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Random Walks and Sticky Surfaces: Single-Molecule Measurements of Solute Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores
Nanoporous anodic aluminum oxide (AAO) membranes are now being explored for use in advanced chemical separations, including in the dehydration of biofuels such as ethanol. Optimization of membrane performance requires an in-depth understanding of how solvent mixtures and solutes behave under nanoconfinement. In this work, the diffusion of rhodamine B (RhB) dye through 10 nm and 20 nm AAO nanopores filled with a series of ethanol/water mixtures (0 - 33% water) is explored by fluorescence correlation spectroscopy (FCS). RhB was found to diffuse through the pores by two distinct mechanisms with mean diffusion coefficients, $D_f$ and $D_s$, reflecting fast and slow diffusive motions, respectively, with values that differ by nearly two orders of magnitude. Further, both $D_f$ and $D_s$ increased with pore size and were significantly smaller than $D_b$, the RhB diffusion coefficient in bulk liquid. Mean $D_f$ values follow a composition-dependent trend that closely mimics the viscosity dependence of $D_b$. Additional slowing of fast RhB diffusion is attributed to both hydrodynamic drag and electrostatic interactions with the nanopore surface. The mean $D_s$ values exhibit a different trend with increasing water content, revealing an increase in $D_s$ and a decrease in the contributions of slow diffusion to the observed dynamics. The fluorescence time transient data used in the analysis show that the slow diffusion process is strongly hindered and likely involves frequent adsorption of RhB to the pore surfaces. These results provide new insights into the detailed molecular-level mechanisms of mass transport in nanoporous AAO membranes.
Universality in the random walk structure function of luminous quasi-stellar objects
Not provided.
The nanocaterpillar's random walk: diffusion with ligand–receptor contacts
Particles with ligand–receptor contacts bind and unbind fluctuating “legs” to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such “nanoscale caterpillars” is a challenge, since binding events often occur on very short time and length scales. Here, in this work, we derive an analytical formula, validated by simulations, for the long time translational diffusion coefficient of an overdamped nanocaterpillar, under a range of modeling assumptions. We demonstrate that the effective diffusion coefficient, which depends on the microscopic parameters governing the legs, can be orders of magnitude smaller than the background diffusion coefficient. Furthermore it varies rapidly with temperature, and reproduces the striking variations seen in existing data and our own measurements of the diffusion of DNA-coated colloids. Our model gives insight into the mechanism of motion, and allows us to ask: when does a nanocaterpillar prefer to move by sliding, where one leg is always linked to the surface, and when does it prefer to move by hopping, which requires all legs to unbind simultaneously? We compare a range of systems (viruses, molecular motors, white blood cells, protein cargos in the nuclear pore complex, bacteria such as Escherichia coli, and DNA-coated colloids) and present guidelines to control the mode of motion for materials design.
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species
Abstract We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.
Random Walks With Tweedie: A Unified View of Score-Based Diffusion Models [In the Spotlight]
We present a concise derivation for several influential score-based diffusion models that relies on only a few textbook results. Diffusion models have recently emerged as powerful tools for generating realistic, synthetic signals—particularly natural images—and often play a role in state-of-the-art algorithms for inverse problems in image processing. While these algorithms are often surprisingly simple, the theory behind them is not, and multiple complex theoretical justifications exist in the literature. Here, in this study, we provide a simple and largely self-contained theoretical justification for score-based diffusion models that is targeted towards the signal processing community. This approach leads to generic algorithmic templates for training and generating samples with diffusion models. We show that several influential diffusion models correspond to particular choices within these templates and demonstrate that alternative, more straightforward algorithmic choices can provide comparable results. This approach has the added benefit of enabling conditional sampling without any likelihood approximation.
Probing black hole microstate evolution with networks and random walks
We model black hole microstates and quantum tunneling transitions between them with networks and simulate their time evolution using well-established tools in network theory. In particular, we consider two models based on Bena-Warner three-charge multi-centered microstates and one model based on the D1-D5 system; we use network theory methods to determine how many centers (or D1-D5 string strands) we expect to see in a typical late-time state. We find three distinct possible phases in parameter space for the late-time behaviour of these networks, which we call ergodic, trapped, and amplified, depending on the relative importance and connectedness of microstates. We analyze in detail how these different phases of late-time behavior are related to the underlying physics of the black hole microstates. Our results indicate that the expected properties of microstates at late times cannot always be determined simply by entropic arguments; typicality is instead a highly non-trivial, emergent property of the full Hilbert space of microstates.
A Comparison of Custom and Standard Neuron Model Random Walks on the Ornstein-Uhlenbeck Equation for Simplified Turbulence
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Examining AGN UV/Optical Variability beyond the Simple Damped Random Walk
We present damped harmonic oscillator (DHO) light-curve modeling for a sample of 12,714 spectroscopically confirmed quasars in the Sloan Digital Sky Survey Stripe 82 region. DHO is a second-order continuous-time autoregressive moving-average process, which can be fully described using four independent parameters: a natural oscillation frequency (ω 0 ), a damping ratio (ξ), a characteristic perturbation timescale (τ perturb ), and an amplitude for the perturbing white noise (σ ϵ ). The asymptotic variability amplitude of a DHO process is quantified by σ DHO —a function of ω 0 , ξ, τ perturb , and σ ϵ . We find that both τ perturb and σ ϵ follow different dependencies with rest-frame wavelength (λ RF ) on either side of 2500 Å, whereas σ DHO follows a single power-law relation with λ RF . After correcting for wavelength dependence, σ DHO exhibits anticorrelations with both the Eddington ratio and the black hole mass, while τ perturb —with a typical value of days in the rest frame—shows an anticorrelation with the bolometric luminosity. Modeling active galactic nuclei (AGN) variability as a DHO offers more insight into the workings of accretion disks close to the supermassive black holes at the center of AGN. The newly discovered short-term variability (characterized by τ perturb and σ ϵ ) and its correlation with bolometric luminosity pave the way for new algorithms that will derive fundamental properties (e.g., Eddington ratio) of AGN using photometric data alone.
Parallelized domain decomposition for multi-dimensional Lagrangian random walk mass-transfer particle tracking schemes
Lagrangian particle tracking schemes allow a wide range of flow and transport processes to be simulated accurately, but a major challenge is numerically implementing the inter-particle interactions in an efficient manner. This article develops a multi-dimensional, parallelized domain decomposition (DDC) strategy for mass-transfer particle tracking (MTPT) methods in which particles exchange mass dynamically. We show that this can be efficiently parallelized by employing large numbers of CPU cores to accelerate run times. In order to validate the approach and our theoretical predictions we focus our efforts on a well-known benchmark problem with pure diffusion, where analytical solutions in any number of dimensions are well established. In this work, we investigate different procedures for “tiling” the domain in two and three dimensions (2-D and 3-D), as this type of formal DDC construction is currently limited to 1-D. An optimal tiling is prescribed based on physical problem parameters and the number of available CPU cores, as each tiling provides distinct results in both accuracy and run time. We further extend the most efficient technique to 3-D for comparison, leading to an analytical discussion of the effect of dimensionality on strategies for implementing DDC schemes. Increasing computational resources (cores) within the DDC method produces a trade-off between inter-node communication and on-node work. For an optimally subdivided diffusion problem, the 2-D parallelized algorithm achieves nearly perfect linear speedup in comparison with the serial run-up to around 2700 cores, reducing a 5 h simulation to 8 s, while the 3-D algorithm maintains appreciable speedup up to 1700 cores.
Leveraging Random Walks to Solve IPDEs on Spiking Neuromorphic Hardware.
Abstract not provided.
A Comparison of Custom and Standard Neuron Model Random Walks on the Ornstein-Uhlenbeck Equation for Simplified Turbulence
An initial investigation into neuron models aimed at efficient stochastic simulation of turbulent flows.
Dark matter halo mass functions and density profiles from mass and energy cascade
Abstract Halo abundance and structure play a central role for modeling structure formation and evolution. Without relying on a spherical or ellipsoidal collapse model, we analytically derive the halo mass function and cuspy halo density (inner slope of −4/3) based on the mass and energy cascade theory in dark matter flow. The hierarchical halo structure formation leads to halo or particle random walk with a position-dependent waiting time $$\tau _g$$ τ g . First, the inverse mass cascade from small to large scales leads to the halo random walk in mass space with $$\tau _g\propto m_h^{-\lambda }$$ τ g ∝ m h - λ , where $$m_h$$ m h is the halo mass and $$\lambda$$ λ is a halo geometry parameter with predicted value of 2/3. The corresponding Fokker-Planck solution for halo random walk in mass space gives rise to the halo mass function with a power-law behavior on small scale and exponential decay on large scale. This can be further improved by considering two different $$\lambda$$ λ for haloes below and above a critical mass scale $$m_h^*$$ m h ∗ , i.e. a double- $$\lambda$$ λ halo mass function. Second, a double- $$\gamma$$ γ density profile can be derived based on the particle random walk in 3D space with a position-dependent waiting time $$\tau _g \propto \Phi (r)^{-1} \propto r^{-\gamma }$$ τ g ∝ Φ ( r ) - 1 ∝ r - γ , where $$\Phi$$ Φ is the gravitational potential and r is the particle distance to halo center. Theory predicts $$\gamma =2/3$$ γ = 2 / 3 that leads to a cuspy density profile with an inner slope of −4/3, consistent with the predicted scaling laws from energy cascade. The Press-Schechter mass function and Einasto density profile are just special cases of proposed models. The small scale permanence can be identified due to the scale-independent rate of mass and energy cascade, where density profiles of different halo masses and redshifts converge to the $$-4/3$$ - 4 / 3 scaling law ( $$\rho _h \propto r^{-4/3}$$ ρ h ∝ r - 4 / 3 ) on small scales. Theory predicts the halo number density scales with halo mass as $$\propto m_h^{-1.9}$$ ∝ m h - 1.9 , while the halo mass density scales as $$\propto m_h^{4/9}$$ ∝ m h 4 / 9 . Results were compared against the Illustris simulations. This new perspective provides a theory for nearly universal halo mass functions and density profiles.
NeuralRW-Loihi: Spiking Discrete Time Markov Chain Simulator for Intel Loihi v
SAND2024-01302O NeuralRW-Loihi: Spiking Discrete Time Markov Chain Simulator for Intel Loihi is a neuromorphic script that generates a random walk simulation of a discrete-time Markov Chain for the Loihi neuromorphic hardware. The code was used to produce the paper "Neuromorphic scaling advantages for energy-efficient random walk computations" by Smith et al., 2021. It was published in Nature Electronics. The software provides code for implementing the discrete time Markov chain random walks on Intel's Loihi Neuromorphic platform. In addition, it provides an example problem through a mini app.
Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning
Motivation: Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. Results: We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement. Availability and implementation: Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.
Delocalization of a non-Hermitian quantum walk on random media in one dimension
Highlights: • We study the localization-delocalization transition of a non-Hermitian quantum walk. • We find that the phase transition is similar to the one in the Hatano-Nelson model. • All eigenvectors get extended and all eigenvalues become complex at the transition. • This implies that the localization lengths of all eigenvectors are the same. We first review the localization–delocalization transition of a non-Hermitian random tight-binding Anderson model, called the Hatano–Nelson model. We then report a new result for a non-Hermitian extension of a discrete-time quantum walk on a one-dimensional random medium; we numerically find a delocalization transition similar to one of the Hatano–Nelson model. As a common feature to both models, at the transition point, an eigenvector gets delocalized and at the same time the corresponding energy eigenvalue (for the latter quantum-walk model, the imaginary unit times the phase of the eigenvalue of the time-evolution operator) becomes complex. One of the unique properties of the present non-Hermitian quantum walk is that the localization length of all eigenvectors is the same, and thereby all eigenstates simultaneously undergo the delocalization transition and all energy eigenvalues become complex at the same time when we turn up a non-Hermitian parameter.
A finite difference informed random walker (FDiRW) solver for strongly inhomogeneous diffusion problems
In nature, many complex multi-physics coupling problems exhibit strong diffusivity inhomogeneity. For instance, in the context of radionuclide absorption by porous wasteform materials within a flowing waste stream, the difference of species’ diffusivity in solid and liquid phases spans by 3~8 orders of magnitude. To solve the diffusion equations with strongly inhomogeneous diffusivity, traditional discretization-based methods, such as the Finite Difference Method (FDM), require infinitesimally small time steps (<10 -10 ) as high spatial resolutions are employed in most microstructure evolution processes, leading to prohibitively high computational costs. Here, this work developed an integrated numerical approach (FDiRW: Finite Difference informed Random Walk) to tackle this challenge. The idea is that utilizing the Random Walk concept, the fast diffusion is modeled as a superposition of point source’s solution for a concentration distribution while FDM is used to obtain the point source’s solution at each node. A mesh-coarsening algorithm is developed to generate an exclusive coarse mesh for FDiRW approach to maximize its efficiency. The effectiveness of the coarse mesh-based FDiRW approach is validated by benchmarking Finite Difference solutions. Numerical results demonstrated that FDiRW achieves a remarkable 1000x computational efficiency improvement over FDM while preserving desired accuracy for a medium-sized model of 192 × 192 × 192 grids. Finally, as models scale up, a floating-point operations (PLOPs) analysis of the FDiRW algorithm reveals that its computational complexity grows quadratically in terms of the number of nodes employed in computation.