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- Hedström, Lucas, et al.
(författare)
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Considerations on the relaxation time in shear-driven jamming
- 2024
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Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 109:6
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Tidskriftsartikel (refereegranskat)abstract
- We study the jamming transition in a model of elastic particles under shear at zero temperature, with a focus on the relaxation time τ1. This relaxation time is from two-step simulations where the first step is the ordinary shearing simulation and the second step is the relaxation of the energy after stopping the shearing. τ1 is determined from the final exponential decay of the energy. Such relaxations are done with many different starting configurations generated by a long shearing simulation in which the shear variable γ slowly increases. We study the correlations of both τ1, determined from the decay, and the pressure, p1, from the starting configurations as a function of the difference in γ. We find that the correlations of p1 are longer lived than the ones of τ1 and find that the reason for this is that the individual τ1 is controlled both by p1 of the starting configuration and a random contribution which depends on the relaxation path length - the average distance moved by the particles during the relaxation. We further conclude that it is γτ, determined from the correlations of τ1, which is the relevant one when the aim is to generate data that may be used for determining the critical exponent that characterizes the jamming transition.
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| 2. |
- Hedström, Lucas, et al.
(författare)
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Modelling chromosome-wide target search
- 2023
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Ingår i: New Journal of Physics. - : Institute of Physics (IOP). - 1367-2630. ; 25:3
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Tidskriftsartikel (refereegranskat)abstract
- The most common gene regulation mechanism is when a transcription factor (TF) protein binds to a regulatory sequence to increase or decrease RNA transcription. However, TFs face two main challenges when searching for these sequences. First, the sequences are vanishingly short relative to the genome length. Second, there are many nearly identical sequences scattered across the genome, causing proteins to suspend the search. But as pointed out in a computational study of LacI regulation in Escherichia coli, such almost-targets may lower search times if considering DNA looping. In this paper, we explore if this also occurs over chromosome-wide distances. To this end, we developed a cross-scale computational framework that combines established facilitated-diffusion models for basepair-level search and a network model capturing chromosome-wide leaps. To make our model realistic, we used Hi-C data sets as a proxy for 3D proximity between long-ranged DNA segments and binding profiles for more than 100 TFs. Using our cross-scale model, we found that median search times to individual targets critically depend on a network metric combining node strength (sum of link weights) and local dissociation rates. Also, by randomizing these rates, we found that some actual 3D target configurations stand out as considerably faster or slower than their random counterparts. This finding hints that chromosomes’ 3D structure funnels essential TFs to relevant DNA regions.
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