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Several Lagrangian methodologies have been proposed in recent years to simulate advection-dispersion of solutes in fluids as a mass exchange between numerical particles carrying the fluid. In this paper, we unify these methodologies,…

Computational Physics · Physics 2019-02-26 Guillem Sole-Mari , Michael J. Schmidt , Stephen D. Pankavich , David A. Benson

Single-particle tracking (SPT) has become a popular tool to study the intracellular transport of molecules in living cells. Inferring the character of their dynamics is important, because it determines the organization and functions of the…

Quantitative Methods · Quantitative Biology 2020-09-09 Joanna Janczura , Patrycja Kowalek , Hanna Loch-Olszewska , Janusz Szwabiński , Aleksander Weron

This paper proposes an effective phase diffusion method to analyze chemical exchange in nuclear magnetic resonance (NMR). The chemical exchange involves spin jumps around different sites where the spin angular frequencies vary, which leads…

Chemical Physics · Physics 2023-07-19 Guoxing Lin

Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…

Quantitative Methods · Quantitative Biology 2016-01-06 Shunsuke Teraguchi , Yutaro Kumagai

Understanding diffusion in microstructures plays a crucial role in many scientific fields, including neuroscience, cancer or energy research. While magnetic resonance (MR) methods are the gold standard for diffusion measurements, spatial…

Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g. about cell membranes. While it has been shown in recent articles, that these…

Medical Physics · Physics 2013-05-08 Frederik Bernd Laun , Tristan Anselm Kuder

Time-dependent diffusion behavior is probed over sub-millisecond timescales in a single shot using an NMR static gradient, time-incremented echo train acquisition (SG-TIETA) framework. The method extends the Carr-Purcell-Meiboom-Gill (CPMG)…

Quantitative Methods · Quantitative Biology 2021-03-18 Teddy X. Cai , Nathan H. Williamson , Velencia J. Witherspoon , Rea Ravin , Peter J. Basser

Transport properties in fluids and confined systems play a central role across a wide range of natural and technological contexts, from geology and environmental sciences to biology, energy storage, and membrane-based separation processes.…

Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…

Biomolecules · Quantitative Biology 2011-07-12 Shannon Kian Zareh , Michael C. DeSantis , Jonathan Kessler , Je-Luen Li , Y. M. Wang

Experimental methods based on single particle tracking (SPT) are being increasingly employed in the physical and biological sciences, where nanoscale objects are visualized with high temporal and spatial resolution. SPT can probe…

Statistical Mechanics · Physics 2015-06-12 Denis Boyer , David S. Dean , Carlos Mejía-Monasterio , Gleb Oshanin

In porous material research, one main interest of nuclear magnetic resonance (NMR) diffusion experiments is the determination of the exact shape of pores. It has been a longstanding ques-tion if this is achievable in principle. In this…

Medical Physics · Physics 2012-05-09 Tristan Anselm Kuder , Frederik Bernd Laun

Systems driven by Brownian motion are ubiquitous. A prevailing challenge is inferring, from data, the diffusion and kinetic parameters that describe these stochastic processes. In this work, we investigate a multi-state diffusion process…

Quantitative Methods · Quantitative Biology 2022-06-20 Lewis R. Baker , Moshe T. Gordon , Brian P. Ziemba , Victoria Gershuny , Joseph J. Falke , David M. Bortz

Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of…

The Eulerian advection-dispersion-reaction equation (ADRE) suffers the well-known scale-effect of reduced apparent reaction rates between chemically dissimilar fluids at larger scales (or dimensional averaging). The dispersion tensor in the…

Fluid Dynamics · Physics 2018-12-05 David A. Benson , Diogo Bolster , Stephen Pankavich

The diffusion motions of individual polymer aggregates in disordered porous media were visualized using the single particle tracking (SPT) method because the motions inside porous media play important roles in various fields of science and…

Soft Condensed Matter · Physics 2024-10-24 Yusaku Abe , Naoki Tomioka , Yu Matsuda

Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…

Methodology · Statistics 2018-04-16 Vincent Briane , Charles Kervrann , Myriam Vimond

We describe methods for the measurement of translational diffusion in very large static magnetic field gradients by NMR. The techniques use a "hole-burning" sequence that, with the use of fringe field gradients of 42 T/m, can image…

Soft Condensed Matter · Physics 2009-11-07 E. E. Sigmund , W. P. Halperin

Single Particle Tracking (SPT) is a powerful class of tools for analyzing the dynamics of individual biological macromolecules moving inside living cells. The acquired data is typically in the form of a sequence of camera images that are…

Biomolecules · Quantitative Biology 2020-01-23 Ye Lin , Sean B. Andersson

This paper introduces the use of statistical distributions based on transport differential equations for clear distinction of transport modes within transient kinetic experiments. More specifically,novel techniques are developed for the…

Applications · Statistics 2025-01-08 M. Ross Kunz , Debtanu Maiti , Gregory Yablonsky , Rebecca Fushimi

We report initial NMR studies of i) xenon gas diffusion in model heterogeneous porous media, and ii) continuous flow laser-polarized xenon gas. Both areas utilize the Pulsed Gradient Spin Echo techniques in the gas-phase, with the aim of…

Soft Condensed Matter · Physics 2007-05-23 R. W. Mair , M. S. Rosen , R. Wang , D. G. Cory , R. L. Walsworth
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