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At least 613 records · Page 34

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler–Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

97 MATHEMATICS AND COMPUTING↗

Ultrafast state-selective tunneling in two-dimensional semiconductors with a phase- and amplitude-controlled THz-scanning tunneling microscope

THz-pulse driven scanning tunneling microscopy (THz-STM) enables access to the ultrafast quantum dynamics of low-dimensional material systems at simultaneous ultrafast temporal and atomic spatial resolution. State-selective tunneling requires precise amplitude and phase control of the THz pulses combined with quantitative near-field waveform characterization. Here, we employ our state-of-the-art THz-STM with multi-MHz repetition rates, efficient THz generation, and precisely tunable THz waveforms to investigate a single sulfur vacancy in monolayer MoS2. We demonstrate that 2D transition metal dichalcogenides (TMDs) are an ideal platform for near-field waveform sampling by THz cross-correlation. Furthermore, we determine the THz voltage via QEV scans, which measure the THz rectified charge Q as a function of THz field amplitude E and dc bias Vdc. Mapping the complex energy landscape of localized states with a resolution down to 0.01 electrons per pulse facilitates state-selective tunneling to the HOMO and LUMO orbitals of a charged sulfur vacancy.

Materials Science↗

Cryogen-free modular scanning tunneling microscope operating at 4-K in high magnetic field on a compact ultra-high vacuum platform

One of the daunting challenges in modern low temperature scanning tunneling microscopy (STM) is the difficulty of combining atomic resolution with cryogen-free cooling. Further functionality needs, such as ultra-high vacuum (UHV), high magnetic field (HF), and compatibility with μm-sized samples, pose additional challenges to an already ambitious build. We present the design, construction, and performance of a cryogen-free, UHV, low temperature, and high magnetic field system for modular STM operation. An internal vibration isolator reduces vibrations in this system, allowing for atomic resolution STM imaging while maintaining a low base temperature of ∼4 K and magnetic fields up to 9 T. Samples and tips can be conditioned in situ utilizing a heating stage, an ion sputtering gun, an e-beam evaporator, a tip treater, and sample exfoliation. In situ sample and tip exchange and alignment are performed in a connected UHV room temperature stage with optical access. Multisite operation without breaking vacuum is enabled by a unique quick-connect STM head design. A novel low-profile vertical transfer mechanism permits transferring the STM between room temperature and the low temperature cryostat.

Instruments & Instrumentation↗

Adaptive tau-leaping methods for microscopic-lattice kinetic Monte Carlo simulations

Traditional Kinetic Monte Carlo (KMC) approaches, rooted in Gillespie’s stochastic simulation algorithm, become computationally demanding in systems with a large range of timescales. The goal of this work is to propose and study new adaptive lattice-KMC time integration strategies for spatially non-uniform systems. To that end, two novel adaptive tau-leaping methods and their corresponding time integration strategies are developed based on the idea of the “n-fold” direct KMC method. These strategies allow for the simultaneous execution of multiple reactions, advancing time by adaptively selected coarse increments. We present numerical experiments comparing the proposed methods with existing approaches in a catalytic surface kinetics application involving ammonia decomposition.

Bimolecular reactions↗

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations in biological samples, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the diffraction-limited three-dimensional distribution of the orientations and positions of ensembles of fluorescent dipoles that label biological structures. We share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model the distributions based on the polarization-dependent efficiency of excitation and detection of emitted fluorescence, using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labeled giant unilamellar vesicles, fast-scarlet-labeled cellulose in xylem cells, and phalloidin-labeled actin in U2OS cells. Additionally, we observe phalloidin-labeled actin in mouse fibroblasts grown on grids of labeled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

Science & Technology - Other Topics↗

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↗

Three-dimensional high-content imaging of unstained soft tissue with subcellular resolution using a laboratory-based X-ray microscope

With increasing interest in studying biological systems across spatial scales—from centimeters down to nanometers—histology continues to be the gold standard for tissue imaging at cellular resolution, providing an essential bridge between macroscopic and nanoscopic analysis. However, its inherently destructive and two-dimensional nature limits its ability to capture the full three-dimensional complexity of tissue architecture. Here, we show that phase-contrast X-ray microscopy can enable three-dimensional virtual histology with subcellular resolution. This technique provides direct quantification of electron density without restrictive assumptions, allowing for direct characterization of cellular nuclei in a standard laboratory setting. By combining high spatial resolution and soft tissue contrast, with automated segmentation of cell nuclei, we demonstrated virtual Hematoxylin and Eosin (H&E) staining using machine learning-based style transfer, yielding volumetric datasets compatible with existing histopathological analysis tools. Furthermore, by integrating electron density and the sensitivity to nanometric features of the dark field contrast channel, we achieve stain-free, high-content imaging capable of distinguishing nuclei and extracellular matrix.

3D virtual histology↗

Microscopic Theory of Nonlinear Hall Effect in Three-Dimensional Magnetic Systems

Abstract Nonlinear Hall effect (NLHE) has been detected in various of condensed matter systems. Unlike linear Hall effect, NLHE may exist in physical systems with broken inversion symmetry in crystals. On the other hand, real space spin texture may also break inversion symmetry and result in NLHE. We employ the Feynman diagrammatic technique to calculate non-linear Hall conductivity (NLHC) in three-dimensional magnetic systems. The results connect NLHE with the physical quantity of emergent electrodynamics which originates from the magnetic texture. The leading order contribution of NLHC, χabb , is proportional to the emergent toroidal moment T a e , which reflects how the spin textures wind in three dimensions.

Hou 侯, Wen-Tao 文涛↗

Form-factor dependence of neutrino-nucleus cross sections using microscopic methods

To achieve its design goals, the next generation of neutrino-oscillation accelerator experiments requires percent-level predictions of neutrino-nucleus cross sections supplemented by robust estimates of the theoretical uncertainties involved. The latter arise from both approximations in solving the nuclear many-body problem and in the determination of the single- and few-nucleon quantities taken as input by many-body methods. To gauge the sensitivity of realistic nuclear many body methods to these few-nucleon quantities, we compute flux-averaged double-differential cross sections using the Green’s function Monte Carlo and spectral function methods as well as different parameterizations of the nucleon axial form factors based on either deuterium bubble-chamber data or lattice quantum chromodynamics calculations. The cross-section results are compared with available experimental data from the MiniBooNE and T2K collaborations. We also discuss the uncertainties associated with N → Δ transition form factors that enter the two-body current operator. We quantify the relations between neutrino-nucleus cross section and nucleon form factor uncertainties. These relations enable us to determine the form factor precision targets required to achieve a given cross-section precision.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

High-resolution analogue of time-domain phonon spectroscopy in the transmission electron microscope

Femtosecond photoexcitation of semiconducting materials leads to the generation of coherent acoustic phonons (CAPs), the behaviours of which are linked to intrinsic and engineered electronic, optical and structural properties. While often studied with pump-probe spectroscopic techniques, the influence of nanoscale structure and morphology on CAP dynamics can be challenging to resolve with these all-optical methods. Here, we used ultrafast electron microscopy (UEM) to resolve variations in CAP dynamics caused by differences in the degree of crystallinity in as-prepared and annealed GaAs lamellae. Following in situ femtosecond photoexcitation, we directly imaged the generation and propagation dynamics of hypersonic CAPs in a mostly amorphous and, following an in situ photothermal anneal, a mostly crystalline lamella. Subtle differences in both the initial hypersonic velocities and the asymptotic relaxation behaviours were resolved via construction of space-time contour plots from phonon wavefronts. Comparison to bulk sound velocities in crystalline and amorphous GaAs reveals the influence of the mixed amorphous-crystalline morphology on CAP dispersion behaviours. Further, an increase in the asymptotic velocity following annealing establishes the sensitivity of quantitative UEM imaging to both structural and compositional variations through differences in bonding and elasticity. Lastly, implications of extending the methods and results reported here to elucidating correlated electronic, optical and structural behaviours in semiconducting materials are discussed.

42 ENGINEERING↗

Self-consistent microscopic calculations for electron captures on nuclei in core-collapse supernovae

Calculations for electron capture rates on nuclei with atomic numbers between 𝑍 = 20 and 𝑍 = 52 are performed in a self-consistent finite-temperature covariant energy density functional theory within the relativistic quasiparticle random-phase approximation. Electron captures on these nuclei contribute most to reducing the electron fraction during the collapse phase of core-collapse supernovae. The rates include contributions from allowed (Gamow-Teller) and first-forbidden (FF) transitions, and it is shown that the latter become dominant at high stellar densities and temperatures. Temperature-dependent effects such as Pauli unblocking and transitions from thermally excited states are also included. The new rates are implemented in a spherically symmetric one-dimensional simulation of the core-collapse phase. The results indicate that the increase in electron capture rates, due to inclusion of FF transitions, leads to reductions of the electron fraction at nuclear saturation density, the peak neutrino luminosity, and enclosed mass at core bounce. The new rates reaffirm that the most relevant nuclei for the deleptonization situate around the 𝑁 = 50 and 82 shell closures, but, compared to previous simulations, nuclei are less proton rich. Here, the new rates developed in this work are available, and will be of benefit to improve the accuracy of multidimensional supernova simulations.

Electron & muon capture↗

Low-energy 17 O(𝑛,𝛾)⁢ 18 O reaction within the microscopic potential model and its role for the weak 𝑟 process

The neutron radiative capture reaction 17 O ⁡(𝑛,𝛾) ⁢18 O plays a pivotal role in both nuclear structure studies and astrophysical nucleosynthesis, particularly in the formation of elements during hydrostatic and explosive stellar environments. We calculated the 17 O ⁡(𝑛,𝛾) ⁢18 O cross section within the Skyrme Hartree-Fock potential model and analyzed electric dipole 𝐸⁢1 transitions to both positive- and negative-parity states below the α-decay threshold in 18 O. Our cross sections are significantly different from the data available in commonly used libraries. We further investigate the impact of the new calculated cross section on weak 𝑟-process nucleosynthesis using large-scale reaction network calculations across a wide range of electron fractions and entropies. Our results show that the 17 O ⁡(𝑛,𝛾) ⁢18 O reaction rate significantly influences the production of first 𝑟-process peak elements, such as strontium, under specific astrophysical conditions. This study highlights the importance of accurate nuclear data for light isotopes in modeling heavy-element synthesis and provides updated reaction rates for future nucleosynthesis simulations.

6 ≤ A ≤ 19↗

Microscopic Imprints of Learned Solutions in Tunable Networks

In physical networks trained using supervised learning, physical parameters are adjusted to produce desired responses to inputs. An example is an electrical contrastive local learning network of nodes connected by edges that adjust their conductances during training. When an edge conductance changes, it upsets the current balance of every node. In response, physics adjusts the node voltages to minimize the dissipated power. Learning in these systems is therefore a coupled double-optimization process, in which the network descends both a cost landscape in the high-dimensional space of edge conductances and a physical landscape—the power dissipation—in the high-dimensional space of node voltages. Because of this coupling, the physical landscape of a trained network contains information about the learned task. Here, we derive a structure-function relation for trained tunable networks and demonstrate that all the physical information relevant to the trained input-output relation can be captured by a tuning susceptibility, an experimentally measurable quantity. We supplement our theoretical results with simulations to show that the tuning susceptibility is correlated with functional importance and that we can extract physical insight into how the system performs the task from the conductances of highly susceptible edges. Our analysis is general and can be applied directly to mechanical networks, such as networks trained for protein-inspired function such as allostery.

36 MATERIALS SCIENCE↗

Microscopic Theory of Pair Density Waves in Spin-Orbit Coupled Kondo Lattice

We demonstrate that the discommensuration between the Fermi surfaces of a conduction sea and an underlying spin liquid provides a natural mechanism for the spontaneous formation of pair density waves. Using a recent formulation of the Kondo lattice model that incorporates a Yao Lee spin liquid proposed by the authors, we demonstrate that doping away from half filling induces finite-momentum electron-Majorana pair condensation, resulting in amplitude-modulated pair density waves (PDWs). Our approach provides a precise, analytically tractable pathway for understanding the spontaneous formation of PDWs in higher dimensions and offers a natural mechanism for PDW formation in the absence of Zeeman splitting.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗