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1.  Nanopore sculpting with noble gas ions 
Journal of applied physics  2006;100(2):024914-024914-6.
We demonstrate that 3 keV ion beams, formed from the common noble gasses, He, Ne, Ar, Kr, and Xe, can controllably “sculpt” nanometer scale pores in silicon nitride films. Single nanometer control of structural dimensions in nanopores can be achieved with all ion species despite a very wide range of sputtering yields and surface energy depositions. Heavy ions shrink pores more efficiently and make thinner pores than lighter ions. The dynamics of nanopore closing is reported for each ion species and the results are fitted to an adatom diffusion model with excellent success. We also present an experimental method for profiling the thickness of the local membrane around the nanopore based on low temperature sputtering and data is presented that provides quantitative measurements of the thickness and its dependence on ion beam species.
doi:10.1063/1.2216880
PMCID: PMC3039599  PMID: 21331305
2.  Surface Morphology Evolution of GaAs by Low Energy Ion Sputtering 
Nanoscale Research Letters  2007;2(10):504-508.
Low energy Ar+ion sputtering, typically below 1,200 eV, of GaAs at normal beam incident angle is investigated. Surface morphology development with respect to varying energy is analyzed and discussed. Dot-like patterns in the nanometer scale are obtained above 600 eV. As the energy approaches upper eV range regular dots have evolved. The energy dependent dot evolution is evaluated based on solutions of the isotropic Kuramoto-Sivashinsky equation. The results are in agreement with the theoretical model which describes a power law dependency of the characteristic wavelength on ion energy in the ion-induced diffusion regime.
doi:10.1007/s11671-007-9090-4
PMCID: PMC3246606
Low energy; Ion sputtering; Surface morphology; GaAs quantum dot
3.  Radioactivity and lung cancer-mathematical models of radionuclide deposition in the human lungs 
Journal of Thoracic Disease  2011;3(4):231-243.
The human respiratory tract is regarded as pathway for radionuclides and other hazardous airborne materials to enter the body. Radioactive particles inhaled and deposited in the lungs cause an irradiation of bronchial/alveolar tissues. At the worst, this results in a malignant cellular transformation and, as a consequence of that, the development of lung cancer. In general, naturally occurring radionuclides (e.g., 222Rn, 40K) are attached to so-called carrier aerosols. The aerodynamic diameters of such radioactively labeled particles generally vary between several nanometers (ultrafine particles) and few micrometers, whereby highest particle fractions adopt sizes around 100 nm. Theoretical simulations of radioactive particle deposition in the human lungs were based on a stochastic lung geometry and a particle transport/deposition model using the random-walk algorithm. Further a polydisperse carrier aerosol (diameter: 1 nm–10 µm, ρ ≈ 1 g cm−3) with irregularly shaped particles and the effect of breathing characteristics and certain respiratory parameters on the transport of radioactive particles to bronchial/alveolar tissues were considered. As clearly shown by the results of deposition modeling, distribution patterns of radiation doses mainly depend on the size of the carrier aerosol. Ultrafine (< 10 nm) and large (> 2 µm) aerosol particles are preferentially deposited in the extrathoracic and upper bronchial region, whereas aerosol particles with intermediate size (10 nm–2 µm) may penetrate to deeper lung regions, causing an enhanced damage of the alveolar tissue by the attached radionuclides.
doi:10.3978/j.issn.2072-1439.2011.04.01
PMCID: PMC3256534  PMID: 22263097
Radionuclides; Carrier aerosol; Monte Carlo model; Stochastic lung geometry
4.  Differences in Phosphorylated Histone H2AX Foci Formation and Removal of Cells Exposed to Low and High Linear Energy Transfer Radiation 
Current Genomics  2012;13(6):418-425.
The use of particle ion beams in cancer radiotherapy has a long history. Today, beams of protons or heavy ions, predominantly carbon ions, can be accelerated to precisely calculated energies which can be accurately targeted to tumors. This particle therapy works by damaging the DNA of tissue cells, ultimately causing their death. Among the different types of DNA lesions, the formation of DNA double strand breaks is considered to be the most relevant of deleterious damages of ionizing radiation in cells. It is well-known that the extremely large localized energy deposition can lead to complex types of DNA double strand breaks. These effects can lead to cell death, mutations, genomic instability, or carcinogenesis. Complex double strand breaks can increase the probability of mis-rejoining by NHEJ. As a consequence differences in the repair kinetics following high and low LET irradiation qualities are attributed mainly to quantitative differences in their contributions of the fast and slow repair component. In general, there is a higher contribution of the slow component of DNA double strand repair after exposure to high LET radiation, which is thought to reflect the increased amount of complex DNA double strand breaks. These can be accurately measured by the γ-H2AX assay, because the number of phosphorylated H2AX foci correlates well with the number of double strand breaks induced by low or / and high LET radiation.
doi:10.2174/138920212802510501
PMCID: PMC3426775  PMID: 23450137
DNA double strand breaks; Linear energy transfer; Radiation; γ-H2AX foci.
5.  Field Emission and Radial Distribution Function Studies of Fractal-like Amorphous Carbon Nanotips 
Nanoscale Research Letters  2009;4(5):431-436.
The short-range order of individual fractal-like amorphous carbon nanotips was investigated by means of energy-filtered electron diffraction in a transmission electron microscope (TEM). The nanostructures were grown in porous silicon substrates in situ within the TEM by the electron beam-induced deposition method. The structure factor S(k) and the reduced radial distribution function G(r) were calculated. From these calculations a bond angle of 124° was obtained which suggests a distorted graphitic structure. Field emission was obtained from individual nanostructures using two micromanipulators with sub-nanometer positioning resolution. A theoretical three-stage model that accounts for the geometry of the nanostructures provides a value for the field enhancement factor close to the one obtained experimentally from the Fowler-Nordheim law.
doi:10.1007/s11671-009-9270-5
PMCID: PMC2894329  PMID: 20596340
Carbon nanotips; Graphite-like a-C; EELS; EFED; Field emission
6.  Field Emission and Radial Distribution Function Studies of Fractal-like Amorphous Carbon Nanotips 
Nanoscale Research Letters  2009;4(5):431-436.
The short-range order of individual fractal-like amorphous carbon nanotips was investigated by means of energy-filtered electron diffraction in a transmission electron microscope (TEM). The nanostructures were grown in porous silicon substrates in situ within the TEM by the electron beam-induced deposition method. The structure factorS(k) and the reduced radial distribution functionG(r) were calculated. From these calculations a bond angle of 124° was obtained which suggests a distorted graphitic structure. Field emission was obtained from individual nanostructures using two micromanipulators with sub-nanometer positioning resolution. A theoretical three-stage model that accounts for the geometry of the nanostructures provides a value for the field enhancement factor close to the one obtained experimentally from the Fowler-Nordheim law.
doi:10.1007/s11671-009-9270-5
PMCID: PMC2894329  PMID: 20596340
Carbon nanotips; Graphite-like a-C; EELS; EFED; Field emission
7.  Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana 
BMC Plant Biology  2011;11:161.
Background
Heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. Heavy-ion beams show high linear energy transfer (LET) and thus more effectively induce DNA double-strand breaks than other mutagenic techniques. Previously, we determined the most effective heavy-ion LET (LETmax: 30.0 keV μm-1) for Arabidopsis mutagenesis by analysing the effect of LET on mutation induction. However, the molecular structure of mutated DNA induced by heavy ions with LETmax remains unclear. Knowledge of the structure of mutated DNA will contribute to the effective exploitation of heavy-ion beam mutagenesis.
Results
Dry Arabidopsis thaliana seeds were irradiated with carbon (C) ions with LETmax at a dose of 400 Gy and with LET of 22.5 keV μm-1 at doses of 250 Gy or 450 Gy. The effects on mutation frequency and alteration of DNA structure were compared. To characterise the structure of mutated DNA, we screened the well-characterised mutants elongated hypocotyls (hy) and glabrous (gl) and identified mutated DNA among the resulting mutants by high-resolution melting curve, PCR and sequencing analyses. The mutation frequency induced by C ions with LETmax was two-fold higher than that with 22.5 keV μm-1 and similar to the mutation frequency previously induced by ethyl methane sulfonate. We identified the structure of 22 mutated DNAs. Over 80% of the mutations caused by C ions with both LETs were base substitutions or deletions/insertions of less than 100 bp. The other mutations involved large rearrangements.
Conclusions
The C ions with LETmax showed high mutation efficiency and predominantly induced base substitutions or small deletions/insertions, most of which were null mutations. These small alterations can be determined by single-nucleotide polymorphism (SNP) detection systems. Therefore, C ions with LETmax might be useful as a highly efficient reverse genetic system in conjunction with SNP detection systems, and will be beneficial for forward genetics and plant breeding.
doi:10.1186/1471-2229-11-161
PMCID: PMC3261129  PMID: 22085561
8.  Drying nano particles solution on an oscillating tip at an air liquid interface: what we can learn, what we can do 
Nanoscale Research Letters  2007;2(7):309-318.
Evaporation of fluid at micro and nanometer scale may be used to self-assemble nanometre-sized particles in suspension. Evaporating process can be used to gently control flow in micro and nanofluidics, thus providing a potential mean to design a fine pattern onto a surface or to functionalize a nanoprobe tip. In this paper, we present an original experimental approach to explore this open and rather virgin domain. We use an oscillating tip at an air liquid interface with a controlled dipping depth of the tip within the range of the micrometer. Also, very small dipping depths of a few ten nanometers were achieved with multi walls carbon nanotubes glued at the tip apex. The liquid is an aqueous solution of functionalized nanoparticles diluted in water. Evaporation of water is the driving force determining the arrangement of nanoparticles on the tip. The results show various nanoparticles deposition patterns, from which the deposits can be classified in two categories. The type of deposit is shown to be strongly dependent on whether or not the triple line is pinned and of the peptide coating of the gold nanoparticle. In order to assess the classification, companion dynamical studies of nanomeniscus and related dissipation processes involved with thinning effects are presented.
doi:10.1007/s11671-007-9065-5
PMCID: PMC3246374
Nanofluidics; Nanoparticles; Micromeniscus; Nanomeniscus; Dynamical mode of atomic force microcopy
9.  Biological consequences of nanoscale energy deposition near irradiated heavy atom nanoparticles 
Scientific Reports  2011;1:18.
Gold nanoparticles (GNPs) are being proposed as contrast agents to enhance X-ray imaging and radiotherapy, seeking to take advantage of the increased X-ray absorption of gold compared to soft tissue. However, there is a great discrepancy between physically predicted increases in X-ray energy deposition and experimentally observed increases in cell killing. In this work, we present the first calculations which take into account the structure of energy deposition in the nanoscale vicinity of GNPs and relate this to biological outcomes, and show for the first time good agreement with experimentally observed cell killing by the combination of X-rays and GNPs. These results are not only relevant to radiotherapy, but also have implications for applications of heavy atom nanoparticles in biological settings or where human exposure is possible because the localised energy deposition high-lighted by these results may cause complex DNA damage, leading to mutation and carcinogenesis.
doi:10.1038/srep00018
PMCID: PMC3216506  PMID: 22355537
10.  The contribution of phosphate–phosphate repulsions to the free energy of DNA bending 
Nucleic Acids Research  2005;33(4):1257-1268.
DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate–phosphate repulsions. In the present work, the electrostatic contribution of phosphate–phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate–phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate–phosphate repulsions account for ∼30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
doi:10.1093/nar/gki272
PMCID: PMC552960  PMID: 15741179
11.  Protein-membrane interactions: Blood clotting on nanoscale bilayers 
Summary
The clotting cascade requires the assembly of protease-cofactor complexes on membranes with exposed anionic phospholipids. Despite their importance, protein-membrane interactions in clotting remain relatively poorly understood. Calcium ions are known to induce anionic phospholipids to cluster, and we propose that clotting proteins assemble preferentially on such anionic lipid-rich microdomains. Until recently, there was no way to control the partitioning of clotting proteins into or out of specific membrane microdomains, so experimenters only knew the average contributions of phospholipids to blood clotting. The development of nanoscale membrane bilayers (Nanodiscs) has now allowed us to probe, with nanometer resolution, how local variations in phospholipid composition regulate the activity of key protease-cofactor complexes in blood clotting. Furthermore, exciting new progress in solid-state NMR and large-scale molecular dynamics simulations are allowing structural insights into interactions between proteins and membrane surfaces with atomic resolution.
doi:10.1111/j.1538-7836.2009.03390.x
PMCID: PMC2839880  PMID: 19630793
membranes; phospholipids; microdomains; GLA-domains; cofactors
12.  Three-dimensional imaging of chemical phase transformations at the nanoscale with full-field transmission X-ray microscopy 
Journal of Synchrotron Radiation  2011;18(Pt 5):773-781.
Two-dimensional and three-dimensional single-pixel and single-voxel speciation of Ni in Li-ion battery electrodes is accomplished combining full-field hard X-ray transmission microscopy and XANES imaging at tens of nanometers resolution.
The ability to probe morphology and phase distribution in complex systems at multiple length scales unravels the interplay of nano- and micrometer-scale factors at the origin of macroscopic behavior. While different electron- and X-ray-based imaging techniques can be combined with spectroscopy at high resolutions, owing to experimental time limitations the resulting fields of view are too small to be representative of a composite sample. Here a new X-ray imaging set-up is proposed, combining full-field transmission X-ray microscopy (TXM) with X-ray absorption near-edge structure (XANES) spectroscopy to follow two-dimensional and three-dimensional morphological and chemical changes in large volumes at high resolution (tens of nanometers). TXM XANES imaging offers chemical speciation at the nanoscale in thick samples (>20 µm) with minimal preparation requirements. Further, its high throughput allows the analysis of large areas (up to millimeters) in minutes to a few hours. Proof of concept is provided using battery electrodes, although its versatility will lead to impact in a number of diverse research fields.
doi:10.1107/S0909049511019364
PMCID: PMC3161818  PMID: 21862859
X-ray microscopy; synchrotron X-ray imaging; Li-ion battery; XANES
13.  Male–male pheromone signalling in a lekking Drosophila 
Interest in sex pheromones has mainly been focused on mate finding, while relatively little attention has been given to the role of sex pheromones in mate choice and almost none to competition over mates. Here, we study male response to male pheromones in the lekking Drosophila grimshawi, where males deposit long-lasting pheromone streaks that attract males and females to the leks and influence mate assessment. We used two stocks of flies and both stocks adjusted their pheromone depositing behaviour in response to experimental manipulation, strongly indicating male ability to distinguish between competitors from qualitative differences in pheromone streaks alone. This is the first example of an insect distinguishing between individual odour signatures. Pheromone signalling influenced competition over mates, as males adjusted their investment in pheromone deposition in response to foreign pheromone streaks. Both sexes adapt their behaviour according to information from olfactory cues in D. grimshawi, but the relative benefits from male–female, as compared to male–male signalling, remain unknown. It seems likely that the pheromone signalling system originally evolved for attracting females to leks. The transition to a signalling system for conveying information about individuals may well, however, at least in part have been driven by benefits from male–male signalling.
doi:10.1098/rspb.2005.3379
PMCID: PMC1560072  PMID: 16608691
individual recognition; scent matching; male competition; mate choice; lekking
14.  Synthesis and Electrochemical Sensing Toward Heavy Metals of Bunch-like Bismuth Nanostructures 
Nanoscale Research Letters  2009;5(2):398-402.
Large-scale bunch-like bismuth (Bi) nanostructures were the first time to be synthesized via two-step electrochemical deposition. The growth mechanism of the nanostructures was discussed. Such a designed bunch-like Bi electrode has high sensitivity to detect the heavy metal ions due to its unique three-dimensional structures and strong ability of adsorbing the heavy metal ions. The bunch-like Bi electrode’s detection of heavy metals was statically performed using anodic stripping voltammetry (ASV). The detection in the Pb(II) concentration range of 2.5–50 μg/l was also performed. Based on the experimental results, this bunch-like Bi electrode can be considered as an interesting alternative to common mercury electrodes and bismuth film electrodes for possible use in electrochemical studies and electroanalytical applications.
doi:10.1007/s11671-009-9495-3
PMCID: PMC2894205  PMID: 20672072
Bismuth; Nanostructure; Electrochemical deposition
15.  Synthesis and Electrochemical Sensing Toward Heavy Metals of Bunch-like Bismuth Nanostructures 
Nanoscale Research Letters  2009;5(2):398-402.
Large-scale bunch-like bismuth (Bi) nanostructures were the first time to be synthesized via two-step electrochemical deposition. The growth mechanism of the nanostructures was discussed. Such a designed bunch-like Bi electrode has high sensitivity to detect the heavy metal ions due to its unique three-dimensional structures and strong ability of adsorbing the heavy metal ions. The bunch-like Bi electrode’s detection of heavy metals was statically performed using anodic stripping voltammetry (ASV). The detection in the Pb(II) concentration range of 2.5–50 μg/l was also performed. Based on the experimental results, this bunch-like Bi electrode can be considered as an interesting alternative to common mercury electrodes and bismuth film electrodes for possible use in electrochemical studies and electroanalytical applications.
doi:10.1007/s11671-009-9495-3
PMCID: PMC2894205  PMID: 20672072
Bismuth; Nanostructure; Electrochemical deposition
16.  Metal site occupancy and allosteric switching in bacterial metal sensor proteins 
All prokaryotes encode a panel of metal sensor or metalloregulatory proteins that govern the expression of genes that allows an organism to quickly adapt to toxicity or deprivation of both biologically essential transition metal ions, e.g., Zn, Cu, Fe, and heavy metal pollutants. As such, metal sensor proteins can be considered arbiters of intracellular transition metal bioavailability and thus potentially control the metallation state of the metalloproteins in the cell. Metal sensor proteins are specialized allosteric proteins that regulate transcription as a result direct binding of one or two cognate metal ions, to the exclusion of all others. In most cases, the binding of the cognate metal ion induces a structural change in a protein oligomer that either activates or inhibits operator DNA binding. A quantitative measure of the degree to which a particular metal drives metalloregulation of operator DNA-binding is the allosteric coupling free energy, ΔGc. In this review, we summarize recent work directed toward understanding metal occupancy and metal selectivity of these allosteric switches in selected families of metal sensor proteins and examine the structural origins of ΔGc in the functional context a thermodynamic “set-point” model of intracellular metal homeostasis.
doi:10.1016/j.abb.2011.11.021
PMCID: PMC3312040  PMID: 22178748
metalloregulation; metal sensor protein; transition metal ions; allosteric coupling free energy; protein-DNA interactions; linkage
17.  Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy 
Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On the end of the microscope's cantilever is a nano-scale probe, which traverses image areas ranging from nanometers to micrometers, measuring the elevation of macromolecules resting on the substrate surface at any given point. Electrostatic forces cause proteins, lipids, and nucleic acids to loosely attach to the substrate in random orientations and permit imaging. The generated data resemble a topographical map, where the macromolecules resolve as three-dimensional particles of discrete sizes (Figure 1) 1,2. Tapping mode AFM involves the repeated oscillation of the cantilever, which permits imaging of relatively soft biomaterials such as DNA and proteins. One of the notable benefits of AFM over other nanoscale microscopy techniques is its relative adaptability to visualize individual proteins and macromolecular complexes in aqueous buffers, including near-physiologic buffered conditions, in real-time, and without staining or coating the sample to be imaged.
The method presented here describes the imaging of DNA and an immunoadsorbed transcription factor (i.e. the glucocorticoid receptor, GR) in buffered solution (Figure 2). Immunoadsorbed proteins and protein complexes can be separated from the immunoadsorbing antibody-bead pellet by competition with the antibody epitope and then imaged (Figure 2A). This allows for biochemical manipulation of the biomolecules of interest prior to imaging. Once purified, DNA and proteins can be mixed and the resultant interacting complex can be imaged as well. Binding of DNA to mica requires a divalent cation 3,such as Ni2+ or Mg2+, which can be added to sample buffers yet maintain protein activity. Using a similar approach, AFM has been utilized to visualize individual enzymes, including RNA polymerase 4 and a repair enzyme 5, bound to individual DNA strands. These experiments provide significant insight into the protein-protein and DNA-protein biophysical interactions taking place at the molecular level. Imaging individual macromolecular particles with AFM can be useful for determining particle homogeneity and for identifying the physical arrangement of constituent components of the imaged particles. While the present method was developed for visualization of GR-chaperone protein complexes 1,2 and DNA strands to which the GR can bind, it can be applied broadly to imaging DNA and protein samples from a variety of sources.
doi:10.3791/3061
PMCID: PMC3196170  PMID: 21788938
18.  DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin 
Nucleic Acids Research  2011;39(15):6489-6499.
DNA double-strand breaks (DSBs) can induce chromosomal aberrations and carcinogenesis and their correct repair is crucial for genetic stability. The cellular response to DSBs depends on damage signaling including the phosphorylation of the histone H2AX (γH2AX). However, a lack of γH2AX formation in heterochromatin (HC) is generally observed after DNA damage induction. Here, we examine γH2AX and repair protein foci along linear ion tracks traversing heterochromatic regions in human or murine cells and find the DSBs and damage signal streaks bending around highly compacted DNA. Given the linear particle path, such bending indicates a relocation of damage from the initial induction site to the periphery of HC. Real-time imaging of the repair protein GFP-XRCC1 confirms fast recruitment to heterochromatic lesions inside murine chromocenters. Using single-ion microirradiation to induce localized DSBs directly within chromocenters, we demonstrate that H2AX is early phosphorylated within HC, but the damage site is subsequently expelled from the center to the periphery of chromocenters within ∼20 min. While this process can occur in the absence of ATM kinase, the repair of DSBs bordering HC requires the protein. Finally, we describe a local decondensation of HC at the sites of ion hits, potentially allowing for DSB movement via physical forces.
doi:10.1093/nar/gkr230
PMCID: PMC3159438  PMID: 21511815
19.  Biomolecular Transport through Hemofiltration Membranes 
A theoretical model for filtration of large solutes through a pore in the presence of transmembrane pressures, applied/induced electric fields, and dissimilar interactions at the pore entrance and exit is developed to characterize and predict the experimental performance of a hemofiltration membrane with nanometer scale pores designed for a proposed implantable Renal Assist Device (RAD). The model reveals that the sieving characteristics of the membrane can be improved by applying an external electric field, and ensuring a smaller ratio of the pore-feed and pore-permeate equilibrium partitioning coefficients when diffusion is present. The model is then customized to study the sieving characteristics for both charged and uncharged solutes in the slit-shaped nanopores of the hemofiltration device for the RAD. The effect of streaming potential or induced fields are found to be negligible under representative operating conditions. Experimental data on the sieving coefficient of bovine serum albumin, carbonic anhydrase and thyroglobulin are reported and compared with the theoretical predictions. Both steric and electrostatic partitioning are considered and the comparison suggests that in general electrostatic effects are present in the filtration of proteins though some data, particularly those recorded in a strongly hypertonic solution (10×PBS), show better agreement with the steric partitioning theory.
doi:10.1007/s10439-009-9642-0
PMCID: PMC2818807  PMID: 19184436
hemofiltration; synthetic nanopore membrane; renal replacement therapy; sieving coefficient; kidney
20.  Biological Cluster Mass Spectrometry 
This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C60, exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining the molecular specificity of mass spectrometry. When the beams are microfocused to a spot on the sample, bioimaging experiments in two and three dimensions are feasible. We describe emerging theoretical models that allow the energy-deposition process to be understood on an atomic and molecular basis. Moreover, experiments on model systems are described that allow protocols for imaging on biological materials to be implemented. Finally, we present recent applications of imaging to biological tissue and single cells to illustrate the future directions of this methodology.
doi:10.1146/annurev.physchem.040808.090249
PMCID: PMC2859288  PMID: 20055679
secondary ion mass spectrometry; bioimaging; molecular depth profiling; three-dimensional molecular imaging; C60; molecular dynamics
21.  Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures 
Nucleic Acids Research  2011;40(7):2862-2868.
DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221–229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.
doi:10.1093/nar/gkr1173
PMCID: PMC3326316  PMID: 22156372
22.  DNA–DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density 
Physical review letters  2010;105(15):158101.
DNA-DNA interactions are important for the assembly of DNA nanostructures and during biological processes such as genome compaction and transcription regulation. In studies of these complex processes, DNA is commonly modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40% of the nominal charge density. These findings were directly supported by atomic-scale molecular dynamics simulations that determined the effective force between two DNA molecules. Our new parameterization has direct impact on many physical models involving DNA-DNA interactions.
PMCID: PMC3170404  PMID: 21230940
DNA; self-assembly; electrostatics; single-molecule; molecular dynamics; super-coiling
23.  Simple Fabrication of Gold Nanobelts and Patterns 
PLoS ONE  2012;7(1):e30469.
Gold nanobelts are of interest in several areas; however, there are only few methods available to produce these belts. We report here on a simple evaporation induced self-assembly (EISA) method to produce porous gold nanobelts with dimensions that scale across nanometer (thickness ∼80 nm) and micrometer (width ∼20 µm), to decimeter (length ∼0.15 m). The gold nanobelts are well packed on the beaker wall and can be easily made to float on the surface of the solution for depositing onto other substrates. Microscopy showed that gold nanobelts had a different structure on the two sides of the belt; the density of gold nanowires on one side was greater than on the other side. Electrical measurements showed that these nanobelts were sensitive to compressive or tensile forces, indicating a potential use as a strain sensor. The patterned nanobelts were further used as a template to grow ZnO nanowires for potential use in applications such as piezo-electronics.
doi:10.1371/journal.pone.0030469
PMCID: PMC3264570  PMID: 22291962
24.  Neurocytotoxic effects of iron-ions on the developing brain measured in vivo using medaka (Oryzias latipes), a vertebrate model 
Purpose: Exposure to heavy-ion radiation is considered a critical health risk on long-term space missions. The developing central nervous system (CNS) is a highly radiosensitive tissue; however, the biological effects of heavy-ion radiation, which are greater than those of low-linear energy transfer (LET) radiation, are not well studied, especially in vivo in intact organisms. Here, we examined the effects of iron-ions on the developing CNS using vertebrate organism, fish embryos of medaka (Oryzias latipes).
Materials and methods: Medaka embryos at developmental stage 28 were irradiated with iron-ions at various doses of 0-1.5 Gy. At 24 h after irradiation, radiation-induced apoptosis was examined using an acridine orange (AO) assay and histo-logically. To estimate the relative biological effectiveness (RBE), we quantified only characteristic AO-stained rosette-shaped apoptosis in the developing optic tectum (OT). At the time of hatching, morphological abnormalities in the irradiated brain were examined histologically.
Results: The dose-response curve utilizing an apoptotic index for the iron-ion irradiated embryos was much steeper than that for X-ray irradiated embryos, with RBE values of 3.7-4.2. Histological examinations of irradiated medaka brain at 24 h after irradiation showed AO-positive rosette-shaped clusters as aggregates of condensed nuclei, exhibiting a circular hole, mainly in the marginal area of the OT and in the retina. However, all of the irradiated embryos hatched normally without apparent histological abnormalities in their brains.
Conclusion: Our present study indicates that the medaka embryo is a useful model for evaluating neurocytotoxic effects on the developing CNS induced by exposure to heavy iron-ions relevant to the aerospace radiation environment.
doi:10.3109/09553002.2011.584944
PMCID: PMC3169016  PMID: 21770703
High-LET radiation; apoptosis; embryonic brain; medaka; relative biological effectiveness (RBE)
25.  Transverse acoustic trapping using a Gaussian focused ultrasound 
The optical tweezer has become a popular device to manipulate particles in nanometer scales, and to study the underlying principles of many cellular or molecular interactions. Theoretical analysis was previously carried out at the authors’ laboratory, to show that similar acoustic trapping of microparticles may be possible with a single beam ultrasound. This paper experimentally presents the transverse trapping of 125 μm lipid droplets under an acoustically transparent mylar film, which is an intermediate step toward achieving acoustic tweezers in 3D. Despite the lack of axial trapping capability in the current experimental arrangement, it was found that a 30 MHz focused beam could be used to laterally direct the droplets towards the focus. The spatial range within which acoustic traps may guide droplet motion was in the range of hundreds of micrometers, much greater than that of optical traps. This suggests that this acoustic device may offer an alternative for manipulating microparticles in a wider spatial range.
doi:10.1016/j.ultrasmedbio.2009.10.005
PMCID: PMC2815109  PMID: 20045590
optical tweezer; scattering force; gradient force; acoustic trapping; transverse force; maximum displacement

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