Rice Unconventional Wisdom
Energy & Environmental Systems Institute

Bio-based Chemicals & Fuels

Life cycle assessment  --  Computational approaches --  Policy analysis --  Carbon cycle assessment  --  Biobutanol   --  Glycerol fermentation  --  Cellulosic biomass   --  Catalysis  --   Process design  --  Reactor design  --  Biodiesel kinetics   

By conservative estimates, biomass (plants, agricultural and other waste) can provide up to 25% of energy demands within the next 20 years. Yet much more research is needed to develop optimized fermentation or thermo-chemical processes.  A major objective is development of highly-integrated processes and biorefineries able to convert biomass to biofuels and bio-based chemicals using efficient, sustainable, environmentally benign, and economical production methods. The conversion of biomass to fuels and chemicals will parallel the route currently used by the petrochemical industry.

EESI - Petrochem & Biobased Industry Chart

What Are the Key Strategies?
Several reports issued by the National Research Council, the Department of Energy, the Department of Agriculture, and other federal agencies and professional organizations have outlined three main research thrusts (or platforms) for the biomass effort. The main objective of all three platforms is the development of commercial biorefinery technology that can reduce (or even end) our dependence on foreign oil.

  1. The sugar platform is based on extracting sugars from plant biomass and using them as substrates (feedstocks) for the production of fuels and chemicals, predominantly via fermentation processes. Enzymatic and chemical processes will also be components of this effort. This is the platform that includes cellulosic ethanol that has recently received so much attention in the press.
  2. The syngas platform proposes to process the plant biomass thermally (pyrolysis/combustion) to obtain heat, power and a gas mix (syngas or synthesis gas) containing CO, CO2, H2, and other compounds. Syngas will then be processed via various chemical or fermentation routes to produce ethanol and other chemicals.
  3. The oil platform is closely related to biodiesel or bio-distillate production. The goal here is to first extract the oil portion of an oil-accumulating plant (e.g., soybean or rapeseed) and then either use this oil to produce biodiesel (a mixture of fatty acid methyl esters) or process it into bio-distillates via conventional refinery technology. Unlike the extraction of sugars, the extraction of biomass oils is technically simple and the subsequent production of methyl esters is a highly efficient process. The rapidly growing biodiesel industry, however, will flood the US and international markets with glycerol, a significant co-product of biodiesel and oleochemical production. For this reason, research into the conversion of glycerin into other useful products (like ethanol, other chemicals or hydrogen) has the potential to revolutionize this industry and dramatically improve its economics.

What can Rice contribute to the development of this industry?
Rice is well positioned to become a key player in the development of bio-refinery technology.

  • The university is located in Houston, the energy capital of the world, and most petrochemical companies have research and/or production facilities in our area.
  • As these energy companies move aggressively into biofuels and bio-based chemicals (see, for example, recent announcements by BP and Chevron), they will want to leverage their existing production and distribution infrastructure.
  • Rice has several interdisciplinary groups working on cross-cutting, enabling technologies across all three platforms. Collaborative research efforts between faculty in the engineering and science schools and their colleagues in the Baker Institute and the social sciences study the policies related to biobased fuels and chemicals, and the environmental implications of their production and use.

Selected Rice research across dominant platforms
& cross-cutting technologies
Click on links (under construction) for more information. 






- Biobutanol
Cellulosic biomass

-  Biodegradable  polymers

-  Catalysis

 -  Process Design 

- Glycerol fermentation

-Reactor design

-  Biodiesel kinetics



- Computational analysis of biosystems & genetic network design

- Life cycle assessment

Carbon cycle assessment

- Energy & environmental policy analysis



Life cycle assessment
Work in this area
 will assess and minimize environmental impacts from the production of renewable fuels from agricultural products, and provide scientific input to address three national interests: (1) minimizing dependence on foreign oil and improving our trade balance, (2) steering the impending growth of biomass-based industries to protect environmental quality, and (3) invigorating agricultural activity and the rural economy for food security in a manner that is environmentally and economically sustainable. This component will not overlap with existing biofuel production efforts. Rather, it will provide a holistic, complementary approach that contributes to national security.
Research will be conducted within the framework of comparative life cycle assessment (LCA) and environmental impact analysis to ensure the sustainable production of transportation biofuels. We will incorporate expertise in industrial ecology, biotechnology, pollutant fate and transport characterization, and risk assessment and management to (1) develop a comprehensive LCA framework for environmental impact evaluation and pollution prevention associated with the production, storage, distribution, and use of biomass-based fuels (i.e., biodiesel, ethanol, butanol and hydrogen), and (2) enhance the economic feasibility and environmental viability of transportation biofuels production. Through the efforts of this group at Rice, safe and economical biofuels will replace the use of foreign oil, generating revenue for U.S. agriculture and promoting strategic independence. By calculating the net environmental benefits of biofuels for transportation, carbon credits will be verified, bought and sold, creating a new commodity crop for farmers. These credits will be exchanged on the emerging  Chicago Climate Exchange, allowing market forces to help improve the environment, rather than using expensive command-and-control regulations as occurred in the past. This center of research will also train graduate students in multidisciplinary areas where there is a shortage of professionals, and will play a crucial role in finding multiple paths to sustainability.  (Top)

Computational approaches
Processes of concern to the metabolic engineer typically involve relatively few metabolites engaged in relatively many reactions. The balance of fluxes therefore leads to significantly underdetermined systems. These extra degrees of freedom then provide organisms and engineers the opportunity to engineer optimal pathways. The optimization problem itself may have many solutions and that this additional freedom would permit one to investigate notions of robustness. However, most studies concentrate on optimization aspects and frequently neglect the implementation constraints imposed by the network. In particular, very few studies have addressed the issue of operating conditions. As such, operating conditions must be taken into account in addition to a traditional pathway optimization approach.
Work in this area is designed to bridge the gap between modeling/theoretical studies and that of experimental implementation. A metabolic network design and optimization framework that will take experimental results and implementation constraints into consideration has been developed and illustrated with a moderate sized system, that of succinate production. This target network is ideal since it is small enough to be implemented and evaluated experimentally and yet large enough to contain the salient features of a large network. We developed a pathway design and optimization scheme that accommodates genetically and/or environmentally derived operational constraints. We expressed the full set of theoretically optimal pathways in terms of the underlying elementary flux modes and then examined the sensitivity of the optimal yield to a wide class of physiological perturbations. Though the scheme is general, it is best appreciated in a concrete context: we here take succinate production as our model system, and the scheme produces novel pathway designs and leads to the construction of optimal succinate production pathway networks. The model predictions compare very favorably with experimental observations.  (Top)

Environmental impact assessment and policy analysis
Drawing on Rice University's interdisciplinary expertise in biology, environmental engineering, energy sustainability, economics, political science, geology, nanotechnology, architecture, and sociology, the  Baker Institute Energy Forum has published major energy studies on topics including global and regional energy security, energy geopolitics, energy resource development, emerging energy technologies, energy and economic growth, energy forecasting, energy and the environment, and energy sector regulation. A conference on the Science and Policy of BioFuels: Assessing Strategic Options and End Goals will be hosted by the Baker Institute in September 2006. 
Work in this area addresses three national interests:  1) minimizing dependence on foreign oil and improving our trade balance;  2)  steering the impending growth of biomass-based industries to protect environmental quality; and 3) invigorating agricultural activity and the rural economy for food security in an environmentally and economically sustainable manner.  (Top)


Among the potential applications of solventogenic Clostridia is the production of butanol and acetone, as was done in large scale until the late 1950's. The traditional process was a batch fermentation. In recent years, substantial interest has been generated for better processes to produce butanol as either a commodity chemical or a gasoline extender. Butanol is currently produced in the USA at over 1.3 billion lbs/yr. Butanol has several features that make it suitable as a fuel extender. It is more hydrophobic than ethanol, thus it mixes better with hydrocarbon fuels and may be relevant as an oxygenate alternative with the current controversy surrounding MTBE contamination. For example it has a much higher flash point and boiling point than MTBE, thus reducing volatiles. The lower vapor pressure (0.33 psi vs 4.5 psi for gasoline) makes it suitable for use as an oxygenate throughout the year. Butanol also has a higher heating value per gal (BTU/gal) than MTBE and a considerably higher value than ethanol. This allows it to be used gal for gal as a replacement for gasoline without engine modifications.
      Rice researchers were the first to genetically engineer high solvent producing strains.  They promulagated the sequencing of the genome of C. acetobutylicum, developed genetic methods, and analyzed the genes and enzymes of solvent production.  A 
2006 international meeting on solvent-producing clostridia was hosted at Rice.  Researchers will further engineer the organism for high production, reduce production of acetone and ethanol, and enhance the ability to convert a wide variety of feedstocks including cellulosic biomass to butanol.  Over fifty  biobutanol-related research papers have been published by Rice researchers.  (Top)

Glycerol fermentation
The worldwide surplus of glycerol generated as an inevitable by-product of biodiesel production is resulting in the shutdown of traditional plants that produce or refine glycerol. Once considered a valuable "co-product", crude glycerol is rapidly becoming a "waste product" with an attached disposal cost. The situation will only become worse as worldwide production of biodiesel grows at an unprecedented pace. In fact, it is well known that some biodiesel companies pay for the appropriate disposal of glycerol-containing streams and in some cases bankruptcy has been attributed to the collapse in glycerol prices. In addition, this glycerol glut is a problem for oleochemical firms, as glycerol refining represents their longtime revenue source.  The need for obtaining new chemicals from glycerol is such that U.S. government agencies such as the Department of Energy have, as one of their main goals, promoting the development of new glycerol platform chemistry and product families. Not only is glycerol cheap and abundant, but the higher reduced state of carbon in glycerol (compared to cellulosic sugars) would significantly increase the yield of chemicals whose production from these sugars is limited by the availability of reducing equivalents.
       Realizing this potential would require the use of microorganisms able to perform glycerol fermentation in the absence of electron acceptors. However, the ability to ferment glycerol is restricted to very few organisms, most of them not amenable to industrial applications. For example, E. coli (the workhorse of modern biotechnology) has been unable to conduct this metabolic process for more than 80 years. However, we recently discovered that this organism is in fact able to metabolize glycerol in a purely fermentative way. Our findings, featured in the August 5, 2006 issue of the journal 
Biotechnology and Bioengineering, should enable the development of an E. coli-based platform for the anaerobic production of reduced chemicals from glycerol. Our current work focuses in two directions: (1) elucidating the pathways and mechanisms mediating the anaerobic fermentation of glycerol in E. coli, and (2) engineering E. coli for the production of fuels and chemicals from glycerol. (Top)

Cellulosic biomass
The fermentation of
5- and 6-carbon sugar mixtures obtained from cellulosic biomass is at the heart of the production of fuels and chemicals through the "sugars" platform, regardless of the chemical and fuel to be produced. Although well established for cornstarch-derived sugars like glucose, this process remains challenging when a mixture of plant biomass sugars is used (i.e., higher capital and operational costs). While the initial goal of simultaneous consumption of 5- and 6-carbon sugar has been achieved, engineered strains do not exhibit significant kinetic advantages over wild-type sequential metabolism of sugars. In other words, sequential and simultaneous metabolism of sugars takes about the same time, and their fermentation is still slower than cornstarch-derived sugars.
       Our initial work in this area was motivated by the need to address these issues and, over the last two years, we have made significant progress toward our goals. For example we are studying the implications of simultaneous vs. sequential metabolism of  5- and 6-C sugars on cellular metabolism, metabolic fluxes, and regulation. We are addressing fundamental questions such as what limits the
glycolytic flux or whether the cells would be able to handle the "excess" glycolytic flux in an engineered organism able to simultaneously consume multiple sugars. We are using a systems biology-based approach that takes advantage of the most recent advances in experimental tools in the area of functional genomics (e.g., DNA microarrays, labeling experiments-based estimation of metabolic fluxes, etc.) as well as new developments in system-wide mathemathical/statistical tools for the analysis of these systems.
       To this end we have made significant contributions in both methodologies and fundamental understanding of the system. We have developed: (1) a superior method for estimating metabolic fluxes using 13C labeling experiments; (2) a novel PCA-based method for the identification of assay-specific signatures in functional genomic studies; and (3) a novel tool (Elementary Network Decomposition, END) to help elucidate the network topology of regulatory systems. These tools and methodologies have been successfully used in the study of the sugar-utilization regulatory systems in E. coli. For example, through END we predicted that a null mutation of Mlc (a glucose PTS repressor) would impair the ability of the cells to consume type II carbon sources (e.g., xylose, arabinose). This was confirmed in experiments with both individual sugars and sugar mixtures, thus demonstrating the utility of END as a discovery tool. In addition, using a combination of metabolic flux analysis and transcriptional profiling we have identified potential genetic and metabolic targets limiting the simultaneous metabolism of 5- and 6-carbon sugars.     
Our future work in this area will continue to address issues related to the optimal utilization of sugar mixtures along with other topics relevant to the production of fuels and chemicals from biomass hydrolysates. These include: (1) study of the cell response to inhibitors present in hydrolysates and inhibition by high concentration of substrates and desired products (e.g., sugars, ethanol, etc.); (2) development and use of evolutionary strategies to create robust biocatalysts for the production of fuels and chemicals from biomass sugars; and (3) development and application of systems biology tools to understand cellular metabolism and manipulate it for the production of biofuels and biochemicals. We are also developing microbial platforms for the conversion of sugars into acetic acid, formic acid, hydrogen, ethanol, and succinic acid. (Top)



Pedro Alvarez
Andrew Barron
George Bennett
Janet Braam

Steven Cox
Ramon Gonzalez
Nikolaos Mantzaris
Ka-Yiu San
Michael Wong
Kyriacos Zygourakis

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