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DOE OSTI2020

Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations

Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Temperature Dependence of Self-diffusion in Cr2O3 from First Principles

Understanding and predicting the dominant diffusion processes in Cr2O3 is essen- tial to its optimization for anti-corrosion coatings, spintronics, and other applications. Despite significant theoretical effort in modeling defect mediated diffusion in Cr2O3 the correlation with experimentally measured diffusivities remains poor partly due to the insufficient accuracy of the theoretical approaches. Here an attempt to resolve these discrepancies is made through high accuracy density functional theory simulations cou- pled with grand canonical formalism of defect thermochemistry. In this approach, point defect formation energies were computed using hybrid exchange correlation functional. This level of theory proved to be essential for achieving the agreement with experi- mental self-diffusion coefficients. The analysis of the resulting self-diffusion coefficients indicate that chromium has higher mobility at low temperatures and high oxygen partial pressures, in particular at standard temperature and pressure conditions. At high vacuum, high temperature conditions, oxygen diffusion becomes dominant. At Cr/Cr2O3 interfaces O vacancies were found to be more mobile than Cr vacancies at all temperatures. Cr diffuses preferentially along the c-axis at low temperatures but switches to basal plane at higher temperatures. O diffusion is primarily bound to basal plane at all temperatures.

Medasani, Bharat K.↗

DOE OSTI2019

Effects of Moisture on Diffusion in Unmodified Wood Cell Walls: A Phenomenological Polymer Science Approach

Despite the importance of cell wall diffusion to nearly all aspects of wood utilization, diffusion mechanisms and the detailed effects of moisture remain poorly understood. In this perspective, we introduce and employ approaches established in polymer science to develop a phenomenological framework for understanding the effects of moisture on diffusion in unmodified wood cell walls. The premise for applying this polymer-science-based approach to wood is that wood polymers (cellulose, hemicelluloses, and lignin) behave like typical solid polymers. Therefore, the movement of chemicals through wood cell walls is a diffusion process through a solid polymer, which is in contrast to previous assertions that transport of some chemicals occurs via aqueous pathways in the cell wall layers. Diffusion in polymers depends on the interrelations between free volume in the polymer matrix, molecular motions of the polymer, diffusant dimensions, and solubility of the diffusant in the polymer matrix. Because diffusion strongly depends on whether a polymer is in a rigid glassy state or soft rubbery state, it is important to understand glass transitions in the amorphous wood polymers. Through a review and analysis of available literature, we conclude that in wood both lignin and the amorphous polysaccharides very likely have glass transitions. After developing and presenting this polymer-science-based perspective of diffusion through unmodified wood cell walls, suggested directions for future research are discussed. A key consideration is that a large difference between diffusion through wood polymers and typical polymers is the high swelling pressures that can develop in unmodified wood cell walls. This pressure likely arises from the hierarchical structure of wood and should be taken into consideration in the development of predictive models for diffusion in unmodified wood cell walls.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Relaxation processes in a lower disorder order transition diblock copolymer

The dynamics of lower disorder-order temperature diblock copolymer leading to phase separation has been observed by X ray photon correlation spectroscopy. Two different modes have been characterized. A non-diffusive mode appears at temperatures below the disorder to order transition, which can be associated to compositional fluctuations, that becomes slower as the interaction parameter increases, in a similar way to the one observed for diblock copolymers exhibiting phase separation upon cooling. At temperatures above the disorder to order transition T{sub ODT}, the dynamics becomes diffusive, indicating that after phase separation in Lower Disorder-Order Transition (LDOT) diblock copolymers, the diffusion of chain segments across the interface is the governing dynamics. As the segregation is stronger, the diffusive process becomes slower. Both observed modes have been predicted by the theory describing upper order-disorder transition systems, assuming incompressibility. However, the present results indicate that the existence of these two modes is more universal as they are present also in compressible diblock copolymers exhibiting a lower disorder-order transition. No such a theory describing the dynamics in LDOT block copolymers is available, and these experimental results may offer some hints to understanding the dynamics in these systems. The dynamics has also been studied in the ordered state, and for the present system, the non-diffusive mode disappears and only a diffusive mode is observed. This mode is related to the transport of segment in the interphase, due to the weak segregation on this system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Decoherence and energy relaxation in the quantum-classical dynamics for charge transport in organic semiconducting crystals: An instantaneous decoherence correction approach

We explore an instantaneous decoherence correction (IDC) approach for the decoherence and energy relaxation in the quantum-classical dynamics of charge transport in organic semiconducting crystals. These effects, originating from environmental fluctuations, are essential ingredients of the carrier dynamics. The IDC is carried out by measurement-like operations in the adiabatic representation. While decoherence is inherent in the IDC, energy relaxation is taken into account by considering the detailed balance through the introduction of energy-dependent reweighing factors, which could be either Boltzmann (IDC-BM) or Miller-Abrahams (IDC-MA) type. For a non-diagonal electron-phonon coupling model, it is shown that IDC tends to enhance diffusion while energy relaxation weakens this enhancement. As expected, both the IDC-BM and IDC-MA achieve a near-equilibrium distribution at finite temperatures in the diffusion process, while in the Ehrenfest dynamics the electronic system tends to infinite temperature limit. The resulting energy relaxation times with the two kinds of factors lie in different regimes and exhibit different dependences on temperature, decoherence time, and electron-phonon coupling strength, due to different dominant relaxation processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

MoRE-Brain: Routed Mixture of Experts for Interpretable and Generalizable Cross-Subject fMRI Visual Decoding

Decoding visual experiences from fMRI offers a powerful avenue to understand human perception and develop advanced brain-computer interfaces. However, current progress often prioritizes maximizing reconstruction fidelity while overlooking interpretability, an essential aspect for deriving neuroscientific insight. To address this gap, we propose MoRE-Brain, a neuro-inspired framework designed for high-fidelity, adaptable, and interpretable visual reconstruction. MoRE-Brain uniquely employs a hierarchical Mixture-of-Experts architecture where distinct experts process fMRI signals from functionally related voxel groups, mimicking specialized brain networks. The experts are first trained to encode fMRI into the frozen CLIP space. A finetuned diffusion model then synthesizes images, guided by expert outputs through a novel dual-stage routing mechanism that dynamically weighs expert contributions across the diffusion process. MoRE-Brain offers three main advancements: First, it introduces a novel Mixture-of-Experts architecture grounded in brain network principles for neuro-decoding. Second, it achieves efficient cross-subject generalization by sharing core expert networks while adapting only subject-specific routers. Third, it provides enhanced mechanistic insight, as the explicit routing reveals precisely how different modeled brain regions shape the semantic and spatial attributes of the reconstructed image. Extensive experiments validate MoRE-Brain’s high reconstruction fidelity, with bottleneck analyses further demonstrating its effective utilization of fMRI signals, distinguishing genuine neural decoding from over-reliance on generative priors. Consequently, MoRE-Brain marks a substantial advance towards more generalizable and interpretable fMRI-based visual decoding.

Wei, Yuxiang [Georgia Institute of Technology]↗

DOE OSTI2016

Review on first-principles study of defect properties of CdTe as a solar cell absorber

CdTe is one of the leading materials for high-efficiency, low-cost, and thin-film solar cells. In this work, we review the recent first-principles study of defect properties of CdTe and present that: (1) When only intrinsic defects are present, p-type doping in CdTe is weak and the hole density is low due to the relatively deep acceptor levels of Cd vacancy. (2) When only intrinsic defects present, the dominant non-radiative recombination center in p-type CdTe is Te-2+/Cd, which limits the carrier lifetime to be around 200 ns. (3) Extrinsic p-type doping in CdTe by replacing Te with group V elements generally will be limited by the formation of AX centers. This could be overcome through a non-equilibrium cooling process and the hole density can achieve 10^17 cm-3. However, the long-term stability will be a challenging issue. (4) Extrinsic p-type doping by replacing Cd with alkaline group I elements is limited by alkaline interstitials and a non-equilibrium cooling process can efficiently enhance the hole density to the order of 10^17 cm-3. (5) Cu and Cl treatments are discussed. In bulk CdTe, Cu can enhance p-type doping, but Cl is found to be unsuitable for this. Both Cu and Cl show segregation at grain boundaries, especially at those with Te-Te wrong bonds. (6) External impurities are usually incorporated by diffusion. Therefore, the diffusion processes in CdTe are investigated. We find that cation interstitial (Nai, Cui) diffusion follows relatively simple diffusion paths, but anion diffusion (Cli, Pi) follows more complicated paths due to the degenerated defect wavefunctions.

14 SOLAR ENERGY↗

DOE OSTI2021

A New Route to Quantum-Scale Structures through a Novel Enhanced Germanium Diffusion Mechanism

This project sought to develop a fundamental understanding of the mechanisms underlying a newly observed enhanced germanium (Ge) diffusion process in silicon germanium (SiGe) semiconductor nanostructures during thermal oxidation. Using a combination of oxidationdiffusion experiments, high resolution imaging, and theoretical modeling, a model for the enhanced Ge diffusion mechanism was proposed. Additionally, a nanofabrication approach utilizing this enhanced Ge diffusion mechanism was shown to be applicable to arbitrary 3D shapes, leading to the fabrication of stacked silicon quantum dots embedded in SiGe nanopillars. A new wet etch-based method for preparing 3D nanostructures for highresolution imaging free of obscuring material or damage was also developed. These results enable a new method for the controlled and scalable fabrication of on-chip silicon nanostructures with sub-10 nm dimensions needed for next generation microelectronics, including low energy electronics, quantum computing, sensors, and integrated photonics.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Structural and phase transformation of apatite and quartz in the indentation process single crystals

Using the method of scanning and high-resolution electron microscopy, the zones of indentation by scratching for apatite and quartz single crystals were investigated. The textural, structural and phase transformations revealed have been conventionally ascribed to “deformation” and “diffusion” processes of plastic deformation. In zones of indentation by scratching of single crystals there have been two levels of structural transformations revealed, with a sharp boundary between them, at a stress equal to the theoretical ultimate stress limit (σ{sub TSL}). In the top zone of scratches, within the range of stress from the microhardness value H{sub s} up to the σ{sub TSL} value the substance undergoes profound structural and phase transformations. In the bed of scratches at the stress value lower than σ{sub TSL} values, single crystal fragmentation occurs with the formation of blocks and steps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Quasielastic neutron scattering studies on glass-forming ionic liquids with imidazolium cations

Relaxation processes for imidazolium-based ionic liquids (ILs) were investigated by means of an incoherent quasielastic neutron scattering technique. In order to clarify the cation and anion effects on the relaxation processes, ten samples were measured. For all of the samples, we found three relaxations at around 1 ps, 10 ps, and 100 ps-10 ns, each corresponding to the alkyl reorientation, the relaxation related to the imidazolium ring, and the ionic diffusion. The activation energy (E{sub a}) for the alkyl relaxation is insensitive to both anion and alkyl chain lengths. On the other hand, for the imidazolium relaxation and the ionic diffusion processes, E{sub a} increases as the anion size decreases but is almost independent of the alkyl chain length. This indicates that the ionic diffusion and imidazolium relaxation are governed by the Coulombic interaction between the core parts of the cations (imidazolium ring) and the anions. This is consistent with the fact that the imidazolium-based ILs have nanometer scale structures consisting of ionic and neutral (alkyl chain) domains. It is also found that there is a clear correlation between the ionic diffusion and viscosity, indicating that the ionic diffusion is mainly associated with the glass transition which is one of the characteristics of imidazolium-based ILs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Analytical estimates of proton acceleration in laser-produced turbulent plasmas

With the advent of high power lasers, new opportunities have opened up for simulating astrophysical processes in the laboratory. We show that second-order Fermi acceleration can be directly investigated at the National Ignition Facility, Livermore. This requires measuring the momentum-space diffusion of 3 MeV protons produced within a turbulent plasma generated by a laser. In conclusion, treating Fermi acceleration as a biased diffusion process, we show analytically that a measurable broadening of the initial proton distribution is then expected for particles exiting the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

CRPropa 3.1—a low energy extension based on stochastic differential equations

The propagation of charged cosmic rays through the Galactic environment influences all aspects of the observation at Earth. Energy spectrum, composition and arrival directions are changed due to deflections in magnetic fields and interactions with the interstellar medium. Today the transport is simulated with different simulation methods either based on the solution of a transport equation (multi-particle picture) or a solution of an equation of motion (single-particle picture). We developed a new module for the publicly available propagation software CRPropa 3.1, where we implemented an algorithm to solve the transport equation using stochastic differential equations. This technique allows us to use a diffusion tensor which is anisotropic with respect to an arbitrary magnetic background field. The source code of CRPropa is written in C++ with python steering via SWIG which makes it easy to use and computationally fast. In this paper, we present the new low-energy propagation code together with validation procedures that are developed to proof the accuracy of the new implementation. Furthermore, we show first examples of the cosmic ray density evolution, which depends strongly on the ratio of the parallel κ{sub ∥} and perpendicular κ{sub ⊥} diffusion coefficients. This dependency is systematically examined as well the influence of the particle rigidity on the diffusion process.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Materials path toward improved energy efficiency for High Energy Physics accelerators

For nearly fifty years researchers working with particle accelerators have envisioned reducing their initial and operating costs by substituting the intermetallic compound Nb 3 Sn for Nb as the cavity interior surface. The goal has remained elusive, stymied especially by the fall of cavity quality factor (representing increasing energy consumption) with increasing gradient (the amount of accelerator need to reach an energy goal). While one research group reported making a few cavities free of the problem, no one has reported how this comes about or has reproduced the improvement. We believe that insufficient understanding is responsible. We report here findings of a detailed, systematic study of the formation of Nb 3 Sn coatings on Nb, relating structure and properties of the coating to the process parameters and substrate materials on the one hand, and RF surface impedance and SRF cavity performance on the other was carried out, focusing on the two step (nucleation – deposition) tin vapor diffusion process. Major outcomes are: The choice of initial surface preparation (BCP etc) has no discernable impact on any quality of the final coating; Though tin chloride serves as the coating nucleant, no trace could be found by any means of chlorine after nucleation or coating; No evidence was found for any substantive impact of the details of the nucleation on the ultimate coating, as long as it was done within the frequently used range; The coating forms as Nb 3 Sn crystals by tin from the vapor diffusing down grain boundaries to the Nb interface and growing there. Higher temperature and longer time lead to larger, but otherwise substantially identical crystals; All coatings exhibited roughness on the micron scale. Testing the effect of coating surface modification technologies in use by the community, only a carefully tailored electropolish showed significant benefit; and, Preliminary results indicate that Ti contamination may be associated with falling gradient. Two particular item appear promising for future work. The effect of surface topography in the range seen here on performance is significant for niobium. The nature and impact on Nb 3 Sn, if any, needs to be understood and managed. At what level Ti, Ta or other impurities affects the performance of Nb 3 Sn needs to be understood.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Empirical correlations between the arrhenius' parameters of impurities' diffusion coefficients in CdTe crystals

Understanding of self- and dopant-diffusion in semiconductor devices is essential to our being able to assure the formation of well-defined doped regions. In this paper, we compare obtained in the literature up to date the Arrhenius’ parameters (D=D 0 exp(–ΔE a /kT)) of point-defect diffusion coefficients and the I-VII groups impurities in CdTe crystals and films. We found that in the diffusion process there was a linear dependence between the pre-exponential factor, D 0 , and the activation energy, ΔE a , of different species: This was evident in the self-diffusivity and isovalent impurity Hg diffusivity as well as for the dominant IIIA and IVA groups impurities and Chlorine, except for the fast diffusing elements (e.g., Cu and Ag), chalcogens O, S, and Se, halogens I and Br as well as the transit impurities Mn, Co, Fe. As a result, reasons of the lack of correspondence of the data to compensative dependence are discussed.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Diffusion of Cd and Te adatoms on CdTe(111) surfaces: A computational study using density functional theory

CdTe is one of the most promising semiconductor for thin-film based solar cells. Here we report a computational study of Cd and Te adatom diffusion on the CdTe (111) A-type (Cd terminated) and B-type (Te terminated) surfaces and their migration paths. The atomic and electronic structure calculations are performed under the DFT formalism and climbing Nudge Elastic Band (cNEB) method has been applied to evaluate the potential barrier of the Te and Cd diffusion. In general the minimum energy site on the surface is labeled as A{sub a} site. In case of Te and Cd on B-type surface, the sub-surface site (a site just below the top surface) is very close in energy to the A site. This is responsible for the subsurface accumulation of adatoms and therefore, expected to influence the defect formation during growth. The diffusion process of adatoms is considered from A{sub a} (occupied) to A{sub a} (empty) site at the nearest distance. We have explored three possible migration paths for the adatom diffusion. The adatom surface interaction is highly dependent on the type of the surface. Typically, Te interaction with both type (5.2 eV for A-type and 3.8 eV for B-type) is stronger than Cd interactions(2.4 eV for B-type and 0.39 eV for A-type). Cd interaction with the A-type surface is very weak. The distinct behavior of the A-type and B-type surfaces perceived in our study explain the need of maintaining the A-type surface during growth for smooth and stoichiometric growth.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Solute Redistribution During Aging in a Laser-Based Powder Bed Fusion-Produced Fe-18Ni-9Co-5Mo-Ti Maraging Steel

Solute distribution during the laser-based powder bed fusion of metals process is highly complex because of solidification. This study builds on a previous investigation of how solute heterogeneities across different scales influence phase distribution and aging physical phenomena in a Fe-18Ni-9Co-5Mo-Ti maraging steel (Santana et al. in Addit Manuf 104494, 2024). Previous work using energy-dispersive X-ray spectroscopy revealed heterogeneous Ni and Mo enrichment at intercellular regions. Using X-ray diffraction, 8 ± 3% retained austenite was quantified in as-built samples. Additionally, electron backscatter diffraction analysis exposed the location of retained austenite along cell boundaries. In this work, scanning transmission electron microscopy results revealed the presence of non-enriched retained austenite in the as-built condition. With increased aging temperature, Ni and Mo enrichment in austenite increased, especially at the austenite/martensite boundary. Solute diffusion was simulated in DICTRA Thermo-Calc® software to assess solute redistribution between the matrix and second phases and to comprehend whether elemental diffusion processes are interconnected. Three different scenarios were considered: (1) solute diffusion in the matrix; (2) diffusion with enriched austenite in the intercellular region; (3) diffusion with non-enriched austenite in the intercellular region. Results showed that Ni partitioning controls austenite growth and that boundary regions exhibit higher element enrichment than the core.

42 ENGINEERING↗

DOE OSTI2015

Anomalous law of cooling

We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergoes a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton’s law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature may oscillate. Despite this anomalous behavior, we show that the variation of entropy remains always positive in accordance with the second law of thermodynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Polarized IR and Raman spectra of (H{sub 2}O){sub n} clusters (n = 2–5) in the c-channels of apatite single crystals

The infrared (IR) and Raman spectra of three samples of fluorapatite single crystals and carbonate fluorapatite single crystal in the region of 7000–400 cm{sup –1} were studied. It has been shown that isomorphic substitution of the Ca{sup 2+} cation and the PO{sub 4}{sup 3-} anion leads to an increase in the size of the c-channels in the apatite crystal, which is accompanied by the formation of water clusters of the (H{sub 2}O){sub n} and H{sub 3}O{sup +} · (H{sub 2}O){sub n} (n = 2–5) types as a result of the diffusion processes in these local sections of the c-channels.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗