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Search · four archives
25 papers · ranked by Valyu relevance
Ion Bica, Thomas Hillen, Kevin J. Painter
Many biological environments display an almost radially-symmetric structure, allowing proteins, cells or animals to move in an oriented fashion. Motivated by specific examples of cell movement in tissues, pigment protein movement in pigment cells and animal movement near watering holes, we consider a class of…
Stephen Smith, Claudia Cianci, Ramon Grima
It is now well established that cell interiors are significantly crowded by macromolecules, which impede diffusion and enhance binding rates. However, it is not fully appreciated that levels of crowding are heterogeneous, and can vary substantially between subcellular regions. In this article, starting from a…
Derik W. Gryczak, Ervin K. Lenzi, Michely P. Rosseto, Luiz R. Evangelista + 2 more
'Luiz R. Evangelista' 'Rafael S. Zola' 'José F. F. Mendes'] The interplay of diffusion with phenomena like stochastic adsorption-desorption, absorption, and reaction-diffusion is essential for life and manifests in diverse natural contexts. Many factors must be considered, including geometry, dimensionality, and the…
Leila Farhadi, Shane A. Fiorenza, Sithara Wijeratne, Konstantinos Nakos + 6 more
How microscopic interactions give rise to cellular-scale order in the crowded environment of cells remains an open problem. Far-from-equilibrium mixtures of active and passive molecules self-organize, but the principles remain unclear. Microtubules are cytoskeletal polymers composed of 13 protofilaments bound by…
Rui Yan, Kun Chen, Ke Xu
Diffusion properties notably determine the behavior of biomembranes. Here we report the concurrent nanoscale fine-mapping of membrane topography, diffusivity, and packing order in live mammalian cells through a synergy of single-molecule and super-resolution methods. By identifying a bright, lipophilic fluorescence…
Mario Heidernätsch, Michael Bauer, Günter Radons
Anisotropic diffusion processes emerge in various fields such as transport in biological tissue and diffusion in liquid crystals. In such systems, the motion is described by a diffusion tensor. For a proper characterization of processes with more than one diffusion coefficient an average description by the mean squared…
Wojciech Szmyt, Carlos Guerra, Ivo Utke, Paul Ziemann
In this work we modelled the diffusive transport of a dilute gas along arrays of randomly distributed, vertically aligned nanocylinders (nanotubes or nanowires) as opposed to gas diffusion in long pores, which is described by the well-known Knudsen theory. Analytical expressions for (i) the gas diffusion coefficient…
Giulia Melchiorre, Francesco Giustiniano, Sundeep Rathore, Giuseppe Pileio
'Giuseppe Pileio'] In this study, long-lived nuclear singlet order methods are combined with diffusion tensor imaging with the purpose of characterizing the full diffusion tensor of molecules diffusing freely in large pores of up to a millimeter in size. Such sizes are out of reach in conventional diffusion tensor…
Kejie Chen, Bogdan I. Epureanu
A generalized persistent random walk (GPRW) model to study anomalous particle diffusion influenced by angular heterogeneity is presented. Consider the motion of a particle is composed of many consecutive straight line segments. At the end of each straight motion, the particle can switch to a new moving direction.…
Oded Farago, Giuseppe Pontrelli
We use Langevin dynamics simulations to study the mass diffusion problem across two adjacent porous layers of different transport property. At the interface between the layers, we impose the Kedem-Katchalsky (KK) interfacial boundary condition that is well suited in a general situation. A detailed algorithm for the…
Jack D. Evans, Simon Krause, Ben L. Feringa
Molecules in gas and liquid states, as well as in solution, exhibit significant and random Brownian motion. Molecules in the solid-state, although strongly immobilized, can still exhibit significant intramolecular dynamics. However, in most framework materials, these intramolecular dynamics are driven by temperature…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Balázs Fábián, Matti Javanainen
Curved membranes are abundant and functionally relevant in living matter, yet they have eluded computational studies due to methodological limitations. With multiple approaches available for setting up simulations on such curved membranes, there is a growing need for efficient and versatile tools to analyze their…
Andreas Wartak, Marco Augustin, Richard Haindl, Florian Beer + 5 more
'Matthias Salas' 'Marie Laslandes' 'Bernhard Baumann' 'Michael Pircher' 'Christoph K. Hitzenberger'] We introduce multi-directional optical coherence tomography (OCT), a technique for investigation of the scattering properties of directionally reflective tissue samples. By combining the concepts of multi-channel and…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Evren Özarslan, Cem Yolcu, Alfredo Ordinola, Deneb Boito + 3 more
'Tom Dela Haije' 'Mathias Højgaard Jensen' 'Magnus Herberthson'] Probing the transport of fluids within confined domains is important in many areas including material science, catalysis, food science, and cell biology. The diffusion propagator fully characterizes the diffusion process, which is highly sensitive to the…
Pauli Losoi, Jukka Konttinen, Ville Santala
Tall vessels equipped with multiple impellers, such as many gas-liquid contactors in bioprocessing, often suffer from poor macromixing of feeds, which leads to heterogeneities and complicates the scale-up. Here, a diffusion equation was used as a simple model of macromixing in multi-impeller tanks, and the model fitted…
Yasushi Saka, Murray MacPherson, Claudiu V. Giuraniuc
Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusionbased gradient generation for cellular assays. A unique…
Ahsan Khawaja, Tariq M. Khan, Mohammad A. U. Khan, Syed Junaid Nawaz
The assessment of transformations in the retinal vascular structure has a strong potential in indicating a wide range of underlying ocular pathologies. Correctly identifying the retinal vessel map is a crucial step in disease identification, severity progression assessment, and appropriate treatment. Marking the…
Matteo Busi, Elisabetta Nocerino, Agnes Åhl, Lennart Bergström + 1 more
multi-directional dark-field neutron tomography Authors: ['Matteo Busi' 'Elisabetta Nocerino' 'Agnes Åhl' 'Lennart Bergström' 'Markus Ströbl'] Hierarchical biomaterials embody nature's intricate design principles, offering advanced functionalities through the complex, multi-level organization of their molecular and…
Authors not listed
A directed-graph model is proposed to describe the concerted ion migration in superionic conductors. Here, each ion hopping during the molecular dynamics simulation is represented as a displacement vector. Multiple hoppings are then timely and spatially connected to reconstruct the concerted ion migration. This enables…
Aishani Ghosal, Yu-Huan Wang, Nguyen Nguyen, Laura Troyer + 1 more
Advances in fluorescence microscopy have enabled high-resolution tracking of individual biomolecules in living cells. However, accurate estimation of diffusion parameters from single-particle trajectories remains challenging due to static and dynamic localization errors inherent in these measurements. While previous…
Kairi Masuda
Molecular dynamics simulation has been widely used to investigate underlying mechanisms of many phenomena from the atomic scale. However, it is often difficult for conventional molecular dynamics to treat a longer time scale because they are based on Newton’s equation. Here, we propose a new molecular dynamics…
Mykhaylo Slobodyanyuk, Alexander T. Bahcheli, Zoe P. Klein, Masroor Bayati + 2 more
'Masroor Bayati' 'Lisa J. Strug' 'Jüri Reimand'] Omics techniques generate comprehensive profiles of biomolecules in cells and tissues. However, a holistic understanding of underlying systems requires joint analyses of multiple data modalities. We present DPM, a data fusion method for integrating omics datasets using…
Mykhaylo Slobodyanyuk, Alexander T. Bahcheli, Zoe P. Klein, Masroor Bayati + 2 more
Omics techniques generate comprehensive profiles of biomolecules in cells and tissues. However, a holistic understanding of the data requires joint multi-omics analyses that are challenging. Here we present DPM, a data fusion method for combining multiple omics datasets using directionality and significance estimates…