References of "van der Schoot, Paul"
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See detailDNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Taghavi, Amirhossein UL; van der Schoot, Paul; Berryman, Josh UL

in Quarterly Reviews of Biophysics (2017), 50

Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of ... [more ▼]

Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure–function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for ‘phase 1’ amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the ‘GADV world’ hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code. [less ▲]

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See detailPercolation in suspensions of hard nanoparticules: From Spheres to needles
Schilling, Tanja UL; Miller, Mark A.; Van der Schoot, Paul

in Europhysics Letters [=EPL] (2015), 111

We investigate geometric percolation and scaling relations in suspensions of nanorods, covering the entire range of aspect ratios from spheres to extremely slender needles. A new version of connectedness ... [more ▼]

We investigate geometric percolation and scaling relations in suspensions of nanorods, covering the entire range of aspect ratios from spheres to extremely slender needles. A new version of connectedness percolation theory is introduced and tested against specialised Monte Carlo simulations. The theory accurately predicts percolation threshold for aspect ratios of length to width as low as 10. The percolation threshold for rod-like particules of aspect ratios below 1000 deviates significantly from the inverse aspect ratio scaling prediction, thought to be valid in the limit of infinitely slender rods and often used as a rule of thumb for nanofibres in composites materials. Hence, most fibres that are currently used as fillers in composite materials cannot be regarded as pratically infinitely slender for the purposes of percolation theory. Comparing percolation thresholds of hard rods and new benchmark results for ideal rods, we find that i) for large aspect ratios, they differ by a factor that is inversely proportional to the connectivity distance between the hard cores, and ii) they approach the slender rod limit differently. [less ▲]

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See detailPercolation in suspensions of polydisperse hard rods: Quasi universality and finite-size effects
Meyer, Hugues UL; Van der Schoot, Paul; Schilling, Tanja UL

in Journal of Chemical Physics (2015), 143(4), 044901

We present a study of connectivity percolation in suspensions of hard spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. We focus attention on polydispersity in the ... [more ▼]

We present a study of connectivity percolation in suspensions of hard spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. We focus attention on polydispersity in the length, the diameter, and the connectedness criterion, and we invoke bimodal, Gaussian, and Weibull distributions for these. The main finding from our simulations is that the percolation threshold shows quasi universal behaviour, i.e., to a good approximation, it depends only on certain cumulants of the full size and connectivity distribution. Our connectedness percolation theory hinges on a Lee-Parsons type of closure recently put forward that improves upon the often-used second virial approximation [T. Schilling, M. Miller, and P. van der Schoot, e-print arXiv:1505.07660 (2015)]. The theory predicts exact universality. Theory and simulation agree quantitatively for aspect ratios in excess of 20, if we include the connectivity range in our definition of the aspect ratio of the particles. We further discuss the mechanism of cluster growth that, remarkably, differs between systems that are polydisperse in length and in width, and exhibits non-universal aspects. [less ▲]

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See detailControlling electrical percolation in multicomponent carbon nanotube dispersions
Kyrylyuk, Andriy V.; Hermant, Marie Claire; Schilling, Tanja UL et al

in Nature Nanotechnology (2011), 6(6), 364-369

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See detailOsmotic compression of droplets of hard rods: A computer simulation study
Trukhina, Yu; Jungblut, S.; van der Schoot, Paul et al

in Journal of Chemical Physics (2009), 130(16),

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See detailIsotropic-nematic interface and wetting in suspensions of colloidal platelets
van der Beek, D.; Reich, H.; van der Schoot, Paul et al

in Physical Review Letters (2006), 111(27), 7825-7835

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