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Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement

Shi Yu, Jiaxin Wu, Xianliang Meng, Ruizhi Chu, Xiao Li, Guoguang Wu
2021 Entropy  
The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically.  ...  Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the  ...  Since the dynamic bacterial chromosome can form "blobs", "branch-like" structures, and cross-links in cylindrical confinement [34] or even between parallel plates [35] , the bacterial chromosome also  ... 
doi:10.3390/e23050542 pmid:33924872 fatcat:mv7zxwtoznbzldugbe4xtmyenq

Wanted: A Positive Control for Anomalous Subdiffusion

Michael J. Saxton
2012 Biophysical Journal  
Anomalous subdiffusion measurements would be strengthened by an experimental standard, particularly one able to cross-calibrate the different types of measurements.  ...  The subject is controversial, especially the hypothesis that crowding causes anomalous subdiffusion.  ...  Pores are irregular with branching, but do not have the sort of fractal structure that leads to anomalous subdiffusion in a percolation cluster near the threshold.  ... 
doi:10.1016/j.bpj.2012.10.038 pmid:23260043 pmcid:PMC3525842 fatcat:atmqkfkczzekbisu25ehzj7j7e

Anomalous transport in the crowded world of biological cells

Felix Höfling, Thomas Franosch
2013 Reports on progress in physics (Print)  
This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures.  ...  A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants  ...  We recall how self-similar, fractal structures emerge and why transport in these systems is naturally subdiffusive.  ... 
doi:10.1088/0034-4885/76/4/046602 pmid:23481518 fatcat:ag4ldxmp4vgddgm5euucicnl6e

Self-similar transport processes in a two-dimensional realization of multiscale magnetic field turbulence [article]

Francesco Chiaravalloti, Alexander V. Milovanov, Gaetano Zimbardo
2004 arXiv   pre-print
Depending on the amplitude of the background field and the input test particle velocity, we observe distinct transport regimes ranging from subdiffusion of guiding centers in the limit of Hamiltonian dynamics  ...  In all cases, we find complex microscopic structure of the particle motion revealing long-time rests and trapping phenomena, sporadically interrupted by the phases of active cross-field propagation reminiscent  ...  The latter is subdiffusive (with the exponent µ ≈ 0.58) on all time scales t ≫ 1/Ω, up to t → ∞.  ... 
arXiv:cond-mat/0404648v3 fatcat:os7yf26i7jcizj2gbmzqjrqmse

Nonclassical Transport and Particle-Field Coupling: from Laboratory Plasmas to the Solar Wind [chapter]

D. Perrone, R. O. Dendy, I. Furno, R. Sanchez, G. Zimbardo, A. Bovet, A. Fasoli, K. Gustafson, S. Perri, P. Ricci, F. Valentini
2013 Space Sciences Series of ISSI  
scales, the influence of coherent structures D.  ...  In all cases, transport depends on the interaction of thermal and suprathermal particles with the electric and magnetic fluctuations in the plasma.  ...  Copyright(2002), American Institute of Physics et al. (2008) and Fig. 5 5 Cross section of the magnetic flux tube structure of an initially circular flux tube, for different degrees of turbulence anisotropy  ... 
doi:10.1007/978-1-4899-7413-6_7 fatcat:sz3rp7ruobh4lewgenz3723izq

Nonclassical Transport and Particle-Field Coupling: from Laboratory Plasmas to the Solar Wind

D. Perrone, R. O. Dendy, I. Furno, R. Sanchez, G. Zimbardo, A. Bovet, A. Fasoli, K. Gustafson, S. Perri, P. Ricci, F. Valentini
2013 Space Science Reviews  
scales, the influence of coherent structures D.  ...  In all cases, transport depends on the interaction of thermal and suprathermal particles with the electric and magnetic fluctuations in the plasma.  ...  Copyright(2002), American Institute of Physics et al. (2008) and Fig. 5 5 Cross section of the magnetic flux tube structure of an initially circular flux tube, for different degrees of turbulence anisotropy  ... 
doi:10.1007/s11214-013-9966-9 fatcat:p7bste4r65es5fbvzmlyllmmhe

Computer Simulation of Cyclic Polymers in Disordered Media

Aleksander Kuriata, Andrzej Sikorski
2015 Computational Methods in Science and Technology  
The differences in the mobility of chains depending on the obstacle density were shown and discussed.  ...  In order to determine the structure and dynamical properties of cyclic polymers (rings) in a random environment we developed and studied an idealized model.  ...  The formation of catenated structures and its influence on the properties of the macromolecular system was also studied [45] .  ... 
doi:10.12921/cmst.2015.21.01.003 fatcat:aviwvo4qinav5lvqbavsv47qmu

Page 8160 of Mathematical Reviews Vol. , Issue 98M [page]

1998 Mathematical Reviews  
Following on this, the authors consider grating-type structures, including strips with dielectric backing. The next chapter deals with problems with translational or rotational symmetry.  ...  98m:76172 of the island deeply modifies the nature of the transport process, leading to subdiffusive behavior.  ... 

Dewetting and spreading transitions for active matter on random pinning substrates

Cs. Sándor, A. Libál, C. Reichhardt, C. J. Olson Reichhardt
2017 Journal of Chemical Physics  
For φ < 0.5 at high F p , interconnections between small branching clusters can no longer percolate across the sample, so there is no giant branching cluster and C l /N s remains low.  ...  F i p , the pinning force exerted by the substrate, is modeled by an array of N p randomly placed circular parabolic traps with a finite radius of R p = 0.5, with F i p = N p k=1 F p (r ik p /R p )Θ(r  ... 
doi:10.1063/1.4983344 pmid:28571342 pmcid:PMC5648553 fatcat:fub3lhyztfa45hvpphtaqbihje

Self-trapped quantum walks [article]

A. R. C. Buarque, W.S. Dias
2019 arXiv   pre-print
Adjusting the nonlinear parameter (χ) and the quantum gates (θ), we will show the existence of different quantum walking regimes, including those with travelling soliton-like structures or localized by  ...  By considering a Kerr-like nonlinearity, we associate an acquisition of the intensity-dependent phase to the walker while it propagates on the lattice.  ...  Disordered nonlinear DTQWs were used to confirm that the subdiffusive spreading of wave-packets (well-known in Gross-Pitaevskii lattices) persists over an additional four decades, which suggests this subdiffusive  ... 
arXiv:1911.10831v1 fatcat:lrplo46xvfgofjwnywptpb6upq

Impact of global structure on diffusive exploration of organelle networks

Aidan I. Brown, Laura M. Westrate, Elena F. Koslover
2020 Scientific Reports  
For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks  ...  The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections.  ...  We investigate the impact of network structure on diffusive search over planar networks with nodes placed homogeneously throughout a circular domain.  ... 
doi:10.1038/s41598-020-61598-8 pmid:32188905 fatcat:nfqdjyekangntduusutm7ac2yy

Geometric universality and anomalous diffusion in frictional fingers

Kristian Stølevik Olsen, Eirik Grude Flekkøy, Luiza Angheluta, James Matthew Campbell, Knut Jorgen Maloy, Bjørnar Sandnes
2019 New Journal of Physics  
The type of self-similarity is a topological one because it only relies on the counting of branches-if the bifurcation ratio is independent of branch order r B (w)=r B the structure has r B more branches  ...  This tree has seven order 1 branches, two order 2 branches and one order 3 branch.  ...  The simulations are based on a discretization of the front into points labeled i which are updated by moving one point at the time a certain length dx along the local unit normal n i at each update, as  ... 
doi:10.1088/1367-2630/ab25bf fatcat:ndhsavivybcozpr72miqj7fwuu

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Vincenzo G Benza, Bruno Bassetti, Kevin D Dorfman, Vittore F Scolari, Krystyna Bromek, Pietro Cicuta, Marco Cosentino Lagomarsino
2012 Reports on progress in physics (Print)  
This has implications on modulating (when not enabling) the core biological processes of replication, transcription, segregation.  ...  The branched plectonemic structure is visible.  ...  The circular chromosome of E. coli is divided into 4 macrodomains and 2 non-structured zones (see figure 1).  ... 
doi:10.1088/0034-4885/75/7/076602 pmid:22790781 fatcat:2b7s5pjzfzf75k3pbd4ulx3sia

Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers [article]

Angelo Rosa, Jan Smrek, Matthew S Turner, Davide Michieletto
2020 arXiv   pre-print
Our findings shed light on how threadings control dynamics and may inform design principles for chimeric polymers with topologically-tunable bulk rheological properties.  ...  the process of constraint release imposed by linear tails on circular heads propagates back to tails too, causing a dramatic and system-wide slowing down.  ...  , on average, and often each threading is made by more than one piercing (see SI).  ... 
arXiv:1908.06638v2 fatcat:t723i2etczb23kjxgir3dlwfzi

Stochastic resetting on comb-like structures [article]

Viktor Domazetoski, Axel Masó-Puigdellosas, Trifce Sandev, Vicenç Méndez, Alexander Iomin, Ljupco Kocarev
2020 arXiv   pre-print
We study a diffusion process on a three-dimensional comb under stochastic resetting.  ...  INTRODUCTION Combs are two-or three-dimensional branched structures with a backbone crossed by perpendicular fingers. These fingers may be one or two dimensional side structures.  ...  They could describe diffusion processes on comb structures with stochastic resetting.  ... 
arXiv:2005.11575v1 fatcat:ma5x5j2ud5dcxk4eaay44v4rne
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