Self-diffusion of reversibly aggregating spheres

Babu, Sujin B.; Gimel, Jean-Christophe; Nicolai, Taco

doi:10.1063/1.2756838

Cited by 10 publications

(14 citation statements)

References 67 publications

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“…clusters are arrested by nearby clusters and thus only the dynamics within the cage is described. The long time limit (region III) also shows linear behavior that is due to crowding effects37. A similar transition from the ballistic regime of individual proteins to region I is also observed but not shown in this plot.…”

Section: Resultssupporting

confidence: 61%

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Allostery through protein-induced DNA bubbles

Traverso

Manoranjan

Bishop

et al. 2015

Sci Rep

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Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.

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Section: Resultssupporting

confidence: 61%

“…In such systems, one expects oligomerization and dissociation events, as well as a reduction of mobility due to oligomerization, crowding, or even dynamically arrested states37. In general, large bubbles induced by TFAM oligomerization are expected to contribute more to DNA compaction than small hinges.…”

Section: Resultsmentioning

confidence: 99%

Allostery through protein-induced DNA bubbles

Traverso

Manoranjan

Bishop

et al. 2015

Sci Rep

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“…Spheres that are part of the network are immobile until the bonds that tie them to the network are broken. A detailed study of the diffusion coefficient of square well fluids forming rigid bonds using BCD2 has been reported recently 30 . It was shown that D decreases with increasing B att following a power law for large B att and only becomes zero when the bonds are irreversible, i.e.…”

Section: Fig 4: Comparison Of the Mean Square Displacement Of Nonintmentioning

confidence: 99%

The influence of bond rigidity and cluster diffusion on the self-diffusion of hard spheres with square well interaction

Babu

Gimel

Nicolai

et al. 2008

The Journal of Chemical Physics

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Hard spheres interacting through a square-well potential were simulated using two different methods: Brownian Cluster Dynamics (BCD) and Event Driven Brownian Dynamics (EDBD). The structure of the equilibrium states obtained by both methods were compared and found to be almost the identical. Self diffusion coefficients (D) were determined as a function of the interaction strength.The same values were found using BCD or EDBD. Contrary the EDBD, BCD allows one to study the effect of bond rigidity and hydrodynamic interaction within the clusters. When the bonds are flexible the effect of attraction on D is relatively weak compared to systems with rigid bonds. D increases first with increasing attraction strength, and then decreases for stronger interaction. Introducing intra-cluster hydrodynamic interaction weakly increases D for a given interaction strength. Introducing bond rigidity causes a strong decrease of D which no longer shows a maximum as function of the attraction strength.

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“…20,37,38,46 Accordingly, z * = P × z represents the bond coordination number, and ⟨z * ⟩ = P × ⟨z⟩ represents the average bond coordination number of the system. By adding up the number of bond clusters of size s, we get the distribution of bond cluster size n * (s).…”

Section: Cluster and Coordination Numbermentioning

confidence: 99%

“…9,14,20,[33][34][35][36][37][38][39] In our study, due to its advantages in dealing with discretized potentials, the event-driven MD 40 is employed to determine the loci of PTs for two types of percolation (namely, contact percolation and bond percolation, see Sec. II) and to investigate the structural properties of the colloidal system.…”

Section: Introductionmentioning

confidence: 99%

Range effect on percolation threshold and structural properties for short-range attractive spheres

Wei

Song

2015

The Journal of Chemical Physics

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Range effect on percolation threshold and structural properties for short-range attractive spheres Percolation or aggregation in colloidal system is important in many fields of science and technology. Using molecular dynamics simulations, we study the percolation behavior for systems consisting of spheres interacting with short-range square-well (SRSW) which mimic colloidal particles, with different interaction ranges. We specifically focus on how the interaction range affects the percolation thresholds in the supercritical region. We find that the contact percolation boundaries are strongly dependent on the interaction ranges of SRSW, especially away from the liquid-liquid critical point. However, varying the interaction ranges of SRSW does not affect much the structure along percolation boundaries especially for low packing fractions. For instance, along the percolation boundary, distributions of coordination number show convergence, and distributions of cluster size are universal for different interaction ranges considered. In addition, either the bond percolation boundaries or isolines of average bond coordination number collapse to those for Baxter sticky model on phase diagram, which confirms the extended law of corresponding states. C 2015 AIP Publishing LLC. [http://dx

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Self-diffusion of reversibly aggregating spheres

Cited by 10 publications

References 67 publications

Allostery through protein-induced DNA bubbles

Allostery through protein-induced DNA bubbles

The influence of bond rigidity and cluster diffusion on the self-diffusion of hard spheres with square well interaction

Range effect on percolation threshold and structural properties for short-range attractive spheres

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