Scholarly Works, Institute for Critical Technology and Applied Science (ICTAS)

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Research articles, presentations, and other scholarship

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Laser-induced exfoliation of amorphous carbon layer on an individual multiwall carbon nanotube
Singh, G.; Rice, P.; Hurst, K. E.; Lehman, John H.; Mahajan, R. L. (AIP Publishing, 2007-07)
Pulsed laser treatment of an individual multiwall carbon nanotube induced selective exfoliation of the amorphous carbon contamination layer. The multiwall carbon nanotube (MWCNT) was exposed to a 248 nm excimer laser. After the treatment, transmission electron microscopy images show that the amorphous layer has expanded and separated from the crystalline MWCNT walls. This interesting observation has implications for laser cleaning and possible thinning of MWCNTs to reduce the radial dimensions. (C) 2007 American Institute of Physics.
Foam-based optical absorber for high-power laser radiometry
Ramadurai, Krishna; Cromer, Christopher L.; Li, Xiaoyu; Mahajan, Roop L.; Lehman, John H. (Optical Society of America, 2007-12-01)
We report damage threshold measurements of novel absorbers comprised of either liquid-cooled silicon carbide or vitreous carbon foams. The measurements demonstrate damage thresholds up to 1.6 x 104 W/cm(2) at an incident circular spot size of 2 mm with an absorbance of 96% at 1.064 mu m. We present a summary of the damage threshold as a function of the water flow velocity and the absorbance measurements. We also present a qualitative description of a damage mechanism based on a two-phase heat transfer between the foam and the flowing water. (c) 2007 Optical Society of America.
High-performance carbon nanotube coatings for high-power laser radiometry
Ramadurai, Krishna; Cromer, Christopher L.; Lewis, Laurence A.; Hurst, Katherine E.; Dillon, Anne C.; Mahajan, Roop L.; Lehman, John H. (American Institute of Physics, 2008-01-01)
Radiometry for the next generation of high-efficiency, high-power industrial lasers requires thermal management at optical power levels exceeding 10 kW. Laser damage and thermal transport present fundamental challenges for laser radiometry in support of common manufacturing processes, such as welding, cutting, ablation, or vaporization. To address this growing need for radiometry at extremely high power densities, we demonstrate multiwalled carbon nanotube (MWCNT) coatings with damage thresholds exceeding 15 000 W/cm(2) and absorption efficiencies over 90% at 1.06 mu m. This result demonstrates specific design advantages not possible with other contemporary high-power laser coatings. Furthermore, the results demonstrate a performance difference between MWCNTs and single-walled carbon nanotube coatings, which is attributed to the lower net thermal resistance of the MWCNT coatings. We explore the behavior of carbon nanotubes at two laser wavelengths (1.06 and 10.6 mu m) and also evaluate the optical-absorption efficiency and bulk properties of the coatings. (c) 2008 American Institute of Physics.
Nanodispersed DO(3)-phase nanostructures observed in magnetostrictive Fe-19% Ga Galfenol alloys
Bhattacharyya, Somnath; Jinschek, J. R.; Khachaturyan, Armen G.; Cao, Hu; Li, Jiefang; Viehland, Dwight D. (American Physical Society, 2008-03-10)
Few nanometer large (<2 nm) inclusions of DO(3)-phase structure have been identified in the A2 matrix of highly magnetostrictive Fe-19% Ga alloys by high-resolution transmission electron microscopy (HRTEM). In addition, we have found that these nanostructures include a high density of {100} line defects with a Burgers vector of a(bcc)/2 < 100 >. This dispersion of DO(3)-phase nanostructures formed within the main A2 matrix and the lifting of their coherency by defects are consistent with a recent theory for the structure and properties of magnetostrictive Fe-Ga and Fe-Al alloys.
Antibacterial efficacy of core-shell nanostructures encapsulating gentamicin against an in vivo intracellular Salmonella model
Ranjan, Ashish; Pothayee, Nikorn; Seleem, Mohamed N.; Tyler, Ronald D.; Brenseke, Bonnie; Sriranganathan, Nammalwar; Riffle, Judy S.; Kasimanickam, Ramanathan K. (Dove Medical Press, 2009-01-01)
Pluronic based core-shell nanostructures encapsulating gentamicin were designed in this study. Block copolymers of (PAA(+/-)Na-b-(PEO-b-PPO-b-PEO)-b-PAA(+/-)Na) were blended with PAA(-) Na(+) and complexed with the polycationic antibiotic gentamicin to form nanostructures. Synthesized nanostructures had a hydrodynamic diameter of 210 nm, zeta potentials of -0.7 (+/-0.2), and incorporated approximately 20% by weight of gentamicin. Nanostructures upon co-incubation with J774A.1 macrophage cells showed no adverse toxicity in vitro. Nanostructures administered in vivo either at multiple dosage of 5 microg g(-1) or single dosage of 15 microg g(-1) in AJ-646 mice infected with Salmonella resulted in significant reduction of viable bacteria in the liver and spleen. Histopathological evaluation for concentration-dependent toxicity at a dosage of 15 microg g(-1) revealed mineralized deposits in 50% kidney tissues of free gentamicin-treated mice which in contrast was absent in nanostructure-treated mice. Thus, encapsulation of gentamicin in nanostructures may reduce toxicity and improve in vivo bacterial clearance.
Large piezoresistivity phenomenon in SiCN-(La,Sr)MnO3 composites
Karmarkar, Makarand; Singh, Gurpreet; Shah, Sandeep; Mahajan, Roop L.; Priya, Shashank (AIP Publishing, 2009-02-01)
We present the results on SiCN-(La,Sr)MnO3 (LSMO) composites correlating the observed large piezoresistance behavior with the microstructural features and defect chemistry. Scanning electron microscopy characterization revealed the presence of self-assembled periodic microvalleys in the microstructure with width of 1-5 mu m and depth of 600-1000 nm. The microvalleys act as stress concentration points providing change in volume with applied stress. High resolution transmission electron microscopy measurements conducted on composites showed that LSMO grains consist of SiCN phase but no inclusions were observed.
Thermal transport in composites of self-assembled nickel nanoparticles embedded in yttria stabilized zirconia
Shukla, Nitin C.; Liao, Hao-Hsiang; Abiade, Jeremiah T.; Murayama, Mitsuhiro; Kumar, Dhananjay; Huxtable, Scott T. (AIP Publishing, 2009-04-01)
We investigate the effect of nickel nanoparticle size on thermal transport in multilayer nanocomposites consisting of alternating layers of nickel nanoparticles and yttria stabilized zirconia (YSZ) spacer layers that are grown with pulsed laser deposition. Using time-domain thermoreflectance, we measure thermal conductivities of k=1.8, 2.4, 2.3, and 3.0 W m(-1) K(-1) for nanocomposites with nickel nanoparticle diameters of 7, 21, 24, and 38 nm, respectively, and k=2.5 W m(-1) K(-1) for a single 80 nm thick layer of YSZ. We use an effective medium theory to estimate the lower limits for interface thermal conductance G between the nickel nanoparticles and the YSZ matrix (G>170 MW m(-2) K(-1)), and nickel nanoparticle thermal conductivity.
Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration
Wang, Yiran; Zhang, Y. H. Percival (2009-06-04)
Background Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes. Results An open reading frame TM0438 from a hyperthermophilic bacterium Thermotoga maritima putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in E. coli. The purified protein was confirmed to have 6PGDH activity with a molecular mass of 53 kDa. The kcat of this enzyme was 325 s-1 and the Km values for 6-phosphogluconate, NADP+, and NAD+ were 11, 10 and 380 μM, respectively, at 80°C. This enzyme had half-life times of 48 and 140 h at 90 and 80°C, respectively. Through numerous approaches including expression vectors, hosts, cultivation conditions, inducers, and codon-optimization of the 6pgdh gene, the soluble 6PGDH expression levels were enhanced to ~250 mg per liter of culture by more than 500-fold. The recombinant 6PGDH accounted for >30% of total E. coli cellular proteins when lactose was used as a low-cost inducer. In addition, this enzyme coupled with glucose-6-phosphate dehydrogenase for the first time was demonstrated to generate two moles of NADPH per mole of glucose-6-phosphate. Conclusion We have achieved a more than 500-fold improvement in the expression of soluble T. maritima 6PGDH in E. coli, characterized its basic biochemical properties, and demonstrated its applicability for NADPH regeneration by a new enzyme cocktail. The methodology for over-expression and simple purification of this thermostable protein would be useful for the production of other thermostable proteins in E. coli.
Cell-free protein synthesis energized by slowly-metabolized maltodextrin
Wang, Yiran; Zhang, Y. H. Percival (2009-06-28)
Background Cell-free protein synthesis (CFPS) is a rapid and high throughput technology for obtaining proteins from their genes. The primary energy source ATP is regenerated from the secondary energy source through substrate phosphorylation in CFPS. Results Distinct from common secondary energy sources (e.g., phosphoenolpyruvate - PEP, glucose-6-phosphate), maltodextrin was used for energizing CFPS through substrate phosphorylation and the glycolytic pathway because (i) maltodextrin can be slowly catabolized by maltodextrin phosphorylase for continuous ATP regeneration, (ii) maltodextrin phosphorylation can recycle one phosphate per reaction for glucose-1-phosphate generation, and (iii) the maltodextrin chain-shortening reaction can produce one ATP per glucose equivalent more than glucose can. Three model proteins, esterase 2 from Alicyclobacillus acidocaldarius, green fluorescent protein, and xylose reductase from Neurospora crassa were synthesized for demonstration. Conclusion Slowly-metabolized maltodextrin as a low-cost secondary energy compound for CFPS produced higher levels of proteins than PEP, glucose, and glucose-6-phospahte. The enhancement of protein synthesis was largely attributed to better-controlled phosphate levels (recycling of inorganic phosphate) and a more homeostatic reaction environment.
Frequency-dependent stability of parallel-plate electrostatic actuators in conductive fluids
Sounart, T. L.; Panchawagh, H. V.; Mahajan, R. L. (AIP Publishing, 2010-05)
We present an electromechanical stability analysis of passivated parallel-plate electrostatic actuators in conductive dielectric media and show that the pull-in instability can be eliminated by tuning the applied frequency below a design-dependent stability limit. A partial instability region is also obtained, where the actuator jumps from the pull-in displacement to another stable position within the gap. The results predict that the stability limit is always greater than the critical actuation frequency, and therefore any device that is feasible to actuate in a conductive fluid can be operated with stability over the full range of motion. (C) 2010 American Institute of Physics. [doi:10.1063/1.3389491]
Renewable Hydrogen Carrier — Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy
Zhang, Y. H. Percival; Mielenz, Jonathan R. (MDPI, 2011-01-31)
The hydrogen economy presents an appealing energy future but its implementation must solve numerous problems ranging from low-cost sustainable production, high-density storage, costly infrastructure, to eliminating safety concern. The use of renewable carbohydrate as a high-density hydrogen carrier and energy source for hydrogen production is possible due to emerging cell-free synthetic biology technology—cell-free synthetic pathway biotransformation (SyPaB). Assembly of numerous enzymes and co-enzymes in vitro can create complicated set of biological reactions or pathways that microorganisms or catalysts cannot complete, for example, C₆H₁₀O₅ (aq) + 7 H₂O (l) à 12 H₂ (g) + 6 CO₂ (g) (PLoS One 2007, 2:e456). Thanks to 100% selectivity of enzymes, modest reaction conditions, and high-purity of generated hydrogen, carbohydrate is a promising hydrogen carrier for end users. Gravimetric density of carbohydrate is 14.8 H₂ mass% if water can be recycled from proton exchange membrane fuel cells or 8.33% H₂ mass% without water recycling. Renewable carbohydrate can be isolated from plant biomass or would be produced from a combination of solar electricity/hydrogen and carbon dioxide fixation mediated by high-efficiency artificial photosynthesis mediated by SyPaB. The construction of this carbon-neutral carbohydrate economy would address numerous sustainability challenges, such as electricity and hydrogen storage, CO₂ fixation and long-term storage, water conservation, transportation fuel production, plus feed and food production.
Network-based functional enrichment
Poirel, Christopher L.; Owens, Clifford C. III; Murali, T. M. (2011-11-30)
Background Many methods have been developed to infer and reason about molecular interaction networks. These approaches often yield networks with hundreds or thousands of nodes and up to an order of magnitude more edges. It is often desirable to summarize the biological information in such networks. A very common approach is to use gene function enrichment analysis for this task. A major drawback of this method is that it ignores information about the edges in the network being analyzed, i.e., it treats the network simply as a set of genes. In this paper, we introduce a novel method for functional enrichment that explicitly takes network interactions into account. Results Our approach naturally generalizes Fisher’s exact test, a gene set-based technique. Given a function of interest, we compute the subgraph of the network induced by genes annotated to this function. We use the sequence of sizes of the connected components of this sub-network to estimate its connectivity. We estimate the statistical significance of the connectivity empirically by a permutation test. We present three applications of our method: i) determine which functions are enriched in a given network, ii) given a network and an interesting sub-network of genes within that network, determine which functions are enriched in the sub-network, and iii) given two networks, determine the functions for which the connectivity improves when we merge the second network into the first. Through these applications, we show that our approach is a natural alternative to network clustering algorithms. Conclusions We presented a novel approach to functional enrichment that takes into account the pairwise relationships among genes annotated by a particular function. Each of the three applications discovers highly relevant functions. We used our methods to study biological data from three different organisms. Our results demonstrate the wide applicability of our methods. Our algorithms are implemented in C++ and are freely available under the GNU General Public License at our supplementary website. Additionally, all our input data and results are available at http://bioinformatics.cs.vt.edu/~murali/supplements/2011-incob-nbe/.
Role of coexisting tetragonal regions in the rhombohedral phase of Na0.5Bi0.5TiO3-xat.%BaTiO3 crystals on enhanced piezoelectric properties on approaching the morphotropic phase boundary
Yao, Jianjun; Monsegue, Niven; Murayama, Mitsuhiro; Leng, W. N.; Reynolds, William T. Jr.; Zhang, Qinhui; Luo, Haosu; Li, Jiefang; Ge, Wenwei; Viehland, Dwight D. (AIP Publishing, 2012-01-01)
The ferroelectric domain and local structures of Na0.5Bi0.5TiO3-xat.%BaTiO3 (NBT-x%BT) crystals for x = 0, 4.5, and 5.5 have been investigated by transmission electron microscopy. The results show that the size of polar nano-regions was refined with increasing xat. %BT. The tetragonal phase volume fraction, as identified by in-phase octahedral tilting, was found to be increased with BT. The findings indicate that the large electric field induced strains in morphotropic phase boundary compositions of NBT-x%BT originate not only from polarization rotation but also polarization extension. (C) 2012 American Institute of Physics. [doi: 10.1063/1.3673832]
Sensitive Detection of Pathway Perturbations in Cancers
Rivera, Corban G.; Tyler, Brett M.; Murali, T. M. (2012-03-21)
Background The normal functioning of a living cell is characterized by complex interaction networks involving many different types of molecules. Associations detected between diseases and perturbations in well-defined pathways within such interaction networks have the potential to illuminate the molecular mechanisms underlying disease progression and response to treatment. Results In this paper, we present a computational method that compares expression profiles of genes in cancer samples to samples from normal tissues in order to detect perturbations of pre-defined pathways in the cancer. In contrast to many previous methods, our scoring function approach explicitly takes into account the interactions between the gene products in a pathway. Moreover, we compute the sub-pathway that has the highest score, as opposed to merely computing the score for the entire pathway. We use a permutation test to assess the statistical significance of the most perturbed sub-pathway. We apply our method to 20 pathways in the Netpath database and to the Global Cancer Map of gene expression in 18 cancers. We demonstrate that our method yields more sensitive results than alternatives that do not consider interactions or measure the perturbation of a pathway as a whole. We perform a sensitivity analysis to show that our approach is robust to modest changes in the input data. Our method confirms numerous well-known connections between pathways and cancers. Conclusions Our results indicate that integrating differential gene expression with the interaction structure in a pathway is a powerful approach for detecting links between a cancer and the pathways perturbed in it. Our results also suggest that even well-studied pathways may be perturbed only partially in any given cancer. Further analysis of cancer-specific sub-pathways may shed new light on the similarities and differences between cancers.
Dielectrophoretic differentiation of mouse ovarian surface epithelial cells, macrophages, and fibroblasts using contactless dielectrophoresis
Salmanzadeh, Alireza; Kittur, Harsha; Sano, Michael B.; Roberts, Paul C.; Schmelz, Eva M.; Davalos, Rafael V. (American Institute of Physics, 2012-06-01)
Ovarian cancer is the leading cause of death from gynecological malignancies in women. The primary challenge is the detection of the cancer at an early stage, since this drastically increases the survival rate. In this study we investigated the dielectrophoretic responses of progressive stages of mouse ovarian surface epithelial (MOSE) cells, as well as mouse fibroblast and macrophage cell lines, utilizing contactless dielectrophoresis (cDEP). cDEP is a relatively new cell manipulation technique that has addressed some of the challenges of conventional dielectrophoretic methods. To evaluate our microfluidic device performance, we computationally studied the effects of altering various geometrical parameters, such as the size and arrangement of insulating structures, on dielectrophoretic and drag forces. We found that the trapping voltage of MOSE cells increases as the cells progress from a non-tumorigenic, benign cell to a tumorigenic, malignant phenotype. Additionally, all MOSE cells display unique behavior compared to fibroblasts and macrophages, representing normal and inflammatory cells found in the peritoneal fluid. Based on these findings, we predict that cDEP can be utilized for isolation of ovarian cancer cells from peritoneal fluid as an early cancer detection tool. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3699973] Actual pdf downloaded from NCBI.
Membranes in Lithium Ion Batteries
Yang, Min; Hou, Junbo (MDPI, 2012-07-04)
Lithium ion batteries have proven themselves the main choice of power sources for portable electronics. Besides consumer electronics, lithium ion batteries are also growing in popularity for military, electric vehicle, and aerospace applications. The present review attempts to summarize the knowledge about some selected membranes in lithium ion batteries. Based on the type of electrolyte used, literature concerning ceramic-glass and polymer solid ion conductors, microporous filter type separators and polymer gel based membranes is reviewed.
Towards the development of latent heat storage electrodes for electroporation-based therapies
Arena, Christopher B.; Mahajan, Roop L.; Rylander, M. Nichole; Davalos, Rafael V. (American Institute of Physics, 2012-08-22)
Phase change materials (PCMs) capable of storing a large amount of heat upon transitioning from the solid-to-liquid state have been widely used in the electronics and construction industries for mitigating temperature development. Here, we show that they are also beneficial for reducing the peak tissue temperature during electroporation-based therapies. A numerical model is developed of irreversible electroporation (IRE) performed with hollow needle electrodes filled with a PCM. Results indicate that this electrode design can be utilized to achieve large ablation volumes while reducing the probability for thermal damage.
Three-Dimensional Characterization of Iron Oxide (alpha-Fe2O3) Nanoparticles: Application of a Compressed Sensing Inspired Reconstruction Algorithm to Electron Tomography
Monsegue, N.; Jin, X.; Echigo, T.; Wang, G.; Murayama, Mitsuhiro (Cambridge University Press, 2012-12)
In this article, we demonstrate the application of a new compressed sensing three-dimensional reconstruction algorithm for electron tomography that increases the accuracy of morphological characterization of nanostructured materials such as nanocrystalline iron oxide particles. A powerful feature of the algorithm is an anisotropic total variation norm for the L1 minimization during algebraic reconstruction that effectively reduces the elongation artifacts caused by limited angle sampling during electron tomography. The algorithm provides faithful morphologies that have not been feasible with existing techniques.
Sequence verification of synthetic DNA by assembly of sequencing reads
Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, Joao C.; Tyler, Brett M.; Peccoud, Jean (2013-01)
Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.
Investigating dielectric properties of different stages of syngeneic murine ovarian cancer cells
Salmanzadeh, Alireza; Sano, Michael B.; Gallo-Villanueva, R. C.; Roberts, Paul C.; Schmelz, Eva M.; Davalos, Rafael V. (American Institute of Physics, 2013-01-01)
In this study, the electrical properties of four different stages of mouse ovarian surface epithelial (MOSE) cells were investigated using contactless dielectrophoresis (cDEP). This study expands the work from our previous report describing for the first time the crossover frequency and cell specific membrane capacitance of different stages of cancer cells that are derived from the same cell line. The specific membrane capacitance increased as the stage of malignancy advanced from 15.39 +/- 1.54 mF m(-2) for a non-malignant benign stage to 26.42 +/- 1.22 mF m(-2) for the most aggressive stage. These differences could be the result of morphological variations due to changes in the cytoskeleton structure, specifically the decrease of the level of actin filaments in the cytoskeleton structure of the transformed MOSE cells. Studying the electrical properties of MOSE cells provides important information as a first step to develop cancer-treatment techniques which could partially reverse the cytoskeleton disorganization of malignant cells to a morphology more similar to that of benign cells. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4788921] Actual pdf downloaded from NCBI.

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