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We introduced a conformational sampling method in an earlier report: The multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD) enhances conformational sampling of a biomolecular system by computer simulations. Herein, new sampling method, a subzone-based mD-VcMD, is presented as an extension of mD-VcMD. Then, the subzone-based method is extended further using a genetic algorithm (GA) named the GA-guided mD-VcMD. In these methods, iterative simulation runs are performed to increase the sampled region gradually. The new methods have the following benefits: (1) They are free from a production run: i.e., all snapshots from all iterations are useful for analyses. (2) They are free from fine tuning of a weight function (probability distribution function or potential of mean force). (3) A canonical ensemble (i.e., a thermally equilibrated ensemble) is generated from a simple procedure. A thermodynamic weight is assigned to each snapshot. (4) Selective sampling can be performed for particularly addressing a poorly sampled region without breaking the proportion of the canonical ensemble if the poorly sampled conformational region emerges in sampling. By applying the methods to a simple system that involves an energy barrier between potential-energy minima, we demonstrated that the new methods have considerably higher sampling efficiency than the original mD-VcMD does.

Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2’s own RNA evades nsp1’s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of the SARS-CoV-2 RNA 5’-untranslated region (SL1) is recognized by both nsp1’s globular region and intrinsically disordered region. The recognition presumably enables selective translation of viral RNAs. Cluster analysis of the binding mode and detailed analysis of the binding poses revealed several residues involved in the SL1 recognition mechanism. The simulation results imply that the nsp1 C-terminal helices are lifted from the 40S ribosome upon the binding of SL1 to nsp1, unblocking translation of the viral RNA.

Criticality experiments are the foundation of the criticality safety validation, the reactor parameter prediction and the nuclear data validation. Criticality experiments have been used in the field of nuclear data adjustment in the last decades. In applications like criticality safety validations and nuclear data adjustments, many criticality experiments are used together in one application. In practice, experts found that some experiments have bad influence in nuclear data adjustments, and they excluded them in these applications. But the reason why these experiments should be excluded is not clear. To give these exclusion a clear physical explanation, we have developed the cross-evaluation method, which could evaluate the random biases of the experimental results by analyzing the C − E (Calculation result - Experiment result) values of similar experiments. In this paper, we use the cross-evaluation method to assess the random biases of some highly enriched metal uranium fast criticality experiments. By the cross-evaluation method, experts could choose criticality experiments which should be used in the applications of criticality safety validations or nuclear data adjustments, and might find the reason why some experiments should be excluded in applications of nuclear data adjustments.

The previous research showed that the application of burnable poison was helpful to improve the criticality safety of space nuclear reactor (SNR). In order to analyze the worth of burnable poison in the SNR’s design, a model of homogeneous reactor had firstly been built based on the design of SAFE400. Comparing its difference with the real design of SAFE400 through criticality calculation, the precise of our model had been verified. Then the influence of the criticality parameters and immersion accident character parameters for this model had been analyzed for the application of the different burnable poisons (such as samarium, europium or gadolinium). The calculation results had shown that the application of the most of the burnable poisons would soften the neutron spectrum and induced a decrement of reactor’s keff in the beginning of life. However, the immersion accident analysis gave out another result that only the reactor using gadolinium could ensure the criticality safety of reactor after it made its initial keff equal with the design value. Meanwhile, compared with the initial design of SAFE400, in one hand, the burn-up results had shown that the decrement of homogeneous reactor’s reactivity using gadolinium as burnable poison was deceased after the 10 years full power operation; in other hand, its neutron spectrum became more softer with the operation time; and what’s more important, the amount of the burnable poison was not decreased with burn-up during its service life-time. These results implied that the application of the burnable poison (especially for gadolinium) could highly ensure the criticality safety and stable operation of SNR.