip vortices may form. Each of these vortices is observed to become fully three-dimensional. In the present study, a numerical model is developed to investigate the noise radiated from the side edge of a flap. The inherent three-dimensionality of this flow forces us to carefully consider a numerical scheme which will be both accurate in its prediction of the flow acoustics and also computationally efficient. Vortex methods have offered a fast and efficient means of simulating many two and three-dimensional, vortex dominated flows. In vortex methods, the time development of the flow is tracked by following exclusively the vorticity containing regions. Through the Biot-Savart law, knowledge of the vorticity field enables one to obtain flow quantities at any desired location during the flow evolution. In the present study, a numerical procedure has been developed which incorporates the Lagrangian approach of vortex methods into a calculation for the noise radiated by a flow-surface interaction. In particular, the noise generated by a vortex in the presence of a flat half plane is considered. This problem serves as a basic model of flap edge flow. It also permits the direct comparison between our computed results and previous acoustic analyses performed for this problem. In our numerical simulations, the mean flow is represented by the complex potential W(z) = Aiz(exp l/2), which is obtained through conformal mapping techniques. The magnitude of the mean flow is controlled by the parameter A. This mean flow has been used in the acoustic analysis by Hardin and is considered a reasonable model of the flow field in the vicinity of the edge and away from the leading and trailing edges of the flap. To represent the primary vortex which occurs near the flap, a point vortex is introduced just below the flat half plane. Using a technique from panel methods, boundary conditions on the flap surface are satisfied by the introduction of a row of stationary point vortices along the extent of the flap. At each time step in the calculation, the strength of these vortices is chosen to eliminate the normal velocity at intermediary collocation points. The time development of the overall flow field is then tracked using standard techniques from vortex methods. Vortex trajectories obtained through this computation are in good agreement with those predicted by the analytical solution given by Hardin, thus verifying the viability of this procedure for more complex flow arrangements. For the flow acoustics, the Ffowcs Williams-Hawkings equation is numerically integrated. This equation supplies the far field acoustic pressure based upon pressures occurring along the flap surface. With our vortex method solution, surface pressures may be obtained with exceptional resolution. The Ffowcs Williams-Hawkings equation is integrated using a spatially fourth order accurate Simpson's rule. Rational function interpolation is used to obtain the surface pressures at the appropriate retarded times. Comparisons between our numerical results for the acoustic pressure and those predicted by the Hardin analysis have been made. Preliminary results indicate the need for an improved integration technique. In the future, the numerical procedure developed in this study will be applied to the case of a rectangular flap of finite thickness and ultimately modified for application to the fully three-dimensional problem.

Martin, James E.↗

Boosting Piezoelectricity by 3D Printing PVDF‐MoS 2 Composite as a Conformal and High‐Sensitivity Piezoelectric Sensor

Abstract Additively manufactured flexible and high‐performance piezoelectric devices are highly desirable for sensing and energy harvesting of 3D conformal structures. Herein, the study reports a significantly enhanced piezoelectricity in polyvinylidene fluoride (PVDF) achieved through the in situ dipole alignment of PVDF within PVDF‐2D molybdenum disulfide (2D MoS 2 ) composite by 3D printing. The shear stress‐induced dipole poling of PVDF and 2D MoS 2 alignment are harnessed during 3D printing to boost piezoelectricity without requiring a post‐poling process. The results show a remarkable, more than the eight‐fold increment in the piezoelectric coefficient ( d 33 ) for 3D printed PVDF‐8wt.% MoS 2 composite over cast neat PVDF. The underlying mechanism of piezoelectric property enhancement is attributed to the increased volume fraction of β phase in PVDF, filler fraction, heterogeneous strain distribution around PVDF‐MoS 2 interfaces, and strain transfer to the nanofillers as confirmed by microstructural analysis and finite element simulation. These results provide a promising route to design and fabricate high‐performance 3D piezoelectric devices via 3D printing for next‐generation sensors and mechanical–electronic conformal devices.

2D MoS2↗

A simulator for evaluating methods for the detection of lesion-deficit associations

Although much has been learned about the functional organization of the human brain through lesion-deficit analysis, the variety of statistical and image-processing methods developed for this purpose precludes a closed-form analysis of the statistical power of these systems. Therefore, we developed a lesion-deficit simulator (LDS), which generates artificial subjects, each of which consists of a set of functional deficits, and a brain image with lesions; the deficits and lesions conform to predefined distributions. We used probability distributions to model the number, sizes, and spatial distribution of lesions, to model the structure-function associations, and to model registration error. We used the LDS to evaluate, as examples, the effects of the complexities and strengths of lesion-deficit associations, and of registration error, on the power of lesion-deficit analysis. We measured the numbers of recovered associations from these simulated data, as a function of the number of subjects analyzed, the strengths and number of associations in the statistical model, the number of structures associated with a particular function, and the prior probabilities of structures being abnormal. The number of subjects required to recover the simulated lesion-deficit associations was found to have an inverse relationship to the strength of associations, and to the smallest probability in the structure-function model. The number of structures associated with a particular function (i.e., the complexity of associations) had a much greater effect on the performance of the analysis method than did the total number of associations. We also found that registration error of 5 mm or less reduces the number of associations discovered by approximately 13% compared to perfect registration. The LDS provides a flexible framework for evaluating many aspects of lesion-deficit analysis.

NASA Program Biomedical Research and Countermeasur↗

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗