Reu pres 8 5
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This document summarizes a student's research using a Monte Carlo lattice model to study diffusion through the nuclear pore complex (NPC). The student built a lattice model from scratch to simulate particle and polymer movements. Various parameters were tested, including FG nup concentration, binding/unbinding probabilities, and gel width. Preliminary results showed diffusion coefficient increases with higher binding probability and lower FG concentration. Future plans include reproducing results from other papers and studying long-time diffusion behavior.
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The nuclear pore complex (NPC) regulates gene expression by facilitating the transport of mRNA from the nucleus to the cytoplasm. Proximal spinal muscular atrophy is caused by a deficiency of the survival motor neuron (SMN) protein, which is involved in small nuclear ribonucleoprotein biogenesis. The NPC structure allows selective transport of molecules between the nucleus and cytoplasm through nuclear transport factors.
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The nucleus is the control center of the cell that contains DNA. It maintains the integrity of genes and controls cell activities through regulating gene expression. The nucleus is enclosed by a nuclear envelope with nuclear pores that regulate molecular trafficking. Within the nucleus are chromatin, nucleolus, and nucleoplasm. The nucleolus forms ribosomes, chromatin contains DNA and proteins, and nucleoplasm scaffolds nuclear components. The nucleus ensures DNA replication, transcription, and transmission to new cells through the cell cycle and mitosis/meiosis.
nuclear envelope
The nuclear envelope consists of an inner and outer nuclear membrane separated by the perinuclear space and punctuated by nuclear pore complexes. It encloses the nuclear DNA and separates the nucleus from the cytoplasm. The nuclear lamina, composed of lamin proteins and membrane proteins, lies underneath the inner nuclear membrane and provides mechanical support. Nuclear pore complexes have an octagonal symmetry and allow regulated transport of macromolecules between the nucleus and cytoplasm through import and export signals and adapter proteins.
Nuclear envelope
The nuclear envelope consists of two nuclear membranes, the nuclear lamina, and nuclear pore complexes. It separates the nucleus from the cytoplasm and provides structure to the nucleus. The nuclear lamina lies between the inner and outer nuclear membranes and is composed of intermediate filaments and associated proteins. Nuclear pore complexes are large protein structures that allow transport of molecules between the nucleus and cytoplasm.
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The nuclear envelope consists of an inner and outer nuclear membrane separated by the perinuclear space and punctuated by nuclear pore complexes. It encloses the nuclear DNA and separates the nucleus from the cytoplasm. The nuclear lamina, composed of lamin proteins and membrane proteins, lies underneath the inner nuclear membrane and provides mechanical support. Nuclear pore complexes have an octagonal symmetry and allow regulated transport of macromolecules between the nucleus and cytoplasm through import and export signals and adapter proteins.
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SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
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Storagedeteriorationisanyformoflossinquantityandqualityofbio-materials.
Themajorcausesofdeteriorationinstorage
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Storageonlypreservesquality.Itneverimprovesquality.
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JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
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Reu pres 8 5
- 1. Using a Lattice Model to Study the Nuclear Pore Complex Samantha Norris Mentors: Meredith Betterton, Loren Hough, Mike Stefferson August 6, 2015
- 2. What is the Nuclear Pore Complex (NPC)? "NuclearPore crop" by The original uploader was R. S. Shaw at English Wikipedia - Transferred from en.wikipediato Commons.. Licensed under CC BY-SA 2.5 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:NuclearPore_crop.png#/media/File:NuclearPore_crop.png protein Transport factor Strands of nucleoporins with FG sequence repeats (FG nups) Nucleus Cytoplasm
- 3. What I Did • To better understand the diffusion of proteins through the NPC • To find the parameters which most significantly affect diffusion Purpose • Built Monte-Carlo lattice model from scratch • Included particle and polymer lattice moves • Tested various sets of parameters
- 4. Experimental Progress • Modelling the NPC with a hydrogel mimic • Hydrogel consists of FG-nups in strands Figure: Loren Hough
- 5. A Lattice Model • Monte Carlo method – each particle (whether TF or FG) takes random walk around the grid • When a TF and FG collide, probability 𝑘 𝑜𝑛 of binding • When separating, probability 𝑘 𝑜𝑓𝑓 of unbinding
- 6. A Lattice Model Probability: 𝑘 𝑜𝑛 Probability: 𝑘 𝑜𝑓𝑓
- 7. A Lattice Model inlet outlet
- 8. Strand Statistics • Movement rules adapted from Haire et. al. • Anchored at one point • If movement breaks strand in 1 place, rest of strand compensates • If movement breaks strand in 2 places, move rejected
- 9. Strand Statistics Deviation from center # 1 strand, length 200, T = 100,000
- 10. Strand Statistics Leftmost figure reprinted from "A Monte Carlo Lattice model for Chain Diffusion in Dense Polymer Systems and its Interlocking with Molecular Dynamics Simulation," by K.R. Haire et. al., 2001, Computational and Theoretical Polymer Science
- 11. Calculating Diffusion Coefficients bindable particles unbindable particles Slope ∝ diffusion coefficient
- 12. Calculating Mean Square Displacement • Old Method: Find distance from starting position for each particle at each time steps, average over particles • New Method: Same as above, but average over different “time origins”, doesn’t choose starting position preferentially
- 13. Parameters • kon, koff (binding and unbinding probability) • Concentration of FG-nups and TFs • Gel width • TF size
- 14. 𝑪𝒐𝒏𝒄𝒆𝒏𝒕𝒓𝒂𝒕𝒊𝒐𝒏 𝒐𝒇 𝑭𝑮𝒔 𝑘 𝑜𝑛 = .5 𝑘 𝑜𝑓𝑓 = 𝑘 𝑜𝑛/10 TF # = 1 Length = 100 Gel width = 50 Conclusion: Lower concentration = Higher diffusion FG %
- 15. 𝒌 𝒐𝒏 FG conc. = 10% 𝑘 𝑜𝑓𝑓 = 𝑘 𝑜𝑛/10 TF # = 1 Length = 100 Gel width = 100 Conclusion: higher 𝑘 𝑜𝑛 = Higher diffusion
- 16. 𝒌 𝒐𝒇𝒇 FG conc. =10% 𝑘 𝑜𝑛 = 0.5 TF # = 1 Length = 100 Gel width = 100 Conclusion: Significant only when 𝒌 𝒐𝒇𝒇 ≈ 𝟎
- 17. FG radius Conclusion: No effect, requires more study FG conc. = 5% of gel 𝑘 𝑜𝑛=0.5 𝑘 𝑜𝑓𝑓 = 𝑘 𝑜𝑛/10 TF # = 1 Length = 100
- 18. Future Plans • Reproduce figures from other papers on diffusion on lattice grid • Study the long-time behavior of diffusion • Possibly add more complex situations (TFs moving and pushing FGs, etc.)
- 19. Thank you! • REU organizers • Meredith Betterton, Loren Hough (mentors) • Mike Stefferson (graduate student) • Jeff Moore, Adam Lamson, Andrea Egan
Editor's Notes
- Done experimentally, don’t understand mechanism
- Periodic boundaries top/bottom, hard walls left/right
- Darker color = lower bindP
- Lower density of FGs, but TF encounters FG faster