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Results for “Brownian dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multitiered computational methodology for extracting three-dimensional rotational diffusion coefficients from x-ray photon correlation spectroscopy data without structural information

X-ray photon correlation spectroscopy (XPCS) is a powerful technique for analyzing particle systems by investigating their dynamics in suspensions across a broad range of temporal and spatial scales. This is done by illuminating samples with coherent x-ray beams and calculating the correlation function of the obtained x-ray scattering images. XPCS is uniquely suited for studying Brownian dynamics, consisting of translational and rotational diffusion. While traditional XPCS image analysis techniques can extract translational diffusion components, they are unable to estimate rotational diffusion coefficients. Here, we introduce a methodology that combines the angular-temporal cross-correlation analysis and a algorithmic framework called Multi-Tiered Estimation for Correlation Spectroscopy in 3D for estimating three-dimensional rotational diffusion coefficients from XPCS images of three-dimensional particle systems. We demonstrate our methodology for extracting rotational diffusion coefficients from XPCS data by applying it to simulated noisy x-ray images of systems of crossing nanotubes and proteins that evolve under translational and rotational Brownian motion for different diffusion rates. Furthermore, our results show that our approach determines rotational diffusion coefficients within a few percent error.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Solvent-Dependent Dynamics of Cellulose Nanocrystals in Process-Relevant Flow Fields

Flow-assisted alignment of anisotropic nanoparticles is a promising route for the bottom-up assembly of advanced materials with tunable properties. While aligning processes could be optimized by controlling factors such as solvent viscosity, flow deformation, and the structure of the particles themselves, it is necessary to understand the relationship between these factors and their effect on the final orientation. In this study, we investigated the flow of surface-charged cellulose nanocrystals (CNCs) with the shape of a rigid rod dispersed in water and propylene glycol (PG) in an isotropic tactoid state. In situ scanning small-angle X-ray scattering (SAXS) and rheo-optical flow-stop experiments were used to quantify the dynamics, orientation, and structure of the assigned system at the nanometer scale. The effects of both shear and extensional flow fields were revealed in a single experiment by using a flow-focusing channel geometry, which was used as a model flow for nanomaterial assembly. Due to the higher solvent viscosity, CNCs in PG showed much slower Brownian dynamics than CNCs in water and thus could be aligned at lower deformation rates. Moreover, CNCs in PG also formed a characteristic tactoid structure but with less ordering than CNCs in water owing to weaker electrostatic interactions. The results indicate that CNCs in water stay assembled in the mesoscale structure at moderate deformation rates but are broken up at higher flow rates, enhancing rotary diffusion and leading to lower overall alignment. Albeit being a study of cellulose nanoparticles, the fundamental interplay between imposed flow fields, Brownian motion, and electrostatic interactions likely apply to many other anisotropic colloidal systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Decoherence and Brownian motion of a polarizable particle near a medium

Optically levitated nanoparticles are ideal experimental testbeds for investigating macroscopic superpositions and microscopic thermodynamics. Integrating such levitated nanoparticles with photonic structures can enable strong coupling between their center-of-mass motion and guided photonic modes, facilitating enhanced control and probing of their motion. When coupling a particle to a photonic structure, such as a waveguide, the effects of fluctuations become prominent at nanoscales. In this work, we analyze the classical and quantized center-of-mass motion of a polarizable particle interacting with the fluctuations of the electromagnetic field in the presence of a medium. We derive a position localization master equation for the particle's quantized center of mass, and examine its classical center-of-mass momentum diffusion, elucidating correspondences between classical and quantum Brownian motion of polarizable particles near media. We study the decoherence rate of the particle in the presence of a planar surface as a function of temperature and distance from the surface, comparing it to common sources of decoherence. Our results are pertinent to experiments aimed at preparing levitated nanospheres in macroscopic quantum states and investigating their Brownian dynamics.

Brownian motion↗
DOE OSTI2024

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phase Separation, Capillarity, and Odd-Surface Flows in Chiral Active Matter

Active phase separations evade canonical thermodynamic descriptions and have thus challenged our understanding of coexistence and interfacial phenomena. Considerable progress has been made towards a nonequilibrium theoretical description of these traditionally thermodynamic concepts. Spatial parity symmetry is conspicuously assumed in much of this progress, despite the ubiquity of chirality in experimentally realized systems. Here, in this Letter, we derive a theory for the phase coexistence and interfacial fluctuations of a system that microscopically violates spatial parity. We find suppression of the phase separation as chirality is increased as well as the development of steady-state currents tangential to the interface dividing the phases. These odd flows are irrelevant to stationary interfacial properties, with stability, capillary fluctuations, and surface area minimization determined entirely by the capillary surface tension. Using large-scale Brownian dynamics simulations, we find excellent agreement with our theoretical scaling predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Nanopores with dynamic pore opening diameter

Solid state nanopores have emerged as model systems for understanding transport properties on the nanoscale. They serve as templates for both preparing mimics of biological channels and designing biological sensors. Unlike their biological inspirations, the majority of nanopores prepared thus far, however, have been structurally static devices such that the pore opening diameter is fixed. If we could prepare nanopores whose opening diameter fluctuated in time with controlled amplitude at known locations in the pore, we could create ionic memristors as well as achieve new transport modes. Here we present ∼10 nm diameter single nanopores drilled through a 10 nm thick gold layer positioned on top of a 30 nm thick silicon nitride film. Two types of devices were prepared; one containing single stranded DNA and the other containing hairpin DNA attached to the discrete layer of gold using thiol chemistry. When an external electric field was applied across a nanopore with single stranded DNA, the nanoconfined DNA molecules exhibited steric and electrical constraints that led to memristor-like behavior in the current–voltage curves. The degree of hysteresis was controlled by salt concentration, magnitude of voltage and pore diameter. In contrast, nanopores containing DNA hairpins conducted similar currents in forward and reverse bias in agreement with the rigidity of the hairpin molecule. The experiments are explained by Brownian dynamics simulations that reveal voltage and salt concentration induced changes in DNA extension. The degree of DNA extension was also found to be dependent on the location of the molecules along the pore axis. The nanopores presented here provide the first steps towards preparation of non-equilibrium nanopore systems.

Vlassiouk, Ivan [ORNL] (ORCID:0000000254940386)↗
DOE OSTI2025

Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport

Nuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargoes, including preribosomes and viral capsids. Our model quantifies how flexible phenylalanine-glycine (FG) repeat proteins create an entropic barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by “fuzzy” multivalent interactions, redundant FG repeat mass, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.

Raveh, Barak [School of Computer Science and Engin↗
DOE OSTI2026

Langevin and Fokker-Planck analyses for diffusion-mediated passing of circular and discorectangular species in two-dimensional channels

The propensity for pairs of diffusing species to pass each other within narrow channels or pores is of basic interest as a first-passage-type problem. It is also of relevance for solution-phase transport in nanoporous materials, and in particular for catalytic conversion reactions where high yield requires that product species can efficiently pass reactant species to exit the pores. Here, we analyze a two-dimensional model with nonoverlapping circular and discorectangular species confined to a rectangular channel, and where passing is mediated by Brownian dynamics in an implicit solvent. For narrower channels where passing is still possible, the discorectangle must align with the channel to pass the circular species. Behavior of the passing propensity, 𝑃, can be assessed by strongly damped Langevin simulations, or within an equivalent Fokker-Planck equation (FPE) formalism. The latter corresponds to a diffusion problem in a “higher-dimensional channel” with a constriction. We assess the variation of the passing propensity, 𝑃, for a broad range of channel width including its scaling just above the threshold where passing is sterically blocked. Analysis of 𝑃 versus the rotational diffusion coefficient 𝐷 𝑟 of the discorectangle reveals a significant decrease in 𝑃 for lower 𝐷 𝑟 for moderate channel width. This prompts a direct analysis of the regime where 𝐷 𝑟 → 0 , for which the FPE can be reduced to a three-dimensional diffusion problem, precise analysis of which is facilitated by adaptive-mesh finite element methods. The dependence of 𝑃 on the aspect ratio of the discorectangle is also assessed.

Rahman, Md Khaledur [Ames Laboratory (AMES), Ames,↗
DOE OSTI2025

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC’s ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model’s predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Multi-Tiered Estimation for Correlation Spectroscopy in 3D (MTECS3D) v0.1

This innovative software estimates rotational diffusion coefficients of particles from X-ray photon correlation spectroscopy (XPCS) data of monodispersed particle systems. It is the first method capable of extracting rotational diffusion information from three-dimensional particle systems using XPCS. Using the angular-temporal cross-correlation of the XPCS images, this software is able to estimate the rotational diffusion coefficients with only a few percent relative errors while requiring minimal prior knowledge of particle structures. This software enhances XPCS analysis capabilities, allowing researchers to study translational and rotational Brownian dynamics of particles in suspension across various temporal and spatial scales.

Hu, Zixi↗
DOE OSTI2026

Diffusion and Solvation Dynamics of Ions in Water: Beyond the Brownian Approximation

The coupled dynamics of ions and water molecules in their first hydration shell impact a variety of processes including ion diffusion, selective ion transport in water-filled nanopores, and the kinetics of ion-pairing, ion adsorption, and metal-ligand binding reactions. In this work, we study these coupled dynamics for alkali metals (Li, Na, K, Rb, Cs), alkaline Earth metals (Mg, Ca, Sr, Ba), and chloride through the lens of their dependence on ion isotopic mass. Results are validated against previous measurements of the isotopic mass-dependence of ion diffusion coefficients in water and previous ab initio calculations of ion high-frequency dynamics in water. We find that the vibrational power spectra of ions in water consistently exhibit either two or three peaks, i.e., ions have several rattling frequencies within their solvations shells as previously reported for a subset of the species examined here. These frequencies have different sensititivies to isotopic mass that may serve as signatures of ion solvation processes (such as the tendency of ions to orient their first-shell water molecules) and that also may relate to Hofmeister-like effects including the relative affinity of different metals for ribonucleic acid (RNA).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Theory of x-ray photon correlation spectroscopy for multiscale flows

Complex multiscale flows associated with instabilities and turbulence are commonly induced under high-energy density (HED) conditions, but accurate measurement of their transport properties has been challenging. X-ray photon correlation spectroscopy (XPCS) with coherent x-ray sources can, in principle, probe material dynamics to infer transport properties using time autocorrelation of density fluctuations. Here we develop a theoretical framework for utilizing XPCS to study material diffusivity in multiscale flows. We extend single-scale shear flow theories to broadband flows using a multiscale analysis that captures shear and diffusion dynamics. Our theory is validated with simulated XPCS for Brownian particles advected in multiscale flows. We demonstrate the versatility of the method over several orders of magnitude in timescale using sequential-pulse XPCS, single-pulse x-ray speckle visibility spectroscopy (XSVS), and double-pulse XSVS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Active-noise-induced dynamic clustering of passive colloidal particles

Active fluids generate spontaneous, often chaotic mesoscale flows. Harnessing these flows to drive soft materials embedded within an active fluid into structures with controlled length scales and lifetimes is a key challenge at the interface between the fields of active matter and nonequilibrium self-assembly. Here, we present a simple and efficient computational approach to model soft materials advected by active fluids, by simulating particles moving in a spatiotemporally correlated noise field. To illustrate our approach, we simulate the dynamical self-organization of repulsive colloids within such an active noise field. The colloids form structures whose sizes and dynamics can be tuned by the correlation time and length of the active fluid, and range from small rotating droplets to clusters with internal flows and system-spanning sizes that vastly exceed the active correlation length. Our results explain how the interplay between active fluid time and length scales and emergent driven assembly can be used to rationally design functional assemblies. More broadly, our approach can be used to efficiently simulate diverse active fluids and other systems with spatiotemporally correlated noise.

Brownian dynamics↗
DOE OSTI2024

Producing entangled photon pairs and quantum squeezed states in plasmas

Plasma is capable of mediating the conversion of two pump photons into two different photons through a relativistic four-wave mixing nonlinearity. Spontaneously created photon pairs are emitted at symmetric angles with respect to the colinear pump direction, and the emission rate is largest if they have identical frequency. Thus, two orthogonally polarized pumps can produce polarization-entangled photon pairs through a millimeter-long homogeneous plasma. Here, the noise from Raman scattering can be avoided if the pump detuning differs from twice the plasma frequency. However, pump detuning exactly equal to twice the plasma frequency can significantly enhance the interaction rate, which allows for the production of strong two-mode squeezed states. Remarkably, the amplified noise from Raman scattering are correlated and hence can be suppressed in one of the output quadratures, thereby maintaining the squeezing magnitude.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Time-resolved atomic-resolution Brownian tomography of single nanocrystals reveals size-dependent dynamics

Atomic-resolution structure identification of nanocrystals by graphene liquid cell electron microscopy (GLC-EM) has revealed that small, solubilized platinum nanocrystals consist of an ordered crystalline core surrounded by mobile surface atoms, which dissociate during oxidative etching, resulting in distinct temporal structural states. Requirements imposed by the 3D reconstruction algorithm limit the number of structural states that can be resolved. We introduce a regularized 3D reconstruction algorithm that exploits the redundancy inherent in the experimental data, allowing us to improve the time resolution. Our developments provide a comprehensive molecular picture at unprecedented spatial and temporal resolution of the nonlinear, linear, and fluctuating dynamic phenomena that single nanocrystals undergo during the GLC-EM experiment. We determined atomic structures of 66 temporal structural states, extracted from 15 time trajectories of individual nanocrystals. Large (478 to 698 atoms) and small (<300 atoms) nanocrystals show etching that preserves a stable core, whereas mid-sized (351 to 571 atoms) nanocrystals present dynamics that change the coordination of the core.

Meana-Pañeda, Rubén↗
DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Janus skyrmion: Interfacial quasiparticle with two-faced helicity

Janus particles are functional particles with at least two surfaces showing asymmetric properties. Here, we show at the interface between two magnetic regions with different antisymmetric exchange interactions, an alternative species of two-dimensional topological quasiparticles can emerge, in which different helicity structures can coexist. We name such an interfacial quasiparticle a “Janus skyrmion,” in analogy to the Janus particle. As the Janus skyrmion shows helicity asymmetry, its size could vary with both the in-plane and out-of-plane magnetic fields. A vertical spin current could drive the Janus skyrmion into one-dimensional motion along the interface without showing the skyrmion Hall effect, at a speed which depends on both the in-plane spin-polarization direction and current density. Thermal fluctuations could also lead to one-dimensional random walk of a Brownian Janus skyrmion. This work uncovers unique dynamics intrinsic to interfacial quasiparticles with exotic helicity, which may be realized in interface-engineered magnetic layers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Machine learning-driven descriptions of protein dynamics at solid-liquid interfaces

This chapter has described how ML has enabled quantitative analysis of HS-AFM data to discover the physical phenomena governing protein dynamics and ordering at solid-liquid interfaces. The research detailed in this chapter modeled the rotation models of protein nanorods, the discovery of which would otherwise not be possible. By tracking the trajectories of individual protein rods from frame to frame, it was possible to model Brownian type motion and behaviors and Levy-flight dynamics that had not previously been shown. We also described the application of the Python package AtomAI, which has been developed specifically to analyze and extract physical phenomena, providing exemplar code for training an ensemble of deep neural networks to produce the semantic segmentation of AFM data and functions for encoding and decoding local environments. We last described a combinatorial approach to analyze very noisy data with a densely covered substrate where the emergence of order for the protein liquid crystals could be elucidated. By combining the methods from Case 1 and 2, it was possible to obtain the center of mass and angle for each rod in the images and track the assembly of the rods over time into a 2D liquid crystal array on the surface of mica.

protein dynamics, solid-liquid interfaces, atomic ↗