Environmental and economic analysis of the fully integrated biorefinery

Cellulosic biofuel systems have the potential to significantly reduce the environmental impact of the world's transportation energy requirements. However, realizing this potential will require systems level thinking and scale integration. Until now, we have lacked modeling tools for studying the behavior of integrated cellulosic biofuel systems. In this paper, we describe a new research tool, the Biorefinery and Farm Integration Tool (BFIT) in which the production of fuel ethanol from cellulosic biomass is integrated with crop and animal (agricultural) production models. Uniting these three subsystems in a single combined model has allowed, for the first time, basic environmental and economic analysis of biomass production, possible secondary products, fertilizer production, and bioenergy production across various regions of the United States. Using BFIT, we simulate cellulosic ethanol production embedded in realistic agricultural landscapes in nine locations under a collection of farm management scenarios. This combined modeling approach permits analysis of economic profitability and highlights key areas for environmental improvement. These results show the advantages of introducing integrated biorefinery systems within agricultural landscapes. This is particularly true in the Midwest, which our results suggest is a good setting for the cellulosic ethanol industry. Specifically, results show that inclusion of cellulosic biofuel systems into existing agriculture enhances farm economics and reduces total landscape emissions. Model results also indicate a limited ethanol price effect from increased biomass transportation distance. Sensitivity analysis using BFIT revealed those variables having the strongest effects on the overall system performance, namely: biorefinery size, switchgrass yield, and biomass farm gate price.     

木质纤维素资源生物精炼技术研究进展

开发利用可再生性的木质纤维素资源来生产液体燃料和大宗化学品,对于解决人类发展面临的资源与环境危机具有重要的意义。然而,作为其代表性工艺的纤维素乙醇生产却因为经济上无法过关而迟迟不能真正实现产业化。采用生物精炼技术,充分利用木质纤维素材料中各种组分,生产包括部分高值产品的多种产品,是克服其转化技术产业化经济可行性问题的有效措施。综述了木质纤维素原料生物精炼技术的研究发展现状,着重阐述了玉米芯的生物精炼技术产业化进展,并对木质纤维素的生物精炼前景进行了展望。     

From a co-production design to an integrated single-cell biorefinery

Engineering microorganisms capable of accumulating multiple products are sometimes attractive because they yield several advantages in balancing the in vivo metabolic flux and restoring the optimal cell physiology. With the development of metabolic engineering and synthetic biology, numerous strategies for minimizing the substrate waste, optimizing the product portfolios, and maximizing the product yield in co-production systems have been designed and applied. This paper reviewed the recent developments in this field and discussed the challenges that may be encountered during the scaling up of the co-production systems. Finally, the importance of product portfolios and biorefinery strategy of single-cell in co-production processes was proposed.     

Valorization of potato peel: a biorefinery approach

Potato is the fourth main crop consumed worldwide and is an important constituent in the human diet. Consequently, potato is widely used in food-processing industries. However, these industries generate massive amounts of potato peel (PP) as a by-product, which is usually considered a waste, and is discarded. Interestingly, recent research suggests that PP is a valuable source of bioactive compounds, which can be converted into value-added products. In this study, we review the physicochemical composition and valorization of PP. In addition to being used as a dietary fiber or medicine, the value-added products obtained by the fermentation of PP have multiple uses, including their use as adsorbents, biocomposites and packaging materials. These products can also be used in energy production, biopolymer film development, corrosion inhibition and the synthesis of cellulose nanocrystals. The biorefinery approach for PP will increase the value of this waste by producing an array of value-added products and reducing extensive waste generation.     

城市生态系统的动力学演化模型研究进展

从系统分析出发,对城市生态系统的动力学演化模型的发展历程、建模的方法和步骤过程、软件开发方法和目前的模型软件等进行了总结。归纳了城市生态系统的动力学演化建模的方法,主要包括模型定义、模拟、实现、验证、分析和应用等六大步骤。目前国内外用于城市生态系统动力学演化模型的主要方法有：基于数理模型的方法、生态控制论和灵敏度模型、系统动力学模型、多目标规划法等。已经开发的用于城市生态系统的动力学模拟的软件可以划分为两类：基于土地利用和交通规划的专业模型和基于系统动力学和灵敏度模型的一般软件。总结了常用的城市演化模型软件,讨论了模型的研究对象和应用范围。分析了城市生态系统的动力学演化模型建模的不确定性的来源,并指出：向宏观和微观两极化发展是城市生态系统动力学演化模型的发展趋势之一,而与人工智能和地理信息系统等新方法的集成是发展的另一趋势。城市生态系统动力学演化模型的开发前景在于对不确定性问题的定性、定量分析,而多模型的耦合和集成是发展的必然趋势。     

Multiscale modeling of lipids and lipid bilayers

A multiscale modeling approach is applied for simulations of lipids and lipid assemblies on mesoscale. First, molecular dynamics simulation of initially disordered system of lipid molecules in water within all-atomic model was carried out. On the next stage, structural data obtained from the molecular dynamics (MD) simulation were used to build a coarse-grained (ten sites) lipid model, with effective interaction potentials computed by the inverse Monte Carlo method. Finally, several simulations of the coarse-grained model on longer length- and time-scale were performed, both within Monte Carlo and molecular dynamics simulations: a periodical sample of lipid molecules ordered in bilayer, a free sheet of such bilayer without periodic boundary conditions, formation of vesicle from a plain membrane, process of self-assembly of lipids randomly dispersed in volume. It was shown that the coarse-grained model, developed exclusively from all-atomic simulation data, reproduces well all the basic features of lipids in water solution.     

Critical applications of Mucor circinelloides within a biorefinery context

The establishment of an efficient and feasible biorefinery model depends on, among other factors, particularly the selection of the most appropriate microorganism. Mucor circinelloides is a dimorphic fungus species able to produce a wide variety of hydrolytic enzymes, lipids prone to biodiesel production, carotenoids, ethanol, and biomass with significant nutritional value. M. circinelloides also has been selected as a model species for genetic modification by being the first filamentous oleaginous species to have its genome fully characterized, as well as being a species characterized as a potential bioremediation agent. Considering the potential of replacing several nonrenewable feedstocks is widely dependent on fossil fuels, the exploitation of microbial processes and products is a desirable solution for promoting a green and sustainable future. Here, we introduce and thoroughly describe the recent and critical applications of this remarkable fungus within the context of developing a fungal-based biorefinery.     

生物炼制细胞工厂:生物制造的技术核心

对生物炼制细胞工厂的发展进行了简要回顾,从微生物糖代谢的分子机制、细胞工厂的代谢网络及调控、细胞工厂的构建技术及细胞工厂的优化4个方面介绍了本期专刊发表的17篇生物炼制细胞工厂方面的论文。     

Sustainable production of eicosapentaenoic acid-rich oil from microalgae: Towards an algal biorefinery

Utilization of sustainable natural resources such as microalgae has been considered for the production of biofuels, aquaculture feed, high-value bioactives such as omega-3 fatty acids, carotenoids, etc. Eicosapentaenoic acid (EPA) is an omega-3 fatty acid present in fish oil, which is of physiological importance to both humans and fish. Marine microalgae are sustainable sources of lipid rich in EPA, and different species have been explored for the production of EPA as a single product. There has been a rising interest in the concept of a multi-product biorefinery, focusing on the maximum valorization of the algal biomass. Targeting one or more value-added compounds in a biorefinery scenario can improve the commercial viability of low-value products such as triglycerides for biofuel. This approach has been viewed by technologists and experts as a sustainable and economically feasible possibility for the large-scale production of microalgae for its potential applications in biodiesel and jet fuel production, nutraceuticals, animal and aquaculture feeds, etc. In this review paper, we describe the recent developments in the production of high-value EPA-rich oil from microalgae, emphasizing the upstream and downstream bioprocess techniques, and the advantages of considering an EPA-rich oil-based biorefinery.     

Production of lignosulfonate in NSSC‐based biorefinery

The spent liquor (SL) of a neutral sulfite semichemical (NSSC) pulping process contains a considerable amount of lignocelluloses and is treated in wastewater systems. The lignocelluloses, however, can be used for producing value‐added products if they are isolated from the SL. In this article, solvent treatment (mixing acetone, ethanol, or isopropyl with SL) was used as a method for isolating lignosulfonate from SL. The maximum lignosulfonate removal was obtained via mixing isopropyl alcohol with SL at the weight ratio of 20/80, room temperature, and 5.7 pH. The results also showed that the molecular weight and anionic charge density of the precipitates were in the range of 5,000–70,000 g/mol and 0.2–1.8 meq/g, respectively. Based on these results, a process was proposed for isolating lignosulfonate from SL and converting the NSSC process to an NSSC‐based biorefinery. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1508–1514, 2015     

秸秆汽爆炼制木质素制备酚醛泡沫材料

以木质纤维素为原料的生物炼制不仅需要考虑到纤维素和半纤维素,同时也需要考虑到木质素的利用,以提高木质纤维素炼制的整体经济效益。利用汽爆处理的玉米秸秆为原料,通过优化碱提取的温度以及碱浓度,获得木质素得率较高,糖含量较少的提取液,同时该提取液经过浓缩后直接部分替代苯酚与甲醛反应制备酚醛泡沫。结果表明:当提取温度120℃,碱浓度1%,固液比1∶10,提取时间2 h,木质素的提取率达到79.67%。由该提取液替代苯酚制备的酚醛泡沫随着替代率的增加,其泡沫的密度逐渐增加,其压缩强度相对于纯酚醛泡沫也得到了提高。而木质素的加入并没有显著影响其热导率以及阻燃性能,同时由于其利用较为低廉的可再生资源木质素替代不可再生的苯酚原料,成本低,环保性好,具有更好的市场应用前景。采用木质素提液直接制备酚醛泡沫材料,工艺流程简单;增加了副产物木质素的经济价值,提高了整个木质纤维素炼制的经济性。     

集成灰色分析和元胞自动机用于景观动态模拟

针对景观生态系统"复杂性"的特点,采用灰色局势确定邻域转换规则,构建元胞自动机,用于模拟和分析景观生态动态变化.在信息不完全的情况下,提高了元胞自动机景观生态动态模型的可靠性和可行性.以中国云南省怒江流域中段作为实例,确定影响元胞转换规则的三因素主要有元胞邻域的聚集程度,土地适宜程度和人类活动影响程度,根据景观这一类复杂系统的动态变化特征其权重随地理空间位置和时间而变化,同时用Monte Carlo法考虑了模拟时转换的随机性.通过计算显示模拟未来发展的情景总的趋势是符合实际的,不但模拟了微观的景观单元的自组织机制,而且在一定程度上反映了宏观的社会经济因素影响,因而更具有针对性、典型性及准确性.     

Multiscale modeling of tumor growth induced by circadian rhythm disruption in epithelial tissue

We propose a multiscale chemo-mechanical model of cancer tumor development in epithelial tissue. The model is based on the transformation of normal cells into a cancerous state triggered by a local failure of spatial synchronization of the circadian rhythm. The model includes mechanical interactions and a chemical signal exchange between neighboring cells, as well as a division of cells and intercalation that allows for modification of the respective parameters following transformation into the cancerous state. The numerical simulations reproduce different dephasing patterns—spiral waves and quasistationary clustering, with the latter being conducive to cancer formation. Modification of mechanical properties reproduces a distinct behavior of invasive and localized carcinoma.     

Multiscale modeling of macromolecular biosystems

In this article, we review the recent progress in multiresolution modeling of structure and dynamics of protein, RNA and their complexes. Many approaches using both physics-based and knowledge-based potentials have been developed at multiple granularities to model both protein and RNA. Coarse graining can be achieved not only in the length, but also in the time domain using discrete time and discrete state kinetic network models. Models with different resolutions can be combined either in a sequential or parallel fashion. Similarly, the modeling of assemblies is also often achieved using multiple granularities. The progress shows that a multiresolution approach has considerable potential to continue extending the length and time scales of macromolecular modeling.     

Multiscale modeling of nucleosome dynamics

Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed “cold sites”, which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.     

江西红壤坡地柑橘园生态水文特征及水土保持效益

在江西省水土保持生态科技园对标准柑橘试验小区生态水文特征进行9年的定位观测,设置7个处理,研究柑橘园生态水文特征及水土保持效益.结果表明： 7个处理的平均减流率和减沙率分别为78.5%和77.2%,其中,林下百喜草(Paspalum natatu)带状覆盖、百喜草全园覆盖和水平梯田+梯壁植草减流率较高,分别为94.8%、94.3%和92.5%;柑橘清耕地减流率较低,为33.1%;林下套种黄豆和萝卜减流率居中,为66.0%和77.5%,且横坡耕作优于纵坡耕作.对2009-2010年发生的43场平均降雨量为20.07 mm的雨水柑橘林冠再分配格局进行观测,穿透降〖JP2〗雨量平均为9.15 mm,树干茎流量平均为4.72 mm,林冠截留量平均为620 mm,分别占林外降雨量的44.7%、25.7%和29.6%.随着林外降雨量的增大,林冠层的穿透雨量、茎流量呈递增趋势.当降雨量<10 mm时,树冠截留率与林外降雨之间呈显著的线性负相关;当降雨量>10 mm时,二者之间的相关性不明显.柑橘枯落物的持水率与浸水时间呈对数回归关系,最大持水率达326%.合理的林下植被配置对柑橘果园的水土保持具有重要作用.     

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks

SUMMARY: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.