26 papers · ranked by Valyu relevance
Mayumi Hamada, Pietro de Anna
Molecular diffusion in liquids is a key process in numerous systems: it is often the reaction rate limiting factor in biological or chemical reaction. Molecular diffusion has been recognized as the ultimate mechanism by which substances concentration get homogenized and, thus, their mixing and dilution occur. Here, we…
Koushik Goswami, Rajarshi Chakrabarti
We propose a model for the motion of a single active particle in a heterogeneous environment where the heterogeneity may arise due to the crowding, conformational fluctuations and/or slow rearrangement of the surroundings. Describing the active particle in terms of the Ornstein-Uhlenbeck process (OUP) and incorporating…
Takuma Akimoto, Jae-Hyung Jeon, Ralf Metzler, Tomoshige Miyaguchi + 2 more
Department of Physics and Astronomy, Tokyo University of Science, Noda, Chiba 278-8510, Japan Asia Pacific Centre for Theoretical Physics, Pohang, 37673, Republic of Korea 3 Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany Department of Systems Engineering, Wakayama University, 930…
Filippo Begarani, Francesca D’Autilia, Gianmarco Ferri, Luca Pesce + 8 more
'Fabio Azzarello' 'Valentina De Lorenzi' 'William Durso' 'Ambra Del Grosso' 'Marco Cecchini' 'Francesco Cardarelli' 'Joseph P. Albanesi' 'David M. Jameson'] Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules…
Sudipta Mandal, Anirban Ghosh
Shape asymmetry is the most abundant in nature and attracted great interest in recent research. The phenomenon is widely recognized: a free ellipsoidal Brownian particle displays anisotropic diffusion during short time intervals, which subsequently transitions to an isotropic diffusion pattern over longer time scales.…
Masahiro Shirataki, Takuma Akimoto
A dynamical transition—seen as a sudden increase in the mean-squared displacement at a characteristic temperature that depends on the observation time—is widely reported in neutron-scattering experiments and molecular dynamics simulations of hydrated proteins. However, its physical origin remains elusive. We show that…
Oliver Schmitt, Christian Nitzsche, Peter Eipert, Vishnu Prathapan + 3 more
'Marc-Thorsten Hütt' 'Claus C. Hilgetag' 'Marcus Kaiser'] Connectomes represent comprehensive descriptions of neural connections in a nervous system to better understand and model central brain function and peripheral processing of afferent and efferent neural signals. Connectomes can be considered as a distinctive and…
Piotr Polanowski, Andrzej Sikorski, Nikolaos Voulgarakis
A coarse-grained model of a two-dimensional colloidal suspension was designed. The model was athermal and, in addition, a lattice approximation was introduced. It consisted of solvent (monomer) molecules, dimer molecules, and immobile impenetrable obstacles that introduced additional heterogeneity into the system.…
Tadeusz Kosztołowicz, Aldona Dutkiewicz, Katarzyna D. Lewandowska
Normal and anomalous diffusion processes are characterized by the time evolution of the mean square displacement of a diffusing molecule $σ2(t)$. When $σ2(t)$ is a power function of time, the process is described by a fractional subdiffusion, fractional superdiffusion or normal diffusion equation. However, for other…
Rushikesh Shinde, Jens‐Uwe Sommer, Hartmut Löwen, Abhinav Sharma
While the dynamics of dimers and polymer chains in a viscous solvent is well understood within the celebrated Rouse model, the effect of an external magnetic field on the dynamics of a charged chain is much less understood. Here we generalize the Rouse model for a charged dimer to include the effect of an external…
András László Szabó, Eszter Nagy-Kanta, Edit Andrea Jáger, Csaba István Pongor + 3 more
The postsynaptic density (PSD) is a complex, multi-layered protein network largely situated on the internal surface of the postsynaptic membrane, with receptor proteins extending it across the membrane. It is the first processing unit for incoming synaptic transmissions, and changes in its internal structure exhibit a…
Kine Ødegård Hanssen, Anders Malthe-Sørenssen
Perineuronal nets (PNNs) are mesh-like extracellular matrix structures that wrap around certain neurons in the central nervous system. They are hypothesized to stabilize memories in the brain and act as a barrier between cell and extracellular space. As a means to study the impact of PNNs on diffusion, the nets were…
Anirban Paul, Jaydeb Chakrabarti
The synergistic interactions between hyaluronic acid (HA) and other cellular components, particularly lipids and water, play a vital role in maintaining cellular structure and function. Variations in HA concentration and chain length lead to changes in the mechanical and viscoelastic properties of diseased cells, such…
Shiwen Zhu, Yi Ting Loo, Sapthaswaran Veerapathiran, Tricia Y. J. Loo + 6 more
Morphogens are intercellular signaling molecules providing spatial information to cells in developing tissues to coordinate cell fate decisions. The spatial information is encoded within long-ranged concentration gradients of the morphogen. Direct measurement of morphogen dynamics in a range of systems suggests that…
Enrico Lorenzetti, Celia Municio-Diaz, Nicolas Minc, Arezki Boudaoud + 1 more
Fluorescence recovery after photobleaching (FRAP) is broadly used to investigate the dynamics of molecules in cells and tissues, notably to quantify diffusion coefficients. FRAP is based on the spatiotemporal imaging of fluorescent molecules following an initial bleaching of fluorescence in a region of the sample.…
Conrad Möckel, Abin Biswas, Simone Reber, Aleksei Chechkin + 2 more
Understanding of the dynamics inherent to biological matter is crucial for illuminating the physical mechanisms underlying cellular processes. In this study, we employ bright-field differential dynamic microscopy (DDM) to investigate density fluctuations inherent in a cell-free model of eukaryotic cytoplasm. Our…
Gregory L. Eyink, Amir Homayoun Jafari
We discuss application of methods from the Kraichnan model of turbulent advection to the study of non-equilibrium concentration fluctuations arising during diffusion in liquid mixtures at high Schmidt numbers. This approach treats nonlinear advection of concentration fluctuations exactly, without linearization.…
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…
Moyassar Meshhal, Oliver Kuehn
Among the carbon-based two-dimensional materials, graphene oxide (GO) has been attracting a growing interest due to its capability to be utilized in the field of water remediation. Therefore, an atomistic understanding of the transport properties of water in layered GO is pivotal for the development of novel GO…
Srijana Pandey, Dinesh Gautam, Jixin Chen
Many interactions between small molecules and particles occur in solutions. They are surrounded by other molecules that do not react, for example, biological processes in water, chemical reactions in gas or liquid solutions, and environmental reactions in air and water. Predicting the rate of such interactions involves…
Timothy Ostler, W. Langbein, Paola Borri, Emily Lewis + 4 more
'Karl Swann' 'Thomas E. Woolley' 'Katerina Kaouri'] During In Vitro Fertilisation (IVF), combining time-lapse contrast microscopy with suitable image processing techniques could facilitate non-invasive classification of oocyte health, driving oocyte selection to maximise success rates. One image processing technique…
Neetu ., Aman Saini, Rishi Ram Mahato, Priyanka . + 1 more
The theory behind origin of life to Darwinian evolution considers emergence of dissipative structures driven by the flow of energy across all length scales. To this end, developing and deeper understanding of non-equilibrium self-assembly processes under continuous supply of energy is a demanding matter, both in…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
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…
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…
Fabian Späth, Michele Stasi, Héctor Soria-Carrera, Judit Sastre + 2 more
Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial…