“大学物理循环教学模式”探索与实践

为了更加切实有效地开展大学物理教学工作,过去5年内,在大学物理实践教学过程中,摸索出一套较为有效的＂大学物理循环教学模式＂,主要对该模式及其实践情况进行简要介绍.

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space,Monte Carlo simulations of DNA compaction in free space,in confined spherical space without crowders and in confined spherical space with crowders were performed separately.The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions.In addition,effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii.In confined spherical space without crowders,the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly.In contrast,with the addition of crowders to the confined spherical space,effects of temperature on the phase transition of DNA compaction become insignificant,whereas the phase transition at different temperatures strongly depends on the size of crowder,and the critical volume fraction of crowders pertains to the diameter of crowder linearly.

Insights into the Discrepancy between Single Molecule Experiments

Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA(ssDNA). Recent FRET singlemolecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor(NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks.

Effect of Temperature on Topological States of Circular DNA

The different topological states of circular double-stranded DNA can be defined by their linking number. The equilibrium distribution of linking number can be obtained by circularizing a linear DNA into a circle by ligase. Based on the recent experimental results that the DNA bending rigidity and twist rigidity strongly depend on temperature, the reduced bending rigidity can be approximated by g = （3.19 x10-19 - T. 4.14s10-22） erg. cm over the temperature interval （5 ~ 53） ~ C, and the temperature dependence of twist rigidity can be fitted by C （ T） = （4588.89 exp（-T/117.04）- 251.33） nm. The temperature dependence of the linking number distribution of circular DNAs can be predicted by using Monte Carlo simulation. The variance of linking number distribution on temperature is in accordance with the previous experimental results. Compared with the temperature dependence of bending rigidity, the temperature dependence of twist rigidity causes a noticeable fluctuation in linking number distribution and mainly contribute towards the variance change of linking number distribution of circular DNA. The variance of the writhe number and twist number in the equation （（ALk）21 = （（ATw）2） -b （（Wr）2） depends on the length of circular DNA. When the length of circular DNA is less than 230 nm, the variance of twist number （（ATw）2） is dominant over the variance of writhe number （（（wr）2））whereas for the condition that the length of the circular DNA is larger than 370 nm.