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(1 - 20 of 149)

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Emergent nonlocal combinatorial design rules for multimodal metamaterials
Mastrigt, R. van; Coulais, C.; Hecke, M.L. van 2023
Emergent nonlocal combinatorial design rules for multimodal metamaterials
Article / Letter to editor
open access
Deterministic, quenched, and annealed parameter estimation for heterogeneous network models
Di Vece, M.; Garlaschelli, D.; Squartini, T. 2023
Deterministic, quenched, and annealed parameter estimation for heterogeneous network models
Article / Letter to editor
open access
Brownian motion of flexibly linked colloidal rings
Verweij, R.W.; Melio, J.; Chakraborty, I.; Kraft, D.J. 2023
Brownian motion of flexibly linked colloidal rings
Article / Letter to editor
open access

Hydrodynamic theory of p-atic liquid crystals
Giomi, L.; Toner, J.; Sarkar, N. 2022
Hydrodynamic theory of p-atic liquid crystals
Article / Letter to editor
open access
We formulate a comprehensive hydrodynamic theory of two-dimensional liquid crystals with generic p-fold rotational symmetry, also known as p-atics, of which nematics (p = 2) and hexatics (p = 6)... Show moreWe formulate a comprehensive hydrodynamic theory of two-dimensional liquid crystals with generic p-fold rotational symmetry, also known as p-atics, of which nematics (p = 2) and hexatics (p = 6) are the two best known examples. Previous hydrodynamic theories of p-atics are characterized by continuous O(2) rotational symmetry, which is higher than the discrete rotational symmetry of p-atic phases. By contrast, here we demonstrate that the discrete rotational symmetry allows the inclusion of additional terms in the hydrodynamic equations, which, in turn, lead to novel phenomena, such as the possibility of flow alignment at high shear rates, even for p > 2. Furthermore, we show that any finite imposed shear will induce long-ranged orientational order in any p-atic liquid crystal, in contrast to the quasi-long-ranged order that occurs in the absence of shear. The induced order parameter scales like a nonuniversal power of the applied shear rate at small shear rates. Show less
Motif structure for the four subgroups within the suprachiasmatic nuclei affects its entrainment ability
Zheng, W.X.; Gu, C.G.; Yang, H.J.; Rohling, J.H.T. 2022
Motif structure for the four subgroups within the suprachiasmatic nuclei affects its entrainment ability
Article / Letter to editor
open access
2022-07-27T00:00:00Z
Circadian rhythms of physiological and behavioral activities are regulated by a central clock. This clock is located in the bilaterally symmetrical suprachiasmatic nucleus (SCN) of mammals. Each... Show moreCircadian rhythms of physiological and behavioral activities are regulated by a central clock. This clock is located in the bilaterally symmetrical suprachiasmatic nucleus (SCN) of mammals. Each nucleus contains a light-sensitive group of neurons, named the ventrolateral (VL) part, with the rest of the neurons being insensitive to light, named the dorsomedial (DM) group. While the coupling between the VL and DM subgroups have been investigated quite well, the communication among the four subgroups across the nuclei did not get a lot of attention. In this article, we theoretically analyzed seven motiflike connection patterns to investigate the network of the two nuclei of the SCN as a whole in relation to the function of the SCN. We investigated the entrainment ability of the SCN and found that the entrainment range is larger in the motifs containing a link between the two VL parts across the nuclei, but it is smaller in the motifs that contain a link between the two DM parts across the nuclei. The SCN may strengthen or weaken connections between the left and right nucleus to accomodate changes in external conditions, such as resynchronization after a jet lag, adjustment to photoperiod or for the aging SCN. Show less
Profusion of transition pathways for interacting hysterons
Hecke, M.L. van 2021
Profusion of transition pathways for interacting hysterons
Article / Letter to editor
open access
Sensitivity of the spectral form factor to short-range level statistics
Buijsman, W.; Cheianov, V.; Gritsev, V. 2020
Sensitivity of the spectral form factor to short-range level statistics
Article / Letter to editor
open access
Generalized priority-based model for smartphone screen touches
Pfister, J.P.; Ghosh, A. 2020
Generalized priority-based model for smartphone screen touches
Article / Letter to editor
open access
Topotaxis of active Brownian particles
Schakenraad, K.; Ravazzano, L.; Sarkar, N.; Wondergem, J.A.J.; Merks, R.M.H.; Giomi, L. 2020
Topotaxis of active Brownian particles
Article / Letter to editor
open access
Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned... Show more

Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned substrate. This phenomenon, known as topotaxis, has been extensively studied for topographical gradients at the subcellular scale, but can also occur in the presence of a spatially varying density of cell-sized features. Such a large-scale topotaxis has recently been observed in highly motile cells that persistently crawl within an array of obstacles with smoothly varying lattice spacing. We introduce a toy model of large-scale topotaxis, based on active Brownian particles. Using numerical simulations and analytical arguments, we demonstrate that topographical gradients introduce a spatial modulation of the particles' persistence, leading to directed motion toward regions of higher persistence. Our results demonstrate that persistent motion alone is sufficient to drive large-scale topotaxis and could serve as a starting point for more detailed studies on self-propelled particles and cells.

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Three-state Potts model on the centered triangular lattice
Fu, Z.; Guo, W.N.; Blöte, H.W.J. 2020
Three-state Potts model on the centered triangular lattice
Article / Letter to editor
open access
Non-Euclidean origami
Waitukaitis, S.; Dieleman, P.; Hecke, M.L. van 2020
Non-Euclidean origami
Article / Letter to editor
open access
Pioneer transcription factors in chromatin remodeling: the kinetic proofreading view
Schiessel, H.; Blossey, R. 2020
Pioneer transcription factors in chromatin remodeling: the kinetic proofreading view
Article / Letter to editor
open access
Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we... Show more

Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows one to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations. Our results demonstrate a way to fine-tune the specificity of processes that modify the chromatin structure in transcriptional initiation.

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    Dislocation screening in crystals with spherical topology
    Garcia-Aguilar, I.; Fonda, P.; Giomi, L. 2020
    Dislocation screening in crystals with spherical topology
    Article / Letter to editor
    open access
    Translational nucleosome positioning: A computational study
    Neipel J., Brandani G., Schiessel H. 2020
    Translational nucleosome positioning: A computational study
    Article / Letter to editor
    open access
    Explosive, oscillatory, and Leidenfrost boiling at the nanoscale
    Jollans, T.G.W.; Orrit, M.A.G.J. 2019
    Explosive, oscillatory, and Leidenfrost boiling at the nanoscale
    Article / Letter to editor
    open access
    We investigate the different boiling regimes around a single continuously laser-heated 80 nm gold nanoparticle and draw parallels to the classical picture of boiling. Initially, nanoscale boiling... Show moreWe investigate the different boiling regimes around a single continuously laser-heated 80 nm gold nanoparticle and draw parallels to the classical picture of boiling. Initially, nanoscale boiling takes the form of transient, inertia-driven, unsustainable boiling events characteristic of a nanoscale boiling crisis. At higher heating power, nanoscale boiling is continuous, with a vapor film being sustained during heating for at least up to 20μs. Only at high heating powers does a substantial stable vapor nanobubble form. At intermediate heating powers, unstable boiling sometimes takes the form of remarkably stable nanobubble oscillations with frequencies between 40 MHz and 60 MHz, frequencies that are consistent with the relevant size scales according to the Rayleigh-Plesset model of bubble oscillation, though how applicable that model is to plasmonic vapor nanobubbles is not clear. Show less
    Revisiting the field-driven edge transition of the tricritical two-dimensional Blume-Capel model
    Blöte, H.W.J.; Deng, Y.J. 2019
    Revisiting the field-driven edge transition of the tricritical two-dimensional Blume-Capel model
    Article / Letter to editor
    open access
    We reconsider the tricritical Blume-Capel model on the square lattice with a magnetic field acting on the open boundaries in one direction. Periodic boundary conditions are applied in the other... Show moreWe reconsider the tricritical Blume-Capel model on the square lattice with a magnetic field acting on the open boundaries in one direction. Periodic boundary conditions are applied in the other direction. We apply three types of Monte Carlo algorithms, local Metropolis updates, and cluster algorithms of the Wolff and geometric type, adapted to the symmetry properties of the model. Statistical analyses of the bulk magnetization, the bulk Binder ratio, the edge magnetization, and the connected product of the edge and bulk magnetizations lead to new results confirming the presence of a singular edge transition at Hsc≈0.68, as we reported earlier [Phys. Rev. E 71, 026109 (2005)]. We provide a plausible answer concerning a discrepancy between the behavior of the edge Binder ratio reported in that work and our new results. Show less
    Shortest paths through synonymous genomes
    Zuiddam, M.; Schiessel, H. 2019
    Shortest paths through synonymous genomes
    Article / Letter to editor
    open access
    The elasticity of the DNA double helix varies with the underlying base pair sequence. This allows one to put mechanical cues into sequences that in turn influence the packaging of DNA into... Show moreThe elasticity of the DNA double helix varies with the underlying base pair sequence. This allows one to put mechanical cues into sequences that in turn influence the packaging of DNA into nucleosomes, DNA-wrapped protein cylinders. Nucleosomes dictate a broad range of biological processes, ranging from gene regulation, recombination, and replication to chromosome condensation. Here we map base pair sequences onto graphs and use shortest paths algorithms to determine which DNA stretches are easiest or hardest to bend inside a nucleosome. We further demonstrate how genetic and mechanical information can be multiplexed by studying paths through graphs of synonymous codons. Using this method we find that nucleosomes can be placed by mechanical cues nearly everywhere on the genome of baker's yeast (Saccharotnyces cerevisiae). Show less
    Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments
    Blossey, R.; Schiessel, H. 2019
    Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments
    Article / Letter to editor
    open access
    Chromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence ``remodel chromatin structure,{''} i.e., they dynamically reorganize nucleosome... Show moreChromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence ``remodel chromatin structure,{''} i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the Imitation Switch family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families.} Show less
    Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments
    Blossey, R.; Schiessel, H. 2019
    Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments
    Article / Letter to editor
    open access
    Chromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence ``remodel chromatin structure,{''} i.e., they dynamically reorganize nucleosome... Show moreChromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence ``remodel chromatin structure,{''} i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the Imitation Switch family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families.} Show less
    Excess floppy modes and multibranched mechanisms in metamaterials with symmetries
    Lubbers, L.A.; Hecke, M.L. van 2019
    Excess floppy modes and multibranched mechanisms in metamaterials with symmetries
    Article / Letter to editor
    open access
    Floppy modes—deformations that cost zero energy—are central to the mechanics of a wide class of systems.For disordered systems, such as random networks and particle packings, it is well-understood... Show moreFloppy modes—deformations that cost zero energy—are central to the mechanics of a wide class of systems.For disordered systems, such as random networks and particle packings, it is well-understood how the numberof floppy modes is controlled by the topology of the connections. Here we uncover that symmetric geometries,present in, e.g., mechanical metamaterials, can feature an unlimited number of excess floppy modes that areabsent in generic geometries, and in addition can support floppy modes that are multibranched. We study thenumber of excess floppy modes by comparing generic and symmetric geometries with identical topologies,and show that is extensive, peaks at intermediate connection densities, and exhibits mean-field scaling. Wethen develop an approximate yet accurate cluster counting algorithm that captures these findings. Finally, weleverage our insights to design metamaterials with multiple folding mechanisms. Show less

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