Chemical and Biomolecular Engineering

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Competing mechanisms and scaling laws for carbon nanotube scission by ultrasonication
(National Academy of Sciences, 2012) Pagani, Guido; Green, Micah J.; Poulin, Philippe; Pasquali, Matteo; Richard E. Smalley Institute for Nanoscale Science and Technology
Dispersion of carbon nanotubes (CNTs) into liquids typically requires ultrasonication to exfoliate individuals CNTs from bundles. Experiments show that CNT length drops with sonication time (or energy) as a power law t?m. Yet the breakage mechanism is not well understood, and the experimentally reported power law exponent m ranges from approximately 0.2 to 0.5. Here we simulate the motion of CNTs around cavitating bubbles by coupling Brownian dynamics with the Rayleigh-Plesset equation. We observe that, during bubble growth, CNTs align tangentially to the bubble surface. Surprisingly, we find two dynamical regimes during the collapse: shorter CNTs align radially, longer ones buckle.We compute the phase diagram for CNT collapse dynamics as a function of CNT length, stiffness, and initial distance from the bubble nuclei and determine the transition from aligning to buckling. We conclude that, depending on their length, CNTs can break due to either buckling or stretching. These two mechanisms yield different power laws for the length decay (0.25 and 0.5, respectively), reconciling the apparent discrepancy in the experimental data.
Synthesis of oligo(poly(ethylene glycol) fumarate)
(Nature Publishing Group, 2012) Kinard, Lucas A.; Kasper, F. Kurtis; Mikos, Antonios G.
This protocol describes the synthesis of oligo(poly(ethylene glycol) fumarate) (OPF) (1-35 kDa)(a polymer useful for tissue engineering applications) by a one-pot reaction of poly(ethylene glycol) (PEG) and fumaryl chloride. The procedure involves three parts: dichloromethane and PEG are first dried; the reaction step follows in which fumaryl chloride and triethylamine are added dropwise to a solution of PEG in dichloromethane; and finally the product solution is filtered to remove byproduct salt, and the OPF product is twice crystallized, washed, and dried under vacuum. The reaction is affected by PEG molecular weight and reactant molar ratio. The OPF product is cross-linked by radical polymerization by either a thermally induced or UV-induced radical initiator, and the physical properties of the OPF oligomer and resulting cross-linked hydrogel are easily tailored by varying PEG molecular weight. OPF hydrogels are injectable, polymerize in situ, and undergo biodegradation by hydrolysis of ester bonds. The expected time required to complete this protocol is 6 d.
Transport mechanism in granular Ni deposited on carbon nanotubes fibers
(American Physical Society, 2012) Salvato, M.; Lucci, M.; Ottaviani, I.; Cirillo, M.; Tamburri, E.; Orlanducci, S.; Terranova, M.L.; Notarianni, M.; Young, C.C.; Behabtu, N.; Pasquali, M.; Richard E. Smalley Institute for Nanoscale Science and Technology
We investigate the transport properties of granular nickel electrodeposited on carbon nanotube fibers by measuring the electrical resistance and the current voltage characteristics as a function of the temperature. The bare fiber is governed by a three-dimensional variable range hopping transport mechanism, however, a semiconducting to metallic transition is observed after the Ni deposition as a consequence of the evolution from weak to strong coupling between the deposited nickel grains. The experimental results indicate that the charge transport in the Ni-coated fiber develops from hopping governed by the Coulomb blockade in the case of small grains dimensions to a metallic electron phonon interaction mechanism for large grains dimensions. Tunneling enhanced by thermal fluctuation is responsible for the transport in the intermediate conductivity range. The role of the fiber and the effects due to the magnetic nature of the nickel grains are also discussed.
A perturbation density functional theory for the competition between inter and intramolecular association
(AIP Publishing LLC, 2012) Marshall, Bennett D.; García-Cuéllar, Alejandro J.; Chapman, Walter G.
Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient.
Wertheim's association theory applied to one site patchy colloids: Beyond the single bonding condition
(American Institute of Physics, 2012) Marshall, Bennett D.; Ballal, Deepti; Chapman, Walter G.
We apply Wertheim's theory to develop an equation of state for one site patchy colloids where the patch can bond multiple times. We allow for the possibility of ring formation without the introduction of empirical parameters and show that for moderate patch coverage the infinite series of chain graphs is well represented by the first two terms. The theory is found to be in excellent agreement with new NVT and NPT Monte Carlo simulations. The approach described here can easily be converted to the form of a density functional theory to describe inhomogeneous patchy colloid systems.
Quantitative Analysis of α-Synuclein Solubility in Living Cells Using Split GFP Complementation
(Public Library of Science, 2012) Kothawala, Ahmed; Kilpatrick, Kiri; Novoa, Jose Andres; Segatori, Laura
Presently incurable, Parkinson's disease (PD) is the most common neurodegenerative movement disorder and affects 1% of the population over 60 years of age. The hallmarks of PD pathogenesis are the loss of dopaminergic neurons in the substantia nigra pars compacta, and the occurrence of proteinaceous cytoplasmic inclusions (Lewy bodies) in surviving neurons. Lewy bodies are mainly composed of the pre-synaptic protein alpha-synuclein (αsyn), an intrinsically unstructured, misfolding-prone protein with high propensity to aggregate. Quantifying the pool of soluble αsyn and monitoring αsyn aggregation in living cells is fundamental to study the molecular mechanisms of αsyn-induced cytotoxicity and develop therapeutic strategies to prevent αsyn aggregation. In this study, we report the use of a split GFP complementation assay to quantify αsyn solubility. Particularly, we investigated a series of naturally occurring and rationally designed αsyn variants and showed that this method can be used to study how αsyn sequence specificity affects its solubility. Furthermore, we demonstrated the utility of this assay to explore the influence of the cellular folding network on αsyn solubility. The results presented underscore the utility of the split GFP assay to quantify αsyn solubility in living cells.
Response behavior of diblock copolymer brushes in explicit solvent
(American Institute of Physics, 2012) Gong, Kai; Marshall, Bennett D.; Chapman, Walter G.
The understanding of phase behavior of copolymer brushes is of fundamental importance for the design of smart materials. In this paper, we have performed classical density functional theory calculations to study diblock copolymer brushes (A-B) in an explicit solvent which prefers the A block to B block. With increasing B-block length (NB), we find a structural transition of the copolymer brush from mixed to collapsed, partial-exposed, and exposed structure, which is qualitatively consistent with experiments. The phase transitions are attributed to the interplay between entropic cost of folding copolymer brushes and enthalpic effect of contact between unlike components. In addition, we examine the effect of different parameters, such as grafting density (ρg), the bottom block length (NA), and the chain length of solvent (NS) on the solvent response of copolymer brushes. The transition chain length (NB) increases with decreasing ρg and NA, and a smaller solvent molecule makes the collapsed structure less stable due to its lower penetration cost. Our results provide the insight to phase behavior of copolymer brushes in selective solvents from a molecular view.
Inexpensive method for producing macroporous silicon particulates (MPSPs) with pyrolyzed polyacrylonitrile for lithium ion batteries
(Springer Nature, 2012) Thakur, Madhuri; Sinsabaugh, Steven L.; Isaacson, Mark J.; Wong, Michael S.; Biswal, Sibani Lisa
One of the most exciting areas in lithium ion batteries is engineering structured silicon anodes. These new materials promise to lead the next generation of batteries with significantly higher reversible charge capacity than current technologies. One drawback of these materials is that their production involves costly processing steps, limiting their application in commercial lithium ion batteries. In this report we present an inexpensive method for synthesizing macroporous silicon particulates (MPSPs). After being mixed with polyacrylonitrile (PAN) and pyrolyzed, MPSPs can alloy with lithium, resulting in capacities of 1000 mAhg−1 for over 600+ cycles. These sponge-like MPSPs with pyrolyzed PAN (PPAN) can accommodate the large volume expansion associated with silicon lithiation. This performance combined with low cost processing yields a competitive anode material that will have an immediate and direct application in lithium ion batteries.
Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coli
(BioMed Central, 2013) Mazumdar, Suman; Blankschien, Matthew D.; Clomburg, James M.; Gonzalez, Ramon
Due to its abundance and low-price, glycerol has become an attractive carbon source for the industrial production of value-added fuels and chemicals. This work reports the engineering of E. coli for the efficient conversion of glycerol into L-lactic acid(L-lactate). Escherichia coli strains have previously been metabolically engineered for the microaerobic production of D-lactic acid from glycerol in defined media by disrupting genes that minimize the synthesis of succinate, acetate, and ethanol, and also overexpressing the respiratory route of glycerol dissimilation (GlpK/GlpD). Here, further rounds of rationale design were performed on these strains for the homofermentative production of L-lactate, not normally produced in E. coli. Specifically, L-lactate production was enabled by: 1), replacing the native D-lactate specific dehydrogenase with Streptococcus bovis L-lactate dehydrogenase (L-LDH), 2) blocking the methylglyoxal bypass pathways to avoid the synthesis of a racemic mixture of D- and L-lactate and prevent the accumulation of toxic intermediate, methylglyoxal, and 3) the native aerobic L-lactate dehydrogenase was blocked to prevent the undesired utilization of L-lactate. The engineered strain produced 50 g/L of L-lactate from 56 g/L of crude glycerol at a yield 93% of the theoretical maximum and with high optical (99.9%) and chemical (97%) purity. This study demonstrates the efficient conversion of glycerol to L-lactate, a microbial process that had not been reported in the literature prior to our work. The engineered biocatalysts produced L-lactate from crude glycerol in defined minimal salts medium at high chemical and optical purity.
Human Omental-Derived Adipose Stem Cells Increase Ovarian Cancer Proliferation, Migration, and Chemoresistance
(Public Library of Science, 2013) Nowicka, Aleksandra; Marini, Frank C.; Solley, Travis N.; Elizondo, Paula B.; Zhang, Yan; Sharp, Hadley J.; Broaddus, Russell; Kolonin, Mikhail; Mok, Samuel C.; Thompson, Melissa S.; Woodward, Wendy A.; Lu, Karen; Salimian, Bahar; Nagrath, Deepak; Klopp, Ann H.
Objectives: Adipose tissue contains a population of multipotent adipose stem cells (ASCs) that form tumor stroma and can promote tumor progression. Given the high rate of ovarian cancer metastasis to the omental adipose, we hypothesized that omental-derived ASC may contribute to ovarian cancer growth and dissemination. Materials and Methods: We isolated ASCs from the omentum of three patients with ovarian cancer, with (O-ASC4, O-ASC5) and without (O-ASC1) omental metastasis. BM-MSCs, SQ-ASCs, O-ASCs were characterized with gene expression arrays and metabolic analysis. Stromal cells effects on ovarian cancer cells proliferation, chemoresistance and radiation resistance was evaluated using co-culture assays with luciferase-labeled human ovarian cancer cell lines. Transwell migration assays were performed with conditioned media from O-ASCs and control cell lines. SKOV3 cells were intraperitionally injected with or without O-ASC1 to track in-vivo engraftment. Results: O-ASCs significantly promoted in vitro proliferation, migration chemotherapy and radiation response of ovarian cancer cell lines. O-ASC4 had more marked effects on migration and chemotherapy response on OVCA 429 and OVCA 433 cells than O-ASC1. Analysis of microarray data revealed that O-ASC4 and O-ASC5 have similar gene expression profiles, in contrast to O-ASC1, which was more similar to BM-MSCs and subcutaneous ASCs in hierarchical clustering. Human O-ASCs were detected in the stroma of human ovarian cancer murine xenografts but not uninvolved ovaries. Conclusions: ASCs derived from the human omentum can promote ovarian cancer proliferation, migration, chemoresistance and radiation resistance in-vitro. Furthermore, clinical O-ASCs isolates demonstrate heterogenous effects on ovarian cancer in-vitro.
Remodeling the Proteostasis Network to Rescue Glucocerebrosidase Variants by Inhibiting ER-Associated Degradation and Enhancing ER Folding
(Public Library of Science, 2013) Wang, Fan; Segatori, Laura
Gaucher’s disease (GD) is characterized by loss of lysosomal glucocerebrosidase (GC) activity. Mutations in the gene encoding GC destabilize the protein’s native folding leading to ER-associated degradation (ERAD) of the misfolded enzyme. Enhancing the cellular folding capacity by remodeling the proteostasis network promotes native folding and lysosomal activity of mutated GC variants. However, proteostasis modulators reported so far, including ERAD inhibitors, trigger cellular stress and lead to induction of apoptosis. We show herein that lacidipine, an L-type Ca2+ channel blocker that also inhibits ryanodine receptors on the ER membrane, enhances folding, trafficking and lysosomal activity of the most severely destabilized GC variant achieved via ERAD inhibition in fibroblasts derived from patients with GD. Interestingly, reprogramming the proteostasis network by combining modulation of Ca2+ homeostasis and ERAD inhibition remodels the unfolded protein response and dramatically lowers apoptosis induction typically associated with ERAD inhibition.
Molecular theory for the phase equilibria and cluster distribution of associating fluids with small bond angles
(AIP Publishing, LLC, 2013) Marshall, Bennett D.; Chapman, Walter G.
We develop a new theory for associating fluids with multiple association sites. The theory accounts for small bond angle effects such as steric hindrance, ring formation, and double bonding. The theory is validated against Monte Carlo simulations for the case of a fluid of patchy colloid particles with three patches and is found to be very accurate. Once validated, the theory is applied to study the phase diagram of a fluid composed of three patch colloids. It is found that bond angle has a significant effect on the phase diagram and the very existence of a liquidﾖvapor transition.
Three new branched chain equations of state based on Wertheim's perturbation theory
(American Institute of Physics, 2013) Marshall, Bennett D.; Chapman, Walter G.
In this work, we present three new branched chain equations of state (EOS) based on Wertheimﾒs perturbation theory. The first represents a slightly approximate general branched chain solution of Wertheimﾒs second order perturbation theory (TPT2) for athermal hard chains, and the second represents the extension of first order perturbation theory with a dimer reference fluid (TPT1-D) to branched athermal hard chain molecules. Each athermal branched chain EOS was shown to give improved results over their linear counterparts when compared to simulation data for branched chain molecules with the branched TPT1-D EOS being the most accurate. Further, it is shown that the branched TPT1-D EOS can be extended to a LennardﾖJones dimer reference system to obtain an equation of state for branched LennardﾖJones chains. The theory is shown to accurately predict the change in phase diagram and vapor pressure which results from branching as compared to experimental data for n-octane and corresponding branched isomers.
Resummed thermodynamic perturbation theory for bond cooperativity in associating fluids
(American Institute of Physics, 2013) Marshall, Bennett D.; Chapman, Walter G.
We develop a resummed thermodynamic perturbation theory for bond cooperativity in associating fluids by extension of Wertheim's multi-density formalism. We specifically consider the case of an associating hard sphere with two association sites and both pairwise and triplet contributions to the energy, such that the first bond in an associated cluster receives an energy −ɛ(1) and each subsequent bond in the cluster receives an energy −ɛ(2). To test the theory we perform new Monte Carlo simulations for potentials of this type. Theory and simulation are found to be in excellent agreement. We show that decreasing the energetic benefit of hydrogen bonding can actually result in a decrease in internal energy in the fluid. We also predict that when ɛ(1) = 0 and ɛ(2) is nonzero there is a transition temperature where the system transitions from a fluid of monomers to a mixture of monomers and very long chains.
Second-order resummed thermodynamic perturbation theory for central-force associating potential: Multi-patch colloidal models
(American Institute of Physics, 2013) Kalyuzhnyi, Y.V.; Marshall, B.D.; Chapman, W.G.; Cummings, P.T.
We propose a second-order version of the resummed thermodynamic perturbation theory for patchy colloidal models with arbitrary number of multiply bondable patches. The model is represented by the hard-sphere fluid system with several attractive patches on the surface and resummation is carried out to account for blocking effects, i.e., when the bonding of a particle restricts (blocks) its ability to bond with other particles. The theory represents an extension of the earlier proposed first order resummed thermodynamic perturbation theory for central force associating potential and takes into account formation of the rings of the particles. In the limiting case of singly bondable patches (total blockage), the theory reduces to Wertheim thermodynamic perturbation theory for associating fluids. Closed-form expressions for the Helmholtz free energy, pressure, internal energy, and chemical potential of the model with an arbitrary number of equivalent doubly bondable patches are derived. Predictions of the theory for the model with two patches appears to be in a very good agreement with predictions of new NVT and NPT Monte Carlo simulations, including the region of strong association.
Thermodynamic perturbation theory for associating fluids with small bond angles: Effects of steric hindrance, ring formation, and double bonding
(American Physical Society, 2013) Marshall, Bennett D.; Chapman, Walter G.
We develop a comprehensive approach to model associating fluids with small bond angles using Wertheim's perturbation theory. We show theoretically and through Monte Carlo simulations that as bond angle is varied various modes of association become dominant. The theory is shown to be in excellent agreement with Monte Carlo simulation for the prediction of the internal energy, pressure, and fractions in rings and chains, double bonded over the full range of bond angles.
Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli
(Pontificia Universidad Cat�lica de Valpara�so, 2013) González, Ramón
Metabolic engineering was formally defined more than two decades ago (Bailey, 1991) and it is now an established discipline. Metabolic engineering is generally defined as the directed improvement of product formation or cellular properties through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant DNA technology (Bailey, 1991; Stephanopoulos et al. 1998). Therefore, the analysis and engineering/synthesis of metabolic pathways is of central importance to metabolic engineering. The analytical part uses a number of experimental and modeling techniques for the systematic study of cellular responses (in terms of RNA, protein and metabolite levels, metabolic fluxes, etc.) to genetic and environmental perturbations. This facilitates a rational design of metabolic modifications, which are implemented using recombinant DNA technology. Both, the analysis and the synthesis of metabolic pathways will be covered in this review. Recent efforts on the engineering of fermentative and biosynthetic pathways for biofuel production in Escherichia coli, as well as those enabling the utilization of novel feedstocks, will be highlighted.
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
(Public Library of Science, 2013) Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay
The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models.
Modeling lower critical solution temperature behavior of associating polymer brushes with classical density functional theory
(AIP Publishing LLC, 2013) Gong, Kai; Marshall, Bennett D.; Chapman, Walter G.
We study the lower critical solution temperature (LCST) behavior of associating polymer brushes (i.e., poly(N-isopropylacrylamide)) using classical density functional theory. Without using any empirical or temperature-dependent parameters, we find the phase transition of polymer brushes from extended to collapsed structure with increasing temperature, indicating the LCST behavior of polymer brushes. The LCST behavior of associating polymer brushes is attributed to the interplay of hydrogen bonding interactions and Lennard-Jones attractions in the system. The effect of grafting density and molecular weight on the phase behavior of associating polymer brushes has been also investigated. We find no LCST behavior at low grafting density or molecular weight. Moreover, increasing grafting density decreases the LCST and swelling ratio of polymer brushes. Similarly, increasing molecular weight decreases the LCST but increases the swelling ratio. At very high grafting density, a partial collapsed structure appears near the LCST. Qualitatively consistent with experiments, our results provide insight into the molecular mechanism of LCST behavior of associating polymer brushes.
Strong, Light, Multifunctional Fibers of Carbon Nanotubes with Ultrahigh Conductivity
(AAAS, 2013) Behabtu, Natnael; Young, Colin C.; Tsentalovich, Dmitri E.; Kleinerman, Olga; Wang, Xuan; Ma, Anson W.K.; Bengio, E. Amram; ter Waarbeek, Ron F.; de Jong, Jorrit J.; Hoogerwerf, Ron E.; Fairchild, Steven B.; Ferguson, John B.; Maruyama, Benji; Kono, Junichiro; Talmon, Yeshayahu; Cohen, Yachin; Otto, Marcin J.; Pasquali, Matteo; Richard E. Smalley Institute for Nanoscale Science and Technology
Broader applications of carbon nanotubes to real-world problems have largely gone unfulfilled because of difficult material synthesis and laborious processing. We report high-performance multifunctional carbon nanotube (CNT) fibers that combine the specific strength, stiffness, and thermal conductivity of carbon fibers with the specific electrical conductivity of metals. These fibers consist of bulk-grown CNTs and are produced by high-throughput wet spinning, the same process used to produce high-performance industrial fibers. These scalable CNT fibers are positioned for high-value applications, such as aerospace electronics and field emission, and can evolve into engineered materials with broad long-term impact, from consumer electronics to long-range power transmission.

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