25 papers · ranked by Valyu relevance
Yann Lanoiselée, Nicolas Moutal, Denis S. Grebenkov
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid rearrangements of the medium constantly change the effective diffusivity felt locally by a diffusing particle and thus impact the distribution of the first-passage…
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…
W. He, H. Song, Y. Su, L. Geng + 3 more
'P. Tong'] The Brownian motion of molecules at thermal equilibrium usually has a finite correlation time and will eventually be randomized after a long delay time, so that their displacement follows the Gaussian statistics. This is true even when the molecules have experienced a complex environment with a finite…
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…
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…
Surajith N. Wanasundara, Raymond J. Spiteri, Richard K. Bowles
Monte Carlo simulation is used to study the dynamical crossover from single file diffusion to normal diffusion in fluids confined to narrow channels. We show that the long time diffusion coefficients for a series of systems involving hard and soft interaction potentials can be described in terms of a hopping time that…
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…
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…
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…
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…
Debabrata Dey, Shir Marciano, Gideon Schreiber
A cell is a densely packed conglomerate of macromolecules, where diffusion is essential for their function. The crowded conditions may affect diffusion both through hard (occluded space) and soft (weak, non-specific) interactions. Multiple-methods have been developed to measure diffusion rates at physiological protein…
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.…
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…
Jia-Xing Gao, Zhen-Yi Wang, Michael Q. Zhang, Min-Ping Qian + 1 more
Dynamic models of gene expression are urgently required. Different from trajectory inference and RNA velocity, our method reveals gene dynamics by learning a jump diffusion process for modeling the biological process directly. The algorithm needs aggregate gene expression data as input and outputs the parameters of the…
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…
Jinggang Lan, David Wilkins, Vladimir Rybkin, Marcella Iannuzzi + 1 more
We report the static and dynamical properties of liquid water at second-order Møller-Plesset perturbation theory level (MP2) with classical and quantum dynamics simulations using a neural network potential. We examined the temperature-dependent radial distribution function, diffusion and vibrational dynamics. MP2…
Suryoday Prodhan, Samuele Giannini, Linjun Wang, David Beljonne
Raising the distance covered by singlet excitons during their lifetimes to values maximizing light absorption (a few hundred nm) would solve the exciton diffusion bottleneck issue and lift the constraint for fine (~10 nm) phase segregation in bulk heterojunction organic solar cells. In that context, the recent report…
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…
Mohammad S. Safari, Ryan Poling-Skutvik, Peter G. Vekilov, Jacinta C. Conrad
'Jacinta C. Conrad'] Research tasks in microgravity include monitoring the dynamics of constituents of varying size and mobility in processes such as aggregation, phase separation, or self-assembly. We use differential dynamic microscopy, a method readily implemented with equipment available on the International Space…
Marcin Mińkowski, Magdalena A. Załuska Kotur
Behavior of the mixture of particles and dimers moving with different jump rates at reconstructed surfaces is described. Collective diffusion coefficient is calculated by the variational approach. Anisotropy of the collective particle motion is analyzed as a function of jump rates and local particle density. Analytic…
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…
James A. Richards, Vincent A. Martinez, Jochen Arlt
Particle size is a key variable in understanding the behaviour of the particulate products that underpin much of our modern lives. Typically obtained from suspensions at rest, measuring the particle size under flowing conditions would enable advances for in-line testing during manufacture and highthroughput testing…
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…
M. Alexander Ardagh, Omar A. Abdelrahman, Paul Dauenhauer
Acceleration of catalytic transformation of molecules via heterogeneous materials occurs through design of active binding sites to optimally balance the requirements of all steps in a catalytic cycle. In accordance with the Sabatier principle, the characteristics of a single binding site are balanced between at least…