Building and deploying a cyberinfrastructure for the data-driven design of chemical systems and the exploration of chemical space

Abstract

The use of modern data science has recently emerged as a promising new path to tackling the complex challenges involved in the creation of next-generation chemistry and materials. However, despite the appeal of this potentially transformative development, the chemistry community has yet to incorporate it as a central tool in every-day work. Our research program is designed to enable and advance this emerging research approach. It is centred around the creation of a software ecosystem that brings together physics-based modelling, high-throughput in silico screening and data analytics (i.e. the use of machine learning and informatics for the validation, mining and modelling of chemical data). This cyberinfrastructure is devised to offer a comprehensive set of data science techniques and tools as well as a general-purpose scope to make it as versatile and widely applicable as possible. It also emphasises user-friendliness to make it accessible to the community at large. It thus provides the means for the large-scale exploration of chemical space and for a better understanding of the hidden mechanisms that determine the properties of complex chemical systems. Such insights can dramatically accelerate, streamline and ultimately transform the way chemical research is conducted. Aside from serving as a production-level tool, our cyberinfrastructure is also designed to facilitate and assess methodological innovation. Both the software and method development work are driven by concrete molecular design problems, which also allow us to assess the efficacy of the overall cyberinfrastructure.     

公共空间安全感研究：以上海城市街景感知为例

在文献基础上梳理了街道安全感影响因素,并采用上海样本检验了“街道眼”等西方街道安全理论。邀请30位学生和30位市民对上海5个不同发展时期社区的300张百度街景图片进行安全感评定。实验发现绿视率、管理程度、车道数等都对安全感起着显著作用,并分别建立了单双车道和多车道街道空间的安全感回归模型。其中发现绿视率（单双车道相关系数R=0.728,p<0.01;多车道相关系数R=0.471,p<0.01）、管理程度（单双车道相关系数R=0.766,p<0.01;多车道相关系数R=0.450,p<0.01）、车道数量因素（相关系数R=0.502,p<0.01）对安全感均有显著的积极作用,界面透明度（单双车道相关系数R=0.222,p<0.01）、独立自行车道（相关系数R=0.309,p<0.01）及设计美感（相关系数R=0.432,p<0.01）等因素在单双车道空间中具有积极影响,而助动车与自行车（单双车道相关系数R=-0.327,p<0.01;多车道相关系数R=-0.281,p<0.01）在对安全感知评价具有消极影响,机动车（单双车道相关系数R=0.251,p<0.01;多车道相关系数R=-0.327,p<0.01）在单双车道与多车道空间中呈现相反的作用。     

对6个国外城市街道规划设计导则的解析——“如何规划步行友好的城市街道开放空间？”

本文将“如何通过街道规划设计,营建步行友好的城市开放空间环境,提高居民生活质量？”作为研究视角,抽取了6个国外城市街道规划设计导则中与“如何规划设计步行友好的城市开放空间？”密切相关的内容,根据相关导则编制的逻辑将内容进行提炼、归纳和重组。针对中国通过改善街道步行环境建设高品质城市的诉求以及相关导则中缺少对使用者需求关注的现状,提出了将需求调查纳入规划规定环节、从环境特征角度出发进行街道分类与定位、关注地域特征与集约性生态设施的环境营造方法以及提升步行道功能多样性和空间相容性的建议。     

绿色校园视角下的校园绿地建设—以北京林业大学为例

绿色校园建设是推进校园可持续发展、促进环境教育开展的校园重要建设工作之一。校园绿地是校园环境营造与教育功能表现的重要载体,也是绿色校园建设的直接体现。在分析《绿色校园评价标准》中对校园绿地建设评价指标的基础上,以北京林业大学为例,将校园绿地建设现状与指标要求进行对比。认为北京林业大学校园绿地建设在校园绿地总体规划、校园绿地营造、校园植物配置3个层面不仅满足指标要求,也形成了自身校园绿地建设特点,包括以植物观赏型绿地为基底、结合互动参与型与科教示范型绿地的建设体系,与科教场所相得益彰、与生活空间相互渗透、与实习基地相辅相成的3种特色绿地营造形式,以及植物与地形、道路结合形成特色的校园植物景观空间。通过以上研究,希望对当前绿色校园视角下的校园绿地建设提供借鉴,同时提出北京林业大学校园绿地未来的建设愿景与方向。     

新加坡·南京生态科技岛滨江风光带（大江侧）示范区景观设计

新加坡·南京生态科技岛滨江风光带（大江侧）示范区景观设计旨在通过广泛的生态种植、森林保护、湿地恢复和栖息地创造等措施,提升自然环境的韧性,同时顺应当地的气候变化。项目组在确保生态不受干扰的前提下,结合现状对部分开放空间节点进行了细致的规划和设计,并在视野开阔的场地设置滨江观景平台。该项目的建成,为场地生态基础设施的建立奠定良好的基础,全面保护、保育长江滨水沿线12km的野生动植物栖息地,提高生态多样性并改善城市生态     

城市地下历史景观的保护实践探析

城市地下考古遗址是城市历史景观的重要组成部分,对城市中心地区地下空间的深度开发是目前发展的重要趋势。在地下空间的规划和设计中对地下历史景观和地下公共空间进行整合,不仅能减少对城市地下历史景观造成破坏,还能充分发挥历史景观的社会文化功能,塑造出富有特色的城市公共空间,促进城市的文化可持续发展。本文以保加利亚谢尔迪卡古文化与交通综合体为例,探讨城市地下空间开发中历史景观的营建经验,以供中国参考。     

Use of space and behavior of weaned piglets kept in enriched two-level housing system

In this study, the possibility of introducing an elevated platform to a piglet pen was explored as a way of increasing available space and creating functional areas. On the platform, nine different manipulable materials were offered. In four batches, 40 weaned piglets were kept for five weeks in the two-level pen. Video recordings were taken two days per week. In the afternoon, more piglets were on the platform than in the morning or at night (7.2 ± 0.1 vs. 4.9 ± 0.1 vs. 0.6 ± 0.1 piglets/5 minutes; p < .05). The area under the platform was preferred more in the morning and at night than in the afternoon (18.5 ± 0.1 vs. 21.6 ± 0.2 vs. 12.5 ± 0.1 piglets/5 minutes; p < .05). Up to 36 piglets were counted there simultaneously, mainly in the recumbent position. On and under the platform, air velocity and ammonia concentration were within the recommended ranges. The study concluded that a two-level pen is a feasible option to increase space allowance and to create functional areas in a piglet pen.     

The environmental zero‐point problem in evolutionary reaction norm modeling

There is a potential problem in present quantitative genetics evolutionary modeling based on reaction norms. Such models are state‐space models, where the multivariate breeder's equation in some form is used as the state equation that propagates the population state forward in time. These models use the implicit assumption of a constant reference environment, in many cases set to zero. This zero‐point is often the environment a population is adapted to, that is, where the expected geometric mean fitness is maximized. Such environmental reference values follow from the state of the population system, and they are thus population properties. The environment the population is adapted to, is, in other words, an internal population property, independent of the external environment. It is only when the external environment coincides with the internal reference environment, or vice versa, that the population is adapted to the current environment. This is formally a result of state‐space modeling theory, which is an important theoretical basis for evolutionary modeling. The potential zero‐point problem is present in all types of reaction norm models, parametrized as well as function‐valued, and the problem does not disappear when the reference environment is set to zero. As the environmental reference values are population characteristics, they ought to be modeled as such. Whether such characteristics are evolvable is an open question, but considering the complexity of evolutionary processes, such evolvability cannot be excluded without good arguments. As a straightforward solution, I propose to model the reference values as evolvable mean traits in their own right, in addition to other reaction norm traits. However, solutions based on an evolvable G matrix are also possible.     

Assessment of a livestock GPS collar based on an open‐source datalogger informs best practices for logging intensity

Ecologists have used Global Positioning Systems (GPS) to track animals for 30 years. Issues today include logging frequency and precision in estimating space use and travel distances, as well as battery life and cost. We developed a low‐cost (~US$125), open‐source GPS datalogger based on Arduino. To test the system, we collected positions at 20‐s intervals for several 1‐week durations from cattle and sheep on rangeland in North Dakota. We tested two questions of broad interest to ecologists who use GPS collars to track animal movements: (1) How closely do collared animals cluster in their herd? (2) How well do different logging patterns estimate patch occupancy and total daily distance traveled? Tested logging patterns included regular logging (one position every 5 or 10 min), and burst logging (positions recorded at 20‐s intervals for 5 or 10 min per hour followed by a sleep period). Collared sheep within the same pasture spent 75% of daytime periods within 51 m of each other (mean = 42 m); collared cattle were within 111 m (mean = 76 m). In our comparison of how well different logging patterns estimate space use versus constant logging, the proportion of positions recorded in 1‐ and 16‐ha patches differed by 2%–3% for burst logging and 1% for regular logging. Although all logging patterns underestimated total daily distance traveled, underestimations were corrected by multiplying estimations by regression coefficients estimated by maximum likelihood. Burst logging can extend battery life by a factor of 7. We conclude that a minimum of two collars programmed with burst logging robustly estimate patch use and spatial distribution of grazing livestock herds. Research questions that require accurately estimating travel of individual animals, however, are probably best addressed with regular logging intervals and will thus have greater battery demands than spatial occupancy questions across all GPS datalogger systems.