Physical modelling of multivalent interactions in the nuclear pore complex

In the nuclear pore complex (NPC), intrinsically disordered proteins (FG Nups) along with their interactions with more globular proteins called nuclear transport receptors (NTRs) are vital to the selectivity of transport into and out of the cell nucleus. While such interactions can be modelled at different levels of coarse graining, in-vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, where the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and non-cohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion, and compare them to experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties, but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences

Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics

In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events

Non-Parametric Analysis of ENSO Impacts on Yield Distributions: Implications for GRP Contract Design

The paper reports preliminary results of non-parametric analysis of historical and crop model generated peanut yield series in the Southwest Georgia. The results suggest ENSO phase dependent differences in yield distributions that are similar for both the simulated and actual series. The differences are magnified in GRP insurance premiums.Crop Production/Industries,

Distribuição espacial das necessidades hídricas das culturas do feijão, milho e soja na bacia do rio Tibaji, PR.

bitstream/item/89786/1/BOP-16.pd

Bistable collective behavior of polymers tethered in a nanopore.

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence the two phases suggests a mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations, which will influence transport through the pore

Imaging the essential role of spin-fluctuations in high-Tc superconductivity

We have used scanning tunneling spectroscopy to investigate short-length electronic correlations in three-layer Bi2Sr2Ca2Cu3O(10+d) (Bi-2223). We show that the superconducting gap and the energy Omega_dip, defined as the difference between the dip minimum and the gap, are both modulated in space following the lattice superstructure, and are locally anti-correlated. Based on fits of our data to a microscopic strong-coupling model we show that Omega_dip is an accurate measure of the collective mode energy in Bi-2223. We conclude that the collective mode responsible for the dip is a local excitation with a doping dependent energy, and is most likely the (pi,pi) spin resonance.Comment: 4 pages, 4 figure

Experiments and data for model evaluation and application

Crop models and decision support systems can be very useful tools for scientists, extension educators, teachers, planners and policy makers to help with the evaluation of alternative management practices. Many of the current crop ­models respond to differences in local weather conditions, soil characteristics, crop management practices and genetics. However, computer-based tools require inputs in order to provide reliable results. Especially for those new to crop modeling, the data requirements are sometimes somewhat overwhelming. In this chapter we provide a clear and concise summary of the input data requirements for crop modeling. We differentiate between requirements for model evaluation, model application and model development and improvement. For model inputs we define daily weather data, soil surface and profile characteristics, and crop management. For model evaluation and improvement we define crop performance data as it relates to growth, development, yield and yield components, as well as additional observations. We expect that this chapter will make the use and application of crop models and ­decision support systems easier for beginning modelers as well as for the more advanced user

Effects of climate change and light limitation on coral recruits

Climate change impacts and light attenuation from suspended sediments due to runoff, natural resuspension or dredging, can both impede the replenishment of coral populations. Here we tested the independent and combined impacts of climate change (current temperature and dissolved CO2, and two future climate scenarios) and a one-month-long light attenuation period at 5 different light levels (0.1 to 4 mol photons m−2 d−1) on early Acropora millepora recruits. Additionally, we evaluated whether the effects were age dependent by comparing responses of recruits that were one-month-old (‘early attenuation’) vs two months old (‘late attenuation’). Recruit survival, size and Symbiodiniaceae densities increased slightly under moderate future climate conditions (current temperature +0.44°C, 692 ppm pCO2), but decreased under a more severe climate scenario (+0.94°C, 985 ppm pCO2). Light attenuation significantly decreased recruit survival, size and Symbiodiniaceae densities only for recruits exposed to the late attenuation, suggesting an increasing reliance on photosynthesis as recruits age. Under the more severe climate scenario tested, recruit survival was diminished by both climate change (≤ 18 ± 4 [SE]% in the early attenuation) and light limitation (≤ 32 ± 6% in the late attenuation) compared with controls. However, there was no interaction between future climate scenarios and light attenuation indicating these effects were additive. This study demonstrates the potential effects of light limitation and future climate conditions on coral recruitment success and highlights the need to manage the timing of sediment-generating activities near reefs to optimise light availability for several months post-settlement

Optical shield: measuring viscosity of turbid fluids using optical tweezers

The viscosity of a fluid can be measured by tracking the motion of a suspended micron-sized particle trapped by optical tweezers. However, when the particle density is high, additional particles entering the trap compromise the tracking procedure and degrade the accuracy of the measurement. In this work we introduce an additional Laguerre–Gaussian, i.e. annular, beam surrounding the trap, acting as an optical shield to exclude contaminating particles