Dragging a polymer chain into a nanotube and subsequent release

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves the tube. MC simulations were performed for a self-avoiding lattice model with a biased chain growth algorithm, the pruned-enriched Rosenbluth method. The nanotube is a long channel opened at one end and its diameter $D$ is much smaller than the size of the polymer coil in solution. We analyze the following characteristics as functions of the chain end position $x$ inside the tube: the free energy of confinement, the average end-to-end distance, the average number of imprisoned monomers, and the average stretching of the confined part of the chain for various values of $D$ and for the number of monomers in the chain, $N$. We show that when the chain end is dragged by a certain critical distance $x^*$ into the tube, the polymer undergoes a first-order phase transition whereby the remaining free tail is abruptly sucked into the tube. This is accompanied by jumps in the average size, the number of imprisoned segments, and in the average stretching parameter. The critical distance scales as $x^*\sim ND^{1-1/\nu}$. The transition takes place when approximately 3/4 of the chain units are dragged into the tube. The theory presented is based on constructing the Landau free energy as a function of an order parameter that provides a complete description of equilibrium and metastable states. We argue that if the trapped chain is released with all monomers allowed to fluctuate, the reverse process in which the chain leaves the confinement occurs smoothly without any jumps. Finally, we apply the theory to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure

Rapid tree carbon stock recovery in managed Amazonian forests.

While around 20% of the Amazonian forest has been cleared for pastures and agriculture, one fourth of the remaining forest is dedicated to wood production [1] . Most of these production forests have been or will be selectively harvested for commercial timber, but recent studies show that even soon after logging, harvested stands retain much of their tree-biomass carbon and biodiversity [2,3] . Comparing species richness of various animal taxa among logged and unlogged forests across the tropics, Burivalova et al.[4] found that despite some variability among taxa, biodiversity loss was generally explained by logging intensity (the number of trees extracted). Here, we use a network of 79 permanent sample plots (376 ha total) located at 10 sites across the Amazon Basin [5] to assess the main drivers of time-to-recovery of post-logging tree carbon ( Table S1 ). Recovery time is of direct relevance to policies governing management practices (i.e., allowable volumes cut and cutting cycle lengths), and indirectly to forest-based climate change mitigation interventions

Accurate estimation of commercial volume in tropical forests.

Accurate estimates of commercial volume in tropical forests are key for the implementation of sustainable forest management plans. Because of the lack of local or generic volumetric equations, most forest managers and forestry services are still using traditional expansion factors (i.e., multiplication of the diameter by a given value) to estimate the volume of commercial tree species in the Amazon. Volumetric models were developed through a unique data set of 1,264 fallen trees fully measured in 150 sample plots located across a broad range of forests in Amapá, Brazil. Forest-specific volumetric models were developed and compared with a generic (i.e., across all forests) model and with published equations developed elsewhere in the Amazon. The generic equation performed well in all forest types and allowed precise predictions. The most efficient sampling design to develop volumetric models consists of measuring approximately 50 trees across four different size classes representing the whole population. The form factors (FF) developed locally generated substantial bias but performed better than the traditional FF (0.7). Overall, our results suggest that it is possible to develop accurate generic models to estimate commercial timber volume, and this study can serve as a guideline for forest managers or scientists interested in calibrating volumetric models in a cost-efficient way. Study Implications: This work provides useful information on volumetric modeling methods for Brazilian Amazon tropical forests. Most of the studies in the literature only investigate the classical modeling using regression models considering only boom metrics with or without bark, and, in this way, they provide incomplete and biased total knowledge and estimates for a given population. Therefore, detailed and accurate analyzes are crucial tools for decisionmaking. If the harvesting interventions are carried out without considering the most appropriate method to estimate the total wood stock, there may be damages or even extinction of some species, as has happened with other forest domains in Brazil and in other rainforest regions in the world. In this work, the results clearly show the importance of testing different methodologies and selecting the one best suited for a particular site, as well as carrying out techniques for the sustainable and correct management of the forest. Because the analysis procedures provide only information on how methodologies behave statistically, our results may contribute to a more refined analysis to be applied in the future in similar environments. Currently, the Brazilian forestry sector is looking for alternatives to obtain forest resources within the concept of sustainability. For the Brazilian Amazon tropical forest domain, it is extremely important to achieve a sustainable management of resources through forest management. Most studies in the literature investigate the management of tropical rainforest, whereas there is a lack of scientific information on the transition range for the cerrado