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At least 505 records · Page 28

System, method, and computer program for creating geometry-compliant lattice structures

A system and method of creating a shape-conforming lattice structure for a part formed via additive manufacturing. The method includes receiving a computer model of the part and generating a finite element mesh. A lattice structure including a number of lattice cellular components may also be generated. Some of the mesh elements of the finite element mesh may be deformed so that the finite element mesh conforms to the overall shape of the part. The lattice structure may then be deformed so that the lattice structure has a cellular periodicity corresponding to the finite elements of the finite element mesh. In this way, the part retains the benefits of its overall shape and the benefits of lattice features without introducing structural weak points, directional stresses, and other structural deficiencies.

Vernon, Gregory John↗

Evaluation of probability density function descriptions for three-component Rayleigh–Taylor mixing

Results from simulations of a three-component Rayleigh–Taylor (RT) mixing problem are presented. These simulations are conducted in heavy–light–heavy and heavy–intermediate–light configurations, and each of these configurations are further considered in high- and low-Reynolds-number regimes. This results in RT-unstable flow with one or both interfaces initially unstable, permitting the influence of problem configuration on the statistical description of three-component RT-driven mixing to be considered. Mass fraction covariances are observed to undergo a sign change through the mixing layer in all four configurations considered. This appears to be unique to the multi-component case and represents another way in which multi-component RT mixing differs from the two-component case. Qualitative and quantitative comparisons of joint and marginal probability density function (PDF) descriptions of species concentration are made. Three-, five-, and six-parameter model PDFs are compared against simulation data to assess how accurately they describe the mixing, and it is found that three-component mixing requires at least a five-parameter model PDF to accurately describe the mixing. Notably, the marginal distributions of three-component mixing do not appear to conform to a beta distribution, representing a departure from the classical two-component RT case. In conclusion, statistical neutrality also appears to influence the optimal choice of model PDF, which is found to be a function of problem configuration.

Large-eddy simulation↗

Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism

Removing glutamate from the synaptic cleft is vital for proper function of the brain. Excitatory amino acid transporters mediate this process by uptaking the neurotransmitter from the synaptic cleft back to the cell after its release. The archaeal homolog, Glt Ph , an aspartate transporter fromPyrococcus horikoshii, presents the best structurally characterized model for this family of transporters. In order to transport, Glt Ph undergoes elevator-like conformational changes between inward-facing (IF) and outward-facing (OF) states. Here, we characterize, at an atomic level, the OF⇌IF transition of Glt Ph in differentapo/bound states using a combination of ensemble-based enhanced sampling techniques, employing more than two thousand of coupled simulation replicas of membrane-embedded Glt Ph . The resulting free-energy profiles portray the transition ofapo/bound states as a complex four-stage process, while sodium binding alone locks the structure in one of its states. Along the transition, the transport domain (TD) disengages from the scaffold domain (SD), allowing it to move as a piston sliding vertically with respect to the membrane during the elevator-like motion of TD. Lipid interactions with residues comprising the SD–TD interface directly influence the large-scale conformational changes and, consequently, the energetics of transport. Structural intermediates formed during the transition leak water molecules and may correlate to the uncoupled Cl − ion conductance observed experimentally in both prokaryotic and mammalian glutamate transporters. Mechanistic insights obtained from our study provide a structural framework for better development of therapeutic for neurological disorders.

Science & Technology - Other Topics↗

A 3d disordered superconformal fixed point

We initiate the study of a three dimensional disordered supersymmetric field theory. Specifically, we consider a $\mathcal{N}$= 2 large N Wess-Zumino like model with cubic superpotential involving couplings drawn from a Gaussian random ensemble. Taking inspiration from analyses of lower dimensional SYK like models we demonstrate that the theory flows to a strongly coupled superconformal fixed point in the infra-red. In particular, we obtain leading large N spectral data and operator product coefficients at the critical point. Moreover, the analytic control accorded by the model allows us to compare our results against those derived in the conformal bootstrap program and demonstrate consistency with general expectations.

1/N expansion↗

Fluorescent toxins as ion channel activity sensors.

Voltage gated ion channels (VGICs) shape the electrical character of cells by undergoing structural changes in response to membrane depolarization. High-resolution techniques have provided a wealth of data on individual VGIC structures, but the conformational changes of endogenous channels in live cell membranes have remained unexplored. Here, we describe methods for imaging structural changes of voltage-gated K + channels in living cells, using peptidyl toxins labeled with fluorophores that report specific protein conformations. These Endogenous Voltage-sensor Activity Probes (EVAPs) enable study of both VGIC allostery and function in the context of endogenous live-cell membranes under different physiological states. In this chapter, we describe methods for the synthesis, imaging, and analysis of dynamic EVAPs, which can report K + channel activity in complex tissue preparations via 2-photon excitation microscopy, and environment-sensitive EVAPs, which report voltage-dependent conformational changes at the VGIC-toxin interface. The methods here present the utility of current EVAPs and lay the groundwork for the development of other probes that act by similar mechanisms. EVAPs can be correlated with electrophysiology, offering insight into the molecular details of endogenous channel function and allostery in live cells. This enables investigation of conformational changes of channels in their native, functional states, putting structures and models into a context of live-cell membranes. The expansive array of state-dependent ligands and optical probes should enable probes more generally for investigating the molecular motions of endogenous proteins.

Stewart, Robert↗

Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence

Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structure of the human PRPK–TPRKB complex

Mutations of the p53-related protein kinase (PRPK) and TP53RK-binding protein (TPRKB) cause Galloway-Mowat syndrome (GAMOS) and are found in various human cancers. We have previously shown that small compounds targeting PRPK showed anti-cancer activity against colon and skin cancer. Here we present the 2.53 Å crystal structure of the human PRPK-TPRKB-AMPPNP (adenylyl-imidodiphosphate) complex. The structure reveals details in PRPK-AMPPNP coordination and PRPK-TPRKB interaction. PRPK appears in an active conformation, albeit lacking the conventional kinase activation loop. We constructed a structural model of the human EKC/KEOPS complex, composed of PRPK, TPRKB, OSGEP, LAGE3, and GON7. Disease mutations in PRPK and TPRKB are mapped into the structure, and we show that one mutation, PRPK K238Nfs*2, lost the binding to OSGEP. Our structure also makes the virtual screening possible and paves the way for more rational drug design.

59 BASIC BIOLOGICAL SCIENCES↗

Robust and scalable uncertainty estimation with conformal prediction for machine-learned interatomic potentials

Abstract Uncertainty quantification (UQ) is important to machine learning (ML) force fields to assess the level of confidence during prediction, as ML models are not inherently physical and can therefore yield catastrophically incorrect predictions. Established a-posteriori UQ methods, including ensemble methods, the dropout method, the delta method, and various heuristic distance metrics, have limitations such as being computationally challenging for large models due to model re-training. In addition, the uncertainty estimates are often not rigorously calibrated. In this work, we propose combining the distribution-free UQ method, known as conformal prediction (CP), with the distances in the neural network’s latent space to estimate the uncertainty of energies predicted by neural network force fields. We evaluate this method (CP+latent) along with other UQ methods on two essential aspects, calibration, and sharpness, and find this method to be both calibrated and sharp under the assumption of independent and identically-distributed (i.i.d.) data. We show that the method is relatively insensitive to hyperparameters selected, and test the limitations of the method when the i.i.d. assumption is violated. Finally, we demonstrate that this method can be readily applied to trained neural network force fields with traditional and graph neural network architectures to obtain estimates of uncertainty with low computational costs on a training dataset of 1 million images to showcase its scalability and portability. Incorporating the CP method with latent distances offers a calibrated, sharp and efficient strategy to estimate the uncertainty of neural network force fields. In addition, the CP approach can also function as a promising strategy for calibrating uncertainty estimated by other approaches.

74 ATOMIC AND MOLECULAR PHYSICS↗

Infinitely many 4D N = 1 SCFTs with a = c

Here, we study a rich set of four-dimensional N = 1 superconformal field theories (SCFTs) with both central charges identical: a = c. We construct them via the diagonal N = 1 gauging of the flavor symmetry G of a collection of N = 2 Argyres–Douglas theories of type D p (G), with or without additional adjoint chiral multiplets. In this way, we construct infinitely many theories that flow to interacting SCFTs with a = c in the infrared. Lastly, we briefly highlight the features of the SCFTs without a = c that arise from generalizing this construction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Pion gravitational form factors in the QCD instanton vacuum. I

The pion form factors of the QCD energy-momentum tensor (EMT) are studied in the instanton liquid model (ILM) of the QCD vacuum. In this approach, the breaking of conformal symmetry is encoded in the form of stronger-than-Poisson fluctuations in the number of instantons. For the trace of the EMT, it is shown that the gluonic trace anomaly term contributes half the pion mass, with the other half coming from the quark-mass-dependent σ term. The Q 2 dependence of the form factors is governed by glueball and scalar meson exchanges. For the EMT, the spin-0 (trace) and spin-2 (traceless rank-2 tensor) form factors are computed at next-to-leading order in the instanton density using effective quark operators. Relations between the gluon and quark contributions to the EMT form factors are derived. The form factors are also expressed in terms of the pion light-front wave functions in the ILM. The results at the low resolution scale of the inverse instanton size are evolved to higher scales using the renormalization group equation. The ILM results compare well with those of recent lattice QCD calculations. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Antipodal self-duality of square fishnet graphs

In strongly deformed planar 𝒩 = 4 super-Yang-Mills theory, or fishnet theory, a point-split single-trace correlation function of four dimension-𝑚 scalar operators is given by a single Feynman integral, which involves integrating over locations of a 𝑚 × 𝑚 grid of points. We show that for any integer 𝑚 this square fishnet graph is invariant under the combined action of a kinematic map and the antipode map of the Hopf algebra on multiple polylogarithms; i.e. it possesses an antipodal self-duality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Design of intrinsically disordered protein variants with diverse structural properties

Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Computational design of IDPs with specific conformational properties has, however, been difficult because of their substantial dynamics and structural complexity. We describe a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs that differ in compaction, long-range contacts, and propensity to phase separate. We experimentally tested and validated our designs and analyzed the sequence features that determine conformations. We show how our results are captured by a machine learning model, enabling us to speed up the algorithm. Our work expands the toolbox for computational protein design and will facilitate the design of proteins whose functions exploit the many properties afforded by protein disorder.

Science & Technology - Other Topics↗

The Atacama Cosmology Telescope: DR6 Gravitational Lensing Map and Cosmological Parameters

We present cosmological constraints from a gravitational lensing mass map covering 9400 deg2 reconstructed from measurements of the cosmic microwave background (CMB) made by the Atacama Cosmology Telescope (ACT) from 2017 to 2021. In combination with measurements of baryon acoustic oscillations and big bang nucleosynthesis, we obtain the clustering amplitude σ8 = 0.819 ± 0.015 at 1.8% precision, S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.840 ± 0.028, and the Hubble constant H 0 = (68.3 ± 1.1) km s -1 Mpc -1 at 1.6% precision. A joint constraint with Planck CMB lensing yields σ 8 = 0.812 ± 0.013, S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.831 ± 0.023 , and H0 = (68.1 ± 1.0) km s -1 Mpc -1 . These measurements agree with ΛCDM extrapolations from the CMB anisotropies measured by Planck. We revisit constraints from the KiDS, DES, and HSC galaxy surveys with a uniform set of assumptions and find that S8 from all three are lower than that from ACT+Planck lensing by levels ranging from 1.7σ to 2.1σ. This motivates further measurements and comparison, not just between the CMB anisotropies and galaxy lensing but also between CMB lensing probing z ~ 0.5–5 on mostly linear scales and galaxy lensing at z 0.5 on smaller scales. We combine with CMB anisotropies to constrain extensions of ΛCDM, limiting neutrino masses to Σm ν < 0.13 eV (95% c.l.), for example. We describe the mass map and related data products that will enable a wide array of cross-correlation science. Our results provide independent confirmation that the universe is spatially flat, conforms with general relativity, and is described remarkably well by the ΛCDM model, while paving a promising path for neutrino physics with lensing from upcoming ground-based CMB surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantum simulation of massive Thirring and Gross--Neveu models for arbitrary number of flavors

The study of fermionic quantum field theories is an important problem for realizing the standard model of particle physics on a quantum computer. As a step towards this goal, we consider the massive Thirring and Gross--Neveu models with arbitrary number of fermion flavors, $N_f$, discretized on a spatial one-dimensional lattice of size $L$ in the Hamiltonian formulation. We compute the gate complexity using the higher-order product formula and using block-encoding/qubitization and quantum singular value transformations in the limit of large $N_f$ and $L$. We also prepare the ground states of both models with excellent fidelity for system sizes up to 20 qubits with $N_f = 1,2,3,4$ using the adaptive-variational quantum imaginary time algorithm. In addition, we also classify the dynamical Lie algebras of these relativistic fermionic models and show that they belong to the same isomorphism class. Our work is a concrete step towards the quantum simulation of real-time dynamics of large $N_f$ fermionic quantum field theories models relevant for chiral symmetry breaking, understanding dimensional transmutation, and exploring the conformal window of field theories on near-term and early fault-tolerant quantum computers.

FOS: Physical sciences↗

Computer Program Re-layers Engineering Drawings

RULCHK computer program aids in structuring layers of information pertaining to part or assembly designed with software described in article "Software for Drawing Design Details Concurrently" (MFS-28444). Checks and optionally updates structure of layers for part. Enables designer to construct model and annotate its documentation without burden of manually layering part to conform to standards at design time.

Crosby, Dewey C., III↗