基于TorchMD的粗粒化分子动力模拟研究

粗粒化模型通过简化原子性质以及原子间的相互作用实现生物大分子长时间尺度的分子动力学模拟.深度学习通过模拟人类的认知过程实现海量数据的准确分类和回归过程.本论文将这两种技术进行融合,利用基于深度学习的粗粒化分子动力学模拟技术研究分子在不同状态之间的变化过程,并提出基于TorchMD的分子动力学模拟的分析框架.在本工作中,MFDP聚类算法被用于在三维的CV变量空间中进行聚类,并确定分子的若干主要状态,在完成聚类的同时,给出各类中的代表分子构象,并给出类之间的分子构象.这为后续利用String算法分析分子在不同状态间的转换路径打下基础.通过String算法,迭代搜索得到分子在不同状态之间的变化路径以及对应的势能变化曲线.通过与已有文献的结果进行对比,验证了基于TorchMD的粗粒化分子动力学模拟的理论框架可以在相对较短的时间尺度里研究分子的变化过程.

A preliminary study of the effects of plastic film-mulched raised beds on soil temperature and crop performance of early-sown short-season spring maize(Zea mays L.) in the North China Plain

To identify a strategy for earlier sowing and harvesting of spring maize(Zea mays L.) in an alternative maize–maize double cropping system, a 2-year field experiment was performed at Quzhou experimental station of China Agricultural University in 2014 and 2015. A short-season cultivar, Demeiya number 1(KX7349), was used in the experiment. Soil temperature to 5 cm depth in the early crop growth stage, crop growth, crop yield, and water use of different treatments(plastic film-mulched raised bed(RF) and flat field without plastic film mulching(CK) in 2014; RF, plastic film-mulched flat field(FF), and CK in 2015)were measured or calculated and compared. Soil temperature in the film-mulched treatments was consistently higher than that in CK(1.6–3.5 °C in average) during the early growth stage. Crops in plastic film-mulched treatments used 214 fewer growing-degree days(GDDs) in 2014 and 262 fewer GDDs in 2015. In 2014, the RF treatment yielded 32.7%higher biomass than CK, although its 9.4% higher grain yield was not statistically significant. Also, RF used 17.9% less water and showed 33.1% higher water use efficiency(WUE) than CK. In 2015, RF and FF showed 56.2% and 49.5% higher yield, 15.0% and 4.5%lower water use(ET), and 63.4% and 75.7% higher WUE, respectively, than CK. RF markedly increased soil temperature in the early crop season, accelerated crop growth, reduced ET,and greatly increased crop yield and WUE. Compared with FF, RF had no obvious effect on crop growth rate, although soil temperature during the period between sowing and stem elongation was slightly increased. However, RF resulted in lower ET and higher WUE than FF. Effects of RF on soil water dynamics as well as its cost-effectiveness remain topics for further study.

分子构象聚类中的K-means密度峰值搜索算法

分子构象的聚类是搜索分子动力学模拟轨迹中代表构象的主要方法。它是分析复杂构象改变或分子间相互作用机制的关键步骤.作为一种基于密度的聚类算法,密度峰值搜索算法因其聚类的准确度而被应用于分子聚类过程中.但随着模拟时长的增长,密度峰值搜索算法较低的计算效率限制了其应用的可能.本文提出K-means密度峰值搜索算法的聚类算法,它是密度峰值搜索算法在计算效率方面的一个扩展版本,用于解决密度峰值搜索算法中巨大的资源消耗问题.在K-means密度峰值搜索算法中,首先,通过高效的聚类算法(例如K-means)进行初始聚类,得到的聚类中心被定义为具有权重的典型点.然后,对加权的典型点通过密度峰值搜索算法实现二次聚类,并细化点为核心点、边界点、加细光晕点.在与密度峰值搜索算法具有相似的精度的同时,计算复杂度由O(n^(2))降至O(n).通过二面角,二级结构,关联图描述的分子构象,将KFDP用于多个模拟轨迹的聚类过程中.并通过与K-means聚类算法,DBSCAN聚类算法的比较结果,验证了K-means密度峰值搜索算法的优势.

Effects of Straw and Biochar Returned to the Soil on Soil Physical Properties and pH Value in Cold Rice Region

[Objectives]In order to explore the feasibility of using straw and biochar returned to the soil to improve soil physical properties and pH value in cold rice regions of China.[Methods]the effects of straw directly returned to the soil and charred straw(biochar)returned to the soil on soil bulk density,porosity,temperature and pH value of cold paddy soil were studied in this paper.[Results]The results showed that compared with conventional production,straw(6 t/ha),a small amount of biochar(2 t/ha)and a large amount of biochar(40 t/ha)returned to the soil reduced paddy soil bulk density at different growth stages by 6.02%-11.86%,2.69%-6.67%and 8.58%-11.32%,respectively,increased total porosity by 7.41%-14.93%,3.19%-8.38%and 9.81%-14.27%,respectively,and increased aeration porosity by 22.28%-192.11%,17.80%-92.11%and 52.44%-157.11%,respectively.Straw and a small amount of biochar returned to the soil had no significant effect on soil temperature and pH value of paddy field,but a large amount of biochar returned to the soil could significantly increase soil temperature by 5.13%-8.79%and pH value by 3.15%-5.96%in the later stage of rice growth.[Conclusions]The straw and biochar returned to the soil could reduce soil bulk density,increase total porosity and aeration porosity,and only a large amount of biochar returned to the soil could significantly increase soil temperature and pH value.

The Differences of Physiological Characteristics and Yield of Northern Japonica Rice in Different Nitrogen Application Patterns

The research performed analysis on differences of physiological property and yield of Tiejing No. 11 by different nitrogen fertilization patterns. The results indicated that while the nitrogen of basal: tillering: panicle was 6 ∶3∶1, the higher amount of nitrogen improved the chlorophyll content, photosynthetic capacity, effective panicle, grain weight and yield; the medium nitrogen level had advantage under the ratio 4:3:3; nitrogen application at lategrowth stage was suitable for low or medium nitrogen level,which could increase photosynthetic capacity and optimize the yield components and increase yield; under the same ratio for basic tiller and ear fertilizer, the increase of nitrogen could improve total nitrogen uptake and protein content, decrease nitrogen physiological efficiency and milled rice and tasting, but nitrogen recovery and harvest index changes had difference; as application at late growth stage in same nitrogen rate, total nitrogen uptake and protein content increased, nitrogen physiological efficiency and milled rice and amylose content and tasting decreased, nitrogen recovery and harvest index increased under low or medium nitrogen level and decreased under high nitrogen level. Nitrogen application 210 kg/hm^2 and the ratio 4 ∶3 ∶3 of basal:tillering: panicle made the yield increase by 2.8%-11.3%, and this is the optimal mode of nitrogen fertilizer application.

SI of Interaction energy prediction of organic molecules using Deep Tensor Neural Network

The support informations of DTNN architecture and prediction results of six testing cases in K-fold are listed here.

Effects of Straw Utilization Methods on Dry Matter Production and Yield of Japonica Rice in Northern China

To study the effects of straw utilization methods on dry matter production and yield of japonica rice in northern China,taking the super japonica rice Shennong 265 as the test material,using the planting method of seedling transplanting,setting four treatments,namely,the conventional production,directly returning straws to field(6 t/ha),returning straws to field at low amount of biochar(2 t/ha)and returning straws to field at high amount of biochar(40 t/ha),this paper analyzed the changes in production and yield of super japonica rice Shennong265.According to the experimental results,compared with the conventional production,after the straws were directly returned to the field,the dry matter accumulation of japonica rice was insufficient,and the leaf output rate and contribution rate were significantly reduced by 41.19%and 34.69%,respectively;the number of filled grains per panicle,1000-grain weight,and panicles per plant showed negative effect,leading to a decline in the yield;under the condition of returning straws to field at high amount of biochar,the dry matter accumulation showed a decline trend,both the leaf and stem sheath significantly reduced by 21.41%and 17.43%,and the number of filled grains per panicle also declined;under the condition of returning straws to field at low amount of biochar,the dry matter accumulation increased,and the leaf contribution rate increased by 11.68%,the number of filled grains per panicle,1000-grain weight,and panicles per plant showed positive effect,showing the potential of yield increase.In conclusion,returning suitable straw biochar to field(2 t/ha)is favorable for promoting the japonica rice production in northern China.

Visible light cross-linking and bioactive peptides loaded integrated hydrogel with sequential release to accelerate wound healing complicated by bacterial infection

The effective management of bacterial infections that are resistant to multiple drugs remains a substantial clinical challenge.The eradication of drug-resistant bacteria and subsequent promotion of angiogenesis are imperative for the regeneration of the infected wounds.Here,a novel and facile peptide containing injectable hydrogel with sustained antibacterial and angiogenic capabilities is developed.The antibacterial peptide that consists of 11 residues(CM11,WKLFKKILKVL)is loaded onto acrylate-modified gelatin through charge interactions.A vascular endothelial growth factor mimetic peptide KLT(KLTWQELYQLKYKGI)with a GCG(Gly-Cys-Gly)modification at the N-terminal is covalently coupled through a visible light-induced thiol-ene reaction.In this reaction,the acrylate gelatin undergoes cross-linkage within seconds.Based on the physical/chemical double crosslinking strategy,the bioactive peptides achieve sustained and sequential release.The results show that the hydrogel significantly inhibits methicillin-resistant Staphylococcus aureus(MRSA)growth through the rapid release of CM11 peptides at early stage;it forms obvious growth inhibition zones against pathogenic bacterial strains.Moreover,cell counting kit-8 assay and scratch test confirm that the CM11/KLT-functionalized hydrogels promote cell proliferation and migration through the later release of KLT peptides.In a mouse skin wound infected with self-luminous MRSA,the CM11/KLT-functionalized hydrogels enhance wound healing,with rapidly bacterial infection reduction,lower expression of inflammatory factors,and neovascularization promotion.These results suggest that the rationally designed,sustained and sequential release CM11/KLT-functionalized hydrogels have huge potential in promoting the healing of multi-drug resistant bacterial infected wounds.