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Sample records for probing cellular dynamics

  1. Probing Cellular Mechanoadaptation Using Cell-Substrate De-Adhesion Dynamics: Experiments and Model

    PubMed Central

    S S, Soumya; Sthanam, Lakshmi Kavitha; Padinhateeri, Ranjith; Inamdar, Mandar M.; Sen, Shamik

    2014-01-01

    Physical properties of the extracellular matrix (ECM) are known to regulate cellular processes ranging from spreading to differentiation, with alterations in cell phenotype closely associated with changes in physical properties of cells themselves. When plated on substrates of varying stiffness, fibroblasts have been shown to exhibit stiffness matching property, wherein cell cortical stiffness increases in proportion to substrate stiffness up to 5 kPa, and subsequently saturates. Similar mechanoadaptation responses have also been observed in other cell types. Trypsin de-adhesion represents a simple experimental framework for probing the contractile mechanics of adherent cells, with de-adhesion timescales shown to scale inversely with cortical stiffness values. In this study, we combine experiments and computation in deciphering the influence of substrate properties in regulating de-adhesion dynamics of adherent cells. We first show that NIH 3T3 fibroblasts cultured on collagen-coated polyacrylamide hydrogels de-adhere faster on stiffer substrates. Using a simple computational model, we qualitatively show how substrate stiffness and cell-substrate bond breakage rate collectively influence de-adhesion timescales, and also obtain analytical expressions of de-adhesion timescales in certain regimes of the parameter space. Finally, by comparing stiffness-dependent experimental and computational de-adhesion responses, we show that faster de-adhesion on stiffer substrates arises due to force-dependent breakage of cell-matrix adhesions. In addition to illustrating the utility of employing trypsin de-adhesion as a biophysical tool for probing mechanoadaptation, our computational results highlight the collective interplay of substrate properties and bond breakage rate in setting de-adhesion timescales. PMID:25197799

  2. Probing cellular behaviors through nanopatterned chitosan membranes

    NASA Astrophysics Data System (ADS)

    Yang, Chung-Yao; Sung, Chun-Yen; Shuai, Hung-Hsun; Cheng, Chao-Min; Yeh, Andrew

    2013-08-01

    This paper describes a high-throughput method for developing physically modified chitosan membranes to probe the cellular behavior of MDCK epithelial cells and HIG-82 fibroblasts adhered onto these modified membranes. To prepare chitosan membranes with micro/nanoscaled features, we have demonstrated an easy-to-handle, facile approach that could be easily integrated with IC-based manufacturing processes with mass production potential. These physically modified chitosan membranes were observed by scanning electron microscopy to gain a better understanding of chitosan membrane surface morphology. After MDCK cells and HIG-82 fibroblasts were cultured on these modified chitosan membranes for various culture durations (i.e. 1, 2, 4, 12 and 24 h), they were investigated to decipher cellular behavior. We found that both cells preferred to adhere onto a flat surface rather than on a nanopatterned surface. However, most (> 80%) of the MDCK cells showed rounded morphology and would suspend in the cultured medium instead of adhering onto the planar surface of negatively nanopatterned chitosan membranes. This means different cell types (e.g. fibroblasts versus epithelia) showed distinct capabilities/preferences of adherence for materials of varying surface roughness. We also showed that chitosan membranes could be re-used at least nine times without significant contamination and would provide us consistency for probing cell-material interactions by permitting reuse of the same substrate. We believe these results would provide us better insight into cellular behavior, specifically, microscopic properties and characteristics of cells grown under unique, nanopatterned cell-interface conditions.

  3. Rapid Cellular Identification by Dynamic Electromechanical Response

    SciTech Connect

    Nikiforov, Maxim; Jesse, Stephen; Kalinin, Sergei V; Reukov, Vladimir V; Vertegel, Alexey; Thompson, Gary L

    2009-01-01

    Coupling between electrical and mechanical phenomena is ubiquitous in living systems. Here, we demonstrate rapid identification of cellular organisms using difference in electromechanical activity in a broad frequency range. Principal component analysis of the dynamic electromechanical response spectra bundled with neural network based recognition provides a robust identification algorithm based on their electromechanical signature, and allows unambiguous differentiation of model Micrococcus Lysodeikticus and Pseudomonas Fluorescens system. This methodology provides a universal pathway for biological identification obviating the need for well-defined analytical models of Scanning Probe Microscopy response.

  4. Plasmonic Nanobubbles as Tunable Cellular Probes for Cancer Theranostics

    PubMed Central

    Lapotko, Dmitri

    2011-01-01

    This review is focused on a novel cellular probe, the plasmonic nanobubble (PNB), which has the dynamically tunable and multiple functions of imaging, diagnosis, delivery, therapy and, ultimately, theranostics. The concept of theranostics was recently introduced in order to unite the clinically important stages of treatment, namely diagnosis, therapy and therapy guidance, into one single, rapid and highly accurate procedure. Cell level theranostics will have far-reaching implications for the treatment of cancer and other diseases at their earliest stages. PNBs were developed to support cell level theranostics as a new generation of on-demand tunable cellular probes. A PNB is a transient vapor nanobubble that is generated within nanoseconds around an overheated plasmonic nanoparticle with a short laser pulse. In the short term, we expect that PNB technology will be rapidly adaptable to clinical medicine, where the single cell resolution it provides will be critical for diagnosing incipient or residual disease and eliminating cancer cells, while leaving healthy cells intact. This review discusses mechanisms of plasmonic nanobubbles and their biomedical applications with the focus on cancer cell theranostics. PMID:21442036

  5. Scientists Probe Pesticide Dynamics

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1974

    1974-01-01

    Summarizes discussions of a symposium on pesticide environmental dynamics with emphases upon pesticide transport processes, environmental reactions, and partitioning in air, soil, water and living organisms. Indicates that the goal is to attain knowledge enough to predict pesticide behavior and describe pesticide distribution with models and…

  6. Active Dynamic Frictional Probes

    NASA Astrophysics Data System (ADS)

    Steimel, Joshua; Aragones, Juan; Alexander-Katz, Alfredo

    2015-03-01

    In biological systems there are a myriad of interactions occurring instantaneously and these interactions can vary drastically in the strength of the interaction, the speed at which this interaction occurs, and the duration of the interaction. When multiple interactions occur any of these factors can determine which particular interaction is dominant. However, currently it is extremely difficult to measure binding affinity, Kon, and Koff rates in a relatively high throughput manner. Here we propose a novel and versatile system that will be able to detect differences in binding affinity of wide range of transient interactions and will be able to extract the relevant time scales of these interactions. Our system will utilize ferromagnetic particles that can be easily functionalized with a receptor of interest and the substrate will be coated in the corresponding ligand. A rotating magnetic field will cause particles, henceforth referred to as rollers, to rotate and this rotational motion will be converted into translational motion via the effective frictional force induced by interaction that is being probed. By measuring the translation of the rollers to a baseline, where only hydrodynamic friction occurs, we can measure the relative strength of the interactions. We can also potentially measure kinetic information by changing the frequency at which the magnetic field rotates, since changing the frequency at which the bead rotates is akin to changing the time allowed for bond formation. We will measure a wide range of interaction including ionic, metal-ion coordination, IgG-Protein A complex, and biotin-streptavidin complex.

  7. From Cnn Dynamics to Cellular Wave Computers

    NASA Astrophysics Data System (ADS)

    Roska, Tamas

    2013-01-01

    Embedded in a historical overview, the development of the Cellular Wave Computing paradigm is presented, starting from the standard CNN dynamics. The theoretical aspects, the physical implementation, the innovation process, as well as the biological relevance are discussed in details. Finally, the latest developments, the physical versus virtual cellular machines, as well as some open questions are presented.

  8. Multi-scale Imaging of Cellular and Sub-cellular Structures using Scanning Probe Recognition Microscopy.

    NASA Astrophysics Data System (ADS)

    Chen, Q.; Rice, A. F.

    2005-03-01

    Scanning Probe Recognition Microscopy is a new scanning probe capability under development within our group to reliably return to and directly interact with a specific nanobiological feature of interest. In previous work, we have successfully recognized and classified tubular versus globular biological objects from experimental atomic force microscope images using a method based on normalized central moments [ref. 1]. In this paper we extend this work to include recognition schemes appropriate for cellular and sub-cellular structures. Globular cells containing tubular actin filaments are under investigation. Thus there are differences in external/internal shapes and scales. Continuous Wavelet Transform with a differential Gaussian mother wavelet is employed for multi- scale analysis. [ref. 1] Q. Chen, V. Ayres and L. Udpa, ``Biological Investigation Using Scanning Probe Recognition Microscopy,'' Proceedings 3rd IEEE Conference on Nanotechnology, vol. 2, p 863-865 (2003).

  9. Intravital FRET: Probing Cellular and Tissue Function in Vivo.

    PubMed

    Radbruch, Helena; Bremer, Daniel; Mothes, Ronja; Günther, Robert; Rinnenthal, Jan Leo; Pohlan, Julian; Ulbricht, Carolin; Hauser, Anja E; Niesner, Raluca

    2015-01-01

    The development of intravital Förster Resonance Energy Transfer (FRET) is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo-ratiometrically and time-resolved by fluorescence lifetime imaging-and show their concrete application in the context of neuroinflammation in adult mice. PMID:26006244

  10. Cellular ubiquitin pool dynamics and homeostasis

    PubMed Central

    Ryu, Kwon-Yul

    2014-01-01

    Ubiquitin (Ub) is a versatile signaling molecule that plays important roles in a variety of cellular processes. Cellular Ub pools, which are composed of free Ub and Ub conjugates, are in dynamic equilibrium inside cells. In particular, increasing evidence suggests that Ub homeostasis, or the maintenance of free Ub above certain threshold levels, is important for cellular function and survival under normal or stress conditions. Accurate determination of various Ub species, including levels of free Ub and specific Ub chain linkages, have become possible in biological specimens as a result of the introduction of the proteomic approach using mass spectrometry. This technology has facilitated research on dynamic properties of cellular Ub pools and has provided tools for in-depth investigation of Ub homeostasis. In this review, we have also discussed the consequences of the disruption of Ub pool dynamics and homeostasis via deletion of polyubiquitin genes or mutations of deubiquitinating enzymes. The common consequence was a reduced availability of free Ub and a significant impact on the function and viability of cells. These observations further indicate that the levels of free Ub are important determinants for cellular protection. [BMB Reports 2014; 47(9): 475-482] PMID:24924398

  11. Design of Environmentally Responsive Fluorescent Polymer Probes for Cellular Imaging.

    PubMed

    Yamada, Arisa; Hiruta, Yuki; Wang, Jian; Ayano, Eri; Kanazawa, Hideko

    2015-08-10

    We report the development of environmentally responsive fluorescent polymers. The reversible temperature-induced phase transition of copolymers composed of N-isopropylacrylamide and a fluorescent monomer based on the fluorescein (FL), coumarin (CO), rhodamine (RH), or dansyl (DA) skeleton was used as a molecular switch to control the fluorescence intensity. The poly(N-isopropylacrylamide) (PNIPAAm) chain showed an expanded coil conformation below the lower critical solution temperature (LCST) due to hydration, but it changed to a globular form above the LCST due to dehydration. Through the combination of a polarity-sensitive fluorophore with PNIPAAm, the synthetic fluorescent polymer displayed a response to external temperature, with the fluorescence strength dramatically changing close to the LCST. Additionally, the P(NIPAAm-co-FL) and P(NIPAAm-co-CO) polymers, containing fluorescein and coumarin groups, respectively, exhibited pH responsiveness. The environmental responsiveness of the reported polymers is derived directly from the PNIPAAm and fluorophore structures, thus allowing for the cellular uptake of the fluorescence copolymer by RAW264.7 cells to be temperature-controlled. Cellular uptake was suppressed below the LCST but enhanced above the LCST. Furthermore, the cellular uptake of both P(NIPAAm-co-CO) and P(NIPAAm-co-RH) conjugated with a fusogenic lipid, namely, l-α-phosphatidylethanolamine, dioleoyl (DOPE), was enhanced. Such lipid-conjugated fluorescence probes are expected to be useful as physiological indicators for intracellular imaging. PMID:26121103

  12. Cellular automatons applied to gas dynamic problems

    NASA Astrophysics Data System (ADS)

    Long, Lyle N.; Coopersmith, Robert M.; McLachlan, B. G.

    1987-06-01

    This paper compares the results of a relatively new computational fluid dynamics method, cellular automatons, with experimental data and analytical results. This technique has been shown to qualitatively predict fluidlike behavior; however, there have been few published comparisons with experiment or other theories. Comparisons are made for a one-dimensional supersonic piston problem, Stokes first problem, and the flow past a normal flat plate. These comparisons are used to assess the ability of the method to accurately model fluid dynamic behavior and to point out its limitations. Reasonable results were obtained for all three test cases, but the fundamental limitations of cellular automatons are numerous. It may be misleading, at this time, to say that cellular automatons are a computationally efficient technique. Other methods, based on continuum or kinetic theory, would also be very efficient if as little of the physics were included.

  13. Cellular automatons applied to gas dynamic problems

    NASA Technical Reports Server (NTRS)

    Long, Lyle N.; Coopersmith, Robert M.; Mclachlan, B. G.

    1987-01-01

    This paper compares the results of a relatively new computational fluid dynamics method, cellular automatons, with experimental data and analytical results. This technique has been shown to qualitatively predict fluidlike behavior; however, there have been few published comparisons with experiment or other theories. Comparisons are made for a one-dimensional supersonic piston problem, Stokes first problem, and the flow past a normal flat plate. These comparisons are used to assess the ability of the method to accurately model fluid dynamic behavior and to point out its limitations. Reasonable results were obtained for all three test cases, but the fundamental limitations of cellular automatons are numerous. It may be misleading, at this time, to say that cellular automatons are a computationally efficient technique. Other methods, based on continuum or kinetic theory, would also be very efficient if as little of the physics were included.

  14. Dynamical Systems Perspective of Wolfram's Cellular Automata

    NASA Astrophysics Data System (ADS)

    Courbage, M.; Kamiński, B.

    2013-01-01

    Leon Chua, following Wolfram, devoted a big effort to understand deeply the wealth of complexity of the rules of all elementary one-dimensional cellular automata from the point of view of the nonlinear dynamicist. Here we complete this point of view by a dynamical system perspective, extending them to the limit of infinite number of sites.

  15. Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations.

    PubMed

    Morita, Ritsuko; Kihira, Miho; Nakatsu, Yousuke; Nomoto, Yohei; Ogawa, Miho; Ohashi, Kazumasa; Mizuno, Kensaku; Tachikawa, Tetsuhiko; Ishimoto, Yukitaka; Morishita, Yoshihiro; Tsuji, Takashi

    2016-01-01

    The morphologies of ectodermal organs are shaped by appropriate combinations of several deformation modes, such as invagination and anisotropic tissue elongation. However, how multicellular dynamics are coordinated during deformation processes remains to be elucidated. Here, we developed a four-dimensional (4D) analysis system for tracking cell movement and division at a single-cell resolution in developing tooth epithelium. The expression patterns of a Fucci probe clarified the region- and stage-specific cell cycle patterns within the tooth germ, which were in good agreement with the pattern of the volume growth rate estimated from tissue-level deformation analysis. Cellular motility was higher in the regions with higher growth rates, while the mitotic orientation was significantly biased along the direction of tissue elongation in the epithelium. Further, these spatio-temporal patterns of cellular dynamics and tissue-level deformation were highly correlated with that of the activity of cofilin, which is an actin depolymerization factor, suggesting that the coordination of cellular dynamics via actin remodeling plays an important role in tooth epithelial morphogenesis. Our system enhances the understanding of how cellular behaviors are coordinated during ectodermal organogenesis, which cannot be observed from histological analyses. PMID:27588418

  16. Two-Photon Enzymatic Probes Visualizing Sub-cellular/Deep-brain Caspase Activities in Neurodegenerative Models

    PubMed Central

    Qian, Linghui; Zhang, Cheng-Wu; Mao, Yanli; Li, Lin; Gao, Nengyue; Lim, Kah-Leong; Xu, Qing-Hua; Yao, Shao Q.

    2016-01-01

    Caspases work as a double-edged sword in maintaining cell homeostasis. Highly regulated caspase activities are essential during animal development, but dysregulation might lead to different diseases, e.g. extreme caspase activation is known to promote neurodegeneration. At present, visualization of caspase activation has mostly remained at the cellular level, in part due to a lack of cell-permeable imaging probes capable of direct, real-time investigations of endogenous caspase activities in deep tissues. Herein, we report a suite of two-photon, small molecule/peptide probes which enable sensitive and dynamic imaging of individual caspase activities in neurodegenerative models under physiological conditions. With no apparent toxicity and the ability of imaging endogenous caspases both in different subcellular organelles of mammalian cells and in brain tissues, these probes serve as complementary tools to conventional histological analysis. They should facilitate future explorations of caspases at molecular, cellular and organism levels and inspire development of novel two-photon probes against other enzymes. PMID:27210613

  17. Two-Photon Enzymatic Probes Visualizing Sub-cellular/Deep-brain Caspase Activities in Neurodegenerative Models.

    PubMed

    Qian, Linghui; Zhang, Cheng-Wu; Mao, Yanli; Li, Lin; Gao, Nengyue; Lim, Kah-Leong; Xu, Qing-Hua; Yao, Shao Q

    2016-01-01

    Caspases work as a double-edged sword in maintaining cell homeostasis. Highly regulated caspase activities are essential during animal development, but dysregulation might lead to different diseases, e.g. extreme caspase activation is known to promote neurodegeneration. At present, visualization of caspase activation has mostly remained at the cellular level, in part due to a lack of cell-permeable imaging probes capable of direct, real-time investigations of endogenous caspase activities in deep tissues. Herein, we report a suite of two-photon, small molecule/peptide probes which enable sensitive and dynamic imaging of individual caspase activities in neurodegenerative models under physiological conditions. With no apparent toxicity and the ability of imaging endogenous caspases both in different subcellular organelles of mammalian cells and in brain tissues, these probes serve as complementary tools to conventional histological analysis. They should facilitate future explorations of caspases at molecular, cellular and organism levels and inspire development of novel two-photon probes against other enzymes. PMID:27210613

  18. Hydrogen Peroxide Probes Directed to Different Cellular Compartments

    PubMed Central

    Malinouski, Mikalai; Zhou, You; Belousov, Vsevolod V.; Hatfield, Dolph L.; Gladyshev, Vadim N.

    2011-01-01

    Background Controlled generation and removal of hydrogen peroxide play important roles in cellular redox homeostasis and signaling. We used a hydrogen peroxide biosensor HyPer, targeted to different compartments, to examine these processes in mammalian cells. Principal Findings Reversible responses were observed to various redox perturbations and signaling events. HyPer expressed in HEK 293 cells was found to sense low micromolar levels of hydrogen peroxide. When targeted to various cellular compartments, HyPer occurred in the reduced state in the nucleus, cytosol, peroxisomes, mitochondrial intermembrane space and mitochondrial matrix, but low levels of the oxidized form of the biosensor were also observed in each of these compartments, consistent with a low peroxide tone in mammalian cells. In contrast, HyPer was mostly oxidized in the endoplasmic reticulum. Using this system, we characterized control of hydrogen peroxide in various cell systems, such as cells deficient in thioredoxin reductase, sulfhydryl oxidases or subjected to selenium deficiency. Generation of hydrogen peroxide could also be monitored in various compartments following signaling events. Conclusions We found that HyPer can be used as a valuable tool to monitor hydrogen peroxide generated in different cellular compartments. The data also show that hydrogen peroxide generated in one compartment could translocate to other compartments. Our data provide information on compartmentalization, dynamics and homeostatic control of hydrogen peroxide in mammalian cells. PMID:21283738

  19. Literature Review on Dynamic Cellular Manufacturing System

    NASA Astrophysics Data System (ADS)

    Nouri Houshyar, A.; Leman, Z.; Pakzad Moghadam, H.; Ariffin, M. K. A. M.; Ismail, N.; Iranmanesh, H.

    2014-06-01

    In previous decades, manufacturers faced a lot of challenges because of globalization and high competition in markets. These problems arise from shortening product life cycle, rapid variation in demand of products, and also rapid changes in manufcaturing technologies. Nowadays most manufacturing companies expend considerable attention for improving flexibility and responsiveness in order to overcome these kinds of problems and also meet customer's needs. By considering the trend toward the shorter product life cycle, the manufacturing environment is towards manufacturing a wide variety of parts in small batches [1]. One of the major techniques which are applied for improving manufacturing competitiveness is Cellular Manufacturing System (CMS). CMS is type of manufacturing system which tries to combine flexibility of job shop and also productivity of flow shop. In addition, Dynamic cellular manufacturing system which considers different time periods for the manufacturing system becomes an important topic and attracts a lot of attention to itself. Therefore, this paper made attempt to have a brief review on this issue and focused on all published paper on this subject. Although, this topic gains a lot of attention to itself during these years, none of previous researchers focused on reviewing the literature of that which can be helpful and useful for other researchers who intend to do the research on this topic. Therefore, this paper is the first study which has focused and reviewed the literature of dynamic cellular manufacturing system.

  20. Complex dynamics of cellular automata rule 119

    NASA Astrophysics Data System (ADS)

    Chen, Fang-Fang; Chen, Fang-Yue

    2009-03-01

    In this paper, the dynamical behaviors of cellular automata rule 119 are studied from the viewpoint of symbolic dynamics in the bi-infinite symbolic sequence space Σ2. It is shown that there exists one Bernoulli-measure global attractor of rule 119, which is also the nonwandering set of the rule. Moreover, it is demonstrated that rule 119 is topologically mixing on the global attractor and possesses the positive topological entropy. Therefore, rule 119 is chaotic in the sense of both Li-Yorke and Devaney on the global attractor. It is interesting that rule 119, a member of Wolfram’s class II which was said to be simple as periodic before, actually possesses a chaotic global attractor in Σ2. Finally, it is noted that the method presented in this work is also applicable to studying the dynamics of other rules, especially the 112 Bernoulli-shift rules therein.

  1. Traffic jam dynamics in stochastic cellular automata

    SciTech Connect

    Nagel, K. |; Schreckenberg, M.

    1995-09-01

    Simple models for particles hopping on a grid (cellular automata) are used to simulate (single lane) traffic flow. Despite their simplicity, these models are astonishingly realistic in reproducing start-stop-waves and realistic fundamental diagrams. One can use these models to investigate traffic phenomena near maximum flow. A so-called phase transition at average maximum flow is visible in the life-times of jams. The resulting dynamic picture is consistent with recent fluid-dynamical results by Kuehne/Kerner/Konhaeuser, and with Treiterer`s hysteresis description. This places CA models between car-following models and fluid-dynamical models for traffic flow. CA models are tested in projects in Los Alamos (USA) and in NRW (Germany) for large scale microsimulations of network traffic.

  2. The Spatiotemporal Cellular Dynamics of Lung Immunity

    PubMed Central

    Lelkes, E.; Headley, M.B.; Thornton, E.E.; Looney, M.R.; Krummel, M.F.

    2014-01-01

    The lung is a complex structure that is interdigitated with immune cells. Understanding the 4-dimensional process of normal and defective lung function and immunity has been a centuries-old problem. Challenges intrinsic to the lung have limited adequate microscopic evaluation of its cellular dynamics in real time, until recently. Because of emerging technologies, we now recognize alveolar-to-airway transport of inhaled antigen. We understand the nature of neutrophil entry during lung injury and are learning more about cellular interactions during inflammatory states. Insights are also accumulating in lung development and the metatastatic niche of the lung. Here we assess the developing technology of lung imaging, its merits for studies of pathophysiology and areas where further advances are needed. PMID:24974157

  3. A Clickable Aminooxy Probe for Monitoring Cellular ADP-Ribosylation

    PubMed Central

    Morgan, Rory K.; Cohen, Michael S.

    2015-01-01

    ADP-ribosylation is essential for cell function, yet there is a dearth of methods for detecting this post-translational modification in cells. Here, we describe a clickable aminooxy alkyne (AO-alkyne) probe that can detect cellular ADP-ribosylation on acidic amino acids following Cu-catalyzed conjugation to an azide-containing reporter. Using AO-alkyne, we show that PARP10 and PARP11 are auto-ADP-ribosylated in cells. We also demonstrate that AO-alkyne can be used to monitor stimulus-induced ADP-ribosylation in cells. Functional studies using AO-alkyne support a previously unknown mechanism for ADP-ribosylation on acidic amino acids, wherein a glutamate or aspartate at the initial C1′-position of ADP-ribose transfers to the C2′ position. This new mechanism for ADP-ribosylation has important implications for how glutamyl/aspartyl-ADP-ribose is recognized by proteins in cells. PMID:25978521

  4. Dynamics of active cellular response under stress

    NASA Astrophysics Data System (ADS)

    de, Rumi; Zemel, Assaf; Safran, Samuel

    2008-03-01

    Forces exerted by and on adherent cells are important for many physiological processes such as wound healing and tissue formation. In addition, recent experiments have shown that stem cell differentiation is controlled, at least in part, by the elasticity of the surrounding matrix. Using a simple theoretical model that includes the forces due to both the mechanosensitive nature of cells and the elastic response of the matrix, we predict the dynamics of orientation of cells. The model predicts many features observed in measurements of cellular forces and orientation including the increase with time of the forces generated by cells in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency. The dependence of the cell orientation angle on the Poisson ratio of the surrounding material can be used to distinguish systems in which cell activity is controlled by stress from those where cell activity is controlled by strain. Reference: Nature Physics, vol. 3, pp 655 (2007).

  5. Dynamic light scattering homodyne probe

    NASA Technical Reports Server (NTRS)

    Meyer, William V. (Inventor); Cannell, David S. (Inventor); Smart, Anthony E. (Inventor)

    2002-01-01

    An optical probe for analyzing a sample illuminated by a laser includes an input optical fiber operably connectable to the laser where the input optical fiber has an entrance end and an exit end. The probe also includes a first beam splitter where the first beam splitter is adapted to transmit an alignment portion of a light beam from the input fiber exit end and to reflect a homodyning portion of the light beam from the input fiber. The probe also includes a lens between the input fiber exit end and the first beam splitter and a first and a second output optical fiber, each having an entrance end and an exit end, each exit end being operably connectable to respective optical detectors. The probe also includes a second beam splitter which is adapted to reflect at least a portion of the reflected homodyning portion into the output fiber entrance ends and to transmit light from the laser scattered by the sample into the entrance ends.

  6. MRNet-based Dynamic Probe Class Library

    Energy Science and Technology Software Center (ESTSC)

    2006-12-19

    The Dynamic Probe Class Library (DPCL) is an API that allows for the modification of running code, or dynamic instrumentation. Dynamic instruction is an attractive technique for implementing performance analysis tools, debugging, or process steering because this method doesn't require the modification of the application's source code and hence avoids recompiling, re-linking, and restarting the application. The DPCL API is machine independent; hence DPCL-based tools built on one platform will work on another platform

  7. Cellular automata modelling of biomolecular networks dynamics.

    PubMed

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  8. Probing reaction dynamics with GDR decay

    SciTech Connect

    Beene, J.R.

    1994-10-01

    The giant dipole resonance (GDR) has been a prolific source of information on the physics of the nucleus. Mostly it has taught us about nuclear structure, but recently experiments have utilized the GDR as a probe of nuclear reaction dynamics. In this report two examples of such investigations are discussed involving very different reactions and probing time scales that differ by a factor of {approximately}10{sup 3}.

  9. Thioflavin T as a fluorescence probe for monitoring RNA metabolism at molecular and cellular levels.

    PubMed

    Sugimoto, Shinya; Arita-Morioka, Ken-ichi; Mizunoe, Yoshimitsu; Yamanaka, Kunitoshi; Ogura, Teru

    2015-08-18

    The intrinsically stochastic dynamics of mRNA metabolism have important consequences on gene regulation and non-genetic cell-to-cell variability; however, no generally applicable methods exist for studying such stochastic processes quantitatively. Here, we describe the use of the amyloid-binding probe Thioflavin T (ThT) for monitoring RNA metabolism in vitro and in vivo. ThT fluoresced strongly in complex with bacterial total RNA than with genomic DNA. ThT bound purine oligoribonucleotides preferentially over pyrimidine oligoribonucleotides and oligodeoxyribonucleotides. This property enabled quantitative real-time monitoring of poly(A) synthesis and phosphorolysis by polyribonucleotide phosphorylase in vitro. Cellular analyses, in combination with genetic approaches and the transcription-inhibitor rifampicin treatment, demonstrated that ThT mainly stained mRNA in actively dividing Escherichia coli cells. ThT also facilitated mRNA metabolism profiling at the single-cell level in diverse bacteria. Furthermore, ThT can also be used to visualise transitions between non-persister and persister cell states, a phenomenon of isogenic subpopulations of antibiotic-sensitive bacteria that acquire tolerance to multiple antibiotics due to stochastically induced dormant states. Collectively, these results suggest that probing mRNA dynamics with ThT is a broadly applicable approach ranging from the molecular level to the single-cell level. PMID:25883145

  10. Continuous waves probing in dynamic acoustoelastic testing

    NASA Astrophysics Data System (ADS)

    Scalerandi, M.; Gliozzi, A. S.; Ait Ouarabi, M.; Boubenider, F.

    2016-05-01

    Consolidated granular media display a peculiar nonlinear elastic behavior, which is normally analysed with dynamic ultrasonic testing exploiting the dependence on amplitude of different measurable quantities, such as the resonance frequency shift, the amount of harmonics generation, or the break of the superposition principle. However, dynamic testing allows measuring effects which are averaged over one (or more) cycles of the exciting perturbation. Dynamic acoustoelastic testing has been proposed to overcome this limitation and allow the determination of the real amplitude dependence of the modulus of the material. Here, we propose an implementation of the approach, in which the pulse probing waves are substituted by continuous waves. As a result, instead of measuring a time-of-flight as a function of the pump strain, we study the dependence of the resonance frequency on the strain amplitude, allowing to derive the same conclusions but with an easier to implement procedure.

  11. The cellular uptake and localization of non-emissive iridium(III) complexes as cellular reaction-based luminescence probes.

    PubMed

    Li, Chunyan; Liu, Yi; Wu, Yongquan; Sun, Yun; Li, Fuyou

    2013-01-01

    Improvement of cellular uptake and subcellular resolution remains a major obstacle in the successful and broad application of cellular optical probes. In this context, we design and synthesize seven non-emissive cyclometalated iridium(III) solvent complexes [Ir(CˆN)(2)(solv)(2)](+)L(-) (LIr2-LIr8, in which CˆN = 2-phenylpyridine (ppy) or its derivative; solv = DMSO, H(2)O or CH(3)CN; L(-) = PF(6)(-) or OTf(-)) applicable in live cell imaging to facilitate selective visualization of cellular structures. Based on the above variations (including different counter ions, solvent ligands, and CˆN ligands), structure-activity relationship analyses reveal a number of clear correlations: (1) variations in counter anions and solvent ligands of iridium(III) complexes do not affect cellular imaging behavior, and (2) length of the side carbon chain in CˆN ligands has significant effects on cellular uptake and localization/accumulation of iridium complexes in living cells. Moreover, investigation of the uptake mechanism via low-temperature and metabolism inhibitor assays reveal that [Ir(4-Meppy)(2)(CH(3)CN)(2)](+)OTf(-) (LIr5) with 2-phenylpyridine derivative with side-chain of methyl group at the 4-position as CˆN ligand permeates the outer and nuclear membranes of living cells through an energy-dependent, non-endocytic entry pathway, and translocation of the complex from the cell periphery towards the perinuclear region possibly occurs through a microtubule-dependent transport pathway. Nuclear pore complexes (NPCs) appear to selectively control the transport of iridium(III) complexes between the cytoplasm and nucleus. A generalization of trends in behavior and structure-activity relationships is presented, which should provide further insights into the design and optimization of future probes. PMID:23131533

  12. Dinuclear ruthenium(II) polypyridyl complexes as single and two-photon luminescence cellular imaging probes.

    PubMed

    Xu, Wenchao; Zuo, Jiarui; Wang, Lili; Ji, Liangnian; Chao, Hui

    2014-02-28

    A new series of dinuclear ruthenium(II) polypyridyl complexes, which possess larger π-conjugated systems, good water solubility and pH resistance, and high photostability, were developed to act as single and two-photon luminescence cellular imaging probes. PMID:24418839

  13. Turn-on trivalent cation selective chemodosimetric probe to image native cellular iron pools.

    PubMed

    Venkateswarulu, M; Mukherjee, Trinetra; Mukherjee, Subhrakanti; Koner, Rik Rani

    2014-04-14

    A new turn-on cell permeable chemodosimetric probe has been developed and its application in the selective detection of trivalent cations (Fe(3+)/Cr(3+)/Al(3+)) at a sub-nanomolar level has been demonstrated. The selectivity of over a broad spectrum of mono- and divalent metal ions was established using fluorescence spectroscopy. Moreover, the changes in the absorption spectra of in the presence of trivalent cations enabled the most bio-relevant metal ion Fe(3+) over Cr(3+)/Al(3+) to be distinguished. The probe was found to be successful in the fluorescence imaging of native cellular iron pools. The fluorescence imaging of the native iron pools of banana pith further supported the high sensitivity of towards Fe(3+) present in living systems. To the best of our knowledge, this is the first example of a turn-on chemodosimetric probe to image native cellular Fe(3+) pools. PMID:24534800

  14. Development of Sulfonamide Photoaffinity Inhibitors for Probing Cellular γ-Secretase.

    PubMed

    Crump, Christina J; Murrey, Heather E; Ballard, T Eric; Am Ende, Christopher W; Wu, Xianzhong; Gertsik, Natalya; Johnson, Douglas S; Li, Yue-Ming

    2016-08-17

    γ-Secretase is a multiprotein complex that catalyzes intramembrane proteolysis associated with Alzheimer's disease and cancer. Here, we have developed potent sulfonamide clickable photoaffinity probes that target γ-secretase in vitro and in cells by incorporating various photoreactive groups and walking the clickable alkyne handle to different positions around the molecule. We found that benzophenone is preferred over diazirine as a photoreactive group within the sulfonamide scaffold for labeling γ-secretase. Intriguingly, the placement of the alkyne at different positions has little effect on probe potency but has a significant impact on the efficiency of labeling of γ-secretase. Moreover, the optimized clickable photoprobe, 163-BP3, was utilized as a cellular probe to effectively assess the target engagement of inhibitors with γ-secretase in primary neuronal cells. In addition, biotinylated 163-BP3 probes were developed and used to capture the native γ-secretase complex in the 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) solubilized state. Taken together, these next generation clickable and biotinylated sulfonamide probes offer new tools to study γ-secretase in biochemical and cellular systems. Finally, the data provide insights into structural features of the sulfonamide inhibitor binding site in relation to the active site and into the design of clickable photoaffinity probes. PMID:27253220

  15. Real-Time Bioluminescent Tracking of Cellular Population Dynamics

    SciTech Connect

    Close, Dan; Sayler, Gary Steven; Xu, Tingting; Ripp, Steven Anthony

    2014-01-01

    Cellular population dynamics are routinely monitored across many diverse fields for a variety of purposes. In general, these dynamics are assayed either through the direct counting of cellular aliquots followed by extrapolation to the total population size, or through the monitoring of signal intensity from any number of externally stimulated reporter proteins. While both viable methods, here we describe a novel technique that allows for the automated, non-destructive tracking of cellular population dynamics in real-time. This method, which relies on the detection of a continuous bioluminescent signal produced through expression of the bacterial luciferase gene cassette, provides a low cost, low time-intensive means for generating additional data compared to alternative methods.

  16. The role of cellular environment in dynamic light scattering

    NASA Astrophysics Data System (ADS)

    An, Ran; Jeong, Kwan; Turek, John; Nolte, David

    2011-03-01

    We have developed motility contrast imaging (MCI) as a coherence-domain volumetric imaging approach that uses subcellular dynamics as an endogenous imaging contrast agent of living tissue. Fluctuation spectroscopy analysis of dynamic light scattering (DLS) from 3-D tissue has identified functional frequency bands related to organelle transport, membrane undulations and cell shape change. In this paper, we track the behavior of dynamic light scattering as we bridge the gap between the two extremes of 2-D cell culture on the one hand, and 3-D tissue spheroids on the other. In a light backscattering geometry, we capture speckle from 2-D cell culture consisting of isolated cells or planar rafts of cells on cell-culture surfaces. DLS from that cell culture shows differences and lower sensitivity to intra-cellular dynamics compared with the 3-D tissue. The motility contrast is weak in this limit. As the cellular density increases to cover the surface, the motility contrast increases. As environmental perturbations or pharmaceuticals are applied, the fluctuation spectral response becomes more dramatic as the dimensionality of the cellular aggregations increases. We show that changing optical thickness of the cellular-to-tissue targets usually causes characteristic frequency shifts in the spectrograms, while changing cellular dimensionality causes characteristic frequencies to be enhanced or suppressed.

  17. Inferring biological dynamics in heterogeneous cellular environments

    NASA Astrophysics Data System (ADS)

    Pressé, Steve

    In complex environments, it often appears that biomolecules such as proteins do not diffuse normally. That is, their mean square displacement does not scale linearly with time. This anomalous diffusion happens for multiple reasons: proteins can bind to structures and other proteins; fluorophores used to label proteins may flicker or blink making it appear that the labeled protein is diffusing anomalously; and proteins can diffuse in differently crowded environments. Here we describe methods for learning about such processes from imaging data collected inside the heterogeneous environment of the living cell. Refs.: ''Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments'' Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J. , 109, 7 (2015). ''A data-driven alternative to the fractional Fokker-Planck equation'' Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , P07009 (2015).

  18. Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

    NASA Astrophysics Data System (ADS)

    Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

    2014-06-01

    Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions.

  19. Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

    PubMed Central

    Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

    2014-01-01

    Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions. PMID:24957323

  20. Metamorphic probing of subduction dynamics and rheology

    NASA Astrophysics Data System (ADS)

    Agard, Philippe

    2015-04-01

    Understanding subduction dynamics and rheology, and particularly the role of fluids and deformation, strongly relies on integrated tectonic, petrological and geochemical studies able to retrieve from our most direct and reliable natural probes (i.e., preserved metamorphic assemblages) their pressure-temperature-time (P-T-t) evolution. I first provide two examples of such integrated studies that allow tracking rock trajectories and exhumation dynamics in subduction zones -- thanks to the considerable progress made over the last ten years on estimating P-T-t conditions. The Oman example shows how EPMA mapping and the detailed study of local, low-temperature equilibria help constrain the behaviour and dynamics of upper crustal units during continental subduction, demonstrating the importance of slicing, accretion at depths of ~30 km and short-lived tectonic expulsion. In the Western Alps, the extensive coverage of field exposures by means of the Raman Spectrometry of carbonaceous matter and by dedicated pseudosection modelling allows to identify the existence of tens of km long, fairly continuous slices of downgoing slab exhumed from similar eclogitic depths (~80 km), and to assess the role of the overall fluid content in enabling their exhumation/preservation. I then illustrate how metamorphic rocks can provide ideal probes (though still partly to be improved) to address key, large-scale tectonic processes and not 'simply' histories, and do stress the importance of adequate field-based data acquisition. Three examples (and present-day limitations) are reviewed here: (1) The regional-scale exhumation of blueschists from the downdip end of the seismogenic zone across thousands of kilometers along the Neotethys (at ~1-1.5 GPa, 350°C) is a major geodynamic event providing insights into changes in interplate mechanical coupling and subduction dynamics. (2) Eclogite breccias recently reported in the Monviso area (W. Alps) allow constraining short-term processes involving

  1. Cellular Particle Dynamics simulation of biomechanical relaxation processes of multi-cellular systems

    NASA Astrophysics Data System (ADS)

    McCune, Matthew; Kosztin, Ioan

    2013-03-01

    Cellular Particle Dynamics (CPD) is a theoretical-computational-experimental framework for describing and predicting the time evolution of biomechanical relaxation processes of multi-cellular systems, such as fusion, sorting and compression. In CPD, cells are modeled as an ensemble of cellular particles (CPs) that interact via short range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through numerical integration of their equations of motion. Here we present CPD simulation results for the fusion of both spherical and cylindrical multi-cellular aggregates. First, we calibrate the relevant CPD model parameters for a given cell type by comparing the CPD simulation results for the fusion of two spherical aggregates to the corresponding experimental results. Next, CPD simulations are used to predict the time evolution of the fusion of cylindrical aggregates. The latter is relevant for the formation of tubular multi-cellular structures (i.e., primitive blood vessels) created by the novel bioprinting technology. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  2. Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology

    PubMed Central

    Byrne, Michael J.; Waxham, M. Neal; Kubota, Yoshihisa

    2010-01-01

    In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations. PMID:20361275

  3. Cellular Uptake and Localization of Polymyxins in Renal Tubular Cells Using Rationally Designed Fluorescent Probes

    PubMed Central

    Yun, Bo; Azad, Mohammad A. K.; Nowell, Cameron J.; Nation, Roger L.; Thompson, Philip E.; Roberts, Kade D.

    2015-01-01

    Polymyxins are cyclic lipopeptide antibiotics that serve as a last line of defense against Gram-negative bacterial superbugs. However, the extensive accumulation of polymyxins in renal tubular cells can lead to nephrotoxicity, which is the major dose-limiting factor in clinical use. In order to gain further insights into the mechanism of polymyxin-induced nephrotoxicity, we have rationally designed novel fluorescent polymyxin probes to examine the localization of polymyxins in rat renal tubular (NRK-52E) cells. Our design strategy focused on incorporating a dansyl fluorophore at the hydrophobic centers of the polymyxin core structure. To this end, four novel regioselectively labeled monodansylated polymyxin B probes (MIPS-9541, MIPS-9542, MIPS-9543, and MIPS-9544) were designed, synthesized, and screened for their antimicrobial activities and apoptotic effects against rat kidney proximal tubular cells. On the basis of the assessment of antimicrobial activities, cellular uptake, and apoptotic effects on renal tubular cells, incorporation of a dansyl fluorophore at either position 6 or 7 (MIPS-9543 and MIPS-9544, respectively) of the polymyxin core structure appears to be an appropriate strategy for generating representative fluorescent polymyxin probes to be utilized in intracellular imaging and mechanistic studies. Furthermore, confocal imaging experiments utilizing these probes showed evidence of partial colocalization of the polymyxins with both the endoplasmic reticulum and mitochondria in rat renal tubular cells. Our results highlight the value of these new fluorescent polymyxin probes and provide further insights into the mechanism of polymyxin-induced nephrotoxicity. PMID:26392495

  4. Advances in fluorescence labeling strategies for dynamic cellular imaging

    PubMed Central

    Dean, Kevin M; Palmer, Amy E

    2014-01-01

    Synergistic advances in optical physics, probe design, molecular biology, labeling techniques and computational analysis have propelled fluorescence imaging into new realms of spatiotemporal resolution and sensitivity. This review aims to discuss advances in fluorescent probes and live-cell labeling strategies, two areas that remain pivotal for future advances in imaging technology. Fluorescent protein– and bio-orthogonal–based methods for protein and RNA imaging are discussed as well as emerging bioengineering techniques that enable their expression at specific genomic loci (for example, CRISPR and TALENs). Important attributes that contribute to the success of each technique are emphasized, providing a guideline for future advances in dynamic live-cell imaging. PMID:24937069

  5. Development of novel FP-based probes for live-cell imaging of nitric oxide dynamics

    PubMed Central

    Eroglu, Emrah; Gottschalk, Benjamin; Charoensin, Suphachai; Blass, Sandra; Bischof, Helmut; Rost, Rene; Madreiter-Sokolowski, Corina T.; Pelzmann, Brigitte; Bernhart, Eva; Sattler, Wolfgang; Hallström, Seth; Malinski, Tadeusz; Waldeck-Weiermair, Markus; Graier, Wolfgang F.; Malli, Roland

    2016-01-01

    Nitric oxide () is a free radical with a wide range of biological effects, but practically impossible to visualize in single cells. Here we report the development of novel multicoloured fluorescent quenching-based probes by fusing a bacteria-derived -binding domain close to distinct fluorescent protein variants. These genetically encoded probes, referred to as geNOps, provide a selective, specific and real-time read-out of cellular dynamics and, hence, open a new era of bioimaging. The combination of geNOps with a Ca2+ sensor allowed us to visualize and Ca2+ signals simultaneously in single endothelial cells. Moreover, targeting of the probes was used to detect signals within mitochondria. The geNOps are useful new tools to further investigate and understand the complex patterns of signalling on the single (sub)cellular level. PMID:26842907

  6. Parameter-less approaches for interpreting dynamic cellular response

    PubMed Central

    2014-01-01

    Cellular response such as cell signaling is an integral part of information processing in biology. Upon receptor stimulation, numerous intracellular molecules are invoked to trigger the transcription of genes for specific biological purposes, such as growth, differentiation, apoptosis or immune response. How complex are such specialized and sophisticated machinery? Computational modeling is an important tool for investigating dynamic cellular behaviors. Here, I focus on certain types of key signaling pathways that can be interpreted well using simple physical rules based on Boolean logic and linear superposition of response terms. From the examples shown, it is conceivable that for small-scale network modeling, reaction topology, rather than parameter values, is crucial for understanding population-wide cellular behaviors. For large-scale response, non-parametric statistical approaches have proven valuable for revealing emergent properties. PMID:25183996

  7. Analysing Dynamical Behavior of Cellular Networks via Stochastic Bifurcations

    PubMed Central

    Zakharova, Anna; Kurths, Jürgen; Vadivasova, Tatyana; Koseska, Aneta

    2011-01-01

    The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types. PMID:21647432

  8. A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells.

    PubMed

    Su, Dongdong; Teoh, Chai Lean; Gao, Nengyue; Xu, Qing-Hua; Chang, Young-Tae

    2016-01-01

    Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM). PMID:27589762

  9. Plant-Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners.

    PubMed

    Toruño, Tania Y; Stergiopoulos, Ioannis; Coaker, Gitta

    2016-08-01

    Plants possess large arsenals of immune receptors capable of recognizing all pathogen classes. To cause disease, pathogenic organisms must be able to overcome physical barriers, suppress or evade immune perception, and derive nutrients from host tissues. Consequently, to facilitate some of these processes, pathogens secrete effector proteins that promote colonization. This review covers recent advances in the field of effector biology, focusing on conserved cellular processes targeted by effectors from diverse pathogens. The ability of effectors to facilitate pathogen entry into the host interior, suppress plant immune perception, and alter host physiology for pathogen benefit is discussed. Pathogens also deploy effectors in a spatial and temporal manner, depending on infection stage. Recent advances have also enhanced our understanding of effectors acting in specific plant organs and tissues. Effectors are excellent cellular probes that facilitate insight into biological processes as well as key points of vulnerability in plant immune signaling networks. PMID:27359369

  10. Application-Aware Dynamic Retransmission Control in Mobile Cellular Networks

    NASA Astrophysics Data System (ADS)

    Halima, Nadhir Ben; Kliazovich, Dzmitry; Granelli, Fabrizio

    This paper proposes an application-aware cross-layer approach between application/transport layers on the mobile terminal and link layer at the wireless base station to enable dynamic control on the strength of per-packet error protection for multimedia and data transfers. Specifically, in the context of cellular networks, the proposed scheme allows to control the desired level of Hybrid ARQ (HARQ) protection by using an in-band control feedback channel. Such protection is dynamically adapted on a per-packet basis and depends on the perceptual importance of different packets as well as on the reception history of the flow.

  11. Maximizing Information on the Environment by Dynamically Controlled Qubit Probes

    NASA Astrophysics Data System (ADS)

    Zwick, Analia; Álvarez, Gonzalo A.; Kurizki, Gershon

    2016-01-01

    We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to the quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic types of bath spectra, and the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.

  12. 7th International Workshop on Microbeam Probes of Cellular Radiation Response

    SciTech Connect

    Brenner, David J.

    2009-07-21

    The extended abstracts that follow present a summary of the Proceedings of the 7th International Workshop: Microbeam Probes of Cellular Radiation Response, held at Columbia University’s Kellogg Center in New York City on March 15–17, 2006. These International Workshops on Microbeam Probes of Cellular Radiation Response have been held regularly since 1993 (1–5). Since the first workshop, there has been a rapid growth (see Fig. 1) in the number of centers developing microbeams for radiobiological research, and worldwide there are currently about 30 microbeams in operation or under development. Single-cell/single-particle microbeam systems can deliver beams of different ionizing radiations with a spatial resolution of a few micrometers down to a few tenths of a micrometer. Microbeams can be used to addressquestions relating to the effects of low doses of radiation (a single radiation track traversing a cell or group of cells), to probe subcellular targets (e.g. nucleus or cytoplasm), and to address questions regarding the propagation of information about DNA damage (for example, the radiation-induced bystander effect). Much of the recent research using microbeams has been to study low-dose effects and ‘‘non-targeted’’ responses such as bystander effects, genomic instability and adaptive responses. This Workshop provided a forum to assess the current state of microbeam technology and current biological applications and to discuss future directions for development, both technological and biological. Over 100 participants reviewed the current state of microbeam research worldwide and reported on new technological developments in the fields of both physics and biology.

  13. Cellular automata and complex dynamics of driven elastic media

    SciTech Connect

    Coppersmith, S.N.; Littlewodd, P.B.; Sibani, P.

    1995-12-01

    Several systems of importance in condensed matter physics can be modelled as an elastic medium in a disordered environment and driven by an external force. In the simplest cases, the equation of motion involves competition between a local non-linear potential (fluctuating in space) and elastic coupling, as well as relaxational (inertialess) dynamics. Despite a simple mathematical description, the interactions between many degrees of freedom lead to the emergence of time and length scales much longer than those set by the microscopic dynamics. Extensive computations have improved the understanding of the behavior of such models, but full solutions of the equations of motion for very large systems are time-consuming and may obscure important physical principles in a massive volume of output. The development of cellular automata models has been crucial, both in conceptual simplification and in allowing the collection of data on many replicas of very large systems. We will discuss how the marriage of cellular automata models and parallel computation on a MasPar MP-1216 computer has helped to elucidate the dynamical properties of these many-degree-of-freedom systems.

  14. Probing ultrafast spin dynamics with optical pump-probe scanning tunnelling microscopy.

    PubMed

    Yoshida, Shoji; Aizawa, Yuta; Wang, Zi-han; Oshima, Ryuji; Mera, Yutaka; Matsuyama, Eiji; Oigawa, Haruhiro; Takeuchi, Osamu; Shigekawa, Hidemi

    2014-08-01

    Studies of spin dynamics in low-dimensional systems are important from both fundamental and practical points of view. Spin-polarized scanning tunnelling microscopy allows localized spin dynamics to be characterized and plays important roles in nanoscale science and technology. However, nanoscale analysis of the ultrafast dynamics of itinerant magnetism, as well as its localized characteristics, should be pursued to advance further the investigation of quantum dynamics in functional structures of small systems. Here, we demonstrate the optical pump-probe scanning tunnelling microscopy technique, which enables the nanoscale probing of spin dynamics with the temporal resolution corresponding, in principle, to the optical pulse width. Spins are optically oriented using circularly polarized light, and their dynamics are probed by scanning tunnelling microscopy based on the optical pump-probe method. Spin relaxation in a single quantum well with a width of 6 nm was observed with a spatial resolution of ∼ 1 nm. In addition to spin relaxation dynamics, spin precession, which provides an estimation of the Landé g factor, was observed successfully. PMID:24974938

  15. Probing ultrafast spin dynamics with optical pump-probe scanning tunnelling microscopy

    NASA Astrophysics Data System (ADS)

    Yoshida, Shoji; Aizawa, Yuta; Wang, Zi-Han; Oshima, Ryuji; Mera, Yutaka; Matsuyama, Eiji; Oigawa, Haruhiro; Takeuchi, Osamu; Shigekawa, Hidemi

    2014-08-01

    Studies of spin dynamics in low-dimensional systems are important from both fundamental and practical points of view. Spin-polarized scanning tunnelling microscopy allows localized spin dynamics to be characterized and plays important roles in nanoscale science and technology. However, nanoscale analysis of the ultrafast dynamics of itinerant magnetism, as well as its localized characteristics, should be pursued to advance further the investigation of quantum dynamics in functional structures of small systems. Here, we demonstrate the optical pump-probe scanning tunnelling microscopy technique, which enables the nanoscale probing of spin dynamics with the temporal resolution corresponding, in principle, to the optical pulse width. Spins are optically oriented using circularly polarized light, and their dynamics are probed by scanning tunnelling microscopy based on the optical pump-probe method. Spin relaxation in a single quantum well with a width of 6 nm was observed with a spatial resolution of ~1 nm. In addition to spin relaxation dynamics, spin precession, which provides an estimation of the Landé g factor, was observed successfully.

  16. Computer-Automated Static, Dynamic and Cellular Bone Histomorphometry

    PubMed Central

    Hong, Seung-Hyun; Jiang, Xi; Chen, Li; Josh, Pujan; Shin, Dong-Guk; Rowe, David

    2013-01-01

    Dynamic and cellular histomorphometry of trabeculae is the most biologically relevant way of assessing steady state bone health. Traditional measurement involves manual visual feature identification by a trained and qualified professional. Inherent with this methodology is the time and cost expenditure, as well as the subjectivity that naturally arises under human visual inspection. In this work, we propose a rapidly deployable, automated, and objective method for dynamic histomorphometry. We demonstrate that our method is highly effective in assessing cellular activities in distal femur and vertebra of mice which are injected with calcein and alizarin complexone 7 and 2 days prior to sacrifice. The mineralized bone tissues of mice are cryosectioned using a tape transfer protocol. A sequential workflow is implemented in which endogenous fluorescent signals (bone mineral, green and red mineralization lines), tartrate resistant acid phosphatase identified by ELF-97 and alkaline phosphatase identified by Fast Red are captured as individual tiled images of the section for each fluorescent color. All the images are then submitted to an image analysis pipeline that automates identification of the mineralized regions of bone and selection of a region of interest. The TRAP and AP stained images are aligned to the mineralized image using strategically placed fluorescent registration beads. Fluorescent signals are identified and are related to the trabecular surface within the ROI. Subsequently, the pipelined method computes static measurements, dynamic measurements, and cellular activities of osteoclast and osteoblast related to the trabecular surface. Our method has been applied to the distal femurs and vertebrae of 8 and 16 week old male and female C57Bl/6J mice. The histomorphometric results reveal a significantly greater bone turnover rate in female in contrast to male irrespective of age, validating similar outcomes reported by other studies. PMID:25019033

  17. Cellular Biotechnology Operations Support System Fluid Dynamics Investigation

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Aboard the International Space Station (ISS), the Tissue Culture Medium (TCM) is the bioreactor vessel in which cell cultures are grown. With its two syringe ports, it is much like a bag used to administer intravenous fluid, except it allows gas exchange needed for life. The TCM contains cell culture medium, and when frozen cells are flown to the ISS, they are thawed and introduced to the TCM through the syringe ports. In the Cellular Biotechnology Operations Support System-Fluid Dynamics Investigation (CBOSS-FDI) experiment, several mixing procedures are being assessed to determine which method achieves the most uniform mixing of growing cells and culture medium.

  18. Dynamic Force Sensing Using an Optically Trapped Probing System.

    PubMed

    Huang, Yanan; Cheng, Peng; Menq, Chia-Hsiang

    2011-12-01

    This paper presents the design of an adaptive observer that is implemented to enable real-time dynamic force sensing and parameter estimation in an optically trapped probing system. According to the principle of separation of estimation and control, the design of this observer is independent of that of the feedback controller when operating within the linear range of the optical trap. Dynamic force sensing, probe steering/clamping, and Brownian motion control can, therefore, be developed separately and activated simultaneously. The adaptive observer utilizes the measured motion of the trapped probe and input control effort to recursively estimate the probe-sample interaction force in real time, along with the estimation of the probing system's trapping bandwidth. This capability is very important to achieving accurate dynamic force sensing in a time-varying process, wherein the trapping dynamics is nonstationary due to local variations of the surrounding medium. The adaptive estimator utilizes the Kalman filter algorithm to compute the time-varying gain in real time and minimize the estimation error for force probing. A series of experiments are conducted to validate the design of and assess the performance of the adaptive observer. PMID:24382944

  19. Does a polymer chain probe solvent dynamics?

    NASA Astrophysics Data System (ADS)

    Peterson, Steve; Echeverria, Isabel; Schrag, John

    2001-03-01

    We have examined the dynamics of polyisoprene (both in bulk and in solution) using viscoelastic and oscillatory flow birefringence measurements. Surprisingly, the breadth of the relaxation time spectrum for the polymer appears to narrow significantly when going from bulk to solution conditions. This suggests an apparent flexibility difference in the polymer that may actually reflect dynamic spatial heterogeneity in the solvent (a glass former). Our results suggest a connection with experimental evidence of dynamic heterogeneities in glass forming liquids (Ediger, M.D., Annu. Rev. Phys. Chem., 2000, 51:99-128) and results of molecular dynamics simulations (Donati, C., et al., PRL, 80, 11, 1998).

  20. Dynamical theory of active cellular response to external stress.

    PubMed

    De, Rumi; Safran, Samuel A

    2008-09-01

    We present a comprehensive, theoretical treatment of the orientational response to external stress of active, contractile cells embedded in a gel-like elastic medium. The theory includes both the forces that arise from the deformation of the matrix as well as forces due to the internal regulation of the stress fibers and focal adhesions of the cell. We calculate the time-dependent response of both the magnitude and the direction of the elastic dipole that characterizes the active forces exerted by the cell, for various situations. For static or quasistatic external stress, cells orient parallel to the stress while for high frequency dynamic external stress, cells orient nearly perpendicular. Both numerical and analytical calculations of these effects are presented. In addition we predict the relaxation time for the cellular response for both slowly and rapidly varying external stresses; several characteristic scaling regimes for the relaxation time as a function of applied frequency are predicted. We also treat the case of cells for which the regulation of the stress fibers and focal adhesions is controlled by strain (instead of stress) and show that the predicted dependence of the cellular orientation on the Poisson ratio of the matrix can differentiate strain vs stress regulation of cellular response. PMID:18851081

  1. Dynamical theory of active cellular response to external stress

    NASA Astrophysics Data System (ADS)

    de, Rumi; Safran, Samuel A.

    2008-09-01

    We present a comprehensive, theoretical treatment of the orientational response to external stress of active, contractile cells embedded in a gel-like elastic medium. The theory includes both the forces that arise from the deformation of the matrix as well as forces due to the internal regulation of the stress fibers and focal adhesions of the cell. We calculate the time-dependent response of both the magnitude and the direction of the elastic dipole that characterizes the active forces exerted by the cell, for various situations. For static or quasistatic external stress, cells orient parallel to the stress while for high frequency dynamic external stress, cells orient nearly perpendicular. Both numerical and analytical calculations of these effects are presented. In addition we predict the relaxation time for the cellular response for both slowly and rapidly varying external stresses; several characteristic scaling regimes for the relaxation time as a function of applied frequency are predicted. We also treat the case of cells for which the regulation of the stress fibers and focal adhesions is controlled by strain (instead of stress) and show that the predicted dependence of the cellular orientation on the Poisson ratio of the matrix can differentiate strain vs stress regulation of cellular response.

  2. Mosquito population dynamics from cellular automata-based simulation

    NASA Astrophysics Data System (ADS)

    Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

    2016-02-01

    In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.

  3. Multiparametric cytometry for exploration of complex cellular dynamics.

    PubMed

    Gondois-Rey, Françoise; Granjeaud, Samuel; Kieu, Suong Le Thi; Herrera, Diana; Hirsch, Ivan; Olive, Daniel

    2012-04-01

    The development of polychromatic cytometry has contributed to significant progress in the field of human immunology. Although numerous functional studies of rare cell populations have been performed using this technology, here we used polychromatic cytometry to explore the dynamics of complex cellular systems implicated in innate immunity. We used PBMC stimulated with live influenza virus as an experimental model. We studied the time course of activation of PBMC, which contain DC, monocytes, and NK cells, all of which are, in addition to their innate immune properties, susceptible to Flu infection. We developed 12 color panels to investigate intracellular expression of IFN-α, TNF-α, IL-12, IL-6, IFN-γ, CD107, and influenza virus nucleoprotein simultaneously in these cell populations. These panels allowed reproducible determination of activation markers induced in DC after their direct exposure to various stimulations or in NK cells by indirect DC-mediated activation within the complex cellular environment. The ability to use a low number of cells and reduced quantities of reagents permitted us to perform kinetic experiments. The power of polychromatic cytometry associated with bioinformatic tools allowed us to analyze the multiple functional data generated as dynamic clustering maps. These maps present a readily understandable view of activation events induced in different populations of PBMC. In addition, it reveals new information on the coordination of the complex pathways induced and on the cellular interactions that sustained indirect DC-mediated NK cell activation. Our work shows that polychromatic cytometry is a tool for discoveries in unexplored complex cell systems, at the crossroads of immunology and virology. © 2012 International Society for Advancement of Cytometry. PMID:22278900

  4. Dynamic Pressure Probes Developed for Supersonic Flow-Field Measurements

    NASA Technical Reports Server (NTRS)

    Porro, A. Robert

    2001-01-01

    A series of dynamic flow-field pressure probes were developed for use in large-scale supersonic wind tunnels at the NASA Glenn Research Center. These flow-field probes include pitot and static pressure probes that can capture fast-acting flow-field pressure transients occurring on a millisecond timescale. The pitot and static probes can be used to determine local Mach number time histories during a transient event. The flow-field pressure probe contains four major components: 1) Static pressure aerodynamic tip; 2) Pressure-sensing cartridge assembly; 3) Pitot pressure aerodynamic tip; 4) Mounting stem. This modular design allows for a variety of probe tips to be used for a specific application. Here, the focus is on flow-field pressure measurements in supersonic flows, so we developed a cone-cylinder static pressure tip and a pitot pressure tip. Alternatively, probe tips optimized for subsonic and transonic flows could be used with this design. The pressure-sensing cartridge assembly allows the simultaneous measurement of steady-state and transient pressure which allows continuous calibration of the dynamic pressure transducer.

  5. The solar probe and coronal dynamics

    NASA Technical Reports Server (NTRS)

    Belcher, J.; Heinemann, M.; Goodrich, C.

    1978-01-01

    The discovery of coronal holes led to basic changes in ideas about the structure of the low corona and its expansion into the solar wind. The nature of the energy flux is not understood. Current ideas include enhanced thermal conductivities, extended MHD wave heating, and wave momentum transfer, all in rapidly diverging geometries. There is little feel for the relative importance of these processes. The Solar Probe, with its penetration deep into the solar corona, could lead to observational constraints on their relative importance, and thus to an understanding of the origin of the solar wind. Observations from the Solar Probe will also bear on such questions as to whether small scale "intrastream" structure is common close to the Sun in open field-line regions, whether the properties of the wind are pronouncedly different over closed and open field-line regions at five solar radii, and many others. The resolution of these questions requires measurements of the magnetic field and of the proton and electron distribution functions.

  6. Probing neutron-proton dynamics by pions

    NASA Astrophysics Data System (ADS)

    Ikeno, Natsumi; Ono, Akira; Nara, Yasushi; Ohnishi, Akira

    2016-04-01

    In order to investigate the nuclear symmetry energy at high density, we study the pion production in central collisions of neutron-rich nuclei 132Sn+124Sn at 300 MeV/nucleon using a new approach that combines antisymmetrized molecular dynamics (AMD) and a hadronic cascade model (JAM). The dynamics of neutrons and protons is solved by AMD, and then pions and Δ resonances in the reaction process are handled by JAM. We see the mechanism by which the Δ resonance and pions are produced, reflecting the dynamics of neutrons and protons. We also investigate the impacts of cluster correlations as well as of the high-density symmetry energy on the nucleon dynamics and consequently on the pion ratio. We find that the Δ-/Δ++ production ratio agrees very well with the neutron-proton squared ratio (N/Z ) 2 in the high-density and high-momentum region. We show quantitatively that the Δ production ratio, and therefore (N/Z ) 2, are directly reflected in the π-/π+ ratio, with modification in the final stage of the reaction.

  7. Dinuclear Ruthenium(II) Complexes as Two-Photon, Time-Resolved Emission Microscopy Probes for Cellular DNA**

    PubMed Central

    Baggaley, Elizabeth; Gill, Martin R; Green, Nicola H; Turton, David; Sazanovich, Igor V; Botchway, Stanley W; Smythe, Carl; Haycock, John W; Weinstein, Julia A; Thomas, Jim A

    2014-01-01

    The first transition-metal complex-based two-photon absorbing luminescence lifetime probes for cellular DNA are presented. This allows cell imaging of DNA free from endogenous fluorophores and potentially facilitates deep tissue imaging. In this initial study, ruthenium(II) luminophores are used as phosphorescent lifetime imaging microscopy (PLIM) probes for nuclear DNA in both live and fixed cells. The DNA-bound probes display characteristic emission lifetimes of more than 160 ns, while shorter-lived cytoplasmic emission is also observed. These timescales are orders of magnitude longer than conventional FLIM, leading to previously unattainable levels of sensitivity, and autofluorescence-free imaging. PMID:24458590

  8. Stochastic cellular automata model for wildland fire spread dynamics

    NASA Astrophysics Data System (ADS)

    Maduro Almeida, Rodolfo; Macau, Elbert E. N.

    2011-03-01

    A stochastic cellular automata model for wildland fire spread under flat terrain and no-wind conditions is proposed and its dynamics is characterized and analyzed. One of three possible states characterizes each cell: vegetation cell, burning cell and burnt cell. The dynamics of fire spread is modeled as a stochastic event with an effective fire spread probability S which is a function of three probabilities that characterize: the proportion of vegetation cells across the lattice, the probability of a burning cell becomes burnt, and the probability of the fire spread from a burning cell to a neighboring vegetation cell. A set of simulation experiments is performed to analyze the effects of different values of the three probabilities in the fire pattern. Monte-Carlo simulations indicate that there is a critical line in the model parameter space that separates the set of parameters which a fire can propagate from those for which it cannot propagate. Finally, the relevance of the model is discussed under the light of computational experiments that illustrate the capability of the model catches both the dynamical and static qualitative properties of fire propagation.

  9. Cellular dynamics of neuronal migration in the hippocampus

    PubMed Central

    Hayashi, Kanehiro; Kubo, Ken-ichiro; Kitazawa, Ayako; Nakajima, Kazunori

    2015-01-01

    A fine structure of the hippocampus is required for proper functions, and disruption of this formation by neuronal migration defects during development may play a role in some psychiatric illnesses. During hippocampal development in rodents, pyramidal neurons in the Ammon's horn are mostly generated in the ventricular zone (VZ), spent as multipolar cells just above the VZ, and then migrate radially toward the pial surface, ultimately settling into the hippocampal plate. Although this process is similar to that of neocortical projection neurons, these are not identical. In addition to numerous histological studies, the development of novel techniques gives a clear picture of the cellular dynamics of hippocampal neurons, as well as neocortical neurons. In this article, we provide an overview of the cellular mechanisms of rodent hippocampal neuronal migration including those of dentate granule cells, especially focusing on the differences of migration modes between hippocampal neurons and neocortical neurons. The unique migration mode of hippocampal pyramidal neurons might enable clonally related cells in the Ammon's horn to distribute in a horizontal fashion. PMID:25964735

  10. Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics

    NASA Astrophysics Data System (ADS)

    Weng, Wenguo; Hasemi, Yuji; Fan, Weicheng

    A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.

  11. Myosins and cell dynamics in cellular slime molds.

    PubMed

    Yumura, Shigehiko; Uyeda, Taro Q P

    2003-01-01

    Myosin is a mechanochemical transducer and serves as a motor for various motile activities such as cell migration, cytokinesis, maintenance of cell shape, phagocytosis, and morphogenesis. Nonmuscle myosin in vivo does not either stay static at specific subcellular regions or construct highly organized structures, such as sarcomere in skeletal muscle cells. The cellular slime mold Dictyostelium discoideum is an ideal "model organism" for the investigation of cell movement and cytokinesis. The advantages of this organism prompted researchers to carry out pioneering cell biological, biochemical, and molecular genetic studies on myosin II, which resulted in elucidation of many fundamental features of function and regulation of this most abundant molecular motor. Furthermore, recent molecular biological research has revealed that many unconventional myosins play various functions in vivo. In this article, how myosins are organized and regulated in a dynamic manner in Dictyostelium cells is reviewed and discussed. PMID:12722951

  12. Cellular Manufacturing System with Dynamic Lot Size Material Handling

    NASA Astrophysics Data System (ADS)

    Khannan, M. S. A.; Maruf, A.; Wangsaputra, R.; Sutrisno, S.; Wibawa, T.

    2016-02-01

    Material Handling take as important role in Cellular Manufacturing System (CMS) design. In several study at CMS design material handling was assumed per pieces or with constant lot size. In real industrial practice, lot size may change during rolling period to cope with demand changes. This study develops CMS Model with Dynamic Lot Size Material Handling. Integer Linear Programming is used to solve the problem. Objective function of this model is minimizing total expected cost consisting machinery depreciation cost, operating costs, inter-cell material handling cost, intra-cell material handling cost, machine relocation costs, setup costs, and production planning cost. This model determines optimum cell formation and optimum lot size. Numerical examples are elaborated in the paper to ilustrate the characterictic of the model.

  13. Nonlinear dynamics of C-terminal tails in cellular microtubules

    NASA Astrophysics Data System (ADS)

    Sekulic, Dalibor L.; Sataric, Bogdan M.; Zdravkovic, Slobodan; Bugay, Aleksandr N.; Sataric, Miljko V.

    2016-07-01

    The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process.

  14. Modeling dynamics of HIV infected cells using stochastic cellular automaton

    NASA Astrophysics Data System (ADS)

    Precharattana, Monamorn; Triampo, Wannapong

    2014-08-01

    Ever since HIV was first diagnosed in human, a great number of scientific works have been undertaken to explore the biological mechanisms involved in the infection and progression of the disease. Several cellular automata (CA) models have been introduced to gain insights into the dynamics of the disease progression but none of them has taken into account effects of certain immune cells such as the dendritic cells (DCs) and the CD8+ T lymphocytes (CD8+ T cells). In this work, we present a CA model, which incorporates effects of the HIV specific immune response focusing on the cell-mediated immunities, and investigate the interaction between the host immune response and the HIV infected cells in the lymph nodes. The aim of our work is to propose a model more realistic than the one in Precharattana et al. (2010) [10], by incorporating roles of the DCs, the CD4+ T cells, and the CD8+ T cells into the model so that it would reproduce the HIV infection dynamics during the primary phase of HIV infection.

  15. Nonlinear dynamics of C-terminal tails in cellular microtubules.

    PubMed

    Sekulic, Dalibor L; Sataric, Bogdan M; Zdravkovic, Slobodan; Bugay, Aleksandr N; Sataric, Miljko V

    2016-07-01

    The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process. PMID:27475079

  16. A full computation-relevant topological dynamics classification of elementary cellular automata

    NASA Astrophysics Data System (ADS)

    Schüle, Martin; Stoop, Ruedi

    2012-12-01

    Cellular automata are both computational and dynamical systems. We give a complete classification of the dynamic behaviour of elementary cellular automata (ECA) in terms of fundamental dynamic system notions such as sensitivity and chaoticity. The "complex" ECA emerge to be sensitive, but not chaotic and not eventually weakly periodic. Based on this classification, we conjecture that elementary cellular automata capable of carrying out complex computations, such as needed for Turing-universality, are at the "edge of chaos."

  17. Ultrasonic Periodontal Probing Based on the Dynamic Wavelet Fingerprint

    NASA Astrophysics Data System (ADS)

    Hinders, Mark K.; Hou, Jidong

    2005-04-01

    Manual pocket depth probing has been widely used as a retrospective diagnosis method in periodontics. However, numerous studies have questioned its ability to accurately measure the anatomic pocket depth. In this paper, an ultrasonic periodontal probing method is described, which involves using a hollow water-filled probe to focus a narrow beam of ultrasound energy into and out of the periodontal pocket, followed by automatic processing of pulse-echo signals to obtain the periodontal pocket depth. The signal processing algorithm consists of three steps: peak detection/characterization, peak classification and peak identification. A dynamic wavelet fingerprint (DWFP) technique was first applied to detect suspected scatterers in the A-scan signal and generate a two-dimensional black and white pattern to characterize the local transient signal corresponding to each scatterer. These DWFP patterns were then classified by a two-dimensional FFT procedure and mapped to an inclination index curve. The location of the pocket bottom was identified as the third broad peak in the inclination index curve. The algorithm was tested on full mouth probing data from two sequential visits of 14 patients. Its performance was evaluated by comparing ultrasonic probing results with that of full-mouth manual probing at the same sites, which was taken as the `gold standard'.

  18. Ultrasonic Periodontal Probing Based on the Dynamic Wavelet Fingerprint

    NASA Astrophysics Data System (ADS)

    Hou, Jidong; Rose, S. Timothy; Hinders, Mark K.

    2005-12-01

    Manual pocket depth probing has been widely used as a retrospective diagnosis method in periodontics. However, numerous studies have questioned its ability to accurately measure the anatomic pocket depth. In this paper, an ultrasonic periodontal probing method is described, which involves using a hollow water-filled probe to focus a narrow beam of ultrasound energy into and out of the periodontal pocket, followed by automatic processing of pulse-echo signals to obtain the periodontal pocket depth. The signal processing algorithm consists of three steps: peak detection/characterization, peak classification, and peak identification. A dynamic wavelet fingerprint (DWFP) technique is first applied to detect suspected scatterers in the A-scan signal and generate a two-dimensional black and white pattern to characterize the local transient signal corresponding to each scatterer. These DWFP patterns are then classified by a two-dimensional FFT procedure and mapped to an inclination index curve. The location of the pocket bottom was identified as the third broad peak in the inclination index curve. The algorithm is tested on full-mouth probing data from two sequential visits of 14 patients. Its performance is evaluated by comparing ultrasonic probing results with that of full-mouth manual probing at the same sites, which is taken as the "gold standard."

  19. Probing the evolution of slow flow dynamics in metallic glasses

    NASA Astrophysics Data System (ADS)

    Luo, P.; Lu, Z.; Li, Y. Z.; Bai, H. Y.; Wen, P.; Wang, W. H.

    2016-03-01

    The dynamics of glass is of paramount importance for understanding glass, while experimental studies of it covering broad time and temperature ranges are fraught with difficulty. We employ a method which can probe the extremely slow dynamics in various glassy states in metallic glass (MG). The flow dynamics of as-cast MG is found to follow a universal Arrhenius behavior in a wide temperature range, and aged MG follows a stretched exponential function with a "magic" exponent number of 3/7. Our observations have implications for understanding the structural evolution of the slow flow and the issue of finite temperature divergence in MGs.

  20. Dynamic involvement of ATG5 in cellular stress responses

    PubMed Central

    Lin, H H; Lin, S-M; Chung, Y; Vonderfecht, S; Camden, J M; Flodby, P; Borok, Z; Limesand, K H; Mizushima, N; Ann, D K

    2014-01-01

    Autophagy maintains cell and tissue homeostasis through catabolic degradation. To better delineate the in vivo function for autophagy in adaptive responses to tissue injury, we examined the impact of compromised autophagy in mouse submandibular glands (SMGs) subjected to main excretory duct ligation. Blocking outflow from exocrine glands causes glandular atrophy by increased ductal pressure. Atg5f/−;Aqp5-Cre mice with salivary acinar-specific knockout (KO) of autophagy essential gene Atg5 were generated. While duct ligation induced autophagy and the expression of inflammatory mediators, SMGs in Atg5f/−;Aqp5-Cre mice, before ligation, already expressed higher levels of proinflammatory cytokine and Cdkn1a/p21 messages. Extended ligation period resulted in the caspase-3 activation and acinar cell death, which was delayed by Atg5 knockout. Moreover, expression of a set of senescence-associated secretory phenotype (SASP) factors was elevated in the post-ligated glands. Dysregulation of cell-cycle inhibitor CDKN1A/p21 and activation of senescence-associated β-galactosidase were detected in the stressed SMG duct cells. These senescence markers peaked at day 3 after ligation and partially resolved by day 7 in post-ligated SMGs of wild-type (WT) mice, but not in KO mice. The role of autophagy-related 5 (ATG5)-dependent autophagy in regulating the tempo, duration and magnitude of cellular stress responses in vivo was corroborated by in vitro studies using MEFs lacking ATG5 or autophagy-related 7 (ATG7) and autophagy inhibitors. Collectively, our results highlight the role of ATG5 in the dynamic regulation of ligation-induced cellular senescence and apoptosis, and suggest the involvement of autophagy resolution in salivary repair. PMID:25341032

  1. Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells.

    PubMed

    Xu, Hua; Gopalsamy, Ariamala; Hett, Erik C; Salter, Shores; Aulabaugh, Ann; Kyne, Robert E; Pierce, Betsy; Jones, Lyn H

    2016-07-14

    Proof of drug-target engagement in physiologically-relevant contexts is a key pillar of successful therapeutic target validation. We developed two orthogonal technologies, the cellular thermal shift assay (CETSA) and a covalent chemical probe reporter approach (harnessing sulfonyl fluoride tyrosine labeling and subsequent click chemistry) to measure the occupancy of the mRNA-decapping scavenger enzyme DcpS by a small molecule inhibitor in live cells. Enzyme affinity determined using isothermal dose response fingerprinting (ITDRFCETSA) and the concentration required to occupy 50% of the enzyme (OC50) using the chemical probe reporter assay were very similar. In this case, the chemical probe method worked well due to the long offset kinetics of the reversible inhibitor (determined using a fluorescent dye-tagged probe). This work suggests that CETSA could become the first choice assay to determine in-cell target engagement due to its simplicity. PMID:27216142

  2. Tracking single particle rotation: Probing dynamics in four dimensions

    DOE PAGESBeta

    Anthony, Stephen Michael; Yu, Yan

    2015-04-29

    Direct visualization and tracking of small particles at high spatial and temporal resolution provides a powerful approach to probing complex dynamics and interactions in chemical and biological processes. Analysis of the rotational dynamics of particles adds a new dimension of information that is otherwise impossible to obtain with conventional 3-D particle tracking. In this review, we survey recent advances in single-particle rotational tracking, with highlights on the rotational tracking of optically anisotropic Janus particles. Furthermore, strengths and weaknesses of the various particle tracking methods, and their applications are discussed.

  3. Probing ultrafast molecular dynamics in O2 using XUV/IR pump-probe studies

    NASA Astrophysics Data System (ADS)

    Ray, D.; Sturm, F. P.; Wright, T. W.; Ranitovic, P.; Shivaram, N. H.; Bocharova, I.; Belkacem, A.; Weber, Th.

    2015-05-01

    We investigate the molecular dynamics via different dissociative and autoionizing pathways in molecular oxygen using a pump-probe scheme with ultrashort extreme ultraviolet (XUV) laser pulses. Our primary focus is to study the molecular dynamics in the superexcited Rydberg states in a time-resolved manner. The O2 molecules are pumped by 20.2 eV and 23.1 eV XUV pulses (13th and 15th harmonics). Probing the relaxation dynamics with an infrared (IR) pulse at very long delays (100s of fs) enables us to measure the lifetimes of these Rydberg states. We also observe an enhancement and suppression of vibrational levels of the O2+ion due to the presence of IR. The high flux XUV pulses used for this experiment are generated in an Ar gas by IR pulses from our state-of-the-art 30 mJ, 50 Hz laser system. The pulses are overlapped with the supersonic jet in our Momentum Imaging for TimE Resolved Studies (MISTERS) setup. The cold target in our setup, combined with a very tight focussing geometry and a 3D momentum detection capability gives a high kinetic energy resolution. Molecular dynamics in other polyatomic molecules are also under investigation. Chemical Sciences Division, Lawrence Berkeley National Laboratory.

  4. Steady-state and time-resolved two-photon fluorescence microscopy: a versatile tool for probing cellular environment and function

    NASA Astrophysics Data System (ADS)

    Denicke, Stefan; Ehlers, Jan-Eric; Niesner, Raluca; Quentmeier, Stefan; Gericke, Karl-Heinz

    2007-09-01

    In the last decade, the two-photon fluorescence laser-scanning microscopy (TPLSM) has become an indispensable tool for the bioscientific and biomedical research. TPLSM techniques as well as their applications are currently experiencing a dramatic evolution and represent the focus of many biophysical research projects. In this work, we compare in detail two steady-state TPLSM techniques, i.e. single-beam scanning microscopy combined with point-detection (SB-PMT) and multi-beam scanning microscopy combined with synchronous detection (MB-CCD), as far as their technical characteristics relevant for the bioscientific research are concerned, i.e. optical performance and imaging speed. We demonstrate that the SB-PMT technique is more adequate for deep-tissue imaging (few 100 μm depth) than the MB-CCD technique, whereas only the MB-CCD technique enables high-speed imaging for characterizing the dynamics of fast biological phenomena. Novel applications of these techniques are additionally discussed. Moreover, we employ a time-resolved TPLSM technique, i.e. biexponential fluorescence lifetime imaging based on the cellular fluorescence of the nicotinamide pyridine dinucleotides NADH and NADPH, which allows us to probe for the first time the redox cellular metabolism of MIN6 cells (mutated insulin producing pancreatic β-cells) as well as to show the potential of this method for the specific and dynamic investigation of NADH- and NADPH-dependent cellular processes.

  5. Ultrafast dynamics in pentacene and tetracene probed using optical pump-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Thorsmølle, Verner; Averitt, Richard; Demsar, Jure; Chi, Xiaoliu; Tretiak, Sergie; Ramirez, Arthur; Taylor, Antoinette

    2004-03-01

    Here we present optical pump-probe measurements of photoinduced (PI) changes in the reflectivity and transmissivity of tetracene and pentacene single crystals. We studied the carrier relaxation dynamics as a function of probe photon energy aiming to elucidate the electronic structure and carrier dynamics in the singlet and triplet manifolds. We observe singlet exciton recombination, singlet fission, and triplet state absorption, which we can identify in the photoinduced (PI) absorption spectrum. In particular, both compounds display a broad long-lived (>>1ns) PI absorption. In tetracene this feature is centered at approximately 1.7 eV, while in pentacene it is centered around 1.4 eV and is very pronounced. The long relaxation time suggests that the state being probed is the triplet state T1 (i.e. T1->Tn). On the other hand, the width of the PI absorption band suggests that the final state is a band-like state at 1.7 eV (1.4 eV) above the triplet state in tetracene (pentacene). This observation supports the semiconductor band model.

  6. Protein-Coupled Fluorescent Probe To Visualize Potassium Ion Transition on Cellular Membranes.

    PubMed

    Hirata, Tomoya; Terai, Takuya; Yamamura, Hisao; Shimonishi, Manabu; Komatsu, Toru; Hanaoka, Kenjiro; Ueno, Tasuku; Imaizumi, Yuji; Nagano, Tetsuo; Urano, Yasuteru

    2016-03-01

    K(+) is the most abundant metal ion in cells, and changes of [K(+)] around cell membranes play important roles in physiological events. However, there is no practical method to selectively visualize [K(+)] at the surface of cells. To address this issue, we have developed a protein-coupled fluorescent probe for K(+), TLSHalo. TLSHalo is responsive to [K(+)] in the physiological range, with good selectivity over Na(+) and retains its K(+)-sensing properties after covalent conjugation with HaloTag protein. By using cells expressing HaloTag on the plasma membrane, we successfully directed TLSHalo specifically to the outer surface of target cells. This enabled us to visualize localized extracellular [K(+)] change with TLSHalo under a fluorescence microscope in real time. To confirm the experimental value of this system, we used TLSHalo to monitor extracellular [K(+)] change induced by K(+) ionophores or by activation of a native Ca(2+)-dependent K(+) channel (BK channel). Further, we show that K(+) efflux via BK channel induced by electrical stimulation at the bottom surface of the cells can be visualized with TLSHalo by means of total internal reflection fluorescence microscope (TIRFM) imaging. Our methodology should be useful to analyze physiological K(+) dynamics with high spatiotemporal resolution. PMID:26894407

  7. Fabrication and operation of GRIN probes for in vivo fluorescence cellular imaging of internal organs in small animals

    PubMed Central

    Kim, Jun Ki; Lee, Woei Ming; Kim, Pilhan; Choi, Myunghwan; Jung, Keehoon; Kim, Seonghoon; Yun, Seok Hyun

    2013-01-01

    Intravital fluorescence microscopy has emerged as a powerful technique to visualize cellular processes in vivo. However, the size of the objective lenses has limited physical accessibility to various tissue sites in the internal organs of small animals. The use of small-diameter probes using graded-index (GRIN) lenses expands the capabilities of conventional intravital microscopes into minimally invasive internal organs imaging. In this protocol, we describe the detailed steps for the fabrication of front- and side-view GRIN probes and the integration and operation of the probes in a confocal microscope for visualizing fluorescent cells and microvasculature in various murine organs. We further present longitudinal imaging of immune cells in renal allografts and the tumor development in the colon. The fabrication and integration can be completed in 5–7 hours, and a typical in vivo imaging session takes 1–2 hours. PMID:22767088

  8. Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics

    PubMed Central

    Li, Xinran; Wang, Xiang; Zhang, Xiaoli; Zhao, Mingkun; Tsang, Wai Lok; Zhang, Yanling; Yau, Richard Gar Wai; Weisman, Lois S.; Xu, Haoxing

    2013-01-01

    Phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] is a low-abundance phosphoinositide presumed to be localized to endosomes and lysosomes, where it recruits cytoplasmic peripheral proteins and regulates endolysosome-localized membrane channel activity. Cells lacking PI(3,5)P2 exhibit lysosomal trafficking defects, and human mutations in the PI(3,5)P2-metabolizing enzymes cause lysosome-related diseases. The spatial and temporal dynamics of PI(3,5)P2, however, remain unclear due to the lack of a reliable detection method. Of the seven known phosphoinositides, only PI(3,5)P2 binds, in the low nanomolar range, to a cytoplasmic phosphoinositide-interacting domain (ML1N) to activate late endosome and lysosome (LEL)-localized transient receptor potential Mucolipin 1 (TRPML1) channels. Here, we report the generation and characterization of a PI(3,5)P2-specific probe, generated by the fusion of fluorescence tags to the tandem repeats of ML1N. The probe was mainly localized to the membranes of Lamp1-positive compartments, and the localization pattern was dynamically altered by either mutations in the probe, or by genetically or pharmacologically manipulating the cellular levels of PI(3,5)P2. Through the use of time-lapse live-cell imaging, we found that the localization of the PI(3,5)P2 probe was regulated by serum withdrawal/addition, undergoing rapid changes immediately before membrane fusion of two LELs. Our development of a PI(3,5)P2-specific probe may facilitate studies of both intracellular signal transduction and membrane trafficking in the endosomes and lysosomes. PMID:24324172

  9. Nanoscale probing of dynamics in local molecular environments.

    PubMed

    Atkin, Joanna M; Sass, Paul M; Teichen, Paul E; Eaves, Joel D; Raschke, Markus B

    2015-11-19

    Vibrational spectroscopy can provide information about structure, coupling, and dynamics underlying the properties of complex molecular systems. While measurements of spectral line broadening can probe local chemical environments, the spatial averaging in conventional spectroscopies limits insight into underlying heterogeneity, in particular in disordered molecular solids. Here, using femtosecond infrared scattering scanning near-field optical microscopy (IR s-SNOM), we resolve in vibrational free-induction decay (FID) measurements a high degree of spatial heterogeneity in polytetrafluoroethylene (PTFE) as a dense molecular model system. In nanoscopic probe volumes as small as 10(3) vibrational oscillators, we approach the homogeneous response limit, with extended vibrational dephasing times of several picoseconds, that is, up to 10 times the inhomogeneous lifetime, and spatial average converging to the bulk ensemble response. We simulate the dynamics of relaxation with a finite set of local vibrational transitions subject to random modulations in frequency. The combined results suggest that the observed heterogeneity arises due to static and dynamic variations in the local molecular environment. This approach thus provides real-space and real-time visualization of the subensemble dynamics that define the properties of many functional materials. PMID:26528865

  10. Extrasynaptic Glutamate Receptor Activation as Cellular Bases for Dynamic Range Compression in Pyramidal Neurons

    PubMed Central

    Oikonomou, Katerina D.; Short, Shaina M.; Rich, Matthew T.; Antic, Srdjan D.

    2012-01-01

    Repetitive synaptic stimulation overcomes the ability of astrocytic processes to clear glutamate from the extracellular space, allowing some dendritic segments to become submerged in a pool of glutamate, for a brief period of time. This dynamic arrangement activates extrasynaptic NMDA receptors located on dendritic shafts. We used voltage-sensitive and calcium-sensitive dyes to probe dendritic function in this glutamate-rich location. An excess of glutamate in the extrasynaptic space was achieved either by repetitive synaptic stimulation or by glutamate iontophoresis onto the dendrites of pyramidal neurons. Two successive activations of synaptic inputs produced a typical NMDA spike, whereas five successive synaptic inputs produced characteristic plateau potentials, reminiscent of cortical UP states. While NMDA spikes were coupled with brief calcium transients highly restricted to the glutamate input site, the dendritic plateau potentials were accompanied by calcium influx along the entire dendritic branch. Once initiated, the glutamate-mediated dendritic plateau potentials could not be interrupted by negative voltage pulses. Activation of extrasynaptic NMDA receptors in cellular compartments void of spines is sufficient to initiate and support plateau potentials. The only requirement for sustained depolarizing events is a surplus of free glutamate near a group of extrasynaptic receptors. Highly non-linear dendritic spikes (plateau potentials) are summed in a highly sublinear fashion at the soma, revealing the cellular bases of signal compression in cortical circuits. Extrasynaptic NMDA receptors provide pyramidal neurons with a function analogous to a dynamic range compression in audio engineering. They limit or reduce the volume of “loud sounds” (i.e., strong glutamatergic inputs) and amplify “quiet sounds” (i.e., glutamatergic inputs that barely cross the dendritic threshold for local spike initiation). Our data also explain why consecutive cortical UP

  11. Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements

    NASA Astrophysics Data System (ADS)

    Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas

    2016-05-01

    Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).

  12. Cellular Automata Models Applied to the Study of Landslide Dynamics

    NASA Astrophysics Data System (ADS)

    Liucci, Luisa; Melelli, Laura; Suteanu, Cristian

    2015-04-01

    Landslides are caused by complex processes controlled by the interaction of numerous factors. Increasing efforts are being made to understand the spatial and temporal evolution of this phenomenon, and the use of remote sensing data is making significant contributions in improving forecast. This paper studies landslides seen as complex dynamic systems, in order to investigate their potential Self Organized Critical (SOC) behavior, and in particular, scale-invariant aspects of processes governing the spatial development of landslides and their temporal evolution, as well as the mechanisms involved in driving the system and keeping it in a critical state. For this purpose, we build Cellular Automata Models, which have been shown to be capable of reproducing the complexity of real world features using a small number of variables and simple rules, thus allowing for the reduction of the number of input parameters commonly used in the study of processes governing landslide evolution, such as those linked to the geomechanical properties of soils. This type of models has already been successfully applied in studying the dynamics of other natural hazards, such as earthquakes and forest fires. The basic structure of the model is composed of three modules: (i) An initialization module, which defines the topographic surface at time zero as a grid of square cells, each described by an altitude value; the surface is acquired from real Digital Elevation Models (DEMs). (ii) A transition function, which defines the rules used by the model to update the state of the system at each iteration. The rules use a stability criterion based on the slope angle and introduce a variable describing the weakening of the material over time, caused for example by rainfall. The weakening brings some sites of the system out of equilibrium thus causing the triggering of landslides, which propagate within the system through local interactions between neighboring cells. By using different rates of

  13. Role of cellular adhesions in tissue dynamics spectroscopy

    NASA Astrophysics Data System (ADS)

    Merrill, Daniel A.; An, Ran; Turek, John; Nolte, David

    2014-02-01

    Cellular adhesions play a critical role in cell behavior, and modified expression of cellular adhesion compounds has been linked to various cancers. We tested the role of cellular adhesions in drug response by studying three cellular culture models: three-dimensional tumor spheroids with well-developed cellular adhesions and extracellular matrix (ECM), dense three-dimensional cell pellets with moderate numbers of adhesions, and dilute three-dimensional cell suspensions in agarose having few adhesions. Our technique for measuring the drug response for the spheroids and cell pellets was biodynamic imaging (BDI), and for the suspensions was quasi-elastic light scattering (QELS). We tested several cytoskeletal chemotherapeutic drugs (nocodazole, cytochalasin-D, paclitaxel, and colchicine) on three cancer cell lines chosen from human colorectal adenocarcinoma (HT-29), human pancreatic carcinoma (MIA PaCa-2), and rat osteosarcoma (UMR-106) to exhibit differences in adhesion strength. Comparing tumor spheroid behavior to that of cell suspensions showed shifts in the spectral motion of the cancer tissues that match predictions based on different degrees of cell-cell contacts. The HT-29 cell line, which has the strongest adhesions in the spheroid model, exhibits anomalous behavior in some cases. These results highlight the importance of using three-dimensional tissue models in drug screening with cellular adhesions being a contributory factor in phenotypic differences between the drug responses of tissue and cells.

  14. Disruption of cellular elements and water in neurotoxicity: Studies using electron probe X-ray microanalysis

    SciTech Connect

    LoPachin, R.M. Jr.; Saubermann, A.J. )

    1990-12-01

    Regulation of elements and water in nerve cells is a complex, multifaceted process which appears to be vulnerable to neurotoxic events. However, much of our knowledge concerning the potential role of elements in nerve cell injury is limited by the relatively gross level of corresponding analyses. If we are to confirm and understand the proposed role, more precise and detailed information is needed. As indicated in this commentary, research employing electron probe microanalysis and digital X-ray imaging has begun to provide this necessary information. Recent EPMA studies of nerve and glial cells in the peripheral and central nervous systems have shown that each cell type and their corresponding morphologic compartments exhibit unique distributions of elements and water. The use of microprobe analysis has allowed us to document precisely how elements and water redistribute in morphological compartments of damaged nerve cells. Accumulating evidence from EPMA studies suggests that, rather than being an epiphenomenon, intracellular changes in diffusible elements might mediate the functional and structural consequences of neurotoxic insult. It is also evident from this research that elements other than Ca might play a pertinent role in the injury response and that changes in intraneuronal elemental composition might develop according to a specific temporal pattern. Therefore, rather than conducting end-point studies, longitudinal investigations are necessary to define the sequential pattern of elemental perturbation associated with a given neurotoxic event. Such research can also help identify the role of individual elements in the injury response. Future microprobe studies should be combined with measurements of ion levels to provide a comprehensive and dynamic view of elemental deregulation. 145 references.

  15. Dynamic piezoresponse force microscopy: Spatially resolved probing of polarization dynamics in time and voltage domains

    SciTech Connect

    Kumar, Amit; Ehara, Y; Wada, A.; Funakubo, Hiroshi; Griggio, Flavio; Trolier-McKinstry, Susan; Jesse, Stephen; Kalinin, Sergei V

    2012-01-01

    An approach for probing dynamic phenomena during hysteresis loop measurements in piezoresponse force microscopy (PFM) is developed. Dynamic PFM (D-PFM) necessitates development of 5-dimensional (5D) data acquisition protocols and associated methods for analysis and visualization of multidimensional data. Using a combination of multivariate statistical analysis and phenomenological fitting, we explore dynamic behavior during polarization switching in model ferroelectric films with dense ferroelastic domain structures and in ferroelectric capacitors. In polydomain films, multivariate analysis of the switching data suggests that ferroelectric and ferroelastic components can be decoupled and time dynamics can be explored. In capacitors, a strong correlation between polarization dynamics and microstructure is observed. The future potential of D-PFM for probing time-dependent hysteretic phenomena in ferroelectrics and ionic systems is discussed.

  16. Types or States? Cellular Dynamics and Regenerative Potential.

    PubMed

    Adler, Carolyn E; Sánchez Alvarado, Alejandro

    2015-11-01

    Many of our organs can maintain and repair themselves during homeostasis and injury, as a result of the action of tissue-specific, multipotent stem cells. However, recent evidence from mammalian systems suggests that injury stimulates dramatic plasticity, or transient changes in cell potential, in both stem cells and more differentiated cells. Planarian flatworms possess abundant stem cells, making them an exceptional model for understanding the cellular behavior underlying homeostasis and regeneration. Recent discoveries of cell lineages and regeneration-specific events provide an initial framework for unraveling the complex cellular contributions to regeneration. In this review, we discuss the concept of cellular plasticity in the context of planarian regeneration, and consider the possibility that pluripotency may be a transient, probabilistic state exhibited by stem cells. PMID:26437587

  17. Pump probe spectroscopy of quasiparticle dynamics in cuprate superconductors

    SciTech Connect

    Segre, Gino P.

    2001-05-01

    Pump probe spectroscopy is used to examine the picosecond response of a BSCCO thin film, and two YBCO crystals in the near infrared. The role of pump fluence and temperature have been closely examined in an effort to clarify the mechanism by which the quasiparticles rejoin the condensate. BSCCO results suggest that the recombination behavior is consistent with the d-wave density of states in that quasiparticles appear to relax to the nodes immediately before they rejoin the condensate. The first substantial investigation of polarized pump probe response in detwinned YBCO crystals is also reported. Dramatic doping dependent anisotropies along the a and b axes are observed in time and temperature resolved studies. Among many results, we highlight the discovery of an anomalous temperature and time dependence of a- axis response in optimally doped YBCO. We also report on the first observation of the photoinduced response in a magnetic field. We find the amplitude of the response, and in some cases, the dynamics considerably changed with the application of a 6T field. Finally, we speculate on two of the many theoretical directions stimulated by our results. We find that the two-fluid model suggests a mechanism to explain how changes at very low energies are visible to a high-energy probe. Also discussed are basic recombination processes which may play a role in the observed decay.

  18. SUPERGRANULES AS PROBES OF SOLAR CONVECTION ZONE DYNAMICS

    SciTech Connect

    Hathaway, David H.

    2012-04-10

    Supergranules are convection cells seen at the Sun's surface as a space filling pattern of horizontal flows. While typical supergranules have diameters of about 35 Mm, they exhibit a broad spectrum of sizes from {approx}10 Mm to {approx}100 Mm. Here we show that supergranules of different sizes can be used to probe the rotation rate in the Sun's outer convection zone. We find that the equatorial rotation rate as a function of depth as measured by global helioseismology matches the equatorial rotation as a function of wavelength for the supergranules. This suggests that supergranules are advected by flows at depths equal to their wavelengths and thus can be used to probe flows at those depths. The supergranule rotation profiles show that the surface shear layer, through which the rotation rate increases inward, extends to depths of {approx}50 Mm and to latitudes of at least 70 Degree-Sign . Typical supergranules are well observed at high latitudes and have a range of sizes that extend to greater depths than those typically available for measuring subsurface flows with local helioseismology. These characteristics indicate that probing the solar convection zone dynamics with supergranules can complement the results of helioseismology.

  19. Probing Dynamical Character of Neural Circuits by Using Fuzzy Logic

    NASA Astrophysics Data System (ADS)

    Hu, Hong; Shi, Zhongzhi

    2008-11-01

    Analytical study or designing of large-scale nonlinear neural circuits, especially for chaotic neural circuits, is a difficult task. Here we analyze the function of neural systems by probing the fuzzy logical framework of the neural cells' dynamical equations. In this paper, the fuzzy logical framework of neural cells is used to understand the nonlinear dynamic attributes of a common neural system, and we proved that if a neural system works in a non-chaotic way, a suitable fuzzy logical framework can be found and we can analyze or design such kind neural system similar to analyze or design a digit computer, but if a neural system works in a chaotic way, an approximation is needed for understanding the function of such neural system.

  20. Probing proton dynamics in molecules on an attosecond timescale

    NASA Astrophysics Data System (ADS)

    Baker, Sarah

    2007-06-01

    A new technique for probing the ultrafast structural rearrangements of light molecules following ionization was demonstrated by our group earlier this year. This technique, termed PACER (probing attosecond dynamics by chirp encoded recollision), interrogates the motion of intramolecular nuclei following ionization via the process of high-harmonic generation (HHG). The strength of harmonic emission on return of the continuum electron wavepacket is weaker the more nuclear motion has occurred in the short time window since ionization. Moreover, since different harmonic orders are emitted at different times, dynamical information is gained by simply recording an harmonic spectrum and examining the change in signal as a function of order (which maps directly to time). Previously the nuclear dynamics of H2^+ and D2^+ were reliably determined at a temporal resolution limited by the difference in emission time of successive harmonic orders (roughly 100 as). The time window accessed in the measurement was 0.9 -- 1.5 fs following ionization. Enlargement of this time window would be a valuable extension to the PACER technique. To this end, we have now performed a PACER measurement in H2 and D2 at longer pump wavelengths (increasing the average electron return time). This work was conducted at the Advanced Laser Light Source facility, using a HE-TOPAS system producing 110 fs pulses in the mid-IR. We observed multiple harmonic orders at pump wavelengths of 1300 nm and 1450 nm using on-target intensities of < 1 x 10^14 Wcm-2. Data at the two pump wavelengths was found to be in qualitative agreement with the known nuclear dynamics of the H2^+ and D2^+ ions to a time 2.1 fs after ionisation. Extension of the time window accessed by the PACER measurement is therefore promising, however, at the pulse durations employed we expect partial alignment of the molecules during the pulse, and therefore the effect of two-centre interference must be carefully examined.

  1. Enhanced cellular uptake of a glutathione selective fluorogenic probe encapsulated in nanoparticles

    NASA Astrophysics Data System (ADS)

    Glówka, Eliza; Lamprecht, Alf; Ubrich, Nathalie; Maincent, Philippe; Lulek, Janina; Coulon, Joël; Leroy, Pierre

    2006-05-01

    Selective fluorogenic probes for the labelling of intracellular reduced glutathione (GSH), i.e. ortho-phthaldialdehyde (OPA) and naphthalene-2,3-dicarboxaldehyde (NDA), have been encapsulated in polymeric nanoparticles (NPs) and the ability of the NPs to enhance uptake of the probe by microbial cells has been evaluated. Preparation of the probe-loaded NPs composed of Eudragit® E was based on an oil-in-water emulsification solvent evaporation method using an ultrasonic probe and polyvinyl alcohol as the surfactant. The encapsulation efficiency of the probes in lyophilized NPs was determined using high performance liquid chromatography (HPLC). A higher encapsulation rate of NDA than OPA was found: 47.6 ± 9.9 (n = 6) and 2.1 ± 0.2% (n = 3), respectively. The NDA-loaded particle diameter and zeta potential were 224.6 ± 14.7 nm and +40.9 ± 6.5 mV, respectively. After 20 min incubation of cultured Candida albicans yeast cells with either free NDA or NDA-loaded NPs (final NDA concentration 100 µM), cells were harvested and corresponding lysates were analysed using HPLC coupled with spectrofluorimetric detection. Incubation of cells with NDA-loaded NPs increased intracellular levels of NDA-GSH adduct by about nine-fold in comparison with the free probe. Adhesion on the cells and the penetration behaviour of NPs loaded with either NDA or fluorescent label (Nile Red) were characterized qualitatively by confocal laser scanning microscopy.

  2. Resolving sub-cellular force dynamics using arrays of magnetic microposts

    NASA Astrophysics Data System (ADS)

    Reich, Daniel

    2010-03-01

    The biological response of cells to mechanical forces is integral to both normal cell function and the progression of many diseases, such as hypertensive vascular wall thickening. This likely results from the fact that mechanical stresses can directly affect many cellular processes, including signal transduction, gene expression, growth, differentiation, and survival. The need to understand the relationship between applied forces and the mechanical response of cells as a critical step towards understanding mechanotransduction calls for tools that can apply forces to cells while measuring their contractile response. This talk will describe an approach that simultaneously allows local mechanical stimulation of the adherent surface of a cell and spatially resolved measurement of the local force fields generated throughout the cell in response to this stimulation. Cells are cultured on the top surfaces of arrays of micrometer-scale posts made from a flexible elastomer (PDMS), and the contractile forces generated by an adherent cell bend the posts. Measurements of the displacement of each post allow the contractile force field of the cell to be mapped out with sub-cellular precision. To apply forces to cells, rod- shaped magnetic nanoparticles are embedded in some of the posts so that externally applied magnetic fields selectively deform these ``magnetic posts,'' thereby exerting tunable local, mechanical stresses to the adherent surface of attached cells. Alternatively, magnetic particles bound to or internalized by the cell may be employed to apply forces and torques to the cell. With either approach, measuring the deflection of the surrounding non-magnetic posts probes the full mechanical response of the cell to these stresses. Results that illustrate the temporal dynamics and spatial distribution of the non-local response of fibroblasts and smooth muscle cells to local stresses will be discussed.

  3. Maria Goeppert-Mayer Award Talk: Probing the structure and dynamics of biological networks

    NASA Astrophysics Data System (ADS)

    Albert, Reka

    2011-03-01

    The relationship between the structure and dynamics of networks is one of the central topics in network science. In the context of biological regulatory networks at the molecular to cellular level, the dynamics in question is often thought of as information propagation through the network. Quantitative dynamic models help to achieve an understanding of this process, but are difficult to construct and validate because of the scarcity of known mechanistic details and kinetic parameters. Structural and qualitative analysis is emerging as a feasible and useful alternative for interpreting biological signal transduction, and at the same time probing the structure-function relation of these networks. This analysis, however, necessitates the extension of current graph theoretical frameworks to incorporate features such as the positive or negative nature of interactions and synergistic behaviors among multiple components. This talk will present a method for structural analysis in an augmented graph framework that can probe the dynamics of information transfer. The first step is to expand the network to a richer representation that incorporates negative and synergistic regulation by the addition of pseudo-nodes and new edges. Our method simulates both knockout and constitutive activation of components as node disruptions, and takes into account the possible cascading effects of a node's disruption. We introduce the concept of elementary signaling mode (ESM), as the minimal set of nodes that can perform signal transduction independently. As a first application of this method we ranked the importance of signaling components by the effects of their perturbation on the ESMs of the network. Validation on various regulatory networks shows that this method can effectively uncover the essentiality of components mediating a signal transduction process and agrees with dynamic simulation results and experimental observations. Future applications include determining the ESMs that (do

  4. Local extracellular matrix alignment directs cellular protrusion dynamics and migration through Rac1 and FAK.

    PubMed

    Carey, Shawn P; Goldblatt, Zachary E; Martin, Karen E; Romero, Bethsabe; Williams, Rebecca M; Reinhart-King, Cynthia A

    2016-08-01

    Cell migration within 3D interstitial microenvironments is sensitive to extracellular matrix (ECM) properties, but the mechanisms that regulate migration guidance by 3D matrix features remain unclear. To examine the mechanisms underlying the cell migration response to aligned ECM, which is prevalent at the tumor-stroma interface, we utilized time-lapse microscopy to compare the behavior of MDA-MB-231 breast adenocarcinoma cells within randomly organized and well-aligned 3D collagen ECM. We developed a novel experimental system in which cellular morphodynamics during initial 3D cell spreading served as a reductionist model for the complex process of matrix-directed 3D cell migration. Using this approach, we found that ECM alignment induced spatial anisotropy of cells' matrix probing by promoting protrusion frequency, persistence, and lengthening along the alignment axis and suppressing protrusion dynamics orthogonal to alignment. Preference for on-axis behaviors was dependent upon FAK and Rac1 signaling and translated across length and time scales such that cells within aligned ECM exhibited accelerated elongation, front-rear polarization, and migration relative to cells in random ECM. Together, these findings indicate that adhesive and protrusive signaling allow cells to respond to coordinated physical cues in the ECM, promoting migration efficiency and cell migration guidance by 3D matrix structure. PMID:27384462

  5. Proceedings of "Optical Probes of Dynamics in Complex Environments"

    SciTech Connect

    Sension, R; Tokmakoff, A

    2008-04-01

    This document contains the proceedings from the symposium on Optical Probes of Dynamics in Complex Environments, which organized as part of the 235th National Meeting of the American Chemical Society in New Orleans, LA from April 6 to 10, 2008. The study of molecular dynamics in chemical reaction and biological processes using time ƒresolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time resolved spectroscopy is central to all of DOEs grand challenges for fundamental energy science. This symposium brought together leaders in the field of ultrafast spectroscopy, including experimentalists, theoretical chemists, and simulators, to discuss the most recent scientific and technological advances. DOE support for this conference was used to help young US and international scientists travel to the meeting. The latest technology in ultrafast infrared, optical, and xray spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  6. Spin probe dynamics of n-hexadecane in confined geometry

    NASA Astrophysics Data System (ADS)

    Lukešová, Miroslava; Švajdlenková, Helena; Sippel, Pit; Macová, Eva; Berek, Dušan; Loidl, Alois; Bartoš, Josef

    2015-02-01

    A combined study of the rotational dynamics of the stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and the phase behavior of n-hexadecane (n-HXD) in the bulk and the confined states in a series of silica gels (SG) by means of ESR and DSC is presented. A slow to fast motion transition of the spin probe TEMPO in the bulk n-HXD occurs at T50 G,bulk ≪ Tm,bulk, i.e., well below the melting temperature due to its trapping and localized mobility in the interlamellar gap of the crystallites [J. Bartoš, H. Švajdlenková, M. Zaleski, M. Edelmann, M. Lukešová, Physica B 430, 99 (2013)]. On the other hand, the dynamics of the TEMPO in the confined systems is strongly slowing down with T50 G (Dpore) >Tm(Dpore) and slightly increases with the pore size Dpore = 60, 100 and 300 Å of the SG's. At the same time, both the corresponding melting temperature, Tm (Dpore), and melting enthalpy, ΔHm (Dpore), decrease with Dpore together with the mutual anti-correlation between T50 G and Tm as a function of the inverse of pore diameter, 1/Dpore. Moreover, the dynamic heterogeneity of the TEMPO in the confined state below T50 G (Dpore) is closely related to the phase transformation. The strong slowing down of the spin probe motion likely results from its preferential localization at the interface layer of the matrix pore due to specific interaction of TEMPO molecules with the polar silanol groups of the SG matrix. This is supported by special study on a series of the variously filled n-HXD/SG systems, other similar experimental findings as well as by theoretical spectral argument.

  7. Dynamic cellular uptake of mixed-monolayer protected nanoparticles.

    PubMed

    Carney, Randy P; Carney, Tamara M; Mueller, Marie; Stellacci, Francesco

    2012-12-01

    Nanoparticles (NPs) are gaining increasing attention for potential application in medicine; consequently, studying their interaction with cells is of central importance. We found that both ligand arrangement and composition on gold nanoparticles play a crucial role in their cellular internalization. In our previous investigation, we showed that 66-34OT nanoparticles coated with stripe-like domains of hydrophobic (octanethiol, OT, 34%) and hydrophilic (11-mercaptoundecane sulfonate, MUS, 66%) ligands permeated through the cellular lipid bilayer via passive diffusion, in addition to endo-/pino-cytosis. Here, we show an analysis of NP internalization by DC2.4, 3T3, and HeLa cells at two temperatures and multiple time points. We study four NPs that differ in their surface structures and ligand compositions and report on their cellular internalization by intracellular fluorescence quantification. Using confocal laser scanning microscopy we have found that all three cell types internalize the 66-34OT NPs more than particles coated only with MUS, or particles coated with a very similar coating but lacking any detectable ligand shell structure, or 'striped' particles but with a different composition (34-66OT) at multiple data points. PMID:22589060

  8. Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy

    SciTech Connect

    Plemmons, DA; Suri, PK; Flannigan, DJ

    2015-05-12

    In this Perspective, we provide an overview,of the field of ultrafast electron microscopy (UEM). We begin by briefly discussing the emergence of methods for probing ultrafast structural dynamics and the information that can be obtained. Distinctions are drawn between the two main types a probes for femtosecond (fs) dynamics fast electrons and X-ray photons and emphasis is placed on hour the nature of charged particles is exploited in ultrafast electron-based' experiments:. Following this, we describe the versatility enabled by the ease with which electron trajectories and velocities can be manipulated with transmission electron microscopy (TEM): hardware configurations, and we emphasize how this is translated to the ability to measure scattering intensities in real, reciprocal, and energy space from presurveyed and selected rianoscale volumes. Owing to decades of ongoing research and development into TEM instrumentation combined with advances in specimen holder technology, comprehensive experiments can be conducted on a wide range of materials in various phases via in situ methods. Next, we describe the basic operating concepts, of UEM, and we emphasize that its development has led to extension of several of the formidable capabilities of TEM into the fs domain, dins increasing the accessible temporal parameter spade by several orders of magnitude. We then divide UEM studies into those conducted in real (imaging), reciprocal (diffraction), and energy (spectroscopy) spate. We begin each of these sections by providing a brief description of the basic operating principles and the types of information that can be gathered followed by descriptions of how these approaches are applied in UM, the type of specimen parameter space that can be probed, and an example of the types of dynamics that can be resolved. We conclude with an Outlook section, wherein we share our perspective on some future directions of the field pertaining to continued instrument development and

  9. Effects of cellular homeostatic intrinsic plasticity on dynamical and computational properties of biological recurrent neural networks.

    PubMed

    Naudé, Jérémie; Cessac, Bruno; Berry, Hugues; Delord, Bruno

    2013-09-18

    Homeostatic intrinsic plasticity (HIP) is a ubiquitous cellular mechanism regulating neuronal activity, cardinal for the proper functioning of nervous systems. In invertebrates, HIP is critical for orchestrating stereotyped activity patterns. The functional impact of HIP remains more obscure in vertebrate networks, where higher order cognitive processes rely on complex neural dynamics. The hypothesis has emerged that HIP might control the complexity of activity dynamics in recurrent networks, with important computational consequences. However, conflicting results about the causal relationships between cellular HIP, network dynamics, and computational performance have arisen from machine-learning studies. Here, we assess how cellular HIP effects translate into collective dynamics and computational properties in biological recurrent networks. We develop a realistic multiscale model including a generic HIP rule regulating the neuronal threshold with actual molecular signaling pathways kinetics, Dale's principle, sparse connectivity, synaptic balance, and Hebbian synaptic plasticity (SP). Dynamic mean-field analysis and simulations unravel that HIP sets a working point at which inputs are transduced by large derivative ranges of the transfer function. This cellular mechanism ensures increased network dynamics complexity, robust balance with SP at the edge of chaos, and improved input separability. Although critically dependent upon balanced excitatory and inhibitory drives, these effects display striking robustness to changes in network architecture, learning rates, and input features. Thus, the mechanism we unveil might represent a ubiquitous cellular basis for complex dynamics in neural networks. Understanding this robustness is an important challenge to unraveling principles underlying self-organization around criticality in biological recurrent neural networks. PMID:24048833

  10. Evaluation of an alpha probe detector for in vitro cellular dosimetry.

    PubMed

    Hui, T E; James, A C; Jostes, R F; Schwartz, J L; Swinth, K L; Cross, F T

    1993-06-01

    This paper describes the design and testing of an alpha probe detector for the continuous measurement of the activity concentrations of alpha emitters in the culture media of in vitro cell suspension irradiation systems. The probe detector consists of a pen-size body housing a small silicon surface-barrier detector with a Mylar window. Theoretical calculations were performed to study the dependence of the alpha-energy spectrum on 1) the thickness of the Mylar barrier; 2) the Mylar-detector distance; and 3) the size of the detector window. These design parameters were selected by taking a compromise between the counting efficiency, the integrity of the detector, and its required range of application. The probe detector was tested using both chelated and unchelated 212Bi and 212Pb standard solutions; plate-out of these radionuclides on the Mylar barrier was observed for unchelated solutions. Alpha energy spectra were analyzed using a total integration technique. The measured activity concentrations and the calibrated values agree to within 4% for the chelated 212Bi and to within 6% for the unchelated 212Bi. The alpha probe detector can be used throughout an entire exposure time period to determine the total dose received by suspended cells, or at different time intervals to determine the dose rate in real time. PMID:8491621

  11. Cell-directed assembly on an integrated nanoelectronic/nanophotonic device for probing cellular responses on the nanoscale.

    SciTech Connect

    Brinker, C. Jeffrey; Dunphy, Darren Robert; Ashley, Carlee E.; Fan, Hongyou; Lopez, DeAnna (University of New Mexico, Albuquerque, NM); Simpson, Regina Lynn; Tallant, David Robert; Burckel, David Bruce; Baca, Helen Kennicott; Carnes, Eric C.; Singh, Seema

    2006-01-01

    Our discovery that the introduction of living cells (Saccharomyces cerevisiae) alters dramatically the evaporation driven self-assembly of lipid-silica nanostructures suggested the formation of novel bio/nano interfaces useful for cellular interrogation at the nanoscale. This one year ''out of the box'' LDRD focused on the localization of metallic and semi-conducting nanocrystals at the fluid, lipid-rich interface between S. cerevisiae and the surrounding phospholipid-templated silica nanostructure with the primary goal of creating Surface Enhanced Raman Spectroscopy (SERS)-active nanostructures and platforms for cellular integration into electrode arrays. Such structures are of interest for probing cellular responses to the onset of disease, understanding of cell-cell communication, and the development of cell-based bio-sensors. As SERS is known to be sensitive to the size and shape of metallic (principally gold and silver) nanocrystals, various sizes and shapes of nanocrystals were synthesized, functionalized and localized at the cellular surface by our ''cell-directed assembly'' approach. Laser scanning confocal microscopy, SEM, and in situ grazing incidence small angle x-ray scattering (GISAXS) experiments were performed to study metallic nanocrystal localization. Preliminary Raman spectroscopy studies were conducted to test for SERS activity. Interferometric lithography was used to construct high aspect ratio cylindrical holes on patterned gold substrates and electro-deposition experiments were performed in a preliminary attempt to create electrode arrays. A new printing procedure was also developed for cellular integration into nanostructured platforms that avoids solvent exposure and may mitigate osmotic stress. Using a different approach, substrates comprised of self-assembled nanoparticles in a phospholipid templated silica film were also developed. When printed on top of these substrates, the cells integrate themselves into the mesoporous silica film and

  12. A cellular automata model of Ebola virus dynamics

    NASA Astrophysics Data System (ADS)

    Burkhead, Emily; Hawkins, Jane

    2015-11-01

    We construct a stochastic cellular automaton (SCA) model for the spread of the Ebola virus (EBOV). We make substantial modifications to an existing SCA model used for HIV, introduced by others and studied by the authors. We give a rigorous analysis of the similarities between models due to the spread of virus and the typical immune response to it, and the differences which reflect the drastically different timing of the course of EBOV. We demonstrate output from the model and compare it with clinical data.

  13. Quantifying cellular interaction dynamics in 3-D fluorescence microscopy data

    PubMed Central

    Klauschen, Frederick; Ishii, Masaru; Qi, Hai; Bajénoff, Marc; Egen, Jackson G.; Germain, Ronald N.; Meier-Schellersheim, Martin

    2012-01-01

    The wealth of information available from advanced fluorescence imaging techniques used to analyze biological processes with high spatial and temporal resolution calls for high-throughput image analysis methods. Here, we describe a fully automated approach to analyzing cellular interaction behavior in 3-D fluorescence microscopy images. As example application we present the analysis of drug-induced and S1P1-knock-out-related changes in bone-osteoclast interactions. Moreover, we apply our approach to images showing the spatial association of dendritic cells with the fibroblastic reticular cell network within lymph nodes and to microscopy data about T-B lymphocyte synapse formation. Such analyses that yield important information about the molecular mechanisms determining cellular interaction behavior would be very difficult to perform with approaches that rely on manual/semi-automated analyses. This protocol integrates adaptive threshold segmentation, object detection, adaptive color channel merging and neighborhood analysis and permits rapid, standardized, quantitative analysis and comparison of the relevant features in large data sets. PMID:19696749

  14. Integrated Circuit-Based Biofabrication with Common Biomaterials for Probing Cellular Biomechanics.

    PubMed

    Sung, Chun-Yen; Yang, Chung-Yao; Yeh, J Andrew; Cheng, Chao-Min

    2016-02-01

    Recent advances in bioengineering have enabled the development of biomedical tools with modifiable surface features (small-scale architecture) to mimic extracellular matrices and aid in the development of well-controlled platforms that allow for the application of mechanical stimulation for studying cellular biomechanics. An overview of recent developments in common biomaterials that can be manufactured using integrated circuit-based biofabrication is presented. Integrated circuit-based biofabrication possesses advantages including mass and diverse production capacities for fabricating in vitro biomedical devices. This review highlights the use of common biomaterials that have been most frequently used to study cellular biomechanics. In addition, the influence of various small-scale characteristics on common biomaterial surfaces for a range of different cell types is discussed. PMID:26708959

  15. Probing cellular traction forces with magnetic nanowires and microfabricated force sensor arrays

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Chia; Kramer, Corinne M.; Chen, Christopher S.; Reich, Daniel H.

    2012-02-01

    In this paper, the use of magnetic nanowires for the study of cellular response to force is demonstrated. High-aspect ratio Ni rods with diameter 300 nm and lengths up to 20 μm were bound to or internalized by pulmonary artery smooth muscle cells (SMCs) cultured on arrays of flexible micropost force sensors. Forces and torques were applied to the cells by driving the nanowires with AC magnetic fields in the frequency range 0.1-10 Hz, and the changes in cellular contractile forces were recorded with the microposts. These local stimulations yield global force reinforcement of the cells’ traction forces, but this contractile reinforcement can be effectively suppressed upon addition of a calcium channel blocker, ruthenium red, suggesting the role of calcium channels in the mechanical response. The responsiveness of the SMCs to actuation depends on the frequency of the applied stimulation. These results show that the combination of magnetic nanoparticles and micropatterned, flexible substrates can provide new approaches to the study of cellular mechanotransduction.

  16. Statistical analysis of nanoparticle dosing in a dynamic cellular system

    NASA Astrophysics Data System (ADS)

    Summers, Huw D.; Rees, Paul; Holton, Mark D.; Rowan Brown, M.; Chappell, Sally C.; Smith, Paul J.; Errington, Rachel J.

    2011-03-01

    The delivery of nanoparticles into cells is important in therapeutic applications and in nanotoxicology. Nanoparticles are generally targeted to receptors on the surfaces of cells and internalized into endosomes by endocytosis, but the kinetics of the process and the way in which cell division redistributes the particles remain unclear. Here we show that the chance of success or failure of nanoparticle uptake and inheritance is random. Statistical analysis of nanoparticle-loaded endosomes indicates that particle capture is described by an over-dispersed Poisson probability distribution that is consistent with heterogeneous adsorption and internalization. Partitioning of nanoparticles in cell division is random and asymmetric, following a binomial distribution with mean probability of 0.52-0.72. These results show that cellular targeting of nanoparticles is inherently imprecise due to the randomness of nature at the molecular scale, and the statistical framework offers a way to predict nanoparticle dosage for therapy and for the study of nanotoxins.

  17. Dynamics of HIV infection on 2D cellular automata

    NASA Astrophysics Data System (ADS)

    Benyoussef, A.; HafidAllah, N. El; ElKenz, A.; Ez-Zahraouy, H.; Loulidi, M.

    2003-05-01

    We use a cellular automata approach to describe the interactions of the immune system with the human immunodeficiency virus (HIV). We study the evolution of HIV infection, particularly in the clinical latency period. The results we have obtained show the existence of four different behaviours in the plane of death rate of virus-death rate of infected T cell. These regions meet at a critical point, where the virus density and the infected T cell density remain invariant during the evolution of disease. We have introduced two kinds of treatments, the protease inhibitors and the RT inhibitors, in order to study their effects on the evolution of HIV infection. These treatments are powerful in decreasing the density of the virus in the blood and the delay of the AIDS onset.

  18. Phenomenological study of a cellular material behaviour under dynamic loadings

    NASA Astrophysics Data System (ADS)

    Bouix, R.; Viot, Ph.; Lataillade, J.-L.

    2006-08-01

    Polypropylene foams are cellular materials, which are often use to fill structures subjected to crash or violent impacts. Therefore, it is necessary to know and to characterise in experiments their mechanical behaviour in compression at high strain rates. So, several apparatus have been used in order to highlight the influence of strain rate, material density and also temperature. A split Hopkinson Pressure Bar has been used for impact tests, a fly wheel to test theses materials at medium strain rate and an electro-mechanical testing machine associated to a climatic chamber for temperature tests. Then, a rheological model has been used in order to describe the material behaviour. The mechanical response to compression of these foams presents three typical domains: a linear elastic step, a wide collapse plateau stress, which leads to a densification, which are related to a standard rheological model.

  19. Statistical analysis of nanoparticle dosing in a dynamic cellular system.

    PubMed

    Summers, Huw D; Rees, Paul; Holton, Mark D; Brown, M Rowan; Chappell, Sally C; Smith, Paul J; Errington, Rachel J

    2011-03-01

    The delivery of nanoparticles into cells is important in therapeutic applications and in nanotoxicology. Nanoparticles are generally targeted to receptors on the surfaces of cells and internalized into endosomes by endocytosis, but the kinetics of the process and the way in which cell division redistributes the particles remain unclear. Here we show that the chance of success or failure of nanoparticle uptake and inheritance is random. Statistical analysis of nanoparticle-loaded endosomes indicates that particle capture is described by an over-dispersed Poisson probability distribution that is consistent with heterogeneous adsorption and internalization. Partitioning of nanoparticles in cell division is random and asymmetric, following a binomial distribution with mean probability of 0.52-0.72. These results show that cellular targeting of nanoparticles is inherently imprecise due to the randomness of nature at the molecular scale, and the statistical framework offers a way to predict nanoparticle dosage for therapy and for the study of nanotoxins. PMID:21258333

  20. Molecular dynamics as observed with probes of different dimensions in thin polymer films

    NASA Astrophysics Data System (ADS)

    Zhao, Jiang; Zhang, Hao; Yang, Jingfa; Wang, Fuyi; Liu, Di

    Rotational motion of individual fluorescence molecules doped in thin films of poly vinylacetate (PVAc) was monitored by single molecule fluorescence de-focus microscopy. Perylendiimide and its derivatives of different dimension were chosen as probes for local dynamics. The results demonstrate that the local vibration mode detected by different molecules probe depends on dimension of the probes - the larger probes the lower frequency. The population of rotating probes is found to increase with temperature elevation, depending on the molecular dimension as well. The comparison of the results with thermo-dynamic measurements helps to shed new light on the physical picture of glass transition. Supported by MoST of China.

  1. Probing scale interaction in brain dynamics through synchronization.

    PubMed

    Barardi, Alessandro; Malagarriga, Daniel; Sancristobal, Belén; Garcia-Ojalvo, Jordi; Pons, Antonio J

    2014-10-01

    The mammalian brain operates in multiple spatial scales simultaneously, ranging from the microscopic scale of single neurons through the mesoscopic scale of cortical columns, to the macroscopic scale of brain areas. These levels of description are associated with distinct temporal scales, ranging from milliseconds in the case of neurons to tens of seconds in the case of brain areas. Here, we examine theoretically how these spatial and temporal scales interact in the functioning brain, by considering the coupled behaviour of two mesoscopic neural masses (NMs) that communicate with each other through a microscopic neuronal network (NN). We use the synchronization between the two NM models as a tool to probe the interaction between the mesoscopic scales of those neural populations and the microscopic scale of the mediating NN. The two NM oscillators are taken to operate in a low-frequency regime with different peak frequencies (and distinct dynamical behaviour). The microscopic neuronal population, in turn, is described by a network of several thousand excitatory and inhibitory spiking neurons operating in a synchronous irregular regime, in which the individual neurons fire very sparsely but collectively give rise to a well-defined rhythm in the gamma range. Our results show that this NN, which operates at a fast temporal scale, is indeed sufficient to mediate coupling between the two mesoscopic oscillators, which evolve dynamically at a slower scale. We also establish how this synchronization depends on the topological properties of the microscopic NN, on its size and on its oscillation frequency. PMID:25180311

  2. Probing carrier dynamics in nanostructures by picosecond cathodoluminescence.

    PubMed

    Merano, M; Sonderegger, S; Crottini, A; Collin, S; Renucci, P; Pelucchi, E; Malko, A; Baier, M H; Kapon, E; Deveaud, B; Ganière, J-D

    2005-11-24

    Picosecond and femtosecond spectroscopy allow the detailed study of carrier dynamics in nanostructured materials. In such experiments, a laser pulse normally excites several nanostructures at once. However, spectroscopic information may also be acquired using pulses from an electron beam in a modern electron microscope, exploiting a phenomenon called cathodoluminescence. This approach offers several advantages. The multimode imaging capabilities of the electron microscope enable the correlation of optical properties (via cathodoluminescence) with surface morphology (secondary electron mode) at the nanometre scale. The broad energy range of the electrons can excite wide-bandgap materials, such as diamond- or gallium-nitride-based structures that are not easily excited by conventional optical means. But perhaps most intriguingly, the small beam can probe a single selected nanostructure. Here we apply an original time-resolved cathodoluminescence set-up to describe carrier dynamics within single gallium-arsenide-based pyramidal nanostructures with a time resolution of 10 picoseconds and a spatial resolution of 50 nanometres. The behaviour of such charge carriers could be useful for evaluating elementary components in quantum computers, optical quantum gates or single photon sources for quantum cryptography. PMID:16306988

  3. FIR line profiles as probes of warm gas dynamics

    NASA Astrophysics Data System (ADS)

    Betz, A. L.; Boreiko, R. T.

    Measurements of the shapes, velocities, and intensities of FIR lines all help to probe the dynamics, physical associations, and excitation conditions of warm gas in molecular clouds. With this in mind, we have observed the J=9-8, 12-11,14-13, and 16-15 lines of (12)CO and the 158 micron line of C II in a number of positions in 4 selected clouds. The data were obtained with a laser heterodyne spectrometer aboard NASA's Kuiper Airborne Observatory. Line measurements at 0.6 km/s resolution allow us to resolve the profiles completely, and thereby to distinguish between UV-and shock-heating mechanisms for the high-excitation gas. For CO, the high-J linewidths lie in the range of 4-20 km/s (FWHM), similar to those observed for low-J (J less than 4) transitions in these sources. This correspondence suggests that the hotter gas (T = 200-600 K) is dynamically linked to the quiescent gas component, perhaps by association with the UV-heated peripheries of the numerous cloud clumps. Much of the C II emission is thought to emanate from these cloud peripheries, but the line profiles generally do not match those seen in CO. None of the observed sources show any evidence in high-J (12)CO emission for shock-excitation (i.e., linewidths greater than 30 km/s).

  4. Probing cytoskeleton dynamics by intracellular particle transport analysis

    NASA Astrophysics Data System (ADS)

    Götz, M.; Hodeck, K. F.; Witzel, P.; Nandi, A.; Lindner, B.; Heinrich, D.

    2015-07-01

    All cellular functions arise from the transport of molecules through a heterogeneous, highly dynamic cell interior for intracellular signaling. Here, the impact of intracellular architecture and cytoskeleton dynamics on transport processes is revealed by high-resolution single particle tracking within living cells, in combination with time-resolved local mean squared displacement (I-MSD) analysis. We apply the I-MSD analysis to trajectories of 200 nm silica particles within living cells of Dictyostelium discoideum obtained by high resolution spinning disc confocal microscopy with a frame rate of 100 fps and imaging in one fixed focal plane. We investigate phases of motor-driven active transport and subdiffusion, normal diffusion, as well as superdiffusion with high spatial and temporal resolution. Active directed intracellular motion is attributed to microtubule associated molecular motor driven transport with average absolute velocities of 2.8 μm s-1 for 200 nm diameter particles. Diffusion processes of these particles within wild-type cells are found to exhibit diffusion constants ranging across two orders of magnitude from subdiffusive to superdiffusive behavior. This type of analysis might prove of ample importance for medical applications, like targeted drug treatment of cells by nano-sized carriers or innovative diagnostic assays.

  5. Dynamic fragmentation of cellular, ice-templated alumina scaffolds

    NASA Astrophysics Data System (ADS)

    Tan, Yi Ming; Cervantes, Octavio; Nam, SeanWoo; Molitoris, John D.; Hooper, Joseph P.

    2016-01-01

    We examine the dynamic failure of ice-templated freeze-cast alumina scaffolds that are being considered as biomimetic hierarchical structures. Three porosities of alumina freeze-cast structures were fabricated, and a systematic variation in microstructural properties such as lamellar width and thickness was observed with changing porosity. Dynamic impact tests were performed in a light-gas gun to examine the failure properties of these materials under high strain-rate loading. Nearly complete delamination was observed following impact, along with characteristic cracking across the lamellar width. Average fragment size decreases with increasing porosity, and a theoretical model was developed to explain this behavior based on microstructural changes. Using an energy balance between kinetic, strain, and surface energies within a single lamella, we are able to accurately predict the characteristic fragment size using only standard material properties of bulk alumina.

  6. Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming

    PubMed Central

    Shchuka, Virlana M.; Malek-Gilani, Nakisa; Singh, Gurdeep; Langroudi, Lida; Dhaliwal, Navroop K.; Moorthy, Sakthi D.; Davidson, Scott; Macpherson, Neil N.; Mitchell, Jennifer A.

    2015-01-01

    Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells. PMID:26193323

  7. Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming.

    PubMed

    Shchuka, Virlana M; Malek-Gilani, Nakisa; Singh, Gurdeep; Langroudi, Lida; Dhaliwal, Navroop K; Moorthy, Sakthi D; Davidson, Scott; Macpherson, Neil N; Mitchell, Jennifer A

    2015-01-01

    Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells. PMID:26193323

  8. Dynamical modeling and analysis of large cellular regulatory networks

    NASA Astrophysics Data System (ADS)

    Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.

    2013-06-01

    The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

  9. Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts.

    PubMed

    Le Bihan, Marie-Catherine; Barrio-Hernandez, Inigo; Mortensen, Tenna Pavia; Henningsen, Jeanette; Jensen, Søren Skov; Bigot, Anne; Blagoev, Blagoy; Butler-Browne, Gillian; Kratchmarova, Irina

    2015-08-01

    Muscle stem cells, or satellite cells, play an important role in the maintenance and repair of muscle tissue and have the capacity to proliferate and differentiate in response to physiological or environmental changes. Although they have been extensively studied, the key regulatory steps and the complex temporal protein dynamics accompanying the differentiation of primary human muscle cells remain poorly understood. Here, we demonstrate the advantages of applying a MS-based quantitative approach, stable isotope labeling by amino acids in cell culture (SILAC), for studying human myogenesis in vitro and characterize the fine-tuned changes in protein expression underlying the dramatic phenotypic conversion of primary mononucleated human muscle cells during in vitro differentiation to form multinucleated myotubes. Using an exclusively optimized triple encoding SILAC procedure, we generated dynamic expression profiles during the course of myogenic differentiation and quantified 2240 proteins, 243 of which were regulated. These changes in protein expression occurred in sequential waves and underlined vast reprogramming in key processes governing cell fate decisions, i.e., cell cycle withdrawal, RNA metabolism, cell adhesion, proteolysis, and cytoskeletal organization. In silico transcription factor target analysis demonstrated that the observed dynamic changes in the proteome could be attributed to a cascade of transcriptional events involving key myogenic regulatory factors as well as additional regulators not yet known to act on muscle differentiation. In addition, we created of a dynamic map of the developing myofibril, providing valuable insights into the formation and maturation of the contractile apparatus in vitro. Finally, our SILAC-based quantitative approach offered the possibility to follow the expression profiles of several muscle disease-associated proteins simultaneously and therefore could be a valuable resource for future studies investigating

  10. Free-Standing Kinked Silicon Nanowires for Probing Inter- and Intracellular Force Dynamics.

    PubMed

    Zimmerman, John F; Murray, Graeme F; Wang, Yucai; Jumper, John M; Austin, Jotham R; Tian, Bozhi

    2015-08-12

    Silicon nanowires (SiNWs) have emerged as a new class of materials with important applications in biology and medicine with current efforts having focused primarily on using substrate bound SiNW devices. However, developing devices capable of free-standing inter- and intracellular operation is an important next step in designing new synthetic cellular materials and tools for biophysical characterization. To demonstrate this, here we show that label free SiNWs can be internalized in multiple cell lines, forming robust cytoskeletal interfaces, and when kinked can serve as free-standing inter- and intracellular force probes capable of continuous extended (>1 h) force monitoring. Our results show that intercellular interactions exhibit ratcheting like behavior with force peaks of ∼69.6 pN/SiNW, while intracellular force peaks of ∼116.9 pN/SiNW were recorded during smooth muscle contraction. To accomplish this, we have introduced a simple single-capture dark-field/phase contrast optical imaging modality, scatter enhanced phase contrast (SEPC), which enables the simultaneous visualization of both cellular components and inorganic nanostructures. This approach demonstrates that rationally designed devices capable of substrate-independent operation are achievable, providing a simple and scalable method for continuous inter- and intracellular force dynamics studies. PMID:26192816

  11. Atlas of Cellular Dynamics during Zebrafish Adult Kidney Regeneration

    PubMed Central

    McCampbell, Kristen K.; Springer, Kristin N.; Wingert, Rebecca A.

    2015-01-01

    The zebrafish is a useful animal model to study the signaling pathways that orchestrate kidney regeneration, as its renal nephrons are simple, yet they maintain the biological complexity inherent to that of higher vertebrate organisms including mammals. Recent studies have suggested that administration of the aminoglycoside antibiotic gentamicin in zebrafish mimics human acute kidney injury (AKI) through the induction of nephron damage, but the timing and details of critical phenotypic events associated with the regeneration process, particularly in existing nephrons, have not been characterized. Here, we mapped the temporal progression of cellular and molecular changes that occur during renal epithelial regeneration of the proximal tubule in the adult zebrafish using a platform of histological and expression analysis techniques. This work establishes the timing of renal cell death after gentamicin injury, identifies proliferative compartments within the kidney, and documents gene expression changes associated with the regenerative response of proliferating cells. These data provide an important descriptive atlas that documents the series of events that ensue after damage in the zebrafish kidney, thus availing a valuable resource for the scientific community that can facilitate the implementation of zebrafish research to delineate the mechanisms that control renal regeneration. PMID:26089919

  12. Microfluidic parallel patterning and cellular delivery of molecules with a nanofountain probe.

    PubMed

    Kang, Wonmo; McNaughton, Rebecca L; Yavari, Fazel; Minary-Jolandan, Majid; Safi, Asmahan; Espinosa, Horacio D

    2014-02-01

    This brief report describes a novel tool for microfluidic patterning of biomolecules and delivery of molecules into cells. The microdevice is based on integration of nanofountain probe (NFP) chips with packaging that creates a closed system and enables operation in liquid. The packaged NFP can be easily coupled to a micro/nano manipulator or atomic force microscope for precise position and force control. We demonstrate here the functionality of the device for continuous direct-write parallel patterning on a surface in air and in liquid. Because of the small volume of the probes (~3 pL), we can achieve flow rates as low as 1 fL/s and have dispensed liquid drops with submicron to 10 µm diameters in a liquid environment. Furthermore, we demonstrate that this microdevice can be used for delivery of molecules into single cells by transient permeabilization of the cell membrane (i.e., electroporation). The significant advantage of NFP-based electroporation compared with bulk electroporation and other transfection techniques is that it allows for precise and targeted delivery while minimizing stress to the cell. We discuss the ongoing development of the tool toward automated operation and its potential as a multifunctional device for microarray applications and time-dependent single-cell studies. PMID:23897012

  13. Use of specific glycosidases to probe cellular interactions in the sea urchin embryo.

    PubMed

    Idoni, Brian; Ghazarian, Haike; Metzenberg, Stan; Hutchins-Carroll, Virginia; Oppenheimer, Steven B; Carroll, Edward J

    2010-08-01

    We present an unusual and novel model for initial investigations of a putative role for specifically conformed glycans in cellular interactions. We have used alpha- and ss-amylase and alpha- and ss-glucosidase in dose-response experiments evaluating their effects on archenteron organization using the NIH designated sea urchin embryo model. In quantitative dose-response experiments, we show that defined activity levels of alpha-glucosidase and ss-amylase inhibited archenteron organization in living Lytechinus pictus gastrula embryos, whereas all concentrations of ss-glucosidase and alpha-amylase were without substantial effects on development. Product inhibition studies suggested that the enzymes were acting by their specific glycosidase activities and polyacrylamide gel electrophoresis suggested that there was no detectable protease contamination in the active enzyme samples. The results provide evidence for a role of glycans in sea urchin embryo cellular interactions with special reference to the possible structural conformation of these glycans based on the differential activities of the alpha- and ss-glycosidases. PMID:20435035

  14. Electric Field Modulation of Semiconductor Quantum Dot Photoluminescence: Insights Into the Design of Robust Voltage-Sensitive Cellular Imaging Probes.

    PubMed

    Rowland, Clare E; Susumu, Kimihiro; Stewart, Michael H; Oh, Eunkeu; Mäkinen, Antti J; O'Shaughnessy, Thomas J; Kushto, Gary; Wolak, Mason A; Erickson, Jeffrey S; Efros, Alexander L; Huston, Alan L; Delehanty, James B

    2015-10-14

    The intrinsic properties of quantum dots (QDs) and the growing ability to interface them controllably with living cells has far-reaching potential applications in probing cellular processes such as membrane action potential. We demonstrate that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect. PMID:26414396

  15. Stochasticity and universal dynamics in communicating cellular populations

    NASA Astrophysics Data System (ADS)

    Noorbakhsh, Javad; Mehta, Pankaj; Allyson Sgro Collaboration; David Schwab Collaboration; Troy Mestler Collaboration; Thomas Gregor Collaboration

    2014-03-01

    A fundamental problem in biology is to understand how biochemical networks within individual cells coordinate and control population-level behaviors. Our knowledge of these biochemical networks is often incomplete, with little known about the underlying kinetic parameters. Here, we present a general modeling approach for overcoming these challenges based on universality. We apply our approach to study the emergence of collective oscillations of the signaling molecule cAMP in populations of the social amoebae Dictyostelium discoideum and show that a simple two-dimensional dynamical system can reproduce signaling dynamics of single cells and successfully predict novel population-level behaviors. We reduce all the important parameters of our model to only two and will study its behavior through a phase diagram. This phase diagram determines conditions under which cells are quiet or oscillating either coherently or incoherently. Furthermore it allows us to study the effect of different model components such as stochasticity, multicellularity and signal preprocessing. A central finding of our model is that Dictyostelium exploit stochasticity within biochemical networks to control population level behaviors.

  16. Efficient Inference of Parsimonious Phenomenological Models of Cellular Dynamics Using S-Systems and Alternating Regression

    PubMed Central

    Daniels, Bryan C.; Nemenman, Ilya

    2015-01-01

    The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action kinetics typically found in cellular dynamics, maintains the efficiency of linear regression. We combine this approach with adaptive model selection to obtain efficient and parsimonious representations of cellular dynamics. The approach is tested by inferring the dynamics of yeast glycolysis from simulated data. With little computing time, it produces dynamical models with high predictive power and with structural complexity adapted to the difficulty of the inference problem. PMID:25806510

  17. Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport

    PubMed Central

    2013-01-01

    Background To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. Results To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the

  18. Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset

    PubMed Central

    Veiseh, Mandana; Kwon, Daniel H.; Borowsky, Alexander D.; Tolg, Cornelia; Leong, Hon S.; Lewis, John D.; Turley, Eva A.; Bissell, Mina J.

    2014-01-01

    Tumor heterogeneity confounds cancer diagnosis and the outcome of therapy, necessitating analysis of tumor cell subsets within the tumor mass. Elevated expression of hyaluronan (HA) and HA receptors, receptor for HA-mediated motility (RHAMM)/HA-mediated motility receptor and cluster designation 44 (CD44), in breast tumors correlates with poor outcome. We hypothesized that a probe for detecting HA–HA receptor interactions may reveal breast cancer (BCa) cell heterogeneity relevant to tumor progression. A fluorescent HA (F-HA) probe containing a mixture of polymer sizes typical of tumor microenvironments (10–480 kDa), multiplexed profiling, and flow cytometry were used to monitor HA binding to BCa cell lines of different molecular subtypes. Formulae were developed to quantify binding heterogeneity and to measure invasion in vivo. Two subsets exhibiting differential binding (HA−/low vs. HAhigh) were isolated and characterized for morphology, growth, and invasion in culture and as xenografts in vivo. F-HA–binding amounts and degree of heterogeneity varied with BCa subtype, were highest in the malignant basal-like cell lines, and decreased upon reversion to a nonmalignant phenotype. Binding amounts correlated with CD44 and RHAMM displayed but binding heterogeneity appeared to arise from a differential ability of HA receptor-positive subpopulations to interact with F-HA. HAhigh subpopulations exhibited significantly higher local invasion and lung micrometastases but, unexpectedly, lower proliferation than either unsorted parental cells or the HA−/low subpopulation. Querying F-HA binding to aggressive tumor cells reveals a previously undetected form of heterogeneity that predicts invasive/metastatic behavior and that may aid both early identification of cancer patients susceptible to metastasis, and detection/therapy of invasive BCa subpopulations. PMID:24733940

  19. Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour

    PubMed Central

    Fokkelman, Michiel; Balcıoğlu, Hayri E.; Klip, Janna E.; Yan, Kuan; Verbeek, Fons J.; Danen, Erik H. J.; van de Water, Bob

    2016-01-01

    Cancer cells migrate from the primary tumour into surrounding tissue in order to form metastasis. Cell migration is a highly complex process, which requires continuous remodelling and re-organization of the cytoskeleton and cell-matrix adhesions. Here, we aimed to identify genes controlling aspects of tumour cell migration, including the dynamic organization of cell-matrix adhesions and cellular traction forces. In a siRNA screen targeting most cell adhesion-related genes we identified 200+ genes that regulate size and/or dynamics of cell-matrix adhesions in MCF7 breast cancer cells. In a subsequent secondary screen, the 64 most effective genes were evaluated for growth factor-induced cell migration and validated by tertiary RNAi pool deconvolution experiments. Four validated hits showed significantly enlarged adhesions accompanied by reduced cell migration upon siRNA-mediated knockdown. Furthermore, loss of PPP1R12B, HIPK3 or RAC2 caused cells to exert higher traction forces, as determined by traction force microscopy with elastomeric micropillar post arrays, and led to considerably reduced force turnover. Altogether, we identified genes that co-regulate cell-matrix adhesion dynamics and traction force turnover, thereby modulating overall motility behaviour. PMID:27531518

  20. Logical Modeling and Dynamical Analysis of Cellular Networks

    PubMed Central

    Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, Claudine

    2016-01-01

    The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle. PMID:27303434

  1. Imaging cellular dynamics in vivo with multicolor fluorescent proteins

    NASA Astrophysics Data System (ADS)

    Hoffman, Robert M.

    2005-04-01

    The new field of in vivo cell biology is being developed with multi-colored fluorescent proteins. With the use of fluorescent proteins, the behavior of individual cells can be visualized in the living animal. An example of the new cell biology is dual-color fluorescence imaging using red fluorescent protein (RFP)-expressing tumors transplanted in green fluorescent protein (GFP)-expressing transgenic mice. These models show with great clarity the details of the tumor-stroma cell-cell interaction especially tumor-induced angiogenesis, tumor-infiltrating lymphocytes, stromal fibroblasts and macrophages. Another example is the color-coding of cells with RFP or GFP such that both cell types and their interaction can be simultaneously visualized in vivo. Stem cells can also be visualized and tracked in vivo with fluorescent proteins. Mice, in which the regulatory elements of the stem-cell marker nestin drive GFP expression, can be used to visualize hair follicle stem cells including their ability to form hair follicles as well as blood vessels. Dual-color cells expressing GFP in the nucleus and RFP in the cytoplasm enable real-time visualization of nuclear-cytoplasm dynamics including cell cycle events and apoptosis. Dual-color cells also enable the in vivo imaging of cell and nuclear deformation as well as trafficking in capillaries in living animals. Multiple-color labeling of cells will enable multiple events to be simultaneously visualized in vivo including cell-cell interaction, gene expression, ion fluxes, protein and organelle trafficking, chromosome dynamics and numerous other processes currently still studied in vitro.

  2. Probing cell membrane dynamics using plasmon coupling microscopy

    NASA Astrophysics Data System (ADS)

    Rong, Guoxin

    The plasma membrane of mammalian cells is depicted as a two-dimensional hybrid material which is compartmentalized into submicron-sized domains. These membrane domains play a pivotal role in cellular signaling processes due to selective recruitment of specific cell surface receptors. The structural dynamics of the membrane domains and their exact biological functions are, however, still unclear, partially due to the wave nature of light, which limits the optical resolution in the visible light to approximately 400 nm in conventional optical microscopy. Here, we provide a non-fluorescence based approach for monitoring distance changes on subdiffraction limit length scales in a conventional far-field optical microscope. This approach, which is referred to as plasmon coupling microscopy (PCM), utilizes the distance dependent near-field coupling between noble metal nanoparticle (NP) labels to resolve close contacts on the length scale of approximately one NP diameter. We firstly utilize this PCM strategy to resolve interparticle separations during individual encounters of gold NP labeled fibronectin-integrin complexes in living HeLa cells. We then further refine this ratiometric detection methodology by augmenting it with a polarization-sensitive detection, which enables simultaneous monitoring of the distance and conformation changes in NP dimers and clusters. We apply this polarization resolved PCM approach to characterize the structural lateral heterogeneity of cell membranes on sub-micron length scales. Finally, we demonstrate that PCM can provide quantitative information about the structural dynamics of individual epidermal growth factor receptor (ErbB1)-enriched membrane domains in living cells.

  3. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

    NASA Astrophysics Data System (ADS)

    Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng

    2008-04-01

    Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, β-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

  4. Complexes of IrIII-Octaethylporphyrin with Peptides as Probes for Sensing Cellular O2

    PubMed Central

    Koren, Klaus; Dmitriev, Ruslan I; Borisov, Sergey M; Papkovsky, Dmitri B; Klimant, Ingo

    2012-01-01

    IrIII–porphyrins are a relatively new group of phosphorescent dyes that have potential for oxygen sensing and labeling of biomolecules. The requirement of two axial ligands for the IrIII ion permits simple linkage of biomolecules by a one-step ligand-exchange reaction, for example, using precursor carbonyl chloride complexes and peptides containing histidine residue(s). Using this approach, we produced three complexes of IrIII–octaethylporphyrin with cell-penetrating (Ir1 and Ir2) and tumor-targeting (Ir3) peptides and studied their photophysical properties. All of the complexes were stable and possessed bright, long-decay (unquenched lifetimes exceeding 45 μs) phosphorescence at around 650 nm, with moderate sensitivity to oxygen. The Ir1 and Ir2 complexes showed positive staining of a number of mammalian cell types, thus demonstrating localization similar to endoplasmic reticulum and ATP- and temperature-independent intracellular accumulation (direct translocation mechanism). Their low photo- and cytotoxicity allows intracellular oxygen to be probed. PMID:22532338

  5. Combined Labelled and Label-free SERS Probes for Triplex Three-dimensional Cellular Imaging

    NASA Astrophysics Data System (ADS)

    Chen, Yong; Bai, Xiangru; Su, Le; Du, Zhanwei; Shen, Aiguo; Materny, Arnulf; Hu, Jiming

    2016-01-01

    Cells are complex chemical systems, where the molecular composition at different cellular locations and specific intracellular chemical interactions determine the biological function. An in-situ nondestructive characterization of the complicated chemical processes (like e.g. apoptosis) is the goal of our study. Here, we present the results of simultaneous and three-dimensional imaging of double organelles (nucleus and membrane) in single HeLa cells by means of either labelled or label-free surface-enhanced Raman spectroscopy (SERS). This combination of imaging with and without labels is not possible when using fluorescence microscopy. The SERS technique is used for a stereoscopic description of the intrinsic chemical nature of nuclei and the precise localization of folate (FA) and luteinizing hormone-releasing hormone (LHRH) on the membrane under highly confocal conditions. We also report on the time-dependent changes of cell nuclei as well as membrane receptor proteins during apoptosis analyzed by statistical multivariate methods. The multiplex three-dimensional SERS imaging technique allows for both temporal (real time) and spatial (multiple organelles and molecules in three-dimensional space) live-cell imaging and therefore provides a new and attractive 2D/3D tracing method in biomedicine on subcellular level.

  6. Tuning the cellular uptake properties of luminescent heterobimetallic iridium(III)-ruthenium(II) DNA imaging probes.

    PubMed

    Wragg, Ashley; Gill, Martin R; Turton, David; Adams, Harry; Roseveare, Thomas M; Smythe, Carl; Su, Xiaodi; Thomas, Jim A

    2014-10-20

    The synthesis of two new luminescent dinuclear Ir(III)-Ru(II) complexes containing tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine (tpphz) as the bridging ligand is reported. Unlike many other complexes incorporating cyclometalated Ir(III) moieties, these complexes display good water solubility, allowing the first cell-based study on Ir(III)-Ru(II) bioprobes to be carried out. Photophysical studies indicate that emission from each complex is from a Ru(II) excited state and both complexes display significant in vitro DNA-binding affinities. Cellular studies show that each complex is rapidly internalised by HeLa cells, in which they function as luminescent nuclear DNA-imaging agents for confocal microscopy. Furthermore, the uptake and nuclear targeting properties of the complex incorporating cyclometalating 2-(4-fluorophenyl)pyridine ligands around its Ir(III) centre is enhanced in comparison to the non-fluorinated analogue, indicating that fluorination may provide a route to promote cell uptake of transition-metal bioprobes. PMID:25208528

  7. Combined Labelled and Label-free SERS Probes for Triplex Three-dimensional Cellular Imaging.

    PubMed

    Chen, Yong; Bai, Xiangru; Su, Le; Du, Zhanwei; Shen, Aiguo; Materny, Arnulf; Hu, Jiming

    2016-01-01

    Cells are complex chemical systems, where the molecular composition at different cellular locations and specific intracellular chemical interactions determine the biological function. An in-situ nondestructive characterization of the complicated chemical processes (like e.g. apoptosis) is the goal of our study. Here, we present the results of simultaneous and three-dimensional imaging of double organelles (nucleus and membrane) in single HeLa cells by means of either labelled or label-free surface-enhanced Raman spectroscopy (SERS). This combination of imaging with and without labels is not possible when using fluorescence microscopy. The SERS technique is used for a stereoscopic description of the intrinsic chemical nature of nuclei and the precise localization of folate (FA) and luteinizing hormone-releasing hormone (LHRH) on the membrane under highly confocal conditions. We also report on the time-dependent changes of cell nuclei as well as membrane receptor proteins during apoptosis analyzed by statistical multivariate methods. The multiplex three-dimensional SERS imaging technique allows for both temporal (real time) and spatial (multiple organelles and molecules in three-dimensional space) live-cell imaging and therefore provides a new and attractive 2D/3D tracing method in biomedicine on subcellular level. PMID:26781186

  8. Combined Labelled and Label-free SERS Probes for Triplex Three-dimensional Cellular Imaging

    PubMed Central

    Chen, Yong; Bai, Xiangru; Su, Le; Du, Zhanwei; Shen, Aiguo; Materny, Arnulf; Hu, Jiming

    2016-01-01

    Cells are complex chemical systems, where the molecular composition at different cellular locations and specific intracellular chemical interactions determine the biological function. An in-situ nondestructive characterization of the complicated chemical processes (like e.g. apoptosis) is the goal of our study. Here, we present the results of simultaneous and three-dimensional imaging of double organelles (nucleus and membrane) in single HeLa cells by means of either labelled or label-free surface-enhanced Raman spectroscopy (SERS). This combination of imaging with and without labels is not possible when using fluorescence microscopy. The SERS technique is used for a stereoscopic description of the intrinsic chemical nature of nuclei and the precise localization of folate (FA) and luteinizing hormone-releasing hormone (LHRH) on the membrane under highly confocal conditions. We also report on the time-dependent changes of cell nuclei as well as membrane receptor proteins during apoptosis analyzed by statistical multivariate methods. The multiplex three-dimensional SERS imaging technique allows for both temporal (real time) and spatial (multiple organelles and molecules in three-dimensional space) live-cell imaging and therefore provides a new and attractive 2D/3D tracing method in biomedicine on subcellular level. PMID:26781186

  9. Dynamic self-organization of microwell-aggregated cellular mixtures.

    PubMed

    Song, Wei; Tung, Chih-Kuan; Lu, Yen-Chun; Pardo, Yehudah; Wu, Mingming; Das, Moumita; Kao, Der-I; Chen, Shuibing; Ma, Minglin

    2016-06-29

    Cells with different cohesive properties self-assemble in a spatiotemporal and context-dependent manner. Previous studies on cell self-organization mainly focused on the spontaneous structural development within a short period of time during which the cell numbers remained constant. However the effect of cell proliferation over time on the self-organization of cells is largely unexplored. Here, we studied the spatiotemporal dynamics of self-organization of a co-culture of MDA-MB-231 and MCF10A cells seeded in a well defined space (i.e. non-adherent microfabricated wells). When cell-growth was chemically inhibited, high cohesive MCF10A cells formed a core surrounded by low cohesive MDA-MB-231 cells on the periphery, consistent with the differential adhesion hypothesis (DAH). Interestingly, this aggregate morphology was completely inverted when the cells were free to grow. At an initial seeding ratio of 1 : 1 (MDA-MB-231 : MCF10A), the fast growing MCF10A cells segregated in the periphery while the slow growing MDA-MB-231 cells stayed in the core. Another morphology developed at an inequal seeding ratio (4 : 1), that is, the cell mixtures developed a side-by-side aggregate morphology. We conclude that the cell self-organization depends not only on the cell cohesive properties but also on the cell seeding ratio and proliferation. Furthermore, by taking advantage of the cell self-organization, we purified human embryonic stem cells-derived pancreatic progenitors (hESCs-PPs) from co-cultured feeder cells without using any additional tools or labels. PMID:27275624

  10. Imaging via complete cantilever dynamic detection: general dynamic mode imaging and spectroscopy in scanning probe microscopy.

    PubMed

    Somnath, Suhas; Collins, Liam; Matheson, Michael A; Sukumar, Sreenivas R; Kalinin, Sergei V; Jesse, Stephen

    2016-10-14

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify the findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip-sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques. PMID:27607339

  11. Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

    DOE PAGESBeta

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; Sukumar, Sreenivas R.; Kalinin, Sergei V.; Jesse, Stephen

    2016-09-08

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify themore » findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.« less

  12. Localization microscopy: mapping cellular dynamics with single molecules.

    PubMed

    Nelson, A J; Hess, S T

    2014-04-01

    has helped to illuminate many dynamic biological processes, such as the trajectories of molecules within living cells. This review discusses the concept and process of SRFLM imaging and investigates recent advances in SRFLM functionality. Since its announcement in 2006, SRFLM has been quickly adopted and modified by many researchers to help investigate questions whose answers lie below the diffraction limit. The versatility of the SRFLM technique has great promise for improving our understanding of cell biology at the molecular level. PMID:24611627

  13. Local collective motion analysis for multi-probe dynamic imaging and microrheology.

    PubMed

    Khan, Manas; Mason, Thomas G

    2016-08-01

    Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches. PMID:27269299

  14. Local collective motion analysis for multi-probe dynamic imaging and microrheology

    NASA Astrophysics Data System (ADS)

    Khan, Manas; Mason, Thomas G.

    2016-08-01

    Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

  15. Statistical analysis of cellular detonation dynamics from numerical simulations: one-step chemistry

    NASA Astrophysics Data System (ADS)

    Sharpe, G. J.; Radulescu, M. I.

    2011-10-01

    In this paper, two methods are developed for statistically analysing the nonlinear cellular dynamics from numerical simulations of gaseous detonations, one use of which is the systematic determination of detonation cell sizes from such simulations. Both these methods rely on signed vorticity records in which the individual families of transverse waves are captured independently. The first method involves an automated extraction of the main triple-point tracks from the vorticity records, allowing statistical analysis of the spacings between neighbouring tracks. The second method uses the autocorrelation function to spectrally analyse the vorticity records. These methods are then employed for a preliminary analysis of the cellular dynamics of the standard, idealized one-step chemistry model. Evidence is found for 'cell size doubling' bifurcations in the one-step model as the cellular dynamics become more irregular (e.g. as the activation is increased). It is also shown that the statistical models converge slowly due to systematic 'shot-to-shot' variation in the cellular dynamics for fixed parameters with different initial perturbations. Instead, it appears that a range of equally probable cell sizes can be obtained for given parameters.

  16. A SIMPLE CELLULAR AUTOMATON MODEL FOR HIGH-LEVEL VEGETATION DYNAMICS

    EPA Science Inventory

    We have produced a simple two-dimensional (ground-plan) cellular automata model of vegetation dynamics specifically to investigate high-level community processes. The model is probabilistic, with individual plant behavior determined by physiologically-based rules derived from a w...

  17. Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

    PubMed Central

    Christensen, Niels J.; Kepp, Kasper P.

    2013-01-01

    Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

  18. Changes in single-molecule integrin dynamics linked to local cellular behavior

    PubMed Central

    Jaqaman, Khuloud; Galbraith, James A.; Davidson, Michael W.; Galbraith, Catherine G.

    2016-01-01

    Recent advances in light microscopy permit visualization of the behavior of individual molecules within dense macromolecular ensembles in live cells. It is now conceptually possible to relate the dynamic organization of molecular machinery to cellular function. However, inherent heterogeneities, as well as disparities between spatial and temporal scales, pose substantial challenges in deriving such a relationship. New approaches are required to link discrete single-molecule behavior with continuous cellular-level processes. Here we combined intercalated molecular and cellular imaging with a computational framework to detect reproducible transient changes in the behavior of individual molecules that are linked to cellular behaviors. Applying our approach to integrin transmembrane receptors revealed a spatial density gradient underlying characteristic molecular density increases and mobility decreases, indicating the subsequent onset of local protrusive activity. Integrin mutants further revealed that these density and mobility transients are separable and depend on different binding domains within the integrin cytoplasmic tail. Our approach provides a generalizable paradigm for dissecting dynamic spatiotemporal molecular behaviors linked to local cellular events. PMID:27009207

  19. Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants.

    PubMed

    Baroux, Célia; Autran, Daphné

    2015-07-01

    Sexual reproduction in flowering plants offers a number of remarkable aspects to developmental biologists. First, the spore mother cells - precursors of the plant reproductive lineage - are specified late in development, as opposed to precocious germline isolation during embryogenesis in most animals. Second, unlike in most animals where meiosis directly produces gametes, plant meiosis entails the differentiation of a multicellular, haploid gametophyte, within which gametic as well as non-gametic accessory cells are formed. These observations raise the question of the factors inducing and modus operandi of cell fate transitions that originate in floral tissues and gametophytes, respectively. Cell fate transitions in the reproductive lineage imply cellular reprogramming operating at the physiological, cytological and transcriptome level, but also at the chromatin level. A number of observations point to large-scale chromatin reorganization events associated with cellular differentiation of the female spore mother cells and of the female gametes. These include a reorganization of the heterochromatin compartment, the genome-wide alteration of the histone modification landscape, and the remodeling of nucleosome composition. The dynamic expression of DNA methyltransferases and actors of small RNA pathways also suggest additional, global epigenetic alterations that remain to be characterized. Are these events a cause or a consequence of cellular differentiation, and how do they contribute to cell fate transition? Does chromatin dynamics induce competence for immediate cellular functions (meiosis, fertilization), or does it also contribute long-term effects in cellular identity and developmental competence of the reproductive lineage? This review attempts to review these fascinating questions. PMID:26031902

  20. Probing cellular processes by long-term live imaging--historic problems and current solutions.

    PubMed

    Coutu, Daniel L; Schroeder, Timm

    2013-09-01

    Living organisms, tissues, cells and molecules are highly dynamic. The importance of their continuous and long-term observation has been recognized for over a century but has been limited by technological hurdles. Improvements in imaging technologies, genetics, protein engineering and data analysis have more recently allowed us to answer long-standing questions in biology using quantitative continuous long-term imaging. This requires a multidisciplinary collaboration between scientists of various backgrounds: biologists asking relevant questions, imaging specialists and engineers developing hardware, and informaticians and mathematicians developing software for data acquisition, analysis and computational modeling. Despite recent improvements, there are still obstacles to be addressed before this technology can achieve its full potential. This Commentary aims at providing an overview of currently available technologies for quantitative continuous long-term single-cell imaging, their limitations and what is required to bring this field to the next level. We provide an historical perspective on the development of this technology and discuss key issues in time-lapse imaging: keeping cells alive, using labels, reporters and biosensors, and hardware and software requirements. We highlight crucial and often non-obvious problems for researchers venturing into the field and hope to inspire experts in the field and from related disciplines to contribute to future solutions. PMID:23943879

  1. A logic gate-based fluorogenic probe for Hg(2+) detection and its applications in cellular imaging.

    PubMed

    Hu, Jiwen; Hu, Zhangjun; Chen, Zhiwen; Gao, Hong-Wen; Uvdal, Kajsa

    2016-05-01

    A new colorimetric and fluorogenic probe (RN3) based on rhodamine-B has been successfully designed and synthesized. It displays a selective response to Hg(2+) in the aqueous buffer solution over the other competing metals. Upon addition of Hg(2+), the solution of RN3 exhibits a 'naked eye' observable color change from colorless to red and an intensive fluorescence with about 105-fold enhancement. The changes in the color and fluorescence are ascribed to the ring-opening of spirolactam in rhodamine fluorophore, which is induced by a binding of the constructed receptor to Hg(2+) with the association and dissociation constants of 0.22 × 10(5) M(-1) and 25.2 μM, respectively. The Job's plot experiment determines a 1:1 binding stoichiometry between RN3 and Hg(2+). The resultant "turn-on" fluorescence in buffer solution, allows the application of a method to determine Hg(2+) levels in the range of 4.0-15.0 μM, with the limit of detection (LOD) calculated at 60.7 nM (3σ/slope). In addition, the fluorescence 'turn-off' and color 'fading-out' happen to the mixture of RN3-Hg(2+) by further addition of I(-) or S(2-). The reversible switching cycles of fluorescence intensity upon alternate additions of Hg(2+) and S(2-) demonstrate that RN3 can perform as an INHIBIT logic gate. Furthermore, the potential of RN3 as a fluorescent probe has been demonstrated for cellular imaging. PMID:27086103

  2. REVIEWS OF TOPICAL PROBLEMS: Study of spatially extended dynamical systems using probabilistic cellular automata

    NASA Astrophysics Data System (ADS)

    Vanag, Vladimir K.

    1999-05-01

    Spatially extended dynamical systems are ubiquitous and include such things as insect and animal populations; complex chemical, technological, and geochemical processes; humanity itself, and much more. It is clearly desirable to have a certain universal tool with which the highly complex behaviour of nonlinear dynamical systems can be analyzed and modelled. For this purpose, cellular automata seem to be good candidates. In the present review, emphasis is placed on the possibilities that various types of probabilistic cellular automata (PCA), such as DSMC (direct simulation Monte Carlo) and LGCA (lattice-gas cellular automata), offer. The methods are primarily designed for modelling spatially extended dynamical systems with inner fluctuations accounted for. For the Willamowskii-Roessler and Oregonator models, PCA applications to the following problems are illustrated: the effect of fluctuations on the dynamics of nonlinear systems; Turing structure formation; the effect of hydrodynamic modes on the behaviour of nonlinear chemical systems (stirring effects); bifurcation changes in the dynamical regimes of complex systems with restricted geometry or low spatial dimension; and the description of chemical systems in microemulsions.

  3. A Mathematical Model to study the Dynamics of Epithelial Cellular Networks

    PubMed Central

    Abate, Alessandro; Vincent, Stéphane; Dobbe, Roel; Silletti, Alberto; Master, Neal; Axelrod, Jeffrey D.; Tomlin, Claire J.

    2013-01-01

    Epithelia are sheets of connected cells that are essential across the animal kingdom. Experimental observations suggest that the dynamical behavior of many single-layered epithelial tissues has strong analogies with that of specific mechanical systems, namely large networks consisting of point masses connected through spring-damper elements and undergoing the influence of active and dissipating forces. Based on this analogy, this work develops a modeling framework to enable the study of the mechanical properties and of the dynamic behavior of large epithelial cellular networks. The model is built first by creating a network topology that is extracted from the actual cellular geometry as obtained from experiments, then by associating a mechanical structure and dynamics to the network via spring-damper elements. This scalable approach enables running simulations of large network dynamics: the derived modeling framework in particular is predisposed to be tailored to study general dynamics (for example, morphogenesis) of various classes of single-layered epithelial cellular networks. In this contribution we test the model on a case study of the dorsal epithelium of the Drosophila melanogaster embryo during early dorsal closure (and, less conspicuously, germband retraction). PMID:23221083

  4. Probing Binding and Cellular Activity of Pyrrolidinone and Piperidinone Small Molecules Targeting the Urokinase Receptor

    PubMed Central

    Mani, Timmy; Liu, Degang; Zhou, Donghui; Li, Liwei; Knabe, William Eric; Wang, Fang; Oh, Kyungsoo; Meroueh, Samy O.

    2014-01-01

    The urokinase receptor (uPAR) is a cell-surface protein that is part of an intricate web of transient and tight protein interactions that promote cancer cell invasion and metastasis. Here we evaluate the binding and biological activity of a new class of pyrrolidinone (3) and piperidinone (4) compounds, along with derivatives of previously-identified pyrazole (1) and propylamine (2) compounds. Competition assays revealed that the compounds displaced a fluorescently-labeled peptide (AE147-FAM) with inhibition constant Ki ranging from 6 to 63 μM. Structure-based computational pharmacophore analysis followed by extensive explicit-solvent molecular dynamics simulations and free energy calculations suggested pyrazole-based 1a and piperidinone-based 4 adopt different binding modes, despite their similar two-dimensional structures. In cells, compounds 1b and 1f showed significant inhibition of breast MDA-MB-231 and pancreatic ductal adenocarcinoma (PDAC) cell proliferation, but 4b exhibited no cytotoxicity even at concentrations of 100 μM. 1f impaired MDA-MB-231 invasion, adhesion, and migration in a concentration-dependent manner, while 4b inhibited only invasion. 1f inhibited gelatinase (MMP-9) activity in a concentration-dependent manner, while 4b showed no effect suggesting different mechanisms for inhibition of cell invasion. Signaling studies further highlighted these differences, showing that pyrazole compounds completely inhibited ERK phosphorylation and impaired HIF1α and NF-κB signaling, while pyrrolidinone and piperidinone (3 and 4b) had no effect. Annexin V staining suggested that the effect of pyrazole-based 1f on proliferation was due to cell killing through an apoptotic mechanism. PMID:24115356

  5. Dynamic compressive behavior of human meniscus correlates with its extra-cellular matrix composition.

    PubMed

    Bursac, P; Arnoczky, S; York, A

    2009-01-01

    The menisci of the knee play a significant role in the complex biomechanics of the joint and are critically important in maintaining articular cartilage health. While a general form-function relationship has been identified for the structural orientation of the extra-cellular matrix of the meniscus, the role of individual biochemical components has yet to be fully explored. To determine if correlations exist between the dynamic and static compressive modulus of human menisci and their major extra-cellular matrix constituents (collagen, glycosoaminoglycan and water content), 12 lateral and 11 medial menisci from 13 adult donors were examined. The results showed that in dynamic compression at high loading frequencies (0.1-1 Hz) the menisci behave as a rubber-like elastic material while at lower frequencies (0.01-0.03 Hz) significant viscous dissipation occurs. While regional variations in compressive moduli and extra-cellular matrix composition were observed, the magnitude of both dynamic and static compressive moduli were found to be insensitive to collagen content (p>0.4). However, this magnitude was found to significantly increase with increasing glycosaminoglycan content (p<0.001) and significantly decrease with increasing water content (p<0.001). The results of this study identify significant relationships between the viscoelastic behavior of the meniscus and its extra-cellular matrix composition. PMID:19581729

  6. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

    SciTech Connect

    Noe, F; Diadone, Isabella; Lollmann, Marc; Sauer, Marcus; Chondera, John D; Smith, Jeremy C

    2011-01-01

    There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.

  7. Prediction of atomic force microscope probe dynamics through the receptance coupling method

    SciTech Connect

    Mehrpouya, M.; Park, S. S.

    2011-12-15

    The increased growth in the use of tip-based sensing, manipulations, and fabrication of devices in atomic force microscopy (AFM) necessitates the accurate prediction of the dynamic behavior of the AFM probe. The chip holder, to which the micro-sensing device is attached, and the rest of the AFM system can affect the overall dynamics of the probe. In order to consider these boundary effects, we propose a novel receptance coupling method to mathematically combine the dynamics of the AFM setup and probe, based on the equilibrium and compatibility conditions at the joint. Once the frequency response functions of displacement over force at the tool tip are obtained, the dynamic interaction forces between the tip and the sample in nanoscale can be determined by measuring the probe tip displacement.

  8. Speckle fluctuations to probe dynamics on the macroscopic to microscopic scales (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Boas, David A.

    2016-03-01

    I will review recent advances and applications in Diffuse Correlation Spectroscopy, Laser Speckle Contrast Imaging, and Optical Coherence Tomography for measuring dynamics arising from cerebral blood flow and intra-cellular organelle motility.

  9. Traffic dynamics of an on-ramp system with a cellular automaton model

    NASA Astrophysics Data System (ADS)

    Li, Xin-Gang; Gao, Zi-You; Jia, Bin; Jiang, Rui

    2010-06-01

    This paper uses the cellular automaton model to study the dynamics of traffic flow around an on-ramp with an acceleration lane. It adopts a parameter, which can reflect different lane-changing behaviour, to represent the diversity of driving behaviour. The refined cellular automaton model is used to describe the lower acceleration rate of a vehicle. The phase diagram and the capacity of the on-ramp system are investigated. The simulation results show that in the single cell model, the capacity of the on-ramp system will stay at the highest flow of a one lane system when the driver is moderate and careful; it will be reduced when the driver is aggressive. In the refined cellular automaton model, the capacity is always reduced even when the driver is careful. It proposes that the capacity drop of the on-ramp system is caused by aggressive lane-changing behaviour and lower acceleration rate.

  10. Asymmetrical Inheritance of Plasmids Depends on Dynamic Cellular Geometry and Volume Exclusion Effects

    PubMed Central

    Marquez-Lago, Tatiana T.

    2015-01-01

    The asymmetrical inheritance of plasmid DNA, as well as other cellular components, has been shown to be involved in replicative aging. In Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms underlying this important asymmetry. Currently proposed models suggest it is established via diffusion, but differ on whether a diffusion barrier is necessary or not. However, no study so far incorporated key aspects to segregation, such as dynamic morphology changes throughout anaphase or plasmids size. Here, we determine the distinct effects and contributions of individual cellular variability, plasmid volume and moving boundaries in the asymmetric segregation of plasmids. We do this by measuring cellular nuclear geometries and plasmid diffusion rates with confocal microscopy, subsequently incorporating this data into a growing domain stochastic spatial simulator. Our modelling and simulations confirms that plasmid asymmetrical inheritance does not require an active barrier to diffusion, and provides a full analysis on plasmid size effects. PMID:26468952

  11. Asymmetrical Inheritance of Plasmids Depends on Dynamic Cellular Geometry and Volume Exclusion Effects.

    PubMed

    Denton, Jai A; Ghosh, Atiyo; Marquez-Lago, Tatiana T

    2015-01-01

    The asymmetrical inheritance of plasmid DNA, as well as other cellular components, has been shown to be involved in replicative aging. In Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms underlying this important asymmetry. Currently proposed models suggest it is established via diffusion, but differ on whether a diffusion barrier is necessary or not. However, no study so far incorporated key aspects to segregation, such as dynamic morphology changes throughout anaphase or plasmids size. Here, we determine the distinct effects and contributions of individual cellular variability, plasmid volume and moving boundaries in the asymmetric segregation of plasmids. We do this by measuring cellular nuclear geometries and plasmid diffusion rates with confocal microscopy, subsequently incorporating this data into a growing domain stochastic spatial simulator. Our modelling and simulations confirms that plasmid asymmetrical inheritance does not require an active barrier to diffusion, and provides a full analysis on plasmid size effects. PMID:26468952

  12. Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion

    PubMed Central

    Garcia, Natalie K.; Lee, Kelly K.

    2016-01-01

    The fusion glycoproteins that decorate the surface of enveloped viruses undergo dramatic conformational changes in the course of engaging with target cells through receptor interactions and during cell entry. These refolding events ultimately drive the fusion of viral and cellular membranes leading to delivery of the genetic cargo. While well-established methods for structure determination such as X-ray crystallography have provided detailed structures of fusion proteins in the pre- and post-fusion fusion states, to understand mechanistically how these fusion glycoproteins perform their structural calisthenics and drive membrane fusion requires new analytical approaches that enable dynamic intermediate states to be probed. Methods including structural mass spectrometry, small-angle X-ray scattering, and electron microscopy have begun to provide new insight into pathways of conformational change and fusion protein function. In combination, the approaches provide a significantly richer portrait of viral fusion glycoprotein structural variation and fusion activation as well as inhibition by neutralizing agents. Here recent studies that highlight the utility of these complementary approaches will be reviewed with a focus on the well-characterized influenza virus hemagglutinin fusion glycoprotein system. PMID:26761026

  13. Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion.

    PubMed

    Garcia, Natalie K; Lee, Kelly K

    2016-01-01

    The fusion glycoproteins that decorate the surface of enveloped viruses undergo dramatic conformational changes in the course of engaging with target cells through receptor interactions and during cell entry. These refolding events ultimately drive the fusion of viral and cellular membranes leading to delivery of the genetic cargo. While well-established methods for structure determination such as X-ray crystallography have provided detailed structures of fusion proteins in the pre- and post-fusion fusion states, to understand mechanistically how these fusion glycoproteins perform their structural calisthenics and drive membrane fusion requires new analytical approaches that enable dynamic intermediate states to be probed. Methods including structural mass spectrometry, small-angle X-ray scattering, and electron microscopy have begun to provide new insight into pathways of conformational change and fusion protein function. In combination, the approaches provide a significantly richer portrait of viral fusion glycoprotein structural variation and fusion activation as well as inhibition by neutralizing agents. Here recent studies that highlight the utility of these complementary approaches will be reviewed with a focus on the well-characterized influenza virus hemagglutinin fusion glycoprotein system. PMID:26761026

  14. Glass-like dynamics in the cell and in cellular collectives

    PubMed Central

    Sadati, Monirosadat; Nourhani, Amir; Qazvini, Nader Taheri

    2014-01-01

    Prominent fluctuations, heterogeneity, and cooperativity dominate the dynamics of the cytoskeleton as well as the dynamics of the cellular collective. Such systems are out of equilibrium, disordered, and remain poorly understood. To explain these findings, here we consider a unifying mechanistic rubric that imagines these systems as comprising phases of soft condensed matter in proximity to a glass or jamming transition, with associated transitions between solid-like versus liquid-like phases. At the scale of the cytoskeleton, data suggest that intermittent dynamics, kinetic arrest and dynamic heterogeneity represent meso-scale features of glassy protein-protein interactions that link underlying biochemical events to integrative cellular behaviors such as crawling, contraction, and remodeling. At the scale of the multicellular collective, jamming has the potential to unify diverse biological factors that previously had been considered mostly as acting separately and independently. Although a quantitative relationship between intra- and intercellular dynamics is still lacking, glassy dynamics and jamming offer insights linking the mechanobiology of cell to human physiology and pathophysiology. PMID:24431332

  15. An investigation of cellular dynamics during the development of intramembranous bones: the scleral ossicles

    PubMed Central

    Jabalee, J; Hillier, S; Franz-Odendaal, T A

    2013-01-01

    The development of intramembranous bone is a dynamic and complex process requiring highly coordinated cellular activities. Although the literature describes the detailed cellular dynamics of early mesoderm-derived endochondral bone, studies regarding neural crest-derived intramembranous bone have failed to keep pace. We analyzed the development of chick scleral ossicles from the onset of osteoid deposition to mineralization at morphological, histological, and ultrastructural levels. We find that the mesenchymal condensations from which ossicles develop change their shape from ellipsoidal to trapezoidal concurrent with an increase in size. Furthermore, the size of an ossicle is dependent upon its time of induction. Our histological analyses of condensation growth reveal cell migration and osteoid secretion as key cellular processes determining condensation size; these processes occur concomitantly to increase both the area and thickness of condensations. We also describe the formation of the zone of overlap between ossicles and conclude that the process is similar to that of cranial suture formation. Finally, transmission electron microscopy of early condensations demonstrates that early osteoblasts secrete collagen parallel to the long axis of the condensation. This study elucidates fundamental mechanisms of intramembranous bone development at the cellular level, furthering our knowledge of this important process among vertebrates. PMID:23930967

  16. An investigation of cellular dynamics during the development of intramembranous bones: the scleral ossicles.

    PubMed

    Jabalee, J; Hillier, S; Franz-Odendaal, T A

    2013-10-01

    The development of intramembranous bone is a dynamic and complex process requiring highly coordinated cellular activities. Although the literature describes the detailed cellular dynamics of early mesoderm-derived endochondral bone, studies regarding neural crest-derived intramembranous bone have failed to keep pace. We analyzed the development of chick scleral ossicles from the onset of osteoid deposition to mineralization at morphological, histological, and ultrastructural levels. We find that the mesenchymal condensations from which ossicles develop change their shape from ellipsoidal to trapezoidal concurrent with an increase in size. Furthermore, the size of an ossicle is dependent upon its time of induction. Our histological analyses of condensation growth reveal cell migration and osteoid secretion as key cellular processes determining condensation size; these processes occur concomitantly to increase both the area and thickness of condensations. We also describe the formation of the zone of overlap between ossicles and conclude that the process is similar to that of cranial suture formation. Finally, transmission electron microscopy of early condensations demonstrates that early osteoblasts secrete collagen parallel to the long axis of the condensation. This study elucidates fundamental mechanisms of intramembranous bone development at the cellular level, furthering our knowledge of this important process among vertebrates. PMID:23930967

  17. Dynamic Finite Element Predictions for Mars Sample Return Cellular Impact Test #4

    NASA Technical Reports Server (NTRS)

    Fasanella, Edwin L.; Billings, Marcus D.

    2001-01-01

    The nonlinear, transient dynamic finite element code, MSC.Dytran, was used to simulate an impact test of an energy absorbing Earth Entry Vehicle (EEV) that will impact without a parachute. EEVOs are designed to return materials from asteroids, comets, or planets for laboratory analysis on Earth. The EEV concept uses an energy absorbing cellular structure designed to contain and limit the acceleration of space exploration samples during Earth impact. The spherical shaped cellular structure is composed of solid hexagonal and pentagonal foam-filled cells with hybrid graphite-epoxy/Kevlar cell walls. Space samples fit inside a smaller sphere at the center of the EEVOs cellular structure. Pre-test analytical predictions were compared with the test results from a bungee accelerator. The model used to represent the foam and the proper failure criteria for the cell walls were critical in predicting the impact loads of the cellular structure. It was determined that a FOAM1 model for the foam and a 20% failure strain criteria for the cell walls gave an accurate prediction of the acceleration pulse for cellular impact.

  18. Dynamics of cellular immune responses in the acute phase of dengue virus infection.

    PubMed

    Yoshida, Tomoyuki; Omatsu, Tsutomu; Saito, Akatsuki; Katakai, Yuko; Iwasaki, Yuki; Kurosawa, Terue; Hamano, Masataka; Higashino, Atsunori; Nakamura, Shinichiro; Takasaki, Tomohiko; Yasutomi, Yasuhiro; Kurane, Ichiro; Akari, Hirofumi

    2013-06-01

    In this study, we examined the dynamics of cellular immune responses in the acute phase of dengue virus (DENV) infection in a marmoset model. Here, we found that DENV infection in marmosets greatly induced responses of CD4/CD8 central memory T and NKT cells. Interestingly, the strength of the immune response was greater in animals infected with a dengue fever strain than in those infected with a dengue hemorrhagic fever strain of DENV. In contrast, when animals were re-challenged with the same DENV strain used for primary infection, the neutralizing antibody induced appeared to play a critical role in sterilizing inhibition against viral replication, resulting in strong but delayed responses of CD4/CD8 central memory T and NKT cells. The results in this study may help to better understand the dynamics of cellular and humoral immune responses in the control of DENV infection. PMID:23381396

  19. Characterization of Probe Dynamic Behaviors in Critical Dimension Atomic Force Microscopy.

    PubMed

    Feng, Shaw C; Joung, Che Bong; Vorburger, Theodore V

    2009-01-01

    This paper describes a detailed computational model of the interaction between an atomic force microscope probe tip and a sample surface. The model provides analyses of dynamic behaviors of the tip to estimate the probe deflections due to surface intermittent contact and the resulting dimensional biases and uncertainties. Probe tip and cantilever beam responses to intermittent contact between the probe tip and sample surface are computed using the finite element method. Intermittent contacts with a wall and a horizontal surface are computed and modeled, respectively. Using a 75 nm Critical Dimension (CD) tip as an example, the responses of the probe to interaction forces between the sample surface and the probe tip are shown in both time and frequency domains. In particular, interaction forces between the tip and both a vertical wall and a horizontal surface of a silicon sample are modeled using Lennard-Jones theory. The Snap-in and Snap-out of the probe tip in surface scanning are calculated and shown in the time domain. Based on the given tip-sample interaction force model, the calculation includes the compliance of the probe and dynamic forces generated by an excitation. Cantilever and probe tip deflections versus interaction forces in the time domain can be derived for both vertical contact with a plateau and horizontal contact with a side wall. Dynamic analysis using the finite element method and Lennard-Jones model provide a unique means to analyze the interaction of the probe and sample, including calculation of the deflection and the gap between the probe tip and the measured sample surface. PMID:27504222

  20. Characterization of Probe Dynamic Behaviors in Critical Dimension Atomic Force Microscopy

    PubMed Central

    Feng, Shaw C.; Joung, Che Bong; Vorburger, Theodore V.

    2009-01-01

    This paper describes a detailed computational model of the interaction between an atomic force microscope probe tip and a sample surface. The model provides analyses of dynamic behaviors of the tip to estimate the probe deflections due to surface intermittent contact and the resulting dimensional biases and uncertainties. Probe tip and cantilever beam responses to intermittent contact between the probe tip and sample surface are computed using the finite element method. Intermittent contacts with a wall and a horizontal surface are computed and modeled, respectively. Using a 75 nm Critical Dimension (CD) tip as an example, the responses of the probe to interaction forces between the sample surface and the probe tip are shown in both time and frequency domains. In particular, interaction forces between the tip and both a vertical wall and a horizontal surface of a silicon sample are modeled using Lennard-Jones theory. The Snap-in and Snap-out of the probe tip in surface scanning are calculated and shown in the time domain. Based on the given tip-sample interaction force model, the calculation includes the compliance of the probe and dynamic forces generated by an excitation. Cantilever and probe tip deflections versus interaction forces in the time domain can be derived for both vertical contact with a plateau and horizontal contact with a side wall. Dynamic analysis using the finite element method and Lennard-Jones model provide a unique means to analyze the interaction of the probe and sample, including calculation of the deflection and the gap between the probe tip and the measured sample surface. PMID:27504222

  1. Ultrafast pump-probe microscopy with high temporal dynamic range.

    PubMed

    Domke, Matthias; Rapp, Stephan; Schmidt, Michael; Huber, Heinz P

    2012-04-23

    Ultrafast pump-probe microscopy is a common method for time and space resolved imaging of short and ultra-short pulse laser ablation. The temporal delay between the ablating pump pulse and the illuminating probe pulse is tuned either by an optical delay, resulting in several hundred femtoseconds temporal resolution for delay times up to a few ns, or by an electronic delay, resulting in several nanoseconds resolution for longer delay times. In this work we combine both delay types for temporally high resolved observations of complete ablation processes ranging from femtoseconds to microseconds, while ablation is initiated by an ultrafast 660 fs laser pump pulse. For this purpose, we also demonstrate the calibration of the delay time zero point, the synchronization of both probe sources, as well as a method for image quality enhancing. In addition, we present for the first time to our knowledge pump-probe microscopy investigations of the complete substrate side selective ablation process of molybdenum films on glass. The initiation of mechanical film deformation is observed at about 400 ps, continues until approximately 15 ns, whereupon a Mo disk is sheared off free from thermal effects due to a directly induced laser lift-off ablation process. PMID:22535122

  2. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    NASA Astrophysics Data System (ADS)

    Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

    2013-11-01

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  3. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    SciTech Connect

    Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

    2013-11-15

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  4. Tempo-spatially resolved cellular dynamics of human immunodeficiency virus transacting activator of transcription (Tat) peptide-modified nanocargos in living cells

    NASA Astrophysics Data System (ADS)

    Wei, Lin; Yang, Qiaoyu; Xiao, Lehui

    2014-08-01

    Understanding the cellular uptake mechanism and intracellular fate of nanocarriers in living cells is of great importance for the rational design of efficient drug delivery cargos as well as the development of robust biomedical diagnostic probes. In present study, with a dual wavelength view darkfield microscope (DWVD), the tempo-spatially resolved dynamics of Tat peptide-functionalized gold nanoparticles (TGNPs, with size similar to viruses) in living HeLa cells were extensively explored. It was found that energy-dependent endocytosis (both clathrin- and caveolae-mediated processes were involved) was the prevailing pathway for the cellular uptake of TGNPs. The time-correlated dynamic spatial distribution information revealed that TGNPs could not actively target the cell nuclei, which is contrary to previous observations based on fixed cell results. More importantly, the inheritance of TGNPs to the daughter cells through mitosis was found to be the major route to metabolize TGNPs by HeLa cells. These understandings on the cellular uptake mechanism and intracellular fate of nanocargos in living cells would provide deep insight on how to improve and controllably manipulate their translocation efficiency for targeted drug delivery.Understanding the cellular uptake mechanism and intracellular fate of nanocarriers in living cells is of great importance for the rational design of efficient drug delivery cargos as well as the development of robust biomedical diagnostic probes. In present study, with a dual wavelength view darkfield microscope (DWVD), the tempo-spatially resolved dynamics of Tat peptide-functionalized gold nanoparticles (TGNPs, with size similar to viruses) in living HeLa cells were extensively explored. It was found that energy-dependent endocytosis (both clathrin- and caveolae-mediated processes were involved) was the prevailing pathway for the cellular uptake of TGNPs. The time-correlated dynamic spatial distribution information revealed that TGNPs

  5. Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants

    PubMed Central

    Baroux, Célia; Autran, Daphné

    2015-01-01

    Sexual reproduction in flowering plants offers a number of remarkable aspects to developmental biologists. First, the spore mother cells – precursors of the plant reproductive lineage – are specified late in development, as opposed to precocious germline isolation during embryogenesis in most animals. Second, unlike in most animals where meiosis directly produces gametes, plant meiosis entails the differentiation of a multicellular, haploid gametophyte, within which gametic as well as non-gametic accessory cells are formed. These observations raise the question of the factors inducing and modus operandi of cell fate transitions that originate in floral tissues and gametophytes, respectively. Cell fate transitions in the reproductive lineage imply cellular reprogramming operating at the physiological, cytological and transcriptome level, but also at the chromatin level. A number of observations point to large-scale chromatin reorganization events associated with cellular differentiation of the female spore mother cells and of the female gametes. These include a reorganization of the heterochromatin compartment, the genome-wide alteration of the histone modification landscape, and the remodeling of nucleosome composition. The dynamic expression of DNA methyltransferases and actors of small RNA pathways also suggest additional, global epigenetic alterations that remain to be characterized. Are these events a cause or a consequence of cellular differentiation, and how do they contribute to cell fate transition? Does chromatin dynamics induce competence for immediate cellular functions (meiosis, fertilization), or does it also contribute long-term effects in cellular identity and developmental competence of the reproductive lineage? This review attempts to review these fascinating questions. PMID:26031902

  6. Dynamics of cellular retinoic acid binding protein I on multiple time scales with implications for ligand binding.

    PubMed

    Krishnan, V V; Sukumar, M; Gierasch, L M; Cosman, M

    2000-08-01

    Cellular retinoic acid binding protein I (CRABPI) belongs to the family of intracellular lipid binding proteins (iLBPs), all of which bind a hydrophobic ligand within an internal cavity. The structures of several iLBPs reveal minimal structural differences between the apo (ligand-free) and holo (ligand-bound) forms, suggesting that dynamics must play an important role in the ligand recognition and binding processes. Here, a variety of nuclear magnetic resonance (NMR) spectroscopy methods were used to systematically study the dynamics of both apo and holo CRABPI at various time scales. Translational and rotational diffusion constant measurements were used to study the overall motions of the proteins. Both apo and holo forms of CRABPI tend to self-associate at high (1.2 mM) concentrations, while at low concentrations (0.2 mM), they are predominantly monomeric. Rapid amide exchange rate and laboratory frame relaxation rate measurements at two spectrometer field strengths (500 and 600 MHz) were used to probe the internal motions of the individual residues. Several residues in the apo form, notably within the ligand recognition region, exhibit millisecond time scale motions that are significantly arrested in the holo form. In contrast, no significant differences in the high-frequency motions were observed between the two forms. These results provide direct experimental evidence for dynamics-induced ligand recognition and binding at a specifically defined time scale. They also exemplify the importance of dynamics in providing a more comprehensive understanding of how a protein functions. PMID:10924105

  7. An efficient ratiometric fluorescent probe for tracking dynamic changes in lysosomal pH.

    PubMed

    Wang, Qianqian; Zhou, Liyi; Qiu, Liping; Lu, Danqing; Wu, Yongxiang; Zhang, Xiao-Bing

    2015-08-21

    Lysosomes are acidic organelles (approximately pH 4.5-5.5) and tracking the changes in lysosomal pH is of great biological importance. To address this issue, quite a few of fluorescent probes have been developed. However, few of these probes can realize the tracking of dynamic changes in lysosomal pH. Herein, we report a new lysosome-targeted ratiometric fluorescent probe (FR-Lys) by hybridizing morpholine with a xanthane derivative and an o-hydroxy benzoxazole group. In this probe, the morpholine group serves as a targeting unit for lysosome, the xanthane derivative exhibits a pH-modulated open/close reaction of the spirocycle, while the o-hydroxy benzoxazole moiety shows a pH modulated excited-state intramolecular proton transfer (ESIPT) process. Such a design affords the probe a ratiometric fluorescence response towards pH with pH values ranging from 4.0 to 6.3. The response of the probe to pH was fast and reversible with high selectivity. Moreover, this probe possesses further advantages such as easy synthesis, high photostability and low cytotoxicity. These features are favorable for tracking dynamic pH changes in biosystems. It was then applied for dynamic imaging pH changes in lysosomes with satisfactory results. PMID:26107774

  8. Investigating local and long-range neuronal network dynamics by simultaneous optogenetics, reverse microdialysis and silicon probe recordings in vivo

    PubMed Central

    Taylor, Hannah; Schmiedt, Joscha T.; Çarçak, Nihan; Onat, Filiz; Di Giovanni, Giuseppe; Lambert, Régis; Leresche, Nathalie; Crunelli, Vincenzo; David, Francois

    2014-01-01

    Background The advent of optogenetics has given neuroscientists the opportunity to excite or inhibit neuronal population activity with high temporal resolution and cellular selectivity. Thus, when combined with recordings of neuronal ensemble activity in freely moving animals optogenetics can provide an unprecedented snapshot of the contribution of neuronal assemblies to (patho)physiological conditions in vivo. Still, the combination of optogenetic and silicone probe (or tetrode) recordings does not allow investigation of the role played by voltage- and transmitter-gated channels of the opsin-transfected neurons and/or other adjacent neurons in controlling neuronal activity. New method and results We demonstrate that optogenetics and silicone probe recordings can be combined with intracerebral reverse microdialysis for the long-term delivery of neuroactive drugs around the optic fiber and silicone probe. In particular, we show the effect of antagonists of T-type Ca2+ channels, hyperpolarization-activated cyclic nucleotide-gated channels and metabotropic glutamate receptors on silicone probe-recorded activity of the local opsin-transfected neurons in the ventrobasal thalamus, and demonstrate the changes that the block of these thalamic channels/receptors brings about in the network dynamics of distant somatotopic cortical neuronal ensembles. Comparison with existing methods This is the first demonstration of successfully combining optogenetics and neuronal ensemble recordings with reverse microdialysis. This combination of techniques overcomes some of the disadvantages that are associated with the use of intracerebral injection of a drug-containing solution at the site of laser activation. Conclusions The combination of reverse microdialysis, silicone probe recordings and optogenetics can unravel the short and long-term effects of specific transmitter- and voltage-gated channels on laser-modulated firing at the site of optogenetic stimulation and the actions that

  9. The Effects of Probe Dynamics on Galactic Exploration Timescales

    NASA Astrophysics Data System (ADS)

    Forgan, Duncan H.; Papadogiannakis, Semeli; Kitching, Thomas

    2013-06-01

    The travel time required for one civilisation to explore the Milky Way using probes is a crucial component of Fermi's Paradox. Previous attempts to estimate this travel time have assumed that the probe's motion is simple, moving at a constant maximum velocity, with powered flight producing the necessary change in velocity required at each star to complete its chosen trajectory. This approach ignores lessons learned from interplanetary exploration, where orbital slingshot maneouvres can provide significant velocity boosts at little to no fuel cost. It is plausible that any attempt to explore the Galaxy would utilise such economising techniques, despite there being an upper limit to these velocity boosts, related to the escape velocity of the object being used to provide the slingshot. In order to investigate the effects of these techniques, we present multiple realisations of single probes exploring a small patch of the Milky Way. We investigate 3 separate scenarios, studying the slingshot effect on trajectories defined by simple heuristics. These scenarios are: i) standard powered flight to the nearest unvisited star without using slingshot techniques; ii) flight to the nearest unvisited star using slingshot techniques, and iii) flight to the next unvisited star which provides the maximal velocity boost under a slingshot trajectory. We find that adding slingshot velocity boosts can decrease the travel time by up to two orders of magnitude over simple powered flight. In the third case, selecting a route which maximises velocity boosts also reduces the travel time relative to powered flight, but by a much reduced factor. From these simulations, we suggest that adding realistic probe trajectories tends to strengthen Fermi's Paradox.

  10. Magneto-optical cellular chip model for intracellular orientational-dynamic-activity detection

    NASA Astrophysics Data System (ADS)

    Miyashita, Y.; Iwasaka, M.; Kurita, S.; Owada, N.

    2012-04-01

    In the present study, a magneto-optical cellular chip model (MoCCM) was developed to detect intracellular dynamics in macromolecules by using magneto-optical effects. For the purpose of cell-measurement under strong static magnetic fields of up to 10 T, we constructed a cellular chip model, which was a thin glass plate with a well for a cell culture. A cell line of osteoblast MC3T3-E1 was incubated in the glass well, and the well, 0.3 mm in depth, was sealed by a cover glass when the MoCCM was set in a fiber optic system. An initial intensity change of the polarized light transmission, which dispersed perpendicular to the cell's attaching surface, was collected for 10 to 60 min, and then magnetic fields were applied parallel and perpendicular to the surface and light direction, respectively. The magnetic birefringence signals that originated from the magnetic orientation of intracellular molecules such as cytoskeletons apparently appeared when the magnetic fields were constant at 10 T. A statistical analysis with 15 experiments confirmed that the cellular components under 10 T magnetic fields caused a stronger alignment, which was transferred into polarizing light intensity that increased more than the case before exposure. Cellular conditions such as generation and cell density affected the magnetic birefringence signals.

  11. Introducing Dynamic Combinatorial Chemistry: Probing the Substrate Selectivity of Acetylcholinesterase

    ERIC Educational Resources Information Center

    Angelin, Marcus; Larsson, Rikard; Vongvilai, Pornrapee; Ramstrom, Olof

    2010-01-01

    In this laboratory experiment, college students are introduced to dynamic combinatorial chemistry (DCC) and apply it to determine the substrate selectivity of acetylcholinesterase (AChE). Initially, the students construct a chemical library of dynamically interchanging thioesters and thiols. Then, AChE is added and allowed to select and hydrolyze…

  12. Ultrafast pump-probe dynamics of iron oxide based earth pigments for applications to ancient pottery manufacture

    NASA Astrophysics Data System (ADS)

    Villafana, Tana E.; Brown, William; Warren, Warren S.; Fischer, Martin

    2015-06-01

    We demonstrate that ultrafast pump-probe microscopy provides unique dynamics for natural iron oxide and iron hydroxide earth pigments, despite their chemical similarity. First, we conducted a pump-probe spectroscopy study on heat-treated hematite (the pure red iron oxide mineral) and found the pump-probe dynamics to be temperature dependent. Second, we investigated pottery fired under known conditions and observed firing dependent pump-probe dynamics. Finally, we imaged a New World potshard from the North Carolina Museum of Art. Our results indicate that pump-probe microscopy could be a useful tool in elucidating pottery manufacture.

  13. Relating the sequential dynamics of excitatory neural networks to synaptic cellular automata.

    PubMed

    Nekorkin, V I; Dmitrichev, A S; Kasatkin, D V; Afraimovich, V S

    2011-12-01

    We have developed a new approach for the description of sequential dynamics of excitatory neural networks. Our approach is based on the dynamics of synapses possessing the short-term plasticity property. We suggest a model of such synapses in the form of a second-order system of nonlinear ODEs. In the framework of the model two types of responses are realized-the fast and the slow ones. Under some relations between their timescales a cellular automaton (CA) on the graph of connections is constructed. Such a CA has only a finite number of attractors and all of them are periodic orbits. The attractors of the CA determine the regimes of sequential dynamics of the original neural network, i.e., itineraries along the network and the times of successive firing of neurons in the form of bunches of spikes. We illustrate our approach on the example of a Morris-Lecar neural network. PMID:22225361

  14. Molecular modeling of the conformational dynamics of the cellular prion protein

    NASA Astrophysics Data System (ADS)

    Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

    2014-03-01

    Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

  15. The spectral gap and the dynamical critical exponent of an exact solvable probabilistic cellular automaton

    NASA Astrophysics Data System (ADS)

    Lazo, M. J.; Ferreira, A. A.; Alcaraz, F. C.

    2015-11-01

    We obtained the exact solution of a probabilistic cellular automaton related to the diagonal-to-diagonal transfer matrix of the six-vertex model on a square lattice. The model describes the flow of ants (or particles), traveling on a one-dimensional lattice whose sites are small craters containing sleeping or awake ants (two kinds of particles). We found the Bethe ansatz equations and the spectral gap for the time-evolution operator of the cellular automaton. From the spectral gap we show that in the asymmetric case it belongs to the Kardar-Parisi-Zhang (KPZ) universality class, exhibiting a dynamical critical exponent value z = 3/2. This result is also obtained from a direct Monte Carlo simulation, by evaluating the lattice-size dependence of the decay time to the stationary state.

  16. Predictive modeling of multicellular structure formation by using Cellular Particle Dynamics simulations

    NASA Astrophysics Data System (ADS)

    McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2014-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  17. Probing Molecular Dynamics by Laser-Induced Backscattering Holography.

    PubMed

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H_{2} and D_{2} molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H_{2} and D_{2} with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules. PMID:27081975

  18. Probing Molecular Dynamics by Laser-Induced Backscattering Holography

    NASA Astrophysics Data System (ADS)

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.

  19. Probing Li-ion Dynamics and Reactivity on the Nanoscale

    SciTech Connect

    Kalinin, Sergei V; Balke, Nina; Jesse, Stephen; Tselev, Alexander; Kumar, Amit; Arruda, Thomas M; Guo, Senli; Proksch, Roger

    2011-01-01

    Progress in development and optimization of energy storage and conversion materials necessitates understanding their ionic and electrochemical functionality on the nanometer scale level of single grain cluster, grain, or extended defect. Classical electrochemical strategies based on Faradaic current detection are fundamentally limited on the nanoscale. Here, we review principles and recent applications of Electrochemical Strain Microscopy (ESM), a scanning probe microscopy (SPM) technique utilizing intrinsic coupling between ionic pehnomena and molar volumes. ESM imaging, as well as time and voltage spectroscopies, are illustrated for several Li-ion cathode and anode materials. Perspectives for future ESM development and applications to other ionic systems are discussed.

  20. Dynamic Finite Element Predictions for Mars Sample Return Cellular Impact Test #4

    NASA Technical Reports Server (NTRS)

    Fasanella, Edwin L.; Billings, Marcus D.

    2001-01-01

    The nonlinear finite element program MSC.Dytran was used to predict the impact pulse for (he drop test of an energy absorbing cellular structure. This pre-test simulation was performed to aid in the design of an energy absorbing concept for a highly reliable passive Earth Entry Vehicle (EEV) that will directly impact the Earth without a parachute. In addition, a goal of the simulation was to bound the acceleration pulse produced and delivered to the simulated space cargo container. EEV's are designed to return materials from asteroids, comets, or planets for laboratory analysis on Earth. The EEV concept uses an energy absorbing cellular structure designed to contain and limit the acceleration of space exploration samples during Earth impact. The spherical shaped cellular structure is composed of solid hexagonal and pentagonal foam-filled cells with hybrid graphite-epoxy/Kevlar cell walls. Space samples fit inside a smaller sphere at the enter of the EEV's cellular structure. The material models and failure criteria were varied to determine their effect on the resulting acceleration pulse. Pre-test analytical predictions using MSC.Dytran were compared with the test results obtained from impact test #4 using bungee accelerator located at the NASA Langley Research Center Impact Dynamics Research Facility. The material model used to represent the foam and the proper failure criteria for the cell walls were critical in predicting the impact loads of the cellular structure. It was determined that a FOAMI model for the foam and a 20% failure strain criteria for the cell walls gave an accurate prediction of the acceleration pulse for drop test #4.

  1. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

    PubMed

    Kirmizialtin, Serdal; Hennelly, Scott P; Schug, Alexander; Onuchic, Jose N; Sanbonmatsu, Karissa Y

    2015-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  2. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    PubMed Central

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  3. Dynamic characterization of small fibers based on the flexural vibrations of a piezoelectric cantilever probe

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaofei; Ye, Xuan; Li, Xide

    2016-08-01

    In this paper, we present a cantilever-probe system excited by a piezoelectric actuator, and use it to measure the dynamic mechanical properties of a micro- and nanoscale fiber. Coupling the fiber to the free end of the cantilever probe, we found the dynamic stiffness and damping coefficient of the fiber from the resonance frequency and the quality factor of the fiber-cantilever-probe system. The properties of Bacillus subtilis fibers measured using our proposed system agreed with tensile measurements, validating our method. Our measurements show that the piezoelectric actuator coupled to cantilever probe can be made equivalent to a clamped cantilever with an effective length, and calculated results show that the errors of measured natural frequency of the system can be ignored if the coupled fiber has an inclination angle of alignment of less than 10°. A sensitivity analysis indicates that the first or second resonant mode is the sensitive mode to test the sample’s dynamic stiffness, while the damping property has different sensitivities for the first four modes. Our theoretical analysis demonstrates that the double-cantilever probe is also an effective sensitive structure that can be used to perform dynamic loading and characterize dynamic response. Our method has the advantage of using amplitude-frequency curves to obtain the dynamic mechanical properties without directly measuring displacements and forces as in tensile tests, and it also avoids the effects of the complex surface structure and deformation presenting in contact resonance method. Our method is effective for measuring the dynamic mechanical properties of fiber-like one-dimensional (1D) materials.

  4. Correlating proton transfer dynamics to probe location in confined environments.

    PubMed

    Sedgwick, Myles; Cole, Richard L; Rithner, Christopher D; Crans, Debbie C; Levinger, Nancy E

    2012-07-25

    The dramatic impact of differing environments on proton transfer dynamics of the photoacid HPTS prompted us to investigate these systems with two highly complementary methods: ultrafast time-resolved transient absorption and two-dimensional NMR spectroscopies. Both ultrafast time-resolved transient absorption spectroscopy and time-resolved anisotropy decays demonstrate the proton transfer dynamics depend intimately on the specific reverse micellar system. For w(0) = 10 reverse micelles formed with anionic AOT surfactant, the HPTS proton transfer dynamics are similar to dynamics in bulk aqueous solution, and the corresponding (1)H 2D NOESY NMR spectra display no cross peaks between HPTS and AOT consistent with the HPTS residing well hydrated by water in the interior of the reverse micelle water pool. In contrast, ultrafast transient absorption experiments show no evidence for HPTS photoinduced proton transfer reaction in reverse micelles formed with the cationic CTAB surfactant. In CTAB reverse micelles, clear cross peaks between HPTS and CTAB in the 2D NMR spectra show that HPTS embeds in the interface. These results indicate that the environment strongly impacts the proton transfer reaction and that complementary experimental techniques develop understanding of how location critically affects molecular responses. PMID:22765228

  5. 3-Picolyl Azide Adenine Dinucleotide as a Probe of Femtosecond to Picosecond Enzyme Dynamics

    PubMed Central

    Dutta, Samrat; Li, Yun-Liang; Rock, William; Houtman, Jon C. D.; Kohen, Amnon; Cheatum, Christopher M.

    2012-01-01

    Functionally relevant femtosecond to picosecond dynamics in enzyme active sites can be difficult to measure because of a lack of spectroscopic probes that can be located in the active site without altering the behavior of the enzyme. We have developed a new NAD+ analog 3-Picolyl Azide Adenine Dinucleotide (PAAD+), which has the potential to be a general spectroscopic probe for NAD-dependent enzymes. This analog is stable and binds in the active site of a typical NAD-dependent enzyme formate dehydrogenase (FDH) with similar characteristics to natural NAD+. It has an isolated infrared transition with high molar absorptivity that makes it suitable for observing enzyme dynamics using 2D IR spectroscopy. 2D IR experiments show that in aqueous solution, the analog undergoes complete spectral diffusion within hundreds of femtoseconds consistent with the water hydrogen bonding dynamics that would be expected. When bound to FDH in a binary complex, it shows picosecond fluctuations and a large static offset, consistent with previous studies of the binary complexes of this enzyme. These results show that PAAD+ is an excellent probe of local dynamics and that it should be a general tool for probing the dynamics of a wide range of NAD-dependent enzymes. PMID:22126535

  6. Micromotion-induced dynamic effects from a neural probe and brain tissue interface

    NASA Astrophysics Data System (ADS)

    Polanco, Michael; Yoon, Hargsoon; Bawab, Sebastian

    2014-04-01

    Neural probes contain the potential to cause injury to surrounding neural cells due to a discrepancy in stiffness values between them and the surrounding brain tissue when subjected to mechanical micromotion of the brain. To evaluate the effects of the mechanical mismatch, a series of dynamic simulations are conducted to better understand the design enhancements required to improve the feasibility of the neuron probe. The simulations use a nonlinear transient explicit finite element code, LS-DYNA. A three-dimensional quarter-symmetry finite element model is utilized for the transient analysis to capture the time-dependent dynamic deformations on the brain tissue from the implant as a function of different frequency shapes and stiffness values. When micromotion-induced pulses are applied, reducing the neuron probe stiffness by three orders of magnitude leads up to a 41.6% reduction in stress and 39.1% reduction in strain. The simulation conditions assume a case where sheath bonding has begun to take place around the probe implantation site, but no full bond to the probe has occurred. The analyses can provide guidance on the materials necessary to design a probe for injury reduction.

  7. Basement membranes in the worm: a dynamic scaffolding that instructs cellular behaviors and shapes tissues

    PubMed Central

    Clay, Matthew R.; Sherwood, David R.

    2015-01-01

    The nematode worm Caenorhabditis elegans has all the major basement membrane proteins found in vertebrates, usually with a smaller gene family encoding each component. With its powerful forward genetics, optical clarity, simple tissue organization, and the capability to functionally tag most basement membrane components with fluorescent proteins, C. elegans has facilitated novel insights into the assembly and function of basement membranes. Although basement membranes are generally thought of as static structures, studies in C. elegans have revealed their active properties and essential functions in tissue formation and maintenance. Here we review discoveries from C. elegans development that highlight dynamic aspects of basement membrane assembly, function, and regulation during organ growth, tissue polarity, cell migration, cell invasion, and tissue attachment. These studies have helped transform our view of basement membranes from static support structures to dynamic scaffoldings that play broad roles in regulating tissue organization and cellular behavior that are essential for development and have important implications in human diseases. PMID:26610919

  8. DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

    NASA Astrophysics Data System (ADS)

    Ohta, Seiichi; Glancy, Dylan; Chan, Warren C. W.

    2016-02-01

    Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments.

  9. TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics.

    PubMed

    Etournay, Raphaël; Merkel, Matthias; Popović, Marko; Brandl, Holger; Dye, Natalie A; Aigouy, Benoît; Salbreux, Guillaume; Eaton, Suzanne; Jülicher, Frank

    2016-01-01

    Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins. PMID:27228153

  10. DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction.

    PubMed

    Ohta, Seiichi; Glancy, Dylan; Chan, Warren C W

    2016-02-19

    Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments. PMID:26912892

  11. Emergence of density dynamics by surface interpolation in elementary cellular automata

    NASA Astrophysics Data System (ADS)

    Seck-Tuoh-Mora, Juan Carlos; Medina-Marin, Joselito; Martínez, Genaro J.; Hernández-Romero, Norberto

    2014-04-01

    A classic problem in elementary cellular automata (ECAs) is the specification of numerical tools to represent and study their dynamical behaviour. Mean field theory and basins of attraction have been commonly used; however, although the first case gives the long term estimation of density, frequently it does not show an adequate approximation for the step-by-step temporal behaviour; mainly for non-trivial behaviour. In the second case, basins of attraction display a complete representation of the evolution of an ECA, but they are limited up to configurations of 32 cells; and for the same ECA, one can obtain tens of basins to analyse. This paper is devoted to represent the dynamics of density in ECAs for hundreds of cells using only two surfaces calculated by the nearest-neighbour interpolation. A diversity of surfaces emerges in this analysis. Consequently, we propose a surface and histogram based classification for periodic, chaotic and complex ECA.

  12. Study of dynamic process of acetic acid induced-whitening in epithelial tissues at cellular level

    NASA Astrophysics Data System (ADS)

    Wu, Tao T.; Qu, Jianan Y.; Cheung, Tak Hong; Yim, So Fan; Wong, Yick Fu

    2005-06-01

    Acetic acid, inducing transient whitening (acetowhitening) when applied to epithelial tissues, is a commonly used contrast agent for detecting early cervical cancer. The goals of this research are to investigate the temporal characteristics of acetowhitening process in cervical epithelial tissue at cellular level and develop a clear understanding of the diagnostic information carried in the acetowhitening signal. A system measuring time-resolved reflectance was built to study the rising and decay processes of acetowhitening signal from the monolayered cell cultures of normal and cancerous cervical squamous cells. It is found that the dynamic processes of acetowhitening in normal and cancerous cells are significantly different. The results of this study provide insight valuable to further understand the acetowhitening process in epithelial cells and to encourage the development of an objective procedure to detect the early cervical cancers based on quantitative monitoring of the dynamic process of acetowhitening

  13. Quantitative scanning thermal microscopy based on determination of thermal probe dynamic resistance.

    PubMed

    Bodzenta, J; Juszczyk, J; Chirtoc, M

    2013-09-01

    Resistive thermal probes used in scanning thermal microscopy provide high spatial resolution of measurement accompanied with high sensitivity to temperature changes. At the same time their sensitivity to variations of thermal conductivity of a sample is relatively low. In typical dc operation mode the static resistance of the thermal probe is measured. It is shown both analytically and experimentally that the sensitivity of measurement can be improved by a factor of three by measuring the dynamic resistance of a dc biased probe superimposed with small ac current. The dynamic resistance can be treated as a complex value. Its amplitude represents the slope of the static voltage-current U-I characteristic for a given I while its phase describes the delay between the measured ac voltage and applied ac current component in the probe. The phase signal also reveals dependence on the sample thermal conductivity. Signal changes are relatively small but very repeatable. In contrast, the difference between dynamic and static resistance has higher sensitivity (the same maximum value as that of the 2nd and 3rd harmonics), and also much higher amplitude than higher harmonics. The proposed dc + ac excitation scheme combines the benefits of dc excitation (mechanical stability of probe-sample contact, average temperature control) with those of ac excitation (base-line stability, rejection of ambient temperature influence, high sensitivity, lock-in signal processing), when the experimental conditions prohibit large ac excitation. PMID:24089831

  14. Probing Molecular Dynamics at Attosecond Resolution with Femtosecond Laser Pulses

    NASA Astrophysics Data System (ADS)

    Tong, X. M.; Zhao, Z. X.; Lin, C. D.

    2003-12-01

    The kinetic energy distribution of D+ ions resulting from the interaction of a femtosecond laser pulse with D2 molecules is calculated based on the rescattering model. From analyzing the molecular dynamics, it is shown that the recollision time between the ionized electron and the D+2 ion can be read from the D+ kinetic energy peaks to attosecond accuracy. We further suggest that a more precise reading of the clock can be achieved by using shorter fs laser pulses (about 15fs).

  15. Actin-binding proteins: the long road to understanding the dynamic landscape of cellular actin networks.

    PubMed

    Lappalainen, Pekka

    2016-08-15

    The actin cytoskeleton supports a vast number of cellular processes in nonmuscle cells. It is well established that the organization and dynamics of the actin cytoskeleton are controlled by a large array of actin-binding proteins. However, it was only 40 years ago that the first nonmuscle actin-binding protein, filamin, was identified and characterized. Filamin was shown to bind and cross-link actin filaments into higher-order structures and contribute to phagocytosis in macrophages. Subsequently many other nonmuscle actin-binding proteins were identified and characterized. These proteins regulate almost all steps of the actin filament assembly and disassembly cycles, as well as the arrangement of actin filaments into diverse three-dimensional structures. Although the individual biochemical activities of most actin-regulatory proteins are relatively well understood, knowledge of how these proteins function together in a common cytoplasm to control actin dynamics and architecture is only beginning to emerge. Furthermore, understanding how signaling pathways and mechanical cues control the activities of various actin-binding proteins in different cellular, developmental, and pathological processes will keep researchers busy for decades. PMID:27528696

  16. Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model

    PubMed Central

    Albert, Philipp J.; Schwarz, Ulrich S.

    2014-01-01

    Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. The third dimension is treated as an area reservoir for spreading. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. We first parameterize our model and show that it accounts for momentum conservation. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We finally predict shapes and forces for micropatterns that have not yet been experimentally studied. PMID:24896113

  17. The effects of Cosmos caudatus (ulam raja) on dynamic and cellular bone histomorphometry in ovariectomized rats

    PubMed Central

    2013-01-01

    Background Cosmos caudatus is a local plant which has antioxidant properties and contains high calcium. It is also reported to be able to strengthen the bone. This report is an extension to previously published article in Evidence Based Complementary and Alternative Medicine (doi:10.1155/2012/817814). In this study, we determined the effectiveness of C. caudatus as an alternative treatment for osteoporosis due to post-menopause by looking at the dynamic and cellular paramaters of bone histomorphometry. Methods Forty female Wistar rats were divided into four groups i.e. sham operated, ovariectomized, ovariectomized treated with calcium 1% ad libitum and ovariectomized force-fed with 500 mg/kg C. caudatus extract. Treatment was given six days a week for eight weeks. Results Dynamic and cellular histomorphometry parameters were measured. C. caudatus increased double-labeled surface (dLS/BS), mineral appositional rate (MAR), osteoid volume (OV/BV) and osteoblast surface (Ob.S/BS). C. caudatus also gave better results compared to calcium 1% in the osteoid volume (OV/BV) parameter. Conclusions C. caudatus at the 500 mg/kg dose may be an alternative treatment in restoring bone damage that may occur in post-menopausal women. PMID:23800238

  18. Development of Dynamic Flow Field Pressure Probes Suitable for Use in Large Scale Supersonic Wind Tunnels

    NASA Technical Reports Server (NTRS)

    Porro, A. Robert

    2000-01-01

    A series of dynamic flow field pressure probes were developed for use in large-scale supersonic wind tunnels at NASA Glenn Research Center. These flow field probes include pitot, static, and five-hole conical pressure probes that are capable of capturing fast acting flow field pressure transients that occur on a millisecond time scale. The pitot and static probes can be used to determine local Mach number time histories during a transient event. The five-hole conical pressure probes are used primarily to determine local flow angularity, but can also determine local Mach number. These probes were designed, developed, and tested at the NASA Glenn Research Center. They were also used in a NASA Glenn 10-by 10-Foot Supersonic Wind Tunnel (SWT) test program where they successfully acquired flow field pressure data in the vicinity of a propulsion system during an engine compressor staff and inlet unstart transient event. Details of the design, development, and subsequent use of these probes are discussed in this report.

  19. Tracing ultrafast dynamics of strong fields at plasma-vacuum interfaces with longitudinal proton probing

    SciTech Connect

    Abicht, F.; Braenzel, J.; Koschitzki, Ch.; Schnürer, M.; Priebe, G.; Andreev, A. A.; Nickles, P. V.; Sandner, W.

    2014-07-21

    If regions of localized strong fields at plasma-vacuum interfaces are probed longitudinally with laser accelerated proton beams their velocity distribution changes sensitively and very fast. Its measured variations provide indirectly a higher temporal resolution as deduced from deflection geometries which rely on the explicit temporal resolution of the proton beam at the position of the object to probe. With help of reasonable models and comparative measurements changes of proton velocity can trace the field dynamics even at femtosecond time scale. In longitudinal probing, the very low longitudinal emittance together with a broad band kinetic energy distribution of laser accelerated protons is the essential prerequisite of the method. With a combination of energy and one-dimensional spatial resolution, we resolve fast field changes down to 100 fs. The used pump probe setup extends previous schemes and allows discriminating simultaneously between electric and magnetic fields in their temporal evolution.

  20. Probing ultrafast dynamics in a solid-density plasma created by an intense femtosecond laser

    NASA Astrophysics Data System (ADS)

    Adak, Amitava; Blackman, Dave; Chatterjee, Gourab; Singh, Prashant Kumar; Lad, Amit D.; Brijesh, P.; Robinson, A. P. L.; Pasley, John; Kumar, G. Ravindra

    2016-03-01

    We report a study on the dynamics of a near-solid density plasma using an ultraviolet (266 nm) femtosecond probe laser pulse, which can penetrate to densities of ∼ 1022 cm-3, nearly an order of magnitude higher than the critical density of the 800 nm, femtosecond pump laser. Time-resolved probe-reflectivity from the plasma shows a rapid decay (picosecond- timescale) while the time-resolved reflected probe spectra show red shifts at early temporal delays and blue shifts at longer delays. This spectral behaviour of the reflected probe can be explained by a laser-driven shock moving inward and a subsequent hydrodynamic free expansion in the outward direction.

  1. Cellular Solid-State NMR Investigation of a Membrane Protein Using Dynamic Nuclear Polarization

    PubMed Central

    Yamamoto, Kazutoshi; Caporini, Marc A.; Im, Sang-Choul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-01-01

    While an increasing number of structural biology studies successfully demonstrate the power of high-resolution structures and dynamics of membrane proteins in fully understanding their function, there is considerable interest in developing NMR approaches to obtain such information in a cellular setting. As long as the proteins inside the living cell tumble rapidly in the NMR timescale, recently developed in-cell solution NMR approaches can be applied towards the determination of 3D structural information. However, there are numerous challenges that need to be overcome to study membrane proteins inside a cell. Research in our laboratory is focused on developing a combination of solid-state NMR and biological approaches to overcome these challenges with a specific emphasis on obtaining high-resolution structural insights into electron transfer biological processes mediated by membrane-bound proteins like mammalian cytochrome b5, cytochrome P450 and cytochrome P450 reductase. In this study, we demonstrate the feasibility of using the signal-enhancement rendered by dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR spectroscopy for in-cell studies on a membrane-anchored protein. Our experimental results obtained from 13C-labeled membrane-anchored cytochrome b5 in native Escherichia coli cells show a ~16-fold DNP signal enhancement (ε). Further, results obtained from a 2D 13C/13C chemical shift correlation MAS experiment demonstrates that it is highly possible to suppress the background signals from other cellular contents for high-resolution structural studies on membrane proteins. We believe that this study would pave new avenues for high-resolution 3D structural studies on a variety of membrane-associated proteins and their complexes in the cellular context to fully understand their functional roles in physiological processes. PMID:25017802

  2. Cellular automata model based on GIS and urban sprawl dynamics simulation

    NASA Astrophysics Data System (ADS)

    Mu, Fengyun; Zhang, Zengxiang

    2005-10-01

    The simulation of land use change process needs the support of Geographical Information System (GIS) and other relative technologies. While the present commercial GIS lack capabilities of distribution, prediction, and simulation of spatial-temporal data. Cellular automata (CA) provide dynamically modeling "from bottom-to-top" framework and posses the capability of modeling spatial-temporal evolvement process of a complicated geographical system, which is composed of a fourfold: cells, states, neighbors and rules. The simplicity and flexibility make CA have the ability to simulate a variety of behaviors of complex systems. One of the most potentially useful applications of cellular automata from the point of view of spatial planning is their use in simulations of urban sprawl at local and regional level. The paper firstly introduces the principles and characters of the cellular automata, and then discusses three methods of the integration of CA and GIS. The paper analyses from a practical point of view the factors that effect urban activities in the science of spatial decision-making. The status of using CA to dynamic simulates of urban expansion at home and abroad is analyzed. Finally, the problems and tendencies that exist in the application of CA model are detailed discussed, such as the quality of the data that the CA needs, the self-organization of the CA roots in the mutual function among the elements of the system, the partition of the space scale, the time calibration of the CA and the integration of the CA with other modular such as artificial nerve net modular and population modular etc.

  3. Probing Dynamical Heterogeneity in Dense Colloidal Suspensions with Depletion Attraction

    NASA Astrophysics Data System (ADS)

    Brown, Zachery; Hogan, Gregory; Gratale, Matthew; Yodh, Arjun G.; Habdas, Piotr

    We directly observe the particle dynamics in dense colloidal suspensions. Using depletion attraction, we vary inter particle potential to study the reentrant glass transition. Confocal microscopy and particle tracking allow us to follow particle trajectories over time. By varying inter particle attraction strength for a fixed volume fraction of colloidal suspensions, we observe three qualitatively different states. Mean square displacement and long time diffusion constant vary with the depletant concentration and indicate a glass state for low attraction strengths, ergodic liquid state for moderate attraction strengths, and attractive arrested state for the highest attraction strengths. Variance in the self overlap function gives the four point susceptibility, a measure of dynamical heterogeneity over a range of length scales and lag times. Results show that the lag times corresponding to the most heterogeneous dynamics are longer for arrested states than for fluid states. The length scale that maximizes four point susceptibility across a range of attraction strengths exhibits a reentrant glass behavior similar to that of the long time diffusion constant. Z.B., G.H., and P.H. acknowledge financial support of the NSF RUI-1306990. M.G. and A.G.Y. acknowledge financial support of the NSF Grant DMR-1205463, NSF MRSEC Grant DMR-1120901, and NASA Grant NNX08AO0G.

  4. Effective Cellular Morphology Analysis for Differentiation Processes by a Fluorescent 1,3a,6a-Triazapentalene Derivative Probe in Live Cells

    PubMed Central

    Kamada, Rui; Tano, Fumi; Kudoh, Fuki; Kimura, Nozomi; Chuman, Yoshiro; Osawa, Ayumi; Namba, Kosuke; Tanino, Keiji; Sakaguchi, Kazuyasu

    2016-01-01

    Nuclear and cytoplasmic morphological changes provide important information about cell differentiation processes, cell functions, and signal responses. There is a strong desire to develop a rapid and simple method for visualizing cytoplasmic and nuclear morphology. Here, we developed a novel and rapid method for probing cellular morphological changes of live cell differentiation process by a fluorescent probe, TAP-4PH, a 1,3a,6a-triazapentalene derivative. TAP-4PH showed high fluorescence in cytoplasmic area, and visualized cytoplasmic and nuclear morphological changes of live cells during differentiation. We demonstrated that TAP-4PH visualized dendritic axon and spine formation in neuronal differentiation, and nuclear structural changes during neutrophilic differentiation. We also showed that the utility of TAP-4PH for visualization of cytoplasmic and nuclear morphologies of various type of live cells. Our visualizing method has no toxicity and no influence on the cellular differentiation and function. The cell morphology can be rapidly observed after addition of TAP-4PH and can continue to be observed in the presence of TAP-4PH in cell culture medium. Moreover, TAP-4PH can be easily removed after observation by washing for subsequent biological assay. Taken together, these results demonstrate that our visualization method is a powerful tool to probe differentiation processes before subsequent biological assay in live cells. PMID:27490470

  5. Digital Holography of Intracellular Dynamics to Probe Tissue Physiology

    PubMed Central

    Merrill, Daniel; An, Ran; Turek, John; Nolte, David D.

    2015-01-01

    Digital holography provides improved capabilities for imaging through dense tissue. Using a short-coherence source, the digital hologram recorded from backscattered light performs laser ranging that maintains fidelity of information acquired from depths much greater than possible by traditional imaging techniques. Biodynamic Imaging (BDI) is a developing technology for live-tissue imaging of up to a millimeter in depth that uses the hologram intensity fluctuations as label-free image contrast and can study tissue behavior in native microenvironments. In this paper BDI is used investigate the change in adhesion-dependent tissue response in 3D cultures. The results show that increasing density of cellular adhesions slows motion inside tissue and alters the response to cytoskeletal drugs. A clear signature of membrane fluctuations was observed in mid frequencies (0.1 – 1 Hz) that was enhanced by the application of cytochalasin-D that degrades the actin cortex inside the cell membrane. This enhancement feature is only observed in tissues that have formed adhesions, because cell pellets initially do not show this signature, but develop this signature only after incubation enables adhesions to form. PMID:25967027

  6. Development of Femtosecond Stimulated Raman Spectroscopy as a Probe of Photoisomerization Dynamics

    NASA Astrophysics Data System (ADS)

    Kieda, Ryan D.; Dunkelberger, Adam D.; Shin, Jaeyoon; Oudenhoven, Tracy; Crim, F. Fleming

    2012-06-01

    Femtosecond stimulated Raman spectroscopy (FSRS) has proven to be a reliable probe of condensed phase dynamics by simultaneously achieving both exceptional temporal and frequency resolution. We report on preliminary attempts to utilize FSRS as a probe of the photoisomerization of dMe-OMe-NAIP (N-alkylated indanylidene pyrroline Schiff base) which is a mimic of the chromophore in Rhodopsin. We implement a 400 nm Raman pump/continuum probe process following a 400 nm actinic pump pulse which initiates photoisomerization. This initial work appears to corroborate previous transient absorption studies of NAIP while granting a vibrational mode specific look at the dynamics involved in relaxation from its excited state and subsequent vibrational relaxation.

  7. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  8. Numerically evaluated functional equivalence between chaotic dynamics in neural networks and cellular automata under totalistic rules.

    PubMed

    Takada, Ryu; Munetaka, Daigo; Kobayashi, Shoji; Suemitsu, Yoshikazu; Nara, Shigetoshi

    2007-09-01

    Chaotic dynamics in a recurrent neural network model and in two-dimensional cellular automata, where both have finite but large degrees of freedom, are investigated from the viewpoint of harnessing chaos and are applied to motion control to indicate that both have potential capabilities for complex function control by simple rule(s). An important point is that chaotic dynamics generated in these two systems give us autonomous complex pattern dynamics itinerating through intermediate state points between embedded patterns (attractors) in high-dimensional state space. An application of these chaotic dynamics to complex controlling is proposed based on an idea that with the use of simple adaptive switching between a weakly chaotic regime and a strongly chaotic regime, complex problems can be solved. As an actual example, a two-dimensional maze, where it should be noted that the spatial structure of the maze is one of typical ill-posed problems, is solved with the use of chaos in both systems. Our computer simulations show that the success rate over 300 trials is much better, at least, than that of a random number generator. Our functional simulations indicate that both systems are almost equivalent from the viewpoint of functional aspects based on our idea, harnessing of chaos. PMID:19003512

  9. Field-free molecular alignment for probing collisional relaxation dynamics

    NASA Astrophysics Data System (ADS)

    Vieillard, Th.; Chaussard, F.; Billard, F.; Sugny, D.; Faucher, O.; Ivanov, S.; Hartmann, J.-M.; Boulet, C.; Lavorel, B.

    2013-02-01

    We report the experimental study of field-free molecular alignment in CO2 gas mixtures induced by intense femtosecond laser pulses in the presence of collisional processes. We demonstrate that the alignment signals exhibit specific features due to nontrivial collisional propensity rules that tend to preserve the orientation of the rotational angular momentum of the molecules. The analysis is performed with a quantum approach based on the modeling of rotational J- and M-dependent state-to-state transfer rates. The present work paves the way for strong-field spectroscopy of collisional dynamics.

  10. Dynamics of the nanoneedle probe in trolling mode AFM.

    PubMed

    Abdi, Ahmad; Pishkenari, Hossein Nejat; Keramati, Ramtin; Minary-Jolandan, Majid

    2015-05-22

    Atomic force microscopy (AFM), as an indispensable tool for nanoscale characterization, presents major drawbacks for operation in a liquid environment arising from the large hydrodynamic drag on the vibrating cantilever. The newly introduced 'Trolling mode' (TR-mode) AFM resolves this complication by using a specialized nanoneedle cantilever that keeps the cantilever outside of the liquid. Herein, a mechanical model with a lumped mass was developed to capture the dynamics of such a cantilever with a nanoneedle tip. This new developed model was applied to investigate the effects of the needle-liquid interface on the performance of the AFM, including the imaging capability in liquid. PMID:25915451

  11. Real-time probing of ultrafast residual charge dynamics

    SciTech Connect

    Li Junjie; Wang Xuan; Zhou Jun; Cao Jianming; Chen Zhaoyang; Mao, Samuel S.

    2011-01-03

    The temporal evolution of residual charges during laser ablation of metal and dielectric materials was investigated by measuring the correlated transient electric field using femtosecond electron shadow imaging and deflectometry. The results indicate that residual charges in metals can redistribute themselves almost instantly, abiding by the boundary conditions and Maxwell equations in the same way as they would at electrostatic equilibrium condition, but residual charges in dielectrics are confined within the excited area for hundreds of picoseconds and beyond. These observations provide an experimental support to the alleged Coulomb explosion phenomenon in previous studies as well as a reference for modeling residual charge dynamics.

  12. Probing Endoplasmic Reticulum Dynamics using Fluorescence Imaging and Photobleaching Techniques

    PubMed Central

    Costantini, Lindsey; Snapp, Erik

    2013-01-01

    This UNIT describes approaches and tools for studying the dynamics and organization of endoplasmic reticulum (ER) membranes and proteins in living cells using commercially available widefield and confocal laser scanning microscopes (CLSM). It has been long appreciated that the ER plays a number of key roles in secretory protein biogenesis, calcium regulation, and lipid synthesis. However, study of these processes has been often restricted to biochemical assays that average the behaviors of millions of lysed cells or to imaging static fixed cells. Now, with new fluorescent protein reporter tools, highly sensitive commercial microscopes, and photobleaching techniques, it is possible to interrogate the behaviors of ER proteins, membranes, and stress pathways in single cells with exquisite spatial and temporal resolution. The ER presents a unique set of imaging challenges including the high mobility of ER membranes, a diverse range of dynamic ER structures, and the influence of post-translational modifications on fluorescent protein reporters. Solutions to these challenges are described and considerations for performing photobleaching assays, especially Fluorescence Recovery after Photobleaching (FRAP) and Fluorescence Loss in Photobleaching (FLIP) for ER proteins will be discussed. In addition, ER reporters and ER-specific pharmacologic compounds are presented with a focus on misfolded secretory protein stress and the Unfolded Protein Response (UPR). PMID:24510787

  13. Novel optical-based methods and analyses for elucidating cellular mechanics and dynamics

    NASA Astrophysics Data System (ADS)

    Koo, Peter K.

    Resolving distinct biochemical interaction states by analyzing the diffusive behaviors of individual protein trajectories is challenging due to the limited statistics provided by short trajectories and experimental noise sources, which are intimately coupled into each proteins localization. In the first part of this thesis, we introduce a novel, a machine-learning based classification methodology, called perturbation expectation-maximization (pEM), which simultaneously analyzes a population of protein trajectories to uncover the system of short-time diffusive behaviors which collectively result from distinct biochemical interactions. We then discuss an experimental application of pEM to Rho GTPase, an integral regulator of cytoskeletal dynamics and cellular homeostasis, inside live cells. We also derive the maximum likelihood estimator (MLE) for driven diffusion, confined diffusion, and fractional Brownian motion. We demonstrate that MLE yields improved estimates in comparison with traditional diffusion analysis, namely mean squared displacement analysis. In addition, we also introduce mleBayes, which is an empirical Bayesian model selection scheme to classify an individual protein trajectory to a given diffusion mode. By employing mleBayes on simulated data, we demonstrate that accurate determination of the underlying diffusive properties, beyond normal diffusion, remains challenging when analyzing particle trajectories on an individual basis. To improve upon the statistical limitations of classification from analyzing trajectories on an individual basis, we extend pEM with a new version (pEMv2) to simultaneously analyzing a collection of particle trajectories to uncover the system of interactions which give rise to unique normal or non-normal diffusive states. We test the performance of pEMv2 on various sets of simulated particle trajectories which transition between various modes of normal and non-normal diffusive states to highlight considerations when

  14. Probing nonlinear magnetization dynamics in Fe/MgO(001) film by all optical pump-probe technique

    SciTech Connect

    He, Wei; Hu, Bo; Zhang, Xiang-Qun; Cheng, Zhao-Hua; Zhan, Qing-Feng

    2014-04-07

    An all-optical pump-probe technique has been employed to investigate the nonlinear magnetization dynamics of a 10 nm Fe/MgO(001) thin film in time domain. The magnetization precession was excited by pump-laser pulses and modulated by laser fluence variations. With increasing the laser fluence up to 7.1 mJ/cm{sup 2}, in addition to the uniform precession mode, a second harmonic signal was detected. The time evolution of the second harmonic signal was obtained in time-frequency domain. Based on the Landau-Lifshitz-Gilbert equation, the numerical simulation was performed to reproduce the observed the frequency doubling behaviors in Fe/MgO(001) film.

  15. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

    Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

  16. A magmatic probe of dynamic topography beneath western North America

    NASA Astrophysics Data System (ADS)

    Klöcking, M.; White, N. J.; Maclennan, J.

    2014-12-01

    A region centered on the Yellowstone hotspot and encompassing the Colorado Plateau sits at an elevation 2 km higher than the cratonic North America. This difference broadly coincides with tomographically observed variations in lithospheric thickness: ~120 km beneath western North America, ~240 km beneath the craton. Thermochronology of the Grand Canyon area, sedimentary flux to the Gulf of Mexico, and river profile inversion all suggest that regional uplift occurred in at least two separate stages. High resolution seismic tomographic models, using USArray data, have identified a ring of low velocity material beneath the edges of the Colorado Plateau. Magmatism coincides with these low velocity zones and shows distinct phases: an overall increase in volume around 40 Ma and a change from lithospheric to asthenospheric signatures around 5 Ma. Volcanism is also observed to migrate north-east with time. Here, we attempt to integrate these different observations with lithospheric thickness. A dynamic topography model of progressive lithospheric erosion over a hot mantle plume might account for uplift as well as the temporal and spatial distribution of magmatism across western North America. Thinning of the lithosphere around the edges of the Colorado Plateau in combination with the hotter mantle potential temperature of a plume could create isostatic and dynamic uplift as well as allowing for melt production. To test this model, we have analysed around 100 samples from volcanic centers across western North America by ICP-MS for rare earth elements (REE). Most of the samples are younger than 5 Ma, and all of them have previously been analysed by XRF. Using trace element ratios such as La/Yb and Nb/Y we assess depth of melting and melt fraction, respectively. In addition, we use REE inversion modelling to estimate melt fractions as a function of depth and temperature of melting. The results are compared to existing constraints on lithospheric thickness and mantle potential

  17. Ideal probe single-molecule experiments reveal the intrinsic dynamic heterogeneity of a supercooled liquid

    PubMed Central

    Paeng, Keewook; Park, Heungman; Hoang, Dat Tien; Kaufman, Laura J.

    2015-01-01

    The concept of dynamic heterogeneity and the picture of the supercooled liquid as a mosaic of environments with distinct dynamics that interchange in time have been invoked to explain the nonexponential relaxations measured in these systems. The spatial extent and temporal persistence of these regions of distinct dynamics have remained challenging to identify. Here, single-molecule fluorescence measurements using a probe similar in size and mobility to the host o-terphenyl unambiguously reveal exponential relaxations distributed in time and space and directly demonstrate ergodicity of the system down to the glass transition temperature. In the temperature range probed, at least 200 times the structural relaxation time of the host is required to recover ensemble-averaged relaxation at every spatial region in the system. PMID:25825739

  18. Sub-Femtosecond Correlated Dynamics Probed with Antiprotons

    SciTech Connect

    Welsch, C. P.; Kuehnel, K. U.; Schroeter, C. D.; Ullrich, J.

    2008-08-08

    Low-energy antiprotons are the ideal and perhaps the only tool to study in detail correlated quantum dynamics of few-electron systems in the femto and sub-femtosecond time regime. Unfortunately cooled beams of antiprotons with the necessary beam quality and luminosity are not yet available and cannot be provided with present scientific infrastructures. In order to pave the way for a next-generation low-energy antiproton facility, challenging developments in both, storing and imaging techniques have been launched at MPI-K. A novel ultra-low energy storage ring (USR) to be integrated at the proposed facility for low-energy antiproton and ion research (FLAIR) is being developed to provide electron-cooled beams of antiprotons and possibly highly charged ions in the energy range between 300 and 20 keV/q, maybe even approaching the sub keV regime. To allow for kinematically complete investigations for a variety of different collision processes, a reaction microscope shall be integrated in the ring thus achieving unprecedented luminosities. In this contribution, the present status of experiments in comparison with theory is highlighted and the layout of the USR as well as of the in-ring and an external single-pass reaction microscope is presented.

  19. Probing the dynamics of amyloidogenic peptides by dielectric relaxation spectroscopy

    NASA Astrophysics Data System (ADS)

    Barry, Donald; Prifti, Fioleda; Stroe, Izabela

    2010-03-01

    Fibrillar amyloidogenic structures have been considered for a long time indicators of neurodegenerative diseases. However, it has been proposed recently that amyloid oligomers are in fact the cytotoxic form and more importantly, they exhibit dynamics which differ from the fibrillar form due to the structure of water around these molecular structures. Here, we report dielectric relaxation measurements of non-amyloidogenic and amyloidogenic peptides in deionized water as a function of time and concentration. Our preliminary data show that the dielectric relaxation time of mixtures of deionized water and amyloidogenic peptides is a sensitive indicator of a transition state dominated by soluble oligomers to one characterized by the formation of large fibrils. Over time, this transition shifts the dielectric signal towards large relaxation time values, similar to those in bulk-like water as more molecules are liberated when small oligomers form fibrils. This is in agreement with recent theoretical models.footnotetextF. Despa et al., J. Biol. Phys. (2008) 34, 577 and references herein.

  20. Dynamics of the HIV infection under antiretroviral therapy: A cellular automata approach

    NASA Astrophysics Data System (ADS)

    González, Ramón E. R.; Coutinho, Sérgio; Zorzenon dos Santos, Rita Maria; de Figueirêdo, Pedro Hugo

    2013-10-01

    The dynamics of human immunodeficiency virus infection under antiretroviral therapy is investigated using a cellular automata model where the effectiveness of each drug is self-adjusted by the concentration of CD4+ T infected cells present at each time step. The effectiveness of the drugs and the infected cell concentration at the beginning of treatment are the control parameters of the cell population’s dynamics during therapy. The model allows describing processes of mono and combined therapies. The dynamics that emerges from this model when considering combined antiretroviral therapies reproduces with fair qualitative agreement the phases and different time scales of the process. As observed in clinical data, the results reproduce the significant decrease in the population of infected cells and a concomitant increase of the population of healthy cells in a short timescale (weeks) after the initiation of treatment. Over long time scales, early treatment with potent drugs may lead to undetectable levels of infection. For late treatment or treatments starting with a low density of CD4+ T healthy cells it was observed that the treatment may lead to a steady state in which the T cell counts are above the threshold associated with the onset of AIDS. The results obtained are validated through comparison to available clinical trial data.

  1. A multi-objective model for designing a group layout of a dynamic cellular manufacturing system

    NASA Astrophysics Data System (ADS)

    Kia, Reza; Shirazi, Hossein; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza

    2013-04-01

    This paper presents a multi-objective mixed-integer nonlinear programming model to design a group layout of a cellular manufacturing system in a dynamic environment, in which the number of cells to be formed is variable. Cell formation (CF) and group layout (GL) are concurrently made in a dynamic environment by the integrated model, which incorporates with an extensive coverage of important manufacturing features used in the design of CMSs. Additionally, there are some features that make the presented model different from the previous studies. These features include the following: (1) the variable number of cells, (2) the integrated CF and GL decisions in a dynamic environment by a multi-objective mathematical model, and (3) two conflicting objectives that minimize the total costs (i.e., costs of intra and inter-cell material handling, machine relocation, purchasing new machines, machine overhead, machine processing, and forming cells) and minimize the imbalance of workload among cells. Furthermore, the presented model considers some limitations, such as machine capability, machine capacity, part demands satisfaction, cell size, material flow conservation, and location assignment. Four numerical examples are solved by the GAMS software to illustrate the promising results obtained by the incorporated features.

  2. Cellular dynamics during early barley pollen embryogenesis revealed by time-lapse imaging

    PubMed Central

    Daghma, Diaa Eldin S.; Hensel, Goetz; Rutten, Twan; Melzer, Michael; Kumlehn, Jochen

    2014-01-01

    Plants display a remarkable capacity for cellular totipotency. An intriguing and useful example is that immature pollen cultured in vitro can pass through embryogenic development to form haploid or doubled haploid plants. However, a lack of understanding the initial mechanisms of pollen embryogenesis hampers the improvement and more effective and widespread employment of haploid technology in plant research and breeding. To investigate the cellular dynamics during the onset of pollen embryogenesis, we used time-lapse imaging along with transgenic barley expressing nuclear localized Green Fluorescent Protein. The results enabled us to identify nine distinct embryogenic and non-embryogenic types of pollen response to the culture conditions. Cell proliferation in embryogenic pollen normally started via a first symmetric mitosis (54.3% of pollen observed) and only rarely did so via asymmetric pollen mitosis I (4.3% of pollen observed). In the latter case, proliferation generally originated from the vegetative-like cell, albeit the division of the generative-like cell was observed in few types of pollen. Under the culture conditions used, fusion of cell nuclei was the only mechanism of genome duplication observed. PMID:25538715

  3. Embedding reach-scale fluvial dynamics within the CAESAR cellular automaton landscape evolution model

    NASA Astrophysics Data System (ADS)

    Van De Wiel, Marco J.; Coulthard, Tom J.; Macklin, Mark G.; Lewin, John

    2007-10-01

    We introduce a new computational model designed to simulate and investigate reach-scale alluvial dynamics within a landscape evolution model. The model is based on the cellular automaton concept, whereby the continued iteration of a series of local process 'rules' governs the behaviour of the entire system. The model is a modified version of the CAESAR landscape evolution model, which applies a suite of physically based rules to simulate the entrainment, transport and deposition of sediments. The CAESAR model has been altered to improve the representation of hydraulic and geomorphic processes in an alluvial environment. In-channel and overbank flow, sediment entrainment and deposition, suspended load and bed load transport, lateral erosion and bank failure have all been represented as local cellular automaton rules. Although these rules are relatively simple and straightforward, their combined and repeatedly iterated effect is such that complex, non-linear geomorphological response can be simulated within the model. Examples of such larger-scale, emergent responses include channel incision and aggradation, terrace formation, channel migration and river meandering, formation of meander cutoffs, and transitions between braided and single-thread channel patterns. In the current study, the model is illustrated on a reach of the River Teifi, near Lampeter, Wales, UK.

  4. Dynamic deformation and fragmentation response of maraging steel linear cellular alloy

    NASA Astrophysics Data System (ADS)

    Jakus, Adam E.; Fredenberg, David A.; McCoy, Tammy; Thadhani, Naresh; Cochran, Joe K.

    2012-03-01

    The dynamic deformation and fragmentation response of 25% dense 9-cell linear cellular alloy (LCA) made of unaged 250 maraging steel, fabricated using a direct reduction and extrusion technique, is investigated. Explicit finite element simulations were implemented using AUTODYN finite element code. The maraging steel properties were defined using a Johnson-Cook strength model with previously validated parameters. Rod-on-anvil impact tests were performed using the 7.6mm helium gas gun and the transient deformation and fragmentation response was recorded with highspeed imaging. Analysis of observed deformation states of specimens and finite element simulations reveal that in the case of the 9-cell LCA, dissipation of stress and strain occurs along the interior cell wells resulting in significant and ubiquitous buckling prior to confined fragmentation.

  5. Cellular computational networks--a scalable architecture for learning the dynamics of large networked systems.

    PubMed

    Luitel, Bipul; Venayagamoorthy, Ganesh Kumar

    2014-02-01

    Neural networks for implementing large networked systems such as smart electric power grids consist of multiple inputs and outputs. Many outputs lead to a greater number of parameters to be adapted. Each additional variable increases the dimensionality of the problem and hence learning becomes a challenge. Cellular computational networks (CCNs) are a class of sparsely connected dynamic recurrent networks (DRNs). By proper selection of a set of input elements for each output variable in a given application, a DRN can be modified into a CCN which significantly reduces the complexity of the neural network and allows use of simple training methods for independent learning in each cell thus making it scalable. This article demonstrates this concept of developing a CCN using dimensionality reduction in a DRN for scalability and better performance. The concept has been analytically explained and empirically verified through application. PMID:24300549

  6. Aurora Borealis: stochastic cellular automata simulations of the excited-state dynamics of oxygen atoms.

    NASA Astrophysics Data System (ADS)

    Seybold, P. G.; Kier, L. B.; Cheng, C.-K.

    1999-12-01

    Emissions from the 1S and 1D excited states of atomic oxygen play a prominent role in creating the dramatic light displays (aurora borealis) seen in the skies over polar regions of the Northern Hemisphere. A probabilistic asynchronous cellular automaton model described previously has been applied to the excited-state dynamics of atomic oxygen. The model simulates the time-dependent variations in ground (3P) and excited-state populations that occur under user-defined probabilistic transition rules for both pulse and steady-state conditions. Although each trial simulation is itself an independent "experiment", deterministic values for the excited-state emission lifetimes and quantum yields emerge as limiting cases for large numbers of cells or large numbers of trials. Stochastic variations in the lifetimes and emission yields can be estimated from repeated trials.

  7. Designing a mathematical model for integrating dynamic cellular manufacturing into supply chain system

    NASA Astrophysics Data System (ADS)

    Aalaei, Amin; Davoudpour, Hamid

    2012-11-01

    This article presents designing a new mathematical model for integrating dynamic cellular manufacturing into supply chain system with an extensive coverage of important manufacturing features consideration of multiple plants location, multi-markets allocation, multi-period planning horizons with demand and part mix variation, machine capacity, and the main constraints are demand of markets satisfaction in each period, machine availability, machine time-capacity, worker assignment, available time of worker, production volume for each plant and the amounts allocated to each market. The aim of the proposed model is to minimize holding and outsourcing costs, inter-cell material handling cost, external transportation cost, procurement & maintenance and overhead cost of machines, setup cost, reconfiguration cost of machines installation and removal, hiring, firing and salary worker costs. Aimed to prove the potential benefits of such a design, presented an example is shown using a proposed model.

  8. Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI)

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Aboard the International Space Station (ISS), the Tissue Culture Module (TCM) is the stationary bioreactor vessel in which cell cultures grow. However, for the Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI), color polystyrene beads are used to measure the effectiveness of various mixing procedures. The beads are similar in size and density to human lymphoid cells. Uniform mixing is a crucial component of CBOSS experiments involving the immune response of human lymphoid cell suspensions. The goal is to develop procedures that are both convenient for the flight crew and are optimal in providing uniform and reproducible mixing of all components, including cells. The average bead density in a well mixed TCM will be uniform, with no bubbles, and it will be measured using the absorption of light. In this photograph, a TCM is shown after mixing protocols, and bubbles of various sizes can be seen.

  9. Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI)

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Aboard the International Space Station (ISS), the Tissue Culture Module (TCM) is the stationary bioreactor vessel in which cell cultures grow. However, for the Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI), color polystyrene beads are used to measure the effectiveness of various mixing procedures. The beads are similar in size and density to human lymphoid cells. Uniform mixing is a crucial component of CBOSS experiments involving the immune response of human lymphoid cell suspensions. The goal is to develop procedures that are both convenient for the flight crew and are optimal in providing uniform and reproducible mixing of all components, including cells. The average bead density in a well mixed TCM will be uniform, with no bubbles, and it will be measured using the absorption of light. In this photograph, beads are trapped in the injection port, with bubbles forming shortly after injection.

  10. Alpha-actinin binding kinetics modulate cellular dynamics and force generation

    PubMed Central

    Ehrlicher, Allen J.; Krishnan, Ramaswamy; Guo, Ming; Bidan, Cécile M.; Weitz, David A.; Pollak, Martin R.

    2015-01-01

    The actin cytoskeleton is a key element of cell structure and movement whose properties are determined by a host of accessory proteins. Actin cross-linking proteins create a connected network from individual actin filaments, and though the mechanical effects of cross-linker binding affinity on actin networks have been investigated in reconstituted systems, their impact on cellular forces is unknown. Here we show that the binding affinity of the actin cross-linker α-actinin 4 (ACTN4) in cells modulates cytoplasmic mobility, cellular movement, and traction forces. Using fluorescence recovery after photobleaching, we show that an ACTN4 mutation that causes human kidney disease roughly triples the wild-type binding affinity of ACTN4 to F-actin in cells, increasing the dissociation time from 29 ± 13 to 86 ± 29 s. This increased affinity creates a less dynamic cytoplasm, as demonstrated by reduced intracellular microsphere movement, and an approximate halving of cell speed. Surprisingly, these less motile cells generate larger forces. Using traction force microscopy, we show that increased binding affinity of ACTN4 increases the average contractile stress (from 1.8 ± 0.7 to 4.7 ± 0.5 kPa), and the average strain energy (0.4 ± 0.2 to 2.1 ± 0.4 pJ). We speculate that these changes may be explained by an increased solid-like nature of the cytoskeleton, where myosin activity is more partitioned into tension and less is dissipated through filament sliding. These findings demonstrate the impact of cross-linker point mutations on cell dynamics and forces, and suggest mechanisms by which such physical defects lead to human disease. PMID:25918384

  11. A Nanocrystal Sensor for Luminescence Detection of Cellular Forces

    SciTech Connect

    Choi, Charina; Chou, Jonathan; Lutker, Katie; Werb, Zena; Alivisatos, Paul

    2011-09-29

    Quantum dots have been used as bright fluorescent tags with high photostability to probe numerous biological systems. In this work we present the tetrapod quantum dot as a dynamic, next-generation nanocrystal probe that fluorescently reports cellular forces with spatial and temporal resolution. Its small size and colloidal state suggest that the tetrapod may be further developed as a tool to measure cellular forces in vivo and with macromolecular spatial resolution.

  12. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics. PMID:23762388

  13. Ultrafast in-situ probing of passively mode-locked VECSEL dynamics

    NASA Astrophysics Data System (ADS)

    Scheller, Maik; Baker, Caleb W.; Gbele, Kokou; Koch, Stephan W.; Jones, R. Jason; Moloney, Jerome V.

    2015-03-01

    While Vertical-External-Cavity-Surface-Emitting-Lasers (VECSELs) have been successfully used as ultrafast laser sources with pulse durations in the hundreds of femtosecond regime, the dynamics within the semiconductor gain structure are not yet completely understood. With the high carrier densities inside the semiconductor, nonequilibrium effects such as kinetic-hole burning are expected to play a major role in pulse formation dynamics. Moreover, the nonlinear phase change by the intense light field can induce a complex dispersion, which may potentially limit the achievable pulse durations. To shed light on such nonequilibrium dynamics, we perform in-situ characterization of mode-locked VECSELs. We probe the gain media as well as the intracavity absorber with a femtosecond fiber laser source. For measuring temporal characteristics, we employ an asynchronous optical sampling technique by phase-locking the repetition rate of the VECSEL to a multiple of the probe laser with an adjustable offset frequency. This allows for probing dynamics from femtosecond to nanosecond time scales with scan rates up to hundreds of Hertz without compromise of measurement precision which can be introduced by mechanical delays covering such large temporal windows. With a resolution in the femtosecond range, we characterize gain depletion by the intracavity pulse as well as the gain recovery timescales for different power levels and operation regimes.

  14. Site-specific probing of charge transfer dynamics in organic photovoltaics

    SciTech Connect

    Arion, Tiberiu; Roth, Friedrich; Hussain, Zahid; Eberhardt, Wolfgang

    2015-03-23

    We report the site-specific probing of charge-transfer dynamics in a prototype system for organic photovoltaics (OPVs) by picosecond time-resolved X-ray photoelectron spectroscopy. A layered system consisting of approximately two monolayers of C{sub 60} deposited on top of a thin film of Copper-Phthalocyanine (CuPC) is excited by an optical pump pulse and the induced electronic dynamics are probed with 590 eV X-ray pulses. Charge transfer from the electron donor (CuPC) to the acceptor (C{sub 60}) and subsequent charge carrier dynamics are monitored by recording the time-dependent C 1s core level photoemission spectrum of the system. The arrival of electrons in the C{sub 60} layer is readily observed as a completely reversible, transient shift of the C{sub 60} associated C 1s core level, while the C 1s level of the CuPC remains unchanged. The capability to probe charge transfer and recombination dynamics in OPV assemblies directly in the time domain and from the perspective of well-defined domains is expected to open additional pathways to better understand and optimize the performance of this emerging technology.

  15. Influence of Solute Charge and Pyrrolidinium Ionic Liquid Alkyl Chain Length on Probe Rotational Reorientation Dynamics

    SciTech Connect

    Guo, Jianchang; Mahurin, Shannon Mark; Baker, Gary A; Hillesheim, Patrick C; Dai, Sheng; Shaw, Robert W

    2014-01-01

    In recent years, the effect of molecular charge on the rotational dynamics of probe solutes in room temperature ionic liquids (RTILs) has been a subject of growing interest. For the purpose of extending our understanding of charged solute behavior within RTILs, we have studied the rotational dynamics of three illustrative xanthene fluorescent probes within a series of N-alkylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([Cnmpyr][Tf2N]) RTILs with different n-alkyl chain lengths (n = 3, 4, 6, 8, or 10) using time-resolved fluorescence anisotropy decay. The rotational dynamics of the neutral probe rhodamine B dye lies between the stick and slip boundary conditions due to the influence of specific hydrogen bonding interactions. The rotation of the negatively-charged sulforhodamine 640 is slower than that of its positively-charged counterpart rhodamine 6G. An analysis based upon Stokes-Einstein-Debye hydrodynamics indicates that SR640 adheres to stick boundary conditions due to specific interactions, whereas the faster rotation of R6G is attributed to weaker electrostatic interactions. No dependence of the rotational dynamics on the solvent alkyl chain length was observed for any of the three dyes, suggesting that the specific interactions between dyes and RTILs are independent of this solvent parameter.

  16. Site-specific probing of charge transfer dynamics in organic photovoltaics

    NASA Astrophysics Data System (ADS)

    Arion, Tiberiu; Neppl, Stefan; Roth, Friedrich; Shavorskiy, Andrey; Bluhm, Hendrik; Hussain, Zahid; Gessner, Oliver; Eberhardt, Wolfgang

    2015-03-01

    We report the site-specific probing of charge-transfer dynamics in a prototype system for organic photovoltaics (OPVs) by picosecond time-resolved X-ray photoelectron spectroscopy. A layered system consisting of approximately two monolayers of C60 deposited on top of a thin film of Copper-Phthalocyanine (CuPC) is excited by an optical pump pulse and the induced electronic dynamics are probed with 590 eV X-ray pulses. Charge transfer from the electron donor (CuPC) to the acceptor (C60) and subsequent charge carrier dynamics are monitored by recording the time-dependent C 1s core level photoemission spectrum of the system. The arrival of electrons in the C60 layer is readily observed as a completely reversible, transient shift of the C60 associated C 1s core level, while the C 1s level of the CuPC remains unchanged. The capability to probe charge transfer and recombination dynamics in OPV assemblies directly in the time domain and from the perspective of well-defined domains is expected to open additional pathways to better understand and optimize the performance of this emerging technology.

  17. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    DOE PAGESBeta

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; et al

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.« less

  18. Back reaction effects on the dynamics of heavy probes in heavy quark cloud

    NASA Astrophysics Data System (ADS)

    Chakrabortty, Shankhadeep; Dey, Tanay K.

    2016-05-01

    We holographically study the effect of back reaction on the hydrodynamical properties of {N}=4 strongly coupled super Yang-Mills (SYM) thermal plasma. The back reaction we consider arises from the presence of static heavy quarks uniformly distributed over {N}=4 SYM plasma. In order to study the hydrodynamical properties, we use heavy quark as well as heavy quark-antiquark bound state as probes and compute the jet quenching parameter, screening length and binding energy. We also consider the rotational dynamics of heavy probe quark in the back-reacted plasma and analyse associated energy loss. We observe that the presence of back reaction enhances the energy-loss in the thermal plasma. Finally, we show that there is no effect of angular drag on the rotational motion of quark-antiquark bound state probing the back reacted thermal plasma.

  19. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics.

    PubMed

    Picón, A; Lehmann, C S; Bostedt, C; Rudenko, A; Marinelli, A; Osipov, T; Rolles, D; Berrah, N; Bomme, C; Bucher, M; Doumy, G; Erk, B; Ferguson, K R; Gorkhover, T; Ho, P J; Kanter, E P; Krässig, B; Krzywinski, J; Lutman, A A; March, A M; Moonshiram, D; Ray, D; Young, L; Pratt, S T; Southworth, S H

    2016-01-01

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site. PMID:27212390

  20. Low magnetic field dynamic nuclear polarization using a single-coil two-channel probe

    SciTech Connect

    TonThat, D.M.; Augustine, M.P.; Pines, A.; Clarke, J. |

    1997-03-01

    We describe the design and construction of a single-coil, two-channel probe for the detection of low-field magnetic resonance using dynamic nuclear polarization (DNP). The high-frequency channel of the probe, which is used to saturate the electron spins, is tuned to the electron Larmor frequency, 75 MHz at 2.7 mT, and matched to 50 {Omega}. Low-field, {sup 1}H nuclear magnetic resonance (NMR) is detected through the second, low-frequency channel at frequencies {lt}1 MHz. The performance of the probe was tested by measuring the DNP of protons in a manganese (II) chloride solution at 2.7 mT. At the proton NMR frequency of 120 kHz, the signal amplitude was enhanced over the value without DNP by a factor of about 200. {copyright} {ital 1997 American Institute of Physics.}

  1. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    NASA Astrophysics Data System (ADS)

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Moonshiram, D.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-05-01

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.

  2. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    PubMed Central

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Moonshiram, D.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-01-01

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site. PMID:27212390

  3. Probing Ultrafast Nuclear Dynamics in Halomethanes by Time-Resolved Electron and Ion Imaging

    NASA Astrophysics Data System (ADS)

    Ziaee, F.; Rudenko, A.; Rolles, D.; Savelyev, E.; Bomme, C.; Boll, R.; Manschwetus, B.; Erk, B.; Trippel, S.; Wiese, J.; Kuepper, J.; Amini, K.; Lee, J.; Brouard, M.; Brausse, F.; Rouzee, A.; Olshin, P.; Mereshchenko, A.; Lahl, J.; Johnsson, P.; Simon, M.; Marchenko, T.; Holland, D.; Underwood, J.

    2016-05-01

    Femtosecond pump-probe experiments provide opportunities to investigate photochemical reaction dynamics and the resulting changes in molecular structure in detail. Here, we present a study of the UV-induced photodissociation of gas-phase halomethane molecules (CH3 I, CH2 IBr, ...) in a pump-probe arrangement using two complementary probe schemes, either using a femtosecond near-infrared laser or the FLASH free-electron laser. We measured electrons and ions produced during the interaction using a double-sided velocity map imaging spectrometer equipped with a CCD camera for electron detection and with the Pixel Imaging Mass Spectrometry (PImMS) camera for ions, which can record the arrival time for up to four ions per pixel. This project is supported by the DOE, Office of Science, BES, Division of Chemical, Geological, and Biological Sciences.

  4. Protein rotational dynamics investigated with a dual EPR/optical molecular probe. Spin-labeled eosin.

    PubMed Central

    Cobb, C E; Hustedt, E J; Beechem, J M; Beth, A H

    1993-01-01

    An acyl spin-label derivative of 5-aminoeosin (5-SLE) was chemically synthesized and employed in studies of rotational dynamics of the free probe and of the probe when bound noncovalently to bovine serum albumin using the spectroscopic techniques of fluorescence anisotropy decay and electron paramagnetic resonance (EPR) and their long-lifetime counterparts phosphorescence anisotropy decay and saturation transfer EPR. Previous work (Beth, A. H., Cobb, C. E., and J. M. Beechem, 1992. Synthesis and characterization of a combined fluorescence, phosphorescence, and electron paramagnetic resonance probe. Society of Photo-Optical Instrumentation Engineers. Time-Resolved Laser Spectroscopy III. 504-512) has shown that the spin-label moiety only slightly altered the fluorescence and phosphorescence lifetimes and quantum yields of 5-SLE when compared with 5-SLE whose nitroxide had been reduced with ascorbate and with the diamagnetic homolog 5-acetyleosin. In the present work, we have utilized time-resolved fluorescence anisotropy decay and linear EPR spectroscopies to observe and quantitate the psec motions of 5-SLE in solution and the nsec motions of the 5-SLE-bovine serum albumin complex. Time-resolved phosphorescence anisotropy decay and saturation transfer EPR studies have been carried out to observe and quantitate the microseconds motions of the 5-SLE-albumin complex in glycerol/buffer solutions of varying viscosity. These latter studies have enabled a rigorous comparison of rotational correlation times obtained from these complementary techniques to be made with a single probe. The studies described demonstrate that it is possible to employ a single molecular probe to carry out the full range of fluorescence, phosphorescence, EPR, and saturation transfer EPR studies. It is anticipated that "dual" molecular probes of this general type will significantly enhance capabilities for extracting dynamics and structural information from macromolecules and their functional

  5. Probing ultrafast electronic and molecular dynamics with free-electron lasers

    NASA Astrophysics Data System (ADS)

    Fang, L.; Osipov, T.; Murphy, B. F.; Rudenko, A.; Rolles, D.; Petrovic, V. S.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Berrah, N.

    2014-06-01

    Molecular dynamics is an active area of research, focusing on revealing fundamental information on molecular structures and photon-molecule interaction and with broad impacts in chemical and biological sciences. Experimental investigation of molecular dynamics has been advanced by the development of new light sources and techniques, deepening our understanding of natural processes and enabling possible control and modification of chemical and biomolecular processes. Free-electron lasers (FELs) deliver unprecedented intense and short photon pulses in the vacuum ultraviolet and x-ray spectral ranges, opening a new era for the study of electronic and nuclear dynamics in molecules. This review focuses on recent molecular dynamics investigations using FELs. We present recent work concerning dynamics of molecular interaction with FELs using an intrinsic clock within a single x-ray pulse as well as using an external clock in a pump-probe scheme. We review the latest developments on correlated and coincident spectroscopy in FEL-based research and recent results revealing photo-induced interaction dynamics using these techniques. We also describe new instrumentations to conduct x-ray pump-x-ray probe experiments with spectroscopy and imaging detectors.

  6. Dynamic analysis of apoptosis using cyanine SYTO probes: From classical to microfluidic cytometry

    SciTech Connect

    Wlodkowic, Donald; Skommer, Joanna; Faley, Shannon; Darzynkiewicz, Zbigniew; Cooper, Jonathan M.

    2009-06-10

    Cell death is a stochastic process, often initiated and/or executed in a multi-pathway/multi-organelle fashion. Therefore, high-throughput single-cell analysis platforms are required to provide detailed characterization of kinetics and mechanisms of cell death in heterogeneous cell populations. However, there is still a largely unmet need for inert fluorescent probes, suitable for prolonged kinetic studies. Here, we compare the use of innovative adaptation of unsymmetrical SYTO dyes for dynamic real-time analysis of apoptosis in conventional as well as microfluidic chip-based systems. We show that cyanine SYTO probes allow non-invasive tracking of intracellular events over extended time. Easy handling and 'stain-no wash' protocols open up new opportunities for high-throughput analysis and live-cell sorting. Furthermore, SYTO probes are easily adaptable for detection of cell death using automated microfluidic chip-based cytometry. Overall, the combined use of SYTO probes and state-of-the-art Lab-on-a-Chip platform emerges as a cost effective solution for automated drug screening compared to conventional Annexin V or TUNEL assays. In particular, it should allow for dynamic analysis of samples where low cell number has so far been an obstacle, e.g. primary cancer stems cells or circulating minimal residual tumors.

  7. Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes

    SciTech Connect

    Popova, Anna; Kalai, Tamas; Hideg, Kalman; Qin, Peter Z.

    2009-09-15

    In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features.

  8. Impact of Resolution on Simulation of Closed Mesoscale Cellular Convection Identified by Dynamically Guided Watershed Segmentation

    SciTech Connect

    Martini, Matus N.; Gustafson, William I.; Yang, Qing; Xiao, Heng

    2014-11-18

    Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. We use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the southeast Pacific. A suite of experiments with 3- and 9-km grid spacing indicates resolution-dependent behavior. The simulations with finer grid spacing have smaller liquid water paths and cloud fractions, while cloud tops are higher. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we develop a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This ensures that the detected cloud fields are dynamically consistent for closed MCC, the most common MCC type over the VOCALS-REx region. We demonstrate that the 3-km simulation is able to reproduce the scaling between horizontal cell size and boundary layer height seen in satellite observations. However, the 9-km simulation is unable to resolve smaller circulations corresponding to shallower boundary layers, instead producing invariant MCC horizontal scale for all simulated boundary layers depths. The results imply that climate models with grid spacing of roughly 3 km or smaller may be needed to properly simulate the MCC structure in the marine stratocumulus regions.

  9. Traffic dynamics around weaving section influenced by accident: Cellular automata approach

    NASA Astrophysics Data System (ADS)

    Kong, Lin-Peng; Li, Xin-Gang; Lam, William H. K.

    2015-07-01

    The weaving section, as a typical bottleneck, is one source of vehicle conflicts and an accident-prone area. Traffic accident will block lanes and the road capacity will be reduced. Several models have been established to study the dynamics around traffic bottlenecks. However, little attention has been paid to study the complex traffic dynamics influenced by the combined effects of bottleneck and accident. This paper presents a cellular automaton model to characterize accident-induced traffic behavior around the weaving section. Some effective control measures are proposed and verified for traffic management under accident condition. The total flux as a function of inflow rates, the phase diagrams, the spatial-temporal diagrams, and the density and velocity profiles are presented to analyze the impact of accident. It was shown that the proposed control measures for weaving traffic can improve the capacity of weaving section under both normal and accident conditions; the accidents occurring on median lane in the weaving section are more inclined to cause traffic jam and reduce road capacity; the capacity of weaving section will be greatly reduced when the accident happens downstream the weaving section.

  10. Cellular context–mediated Akt dynamics regulates MAP kinase signaling thresholds during angiogenesis

    PubMed Central

    Hellesøy, Monica; Lorens, James B.

    2015-01-01

    The formation of new blood vessels by sprouting angiogenesis is tightly regulated by contextual cues that affect angiogeneic growth factor signaling. Both constitutive activation and loss of Akt kinase activity in endothelial cells impair angiogenesis, suggesting that Akt dynamics mediates contextual microenvironmental regulation. We explored the temporal regulation of Akt in endothelial cells during formation of capillary-like networks induced by cell–cell contact with vascular smooth muscle cells (vSMCs) and vSMC-associated VEGF. Expression of constitutively active Akt1 strongly inhibited network formation, whereas hemiphosphorylated Akt1 epi-alleles with reduced kinase activity had an intermediate inhibitory effect. Conversely, inhibition of Akt signaling did not affect endothelial cell migration or morphogenesis in vSMC cocultures that generate capillary-like structures. We found that endothelial Akt activity is transiently blocked by proteasomal degradation in the presence of SMCs during the initial phase of capillary-like structure formation. Suppressed Akt activity corresponded to the increased endothelial MAP kinase signaling that was required for angiogenic endothelial morphogenesis. These results reveal a regulatory principle by which cellular context regulates Akt protein dynamics, which determines MAP kinase signaling thresholds necessary drive a morphogenetic program during angiogenesis. PMID:26023089

  11. Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

    NASA Technical Reports Server (NTRS)

    Greenberg, Albert G.; Lubachevsky, Boris D.; Nicol, David M.; Wright, Paul E.

    1994-01-01

    Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times.

  12. TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics

    PubMed Central

    Etournay, Raphaël; Merkel, Matthias; Popović, Marko; Brandl, Holger; Dye, Natalie A; Aigouy, Benoît; Salbreux, Guillaume; Eaton, Suzanne; Jülicher, Frank

    2016-01-01

    Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins. DOI: http://dx.doi.org/10.7554/eLife.14334.001 PMID:27228153

  13. Cellular internalization of a membrane binding two-photon probe by a complex of anionic diblock copolymer and cationic surfactant

    NASA Astrophysics Data System (ADS)

    Nag, Okhil Kumar; Woo, Han Young; Chen, Wei R.

    2012-03-01

    We report a two-photon (TP) absorbing molecular probe 1,4-bis(4'-(N,N-bis(6''-(N,N,N-trimethylammonium)hexyl)amino)-styryl)benzene tetrabromide (C1) and its interaction with cells upon encapsulation with polymeric vesicles. Two-photon microscopy (TPM) revealed that the free C1 specifically could bind to the plasma membrane and shows bright TP emission. However, C1 encapsulated with polymeric vesicles internalized into the cytosol. In addition, fluorescence quantum efficiency and TP cross section of encapsulated C1 enhanced by 2-fold. These results not only show useful guidelines for the development of efficient TP probes, but also underscore the possibility of using this type of nanostructure for intracellular delivery of the bioactive therapeutics.

  14. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    SciTech Connect

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly, this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  15. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes.

    PubMed

    Li, Y; Zakharov, D; Zhao, S; Tappero, R; Jung, U; Elsen, A; Baumann, Ph; Nuzzo, R G; Stach, E A; Frenkel, A I

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  16. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    NASA Astrophysics Data System (ADS)

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  17. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    PubMed Central

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R.G.; Stach, E.A.; Frenkel, A.I.

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  18. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    DOE PAGESBeta

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly,more » this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.« less

  19. Probing the dynamics of Andreev states in a coherent Normal/Superconducting ring

    PubMed Central

    Chiodi, F.; Ferrier, M.; Tikhonov, K.; Virtanen, P.; Heikkilä, T. T.; Feigelman, M.; Guéron, S.; Bouchiat, H.

    2011-01-01

    The supercurrent that establishes between two superconductors connected through a normal N mesoscopic link is carried by quasiparticule states localized within the link, the “Andreev bound states (ABS)”. Whereas the dc properties of this supercurrent in SNS junctions are now well understood, its dynamical properties are still an unresolved issue. In this letter we probe this dynamics by inductively coupling an NS ring to a multimode superconducting resonator, thereby implementing both a phase bias and current detection at high frequency. Whereas at very low temperatures we essentially measure the phase derivative of the supercurrent, at higher temperature we find a surprisingly strong frequency dependence in the current response of the ring: the ABS do not follow adiabatically the phase modulation. This experiment also illustrates a new tool to probe the fundamental time scales of phase coherent systems that are decoupled from macroscopic normal contacts and thermal baths. PMID:22355522

  20. Functional Contributions of Strong and Weak Cellular Oscillators to Synchrony and Light-shifted Phase Dynamics.

    PubMed

    Roberts, Logan; Leise, Tanya L; Welsh, David K; Holmes, Todd C

    2016-08-01

    Light is the primary signal that calibrates circadian neural circuits and thus coordinates daily physiological and behavioral rhythms with solar entrainment cues. Drosophila and mammalian circadian circuits consist of diverse populations of cellular oscillators that exhibit a wide range of dynamic light responses, periods, phases, and degrees of synchrony. How heterogeneous circadian circuits can generate robust physiological rhythms while remaining flexible enough to respond to synchronizing stimuli has long remained enigmatic. Cryptochrome is a short-wavelength photoreceptor that is endogenously expressed in approximately half of Drosophila circadian neurons. In a previous study, physiological light response was measured using real-time bioluminescence recordings in Drosophila whole-brain explants, which remain intrinsically light-sensitive. Here we apply analysis of real-time bioluminescence experimental data to show detailed dynamic ensemble representations of whole circadian circuit light entrainment at single neuron resolution. Organotypic whole-brain explants were either maintained in constant darkness (DD) for 6 days or exposed to a phase-advancing light pulse on the second day. We find that stronger circadian oscillators support robust overall circuit rhythmicity in DD, whereas weaker oscillators can be pushed toward transient desynchrony and damped amplitude to facilitate a new state of phase-shifted network synchrony. Additionally, we use mathematical modeling to examine how a network composed of distinct oscillator types can give rise to complex dynamic signatures in DD conditions and in response to simulated light pulses. Simulations suggest that complementary coupling mechanisms and a combination of strong and weak oscillators may enable a robust yet flexible circadian network that promotes both synchrony and entrainment. A more complete understanding of how the properties of oscillators and their signaling mechanisms facilitate their distinct roles

  1. Exploring Ultrafast Molecular Dynamics using Photoelectron Spectra from UV/XUV Pump-Probe Experiments

    NASA Astrophysics Data System (ADS)

    Champenois, Elio; Cryan, James; Shivaram, Niranjan; Wright, Travis; Belkacem, Ali

    2015-05-01

    The motion of atoms in molecules can drive electron dynamics via non-adiabatic couplings. In small molecules such as Ethylene, Carbon Dioxide, and Nitrophenol, this can lead to isomerization, electronic relaxation, or other time-dependent effects following excitation from a bonding to an anti-bonding molecular orbital. To study these mechanisms, we use ultraviolet photons of various energies from a bright High Harmonic Generation source to first initiate dynamics and subsequently probe the system through ionization. We record the kinetic energy and angular distribution of the resultant photoelectrons using a Velocity Map Imaging spectrometer, allowing us to track the evolution of the electronic state.

  2. Probing dynamics of fusion reactions through cross-section and spin distribution measurement

    NASA Astrophysics Data System (ADS)

    Kaur, Maninder; Behera, B. R.; Singh, Gulzar; Singh, Varinderjit; Madhavan, N.; Muralithar, S.; Nath, S.; Gehlot, J.; Mohanto, G.; Mukul, Ish; Siwal, D.; Thakur, M.; Kapoor, K.; Sharma, P.; Banerjee, T.; Jhingan, A.; Varughese, T.; Bala, Indu; Nayak, B. K.; Saxena, A.; Chatterjee, M. B.; Stevenson, P. D.

    2016-05-01

    Present work aims to explicate the effect of entrance channel mass asymmetry on fusion dynamics for the Compound Nucleus 80Sr populated through two different channels, 16O+64Zn and 32S+48Ti, using cross-section and spin distribution measurements as probes. The evaporation spectra studies for these systems, reported earlier indicate the presence of dynamical effects for mass symmetric 32S+48Ti system.The CCDEF and TDHF calculations have been performed for both the systems and an attempt has been made to explain the reported deviations in the α-particle spectrum for the mass symmetric system.

  3. Probing superfluidity in a quasi two-dimensional Bose gas through its local dynamics

    NASA Astrophysics Data System (ADS)

    De Rossi, Camilla; Dubessy, Romain; Merloti, Karina; de Goër de Herve, Mathieu; Badr, Thomas; Perrin, Aurélien; Longchambon, Laurent; Perrin, Hélène

    2016-06-01

    We report direct evidence of superfluidity in a quasi two-dimensional Bose gas by observing its dynamical response to a collective excitation, the scissors mode. Relying on a novel local average analysis, we are able to probe inhomogeneous clouds and reveal their local dynamics. We identify in this way the superfluid and thermal phases inside the gas and locate the boundary at which the Berezinskii–Kosterlitz–Thouless crossover occurs. This new analysis also allows to evidence the coupling of the two fluids which induces at finite temperatures damping rates larger than the usual Landau damping.

  4. Automated Identification of Closed Mesoscale Cellular Convection and Impact of Resolution on Related Mesoscale Dynamics

    NASA Astrophysics Data System (ADS)

    Martini, M.; Gustafson, W. I.; Yang, Q.; Xiao, H.

    2013-12-01

    Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. Cloud resolving models begin to resolve some, but not all, of these processes with less of the mesoscale dynamics resolved as one progresses from <1 km to 10 km grid spacing. While limited domain cloud resolving models can use high resolution to simulate MCC, global cloud resolving models must resort to using grid spacings closer to 5 to 10 km. This effectively truncates the scales through which the dynamics can act and impacts the MCC characteristics, potentially altering the climate impact of these clouds in climate models. To understand the impact of this truncation, we use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the Southeast Pacific. A suite of experiments with 1-, 3- and 9-km grid spacing indicates resolution dependent behavior. The simulations with finer grid spacing have lower liquid water paths and cloud fractions, while cloud tops are higher. When compared to observed liquid water paths from GOES and MODIS, the 3-km simulation has better agreement over the coastal regions while the 9-km simulation better agrees over remote regions. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we developed a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This has the advantage of ensuring that the detected cloud fields are dynamically consistent for closed MCC and helps minimize false detections from secondary circulations. We demonstrate that the 3-km simulation is able to reproduce the scaling between

  5. Dynamical surface affinity of diphasic liquids as a probe of wettability of multimodal porous media.

    PubMed

    Korb, J-P; Freiman, G; Nicot, B; Ligneul, P

    2009-12-01

    We introduce a method for estimating the wettability of rock/oil/brine systems using noninvasive in situ nuclear magnetic relaxation dispersion. This technique scans over a large range of applied magnetic fields and yields unique information about the extent to which a fluid is dynamically correlated with a solid rock surface. Unlike conventional transverse relaxation studies, this approach is a direct probe of the dynamical surface affinity of fluids. To quantify these features we introduce a microscopic dynamical surface affinity index which measures the dynamical correlation (i.e., the microscopic wettability) between the diffusive fluid and the fixed paramagnetic relaxation sources at the pore surfaces. We apply this method to carbonate reservoir rocks which are known to hold about two thirds of the world's oil reserves. Although this nondestructive method concerns here an application to rocks, it could be generalized as an in situ liquid/surface affinity indicator for any multimodal porous medium including porous biological media. PMID:20365175

  6. Nanobodies as Probes for Protein Dynamics in Vitro and in Cells.

    PubMed

    Dmitriev, Oleg Y; Lutsenko, Svetlana; Muyldermans, Serge

    2016-02-19

    Nanobodies are the recombinant antigen-recognizing domains of the minimalistic heavy chain-only antibodies produced by camels and llamas. Nanobodies can be easily generated, effectively optimized, and variously derivatized with standard molecular biology protocols. These properties have triggered the recent explosion in the nanobody use in basic and clinical research. This review focuses on the emerging use of nanobodies for understanding and monitoring protein dynamics on the scales ranging from isolated protein domains to live cells, from nanoseconds to hours. The small size and high solubility make nanobodies uniquely suited for studying protein dynamics by NMR. The ability to produce conformation-sensitive nanobodies in cells enables studies that link structural dynamics of a target protein to its cellular behavior. The link between in vitro and in-cell dynamics, afforded by nanobodies, brings the analysis of such important events as receptor signaling, membrane protein trafficking, and protein interactions to the next level of resolution. PMID:26677230

  7. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes.

    PubMed

    Chang, Xingmao; Yu, Chunmeng; Wang, Gang; Fan, Jiayun; Zhang, Jianyun; Qi, Yanyu; Liu, Kaiqiang; Fang, Yu

    2015-06-01

    Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively. PMID:25985384

  8. Small-Scale Perfusion Bioreactor of Red Blood Cells for Dynamic Studies of Cellular Pathways: Proof-of-Concept.

    PubMed

    Prudent, Michel; Stauber, Frédéric; Rapin, Alexis; Hallen, Sonia; Pham, Nicole; Abonnenc, Mélanie; Marvin, Laure; Rochat, Bertrand; Tissot, Jean-Daniel; Lion, Niels

    2016-01-01

    To date, the development of bioreactors for the study of red blood cells (RBCs, daily transfused in the case of disease or hemorrhage) has focused on hematopoietic stem cells. Despite the fact that mature RBCs are enucleated and do not expand, they possess complex cellular and metabolic pathways, as well as post-translation modification signaling and gas-exchange regulation. In order to dynamically study the behavior of RBCs and their signaling pathways under various conditions, a small-scale perfusion bioreactor has been developed. The most advanced design developed here consists of a fluidized bed of 7.6 mL containing 3·10(9) cells and perfused at 8.5 μL/min. Mimicking RBC storage conditions in transfusion medicine, as a proof-of-concept, we investigated the ex vivo aging of RBCs under both aerobic and anaerobic conditions. Hence, RBCs stored in saline-adenine-glucose-mannitol (SAGM) were injected in parallel into two bioreactors and perfused with a modified SAGM solution over 14 days at room temperature under air or argon. The formation of a fluidized bed enabled easy sampling of the extracellular medium over the storage period used for the quantitation of glucose consumption and lactate production. Hemolysis and microvesiculation increased during aging and were reduced under anaerobic (argon) conditions, which is consistent with previously reported findings. Glucose and lactate levels showed expected trends, i.e., decreased and increased during the 2-week period, respectively; whereas extracellular glucose consumption was higher under aerobic conditions. Metabolomics showed depletion of glycolsis and pentose phosphate pathway metabolites, and an accumulation of purine metabolite end-products. This novel approach, which takes advantage of a fluidized bed of cells in comparison to traditional closed bags or tubes, does not require agitation and limit shear stress, and constantly segragates extracellular medium from RBCs. It thus gives access to several

  9. Small-Scale Perfusion Bioreactor of Red Blood Cells for Dynamic Studies of Cellular Pathways: Proof-of-Concept

    PubMed Central

    Prudent, Michel; Stauber, Frédéric; Rapin, Alexis; Hallen, Sonia; Pham, Nicole; Abonnenc, Mélanie; Marvin, Laure; Rochat, Bertrand; Tissot, Jean-Daniel; Lion, Niels

    2016-01-01

    To date, the development of bioreactors for the study of red blood cells (RBCs, daily transfused in the case of disease or hemorrhage) has focused on hematopoietic stem cells. Despite the fact that mature RBCs are enucleated and do not expand, they possess complex cellular and metabolic pathways, as well as post-translation modification signaling and gas-exchange regulation. In order to dynamically study the behavior of RBCs and their signaling pathways under various conditions, a small-scale perfusion bioreactor has been developed. The most advanced design developed here consists of a fluidized bed of 7.6 mL containing 3·109 cells and perfused at 8.5 μL/min. Mimicking RBC storage conditions in transfusion medicine, as a proof-of-concept, we investigated the ex vivo aging of RBCs under both aerobic and anaerobic conditions. Hence, RBCs stored in saline-adenine-glucose-mannitol (SAGM) were injected in parallel into two bioreactors and perfused with a modified SAGM solution over 14 days at room temperature under air or argon. The formation of a fluidized bed enabled easy sampling of the extracellular medium over the storage period used for the quantitation of glucose consumption and lactate production. Hemolysis and microvesiculation increased during aging and were reduced under anaerobic (argon) conditions, which is consistent with previously reported findings. Glucose and lactate levels showed expected trends, i.e., decreased and increased during the 2-week period, respectively; whereas extracellular glucose consumption was higher under aerobic conditions. Metabolomics showed depletion of glycolsis and pentose phosphate pathway metabolites, and an accumulation of purine metabolite end-products. This novel approach, which takes advantage of a fluidized bed of cells in comparison to traditional closed bags or tubes, does not require agitation and limit shear stress, and constantly segragates extracellular medium from RBCs. It thus gives access to several difficult

  10. Hygromorphic behaviour of cellular material: hysteretic swelling and shrinkage of wood probed by phase contrast X-ray tomography

    NASA Astrophysics Data System (ADS)

    Derome, Dominique; Rafsanjani, Ahmad; Patera, Alessandra; Guyer, Robert; Carmeliet, Jan

    2012-10-01

    Wood is a hygromorphic material, meaning it responds to changes in environmental humidity by changing its geometry. Its cellular biological structure swells during wetting and shrinks during drying. The origin of the moisture-induced deformation lies at the sub-cellular scale. The cell wall can be considered a composite material with stiff cellulose fibrils acting as reinforcement embedded in a hemicellulose/lignin matrix. The bulk of the cellulose fibrils, forming 50% of the cell wall, are oriented longitudinally, forming long-pitched helices. Both components of cell wall matrix are displaying swelling. Moisture sorption and, to a lesser degree, swelling/shrinkage are known to be hysteretic. We quantify the affine strains during the swelling and shrinkage using high resolution images obtained by phase contrast synchrotron X-ray tomography of wood samples of different porosities. The reversibility of the swelling/shrinkage is found for samples with controlled moisture sorption history. The deformation is more hysteretic for high than for low density samples. Swelling/shrinkage due to ad/desorption of water vapour displays also a non-affine component. The reversibility of the swelling/shrinkage indicates that the material has a structural capacity to show a persistent cellular geometry for a given moisture state and a structural composition that allows for moisture-induced transitional states. A collection of qualitative observations of small subsets of cells during swelling/shrinkage is further studied by simulating the observed behaviour. An anisotropic swelling coefficient of the cell wall is found to emerge and its origin is linked to the anisotropy of the cellulose fibrils arrangement in cell wall layers.

  11. Cellular imaging using biocompatible dendrimer-functionalized graphene oxide-based fluorescent probe anchored with magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Wate, Prateek S.; Banerjee, Shashwat S.; Jalota-Badhwar, Archana; Mascarenhas, Russel R.; Zope, Khushbu R.; Khandare, Jayant; Misra, R. Devesh K.

    2012-10-01

    We describe a novel multicomponent graphene nanostructured system that is biocompatible, and has strong NIR optical absorbance and superparamagnetic properties. The fabrication of the multicomponent nanostructure system involves the covalent attachment of 3 components; Fe3O4(Fe) nanoparticles, PAMAM-G4-NH2 (G4) dendrimer and Cy5 (Cy) on a graphene oxide (GO) surface to synthesize a biologically relevant multifunctional system. The resultant GO-G4-Fe-Cy nanosystem exhibits high dispersion in an aqueous medium, and is magnetically responsive and fluorescent. In vitro experiments provide a clear indication of successful uptake of the GO-G4-Fe-Cy nanosystem by MCF-7 breast cancer cells, and it is seen to behave as a bright and stable fluorescent marker. The study also reveals varied cellular distribution kinetics profile for the GO nanostructured system compared to free Cy. Furthermore, the newly developed GO nanostructured system is observed to be non-toxic to MDA-MB-231 cell growth, in striking contrast to free G4 dendrimer and GO-G4 conjugate. The GO-G4-Fe-Cy nanostructured system characterized by multifunctionality suggests the merits of graphene for cellular bioimaging and the delivery of bioactives.

  12. Autofluorescence multiphoton microscopy for visualization of tissue morphology and cellular dynamics in murine and human airways

    PubMed Central

    Kretschmer, Sarah; Pieper, Mario; Hüttmann, Gereon; Bölke, Torsten; Wollenberg, Barbara; Marsh, Leigh M; Garn, Holger; König, Peter

    2016-01-01

    The basic understanding of inflammatory airway diseases greatly benefits from imaging the cellular dynamics of immune cells. Current imaging approaches focus on labeling specific cells to follow their dynamics but fail to visualize the surrounding tissue. To overcome this problem, we evaluated autofluorescence multiphoton microscopy for following the motion and interaction of cells in the airways in the context of tissue morphology. Freshly isolated murine tracheae from healthy mice and mice with experimental allergic airway inflammation were examined by autofluorescence multiphoton microscopy. In addition, fluorescently labeled ovalbumin and fluorophore-labeled antibodies were applied to visualize antigen uptake and to identify specific cell populations, respectively. The trachea in living mice was imaged to verify that the ex vivo preparation reflects the in vivo situation. Autofluorescence multiphoton microscopy was also tested to examine human tissue from patients in short-term tissue culture. Using autofluorescence, the epithelium, underlying cells, and fibers of the connective tissue, as well as blood vessels, were identified in isolated tracheae. Similar structures were visualized in living mice and in the human airway tissue. In explanted murine airways, mobile cells were localized within the tissue and we could follow their migration, interactions between individual cells, and their phagocytic activity. During allergic airway inflammation, increased number of eosinophil and neutrophil granulocytes were detected that moved within the connective tissue and immediately below the epithelium without damaging the epithelial cells or connective tissues. Contacts between granulocytes were transient lasting 3 min on average. Unexpectedly, prolonged interactions between granulocytes and antigen-uptaking cells were observed lasting for an average of 13 min. Our results indicate that autofluorescence-based imaging can detect previously unknown immune cell

  13. Autofluorescence multiphoton microscopy for visualization of tissue morphology and cellular dynamics in murine and human airways.

    PubMed

    Kretschmer, Sarah; Pieper, Mario; Hüttmann, Gereon; Bölke, Torsten; Wollenberg, Barbara; Marsh, Leigh M; Garn, Holger; König, Peter

    2016-08-01

    The basic understanding of inflammatory airway diseases greatly benefits from imaging the cellular dynamics of immune cells. Current imaging approaches focus on labeling specific cells to follow their dynamics but fail to visualize the surrounding tissue. To overcome this problem, we evaluated autofluorescence multiphoton microscopy for following the motion and interaction of cells in the airways in the context of tissue morphology. Freshly isolated murine tracheae from healthy mice and mice with experimental allergic airway inflammation were examined by autofluorescence multiphoton microscopy. In addition, fluorescently labeled ovalbumin and fluorophore-labeled antibodies were applied to visualize antigen uptake and to identify specific cell populations, respectively. The trachea in living mice was imaged to verify that the ex vivo preparation reflects the in vivo situation. Autofluorescence multiphoton microscopy was also tested to examine human tissue from patients in short-term tissue culture. Using autofluorescence, the epithelium, underlying cells, and fibers of the connective tissue, as well as blood vessels, were identified in isolated tracheae. Similar structures were visualized in living mice and in the human airway tissue. In explanted murine airways, mobile cells were localized within the tissue and we could follow their migration, interactions between individual cells, and their phagocytic activity. During allergic airway inflammation, increased number of eosinophil and neutrophil granulocytes were detected that moved within the connective tissue and immediately below the epithelium without damaging the epithelial cells or connective tissues. Contacts between granulocytes were transient lasting 3 min on average. Unexpectedly, prolonged interactions between granulocytes and antigen-uptaking cells were observed lasting for an average of 13 min. Our results indicate that autofluorescence-based imaging can detect previously unknown immune cell

  14. Probing ultrafast valley dynamics in 2D semiconductors via time-resolved Kerr rotation

    NASA Astrophysics Data System (ADS)

    Huang, Jiani; Hoang, Thang; Ming, Tian; Kong, Jing; Mikkelsen, Maiken

    Monolayer transition metal dichalcogenides (TMDCs) offer a tantalizing platform for controlling spin and valley degrees of freedom, enabling future optoelectronic devices with enhanced and novel functionalities. Here, we experimentally probe the valley dynamics in monolayer MoS2 and WSe2 using time-resolved Kerr rotation (TRKR) from T = 10 K to 300 K . This pump-probe technique offers sub-picosecond temporal resolution, providing insight into ultrafast valley dynamics inaccessible by polarized and time-resolved photoluminescence spectroscopy. Bi-exponential decay dynamics were observed for both materials at low temperatures. Strong long-range exchange interactions between the K valleys led to a rapid exciton valley depolarization time (< 10 ps), while the valley polarization of the trion and defect states decays within several tens of ps. Moreover, spatial distributions of the TRKR amplitude across monolayer flakes indicated weaker valley polarizations near the edges of MoS2, which is likely associated with the Mo- or S-zigzag terminations at the boundaries. These temporal and spatial TRKR measurements reveal insight into the complex dynamics of valley excitonic states in monolayer TMDCs.

  15. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    SciTech Connect

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  16. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy.

    PubMed

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O-H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm(-1). We observe rapid vibrational relaxation processes on 150-250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1-2 ps time scales. Furthermore, the O-H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions. PMID:26590536

  17. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-01

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O-H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm-1. We observe rapid vibrational relaxation processes on 150-250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1-2 ps time scales. Furthermore, the O-H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ˜200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  18. Dynamic Deformation and Fragmentation Response of Maraging Steel Linear Cellular Alloy

    NASA Astrophysics Data System (ADS)

    Jakus, Adam; Fredenburg, D. A.; McCoy, T.; Thadhani, N. N.; Cochran, J.

    2011-06-01

    The dynamic deformation and fragmentation response of 25% dense 9-cell linear cellular alloy (LCA) made of unaged 250 maraging steel, fabricated using a direct reduction and extrusion technique, is investigated. Explicit finite element simulations were implemented using AUTODYN. The maraging steel properties were defined using a Johnson-Cook strength model with previously validated parameters. Rod-on-anvil impact tests were performed using the 7.6 mm helium gas gun and the transient deformation and fragmentation response was recorded with high-speed imaging. For purpose of comparison, the response of 25% dense hollow cylinders of same density as the 9-cell LCA was also studied. Analysis of observed states of specimens and finite element simulations reveal that in the case of the 9-cell LCA, dissipation of stress and strain occurs along the interior cell wells resulting in significant and ubiquitous buckling prior to confined fragmentation. In comparison, the simple hollow cylinder undergoes significant radial lipping, eventually producing larger sized, external fragments. DTRA Grant No. HDTRA1-07-1-0018 and NDSEG Fellowship Program.

  19. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    PubMed

    Shalek, Alex K; Satija, Rahul; Shuga, Joe; Trombetta, John J; Gennert, Dave; Lu, Diana; Chen, Peilin; Gertner, Rona S; Gaublomme, Jellert T; Yosef, Nir; Schwartz, Schraga; Fowler, Brian; Weaver, Suzanne; Wang, Jing; Wang, Xiaohui; Ding, Ruihua; Raychowdhury, Raktima; Friedman, Nir; Hacohen, Nir; Park, Hongkun; May, Andrew P; Regev, Aviv

    2014-06-19

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses. PMID:24919153

  20. An archived multi-objective simulated annealing for a dynamic cellular manufacturing system

    NASA Astrophysics Data System (ADS)

    Shirazi, Hossein; Kia, Reza; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza

    2014-05-01

    To design a group layout of a cellular manufacturing system (CMS) in a dynamic environment, a multi-objective mixed-integer non-linear programming model is developed. The model integrates cell formation, group layout and production planning (PP) as three interrelated decisions involved in the design of a CMS. This paper provides an extensive coverage of important manufacturing features used in the design of CMSs and enhances the flexibility of an existing model in handling the fluctuations of part demands more economically by adding machine depot and PP decisions. Two conflicting objectives to be minimized are the total costs and the imbalance of workload among cells. As the considered objectives in this model are in conflict with each other, an archived multi-objective simulated annealing (AMOSA) algorithm is designed to find Pareto-optimal solutions. Matrix-based solution representation, a heuristic procedure generating an initial and feasible solution and efficient mutation operators are the advantages of the designed AMOSA. To demonstrate the efficiency of the proposed algorithm, the performance of AMOSA is compared with an exact algorithm (i.e., ∈-constraint method) solved by the GAMS software and a well-known evolutionary algorithm, namely NSGA-II for some randomly generated problems based on some comparison metrics. The obtained results show that the designed AMOSA can obtain satisfactory solutions for the multi-objective model.

  1. Identification of Dynamic Changes in Proteins Associated with the Cellular Cytoskeleton after Exposure to Okadaic Acid

    PubMed Central

    Opsahl, Jill A.; Ljostveit, Sonja; Solstad, Therese; Risa, Kristin; Roepstorff, Peter; Fladmark, Kari E.

    2013-01-01

    Exposure of cells to the diarrhetic shellfish poison, okadaic acid, leads to a dramatic reorganization of cytoskeletal architecture and loss of cell-cell contact. When cells are exposed to high concentrations of okadaic acid (100–500 nM), the morphological rearrangement is followed by apoptotic cell death. Okadaic acid inhibits the broad acting Ser/Thr protein phosphatases 1 and 2A, which results in hyperphosphorylation of a large number of proteins. Some of these hyperphosphorylated proteins are most likely key players in the reorganization of the cell morphology induced by okadaic acid. We wanted to identify these phosphoproteins and searched for them in the cellular lipid rafts, which have been found to contain proteins that regulate cytoskeletal dynamics and cell adhesion. By using stable isotope labeling by amino acids in cell culture cells treated with okadaic acid (400 nM) could be combined with control cells before the isolation of lipid rafts. Protein phosphorylation events and translocations induced by okadaic acid were identified by mass spectrometry. Okadaic acid was shown to regulate the phosphorylation status and location of proteins associated with the actin cytoskeleton, microtubules and cell adhesion structures. A large number of these okadaic acid-regulated proteins have previously also been shown to be similarly regulated prior to cell proliferation and migration. Our results suggest that okadaic acid activates general cell signaling pathways that induce breakdown of the cortical actin cytoskeleton and cell detachment. PMID:23708184

  2. Complex dynamics of selection and cellular memory in adaptation to a changing environment

    NASA Astrophysics Data System (ADS)

    Kussell, Edo; Lin, Wei-Hsiang

    We study a synthetic evolutionary system in bacteria in which an antibiotic resistance gene is controlled by a stochastic on/off switching promoter. At the population level, this system displays all the basic ingredients for evolutionary selection, including diversity, fitness differences, and heritability. At the single cell level, physiological processes can modulate the ability of selection to act. We expose the stochastic switching strains to pulses of antibiotics of different durations in periodically changing environments using microfluidics. Small populations are tracked over a large number of periods at single cell resolution, allowing the visualization and quantification of selective sweeps and counter-sweeps at the population level, as well as detailed single cell analysis. A simple model is introduced to predict long-term population growth rates from single cell measurements, and reveals unexpected aspects of population dynamics, including cellular memory that acts on a fast timescale to modulate growth rates. This work is supported by NIH Grant No. R01-GM097356.

  3. Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

    NASA Astrophysics Data System (ADS)

    Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

    2012-03-01

    Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

  4. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

    NASA Astrophysics Data System (ADS)

    Shalek, Alex K.; Satija, Rahul; Shuga, Joe; Trombetta, John J.; Gennert, Dave; Lu, Diana; Chen, Peilin; Gertner, Rona S.; Gaublomme, Jellert T.; Yosef, Nir; Schwartz, Schraga; Fowler, Brian; Weaver, Suzanne; Wang, Jing; Wang, Xiaohui; Ding, Ruihua; Raychowdhury, Raktima; Friedman, Nir; Hacohen, Nir; Park, Hongkun; May, Andrew P.; Regev, Aviv

    2014-06-01

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a `core' module of antiviral genes is expressed very early by a few `precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced `peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.

  5. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.

    PubMed

    Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B

    2015-01-15

    Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn(-/-) mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn(-/-) mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259

  6. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling

    PubMed Central

    Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B

    2015-01-01

    Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn–/– mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn–/– mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259

  7. Highly Dynamic Cellular-Level Response of Symbiotic Coral to a Sudden Increase in Environmental Nitrogen

    PubMed Central

    Kopp, C.; Pernice, M.; Domart-Coulon, I.; Djediat, C.; Spangenberg, J. E.; Alexander, D. T. L.; Hignette, M.; Meziane, T.; Meibom, A.

    2013-01-01

    ABSTRACT Metabolic interactions with endosymbiotic photosynthetic dinoflagellate Symbiodinium spp. are fundamental to reef-building corals (Scleractinia) thriving in nutrient-poor tropical seas. Yet, detailed understanding at the single-cell level of nutrient assimilation, translocation, and utilization within this fundamental symbiosis is lacking. Using pulse-chase 15N labeling and quantitative ion microprobe isotopic imaging (NanoSIMS; nanoscale secondary-ion mass spectrometry), we visualized these dynamic processes in tissues of the symbiotic coral Pocillopora damicornis at the subcellular level. Assimilation of ammonium, nitrate, and aspartic acid resulted in rapid incorporation of nitrogen into uric acid crystals (after ~45 min), forming temporary N storage sites within the dinoflagellate endosymbionts. Subsequent intracellular remobilization of this metabolite was accompanied by translocation of nitrogenous compounds to the coral host, starting at ~6 h. Within the coral tissue, nitrogen is utilized in specific cellular compartments in all four epithelia, including mucus chambers, Golgi bodies, and vesicles in calicoblastic cells. Our study shows how nitrogen-limited symbiotic corals take advantage of sudden changes in nitrogen availability; this opens new perspectives for functional studies of nutrient storage and remobilization in microbial symbioses in changing reef environments. PMID:23674611

  8. Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI)

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Aboard the International Space Station (ISS), the Tissue Culture Module (TCM) is the stationary bioreactor vessel in which cell cultures grow. However, for the Cellular Biotechnology Operations Support Systems-Fluid Dynamics Investigation (CBOSS-FDI), color polystyrene beads are used to measure the effectiveness of various mixing procedures. Uniform mixing is a crucial component of CBOSS experiments involving the immune response of human lymphoid cell suspensions. In this picture, the beads are trapped in the injection port shortly after injection. Swirls of beads indicate, event to the naked eye, the contents of the TCM are not fully mixed. The beads are similar in size and density to human lymphoid cells. The goal is to develop procedures that are both convenient for the flight crew and are optimal in providing uniform and reproducible mixing of all components, including cells. The average bead density in a well mixed TCM will be uniform, with no bubbles, and it will be measured using the absorption of light

  9. Laminar, cellular, transverse, and multiheaded pulsating detonations in condensed phase energetic materials from molecular dynamics simulations.

    PubMed

    Zhakhovsky, Vasily V; Budzevich, Mikalai M; Landerville, Aaron C; Oleynik, Ivan I; White, Carter T

    2014-09-01

    The development of condensed-phase detonation instabilities is simulated using moving window molecular dynamics and a generic AB model of a high explosive. It is found that an initially planar detonation front with one-dimensional flow can become unstable through development of transverse perturbations resulting in highly inhomogeneous and complex two- and three-dimensional distributions of pressure and other variables within the detonation front. Chemical reactions are initiated in localized transverse shock fronts and Mach stems with a pressure and temperature higher than those predicted by classic Zel'dovich, von Neumann, and Doering detonation theory. The two-dimensional cellular and transverse and three-dimensional pulsating detonation structures are found by varying the physico-chemical properties of AB energetic material, sample geometry, and boundary conditions. The different regimes of condensed-phase detonation that can develop from instabilities within a planar detonation front exhibit structures, although at a much smaller scale, that are similar to those observed in gases and diluted liquids. PMID:25314569

  10. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics

    PubMed Central

    Keränen, Soile VE; Fowlkes, Charless C; Luengo Hendriks, Cris L; Sudar, Damir; Knowles, David W; Malik, Jitendra; Biggin, Mark D

    2006-01-01

    Background To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos. Results Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms. Conclusion Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis. PMID:17184547

  11. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    SciTech Connect

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  12. XPS for probing the dynamics of surface voltage and photovoltage in GaN

    NASA Astrophysics Data System (ADS)

    Sezen, Hikmet; Ozbay, Ekmel; Suzer, Sefik

    2014-12-01

    We describe application of two different data gathering techniques of XPS for probing the dynamics of surface voltage and surface photovoltage (SPV) developed in microseconds to seconds time-domain, in addition to the conventional steady-state measurements. For the longer (seconds to milliseconds) regime, capturing the data in the snapshot fashion is used, but for the faster one (down to microseconds), square wave (SQW) electrical pulses at different frequencies are utilized to induce and probe the dynamics of various processes causing the surface voltage, including the SPV, via the changes in the peak positions. The frequency range covers anywhere from 10-3 to 105 Hz for probing changes due to charging (slow), dipolar (intermediate), and electronic (fast) processes associated with the external stresses imposed. We demonstrate its power by application to n- and p-GaN, and discuss the chemical/physical information derived thereof. In addition, the method allows us to decompose and identify the peaks with respect to their charging nature for a composite sample containing both n- and p-GaN moieties.

  13. Valley dynamics probed through charged and neutral exciton emission in monolayer WSe2

    NASA Astrophysics Data System (ADS)

    Wang, G.; Bouet, L.; Lagarde, D.; Vidal, M.; Balocchi, A.; Amand, T.; Marie, X.; Urbaszek, B.

    2014-08-01

    Optical interband transitions in monolayer transition metal dichalcogenides such as WSe2 and MoS2 are governed by chiral selection rules. This allows efficient optical initialization of an electron in a specific K valley in momentum space. Here we probe the valley dynamics in monolayer WSe2 by monitoring the emission and polarization dynamics of the well-separated neutral excitons (bound electron-hole pairs) and charged excitons (trions) in photoluminescence. The neutral exciton photoluminescence intensity decay time is about 4 ps, whereas the trion emission occurs over several tens of ps. The trion polarization dynamics shows a partial, fast initial decay within tens of ps before reaching a stable polarization of ≈20%, for which a typical valley polarization decay time of the order of 1 ns can be inferred.

  14. Real-Time Probing of Electron Dynamics Using Attosecond Time-Resolved Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ramasesha, Krupa; Leone, Stephen R.; Neumark, Daniel M.

    2016-05-01

    Attosecond science has paved the way for direct probing of electron dynamics in gases and solids. This review provides an overview of recent attosecond measurements, focusing on the wealth of knowledge obtained by the application of isolated attosecond pulses in studying dynamics in gases and solid-state systems. Attosecond photoelectron and photoion measurements in atoms reveal strong-field tunneling ionization and a delay in the photoemission from different electronic states. These measurements applied to molecules have shed light on ultrafast intramolecular charge migration. Similar approaches are used to understand photoemission processes from core and delocalized electronic states in metal surfaces. Attosecond transient absorption spectroscopy is used to follow the real-time motion of valence electrons and to measure the lifetimes of autoionizing channels in atoms. In solids, it provides the first measurements of bulk electron dynamics, revealing important phenomena such as the timescales governing the switching from an insulator to a metallic state and carrier-carrier interactions.

  15. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution

    PubMed Central

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H. A.; Vogel, Martin

    2016-01-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  16. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution.

    PubMed

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H A; Vogel, Martin

    2016-02-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  17. Real-Time Probing of Electron Dynamics Using Attosecond Time-Resolved Spectroscopy.

    PubMed

    Ramasesha, Krupa; Leone, Stephen R; Neumark, Daniel M

    2016-05-27

    Attosecond science has paved the way for direct probing of electron dynamics in gases and solids. This review provides an overview of recent attosecond measurements, focusing on the wealth of knowledge obtained by the application of isolated attosecond pulses in studying dynamics in gases and solid-state systems. Attosecond photoelectron and photoion measurements in atoms reveal strong-field tunneling ionization and a delay in the photoemission from different electronic states. These measurements applied to molecules have shed light on ultrafast intramolecular charge migration. Similar approaches are used to understand photoemission processes from core and delocalized electronic states in metal surfaces. Attosecond transient absorption spectroscopy is used to follow the real-time motion of valence electrons and to measure the lifetimes of autoionizing channels in atoms. In solids, it provides the first measurements of bulk electron dynamics, revealing important phenomena such as the timescales governing the switching from an insulator to a metallic state and carrier-carrier interactions. PMID:26980312

  18. Probing the dynamics of elliptical galaxies by planetary nebulae in the framework of MOdified Newtonian Dynamics

    NASA Astrophysics Data System (ADS)

    Tian, Yong; Ko, Chung-Ming

    2015-08-01

    Planetary nebulae (PNe) at large distances from the centre of a galaxy provide us a tool to study its dynamics there. Romanowsky et al. (2003) reported the dynamics of three luminous elliptical galaxies up to 6 effective radii, and all of them can be explained by Newtonian dynamics without dark matter. Milgrom & Sanders (2003) deem that the result can be understood in the framework of MOND (MOdified Newtonian dynamics). We revisit this problem as more measurements are available in the past decade. In this contribution, we present our result on 7 elliptical galaxies with PNe data up to 6-8 effective radii and also stellar data from SAURON. We conclude that MOND can well explain the dynamics of all these galaxies.

  19. Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy

    PubMed Central

    Nishida, Jun; Tamimi, Amr; Fei, Honghan; Pullen, Sonja; Ott, Sascha; Cohen, Seth M.; Fayer, Michael D.

    2014-01-01

    The structural elasticity of metal–organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer. PMID:25512539

  20. Acoustic wave absorption as a probe of dynamical geometrical response of fractional quantum Hall liquids

    NASA Astrophysics Data System (ADS)

    Yang, Kun

    2016-04-01

    We show that an acoustic crystalline wave gives rise to an effect similar to that of a gravitational wave to an electron gas. Applying this idea to a two-dimensional electron gas in the fractional quantum Hall regime, this allows for experimental study of its intra-Landau level dynamical response in the long-wavelength limit. To study such response we generalize Haldane's geometrical description of fractional quantum Hall states to situations where the external metric is time dependent. We show that such time-dependent metric (generated by acoustic wave) couples to collective modes of the system, including a quadrapolar mode at long wavelength, and magnetoroton at finite wavelength. Energies of these modes can be revealed in spectroscopic measurements, controlled by strain-induced Fermi velocity anisotropy. We argue that such geometrical probe provides a potentially highly useful alternative probe of quantum Hall liquids, in addition to the usual electromagnetic response.

  1. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level.

    PubMed

    Dopfer, Otto; Fujii, Masaaki

    2016-05-11

    Solvation processes play a crucial role in chemical reactions and biomolecular recognition phenomena. Although solvation dynamics of interfacial or biological water has been studied extensively in aqueous solution, the results are generally averaged over several solvation layers and the motion of individual solvent molecules is difficult to capture. This review describes the development and application of a new experimental approach, namely, picosecond time-resolved pump-probe infrared spectroscopy of size- and isomer-selected aromatic clusters, in which for the first time the dynamics of a single individual solvent molecule can be followed in real time. The intermolecular isomerization reaction is triggered by resonant photoionization (pump), and infrared photodissociation (probe) at variable delay generates the spectroscopic signature of salient properties of the reaction, including rates, yields, pathways, branching ratios of competing reactions, existence of reaction intermediates, occurrence of back reactions, and time scales of energy relaxation processes. It is shown that this relevant information can reliably be decoded from the experimental spectra by sophisticated molecular dynamics simulations. This review covers a description of the experimental strategies and spectroscopic methods along with all applications to date, which range from aromatic clusters with nonpolar solvent molecules to aromatic monohydrated biomolecules. PMID:27054835

  2. Closed-form stochastic solutions for non-equilibrium dynamics and inheritance of cellular components over many cell divisions

    PubMed Central

    Johnston, Iain G.; Jones, Nick S.

    2015-01-01

    Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for treating several important examples of these stochastic processes, most notably gene expression and random partitioning at single-cell divisions or after a steady state has been reached. Comparatively little work exists exploring different and specific ways that repeated cell divisions can lead to stochastic inheritance of unequilibrated cellular populations. Here we introduce a mathematical formalism to describe cellular agents that are subject to random creation, replication and/or degradation, and are inherited according to a range of random dynamics at cell divisions. We obtain closed-form generating functions describing systems at any time after any number of cell divisions for binomial partitioning and divisions provoking a deterministic or random, subtractive or additive change in copy number, and show that these solutions agree exactly with stochastic simulation. We apply this general formalism to several example problems involving the dynamics of mitochondrial DNA during development and organismal lifetimes. PMID:26339194

  3. Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory

    PubMed Central

    Hasselmo, Michael E.; Giocomo, Lisa M.; Yoshida, Motoharu

    2010-01-01

    Understanding the mechanisms of episodic memory requires linking behavioural data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within these brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action. PMID:20018213

  4. Implementation and characterization of a quartz tuning fork based probe consisted of discrete resonators for dynamic mode atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Akiyama, Terunobu; de Rooij, Nicolaas F.; Staufer, Urs; Detterbeck, Manfred; Braendlin, Dominik; Waldmeier, Simon; Scheidiger, Martin

    2010-06-01

    The quartz tuning fork based probe {e.g., Akiyama et al. [Appl. Surf. Sci. 210, 18 (2003)]}, termed "A-Probe," is a self-sensing and self-actuating (exciting) probe for dynamic mode atomic force microscope (AFM) operation. It is an oscillatory force sensor consisting of the two discrete resonators. This paper presents the investigations on an improved A-Probe: its batch fabrication and assembly, mounting on an AFM head, electrical setup, characterization, and AFM imaging. The fundamental features of the A-Probe are electrically and optically characterized in "approach-withdraw" experiments. Further investigations include the frequency response of an A-Probe to small mechanical vibrations externally applied to the tip and the effective loading force yielding between the tip and the sample during the periodic contact. Imaging of an electronic chip, a compact disk stamper, carbon nanotubes, and Si beads is demonstrated with this probe at ambient conditions in the so-called frequency modulation mode. A special probe substrate, which can snap on a receptacle fixed on an AFM head, and a special holder including a preamplifier electronic are introduced. We hope that the implementation and characterization of the A-Probe described in this paper will provide hints for new scanning probe techniques.

  5. Computational model of cellular metabolic dynamics: effect of insulin on glucose disposal in human skeletal muscle

    PubMed Central

    Li, Yanjun; Solomon, Thomas P. J.; Haus, Jacob M.; Saidel, Gerald M.; Cabrera, Marco E.

    2010-01-01

    Identifying the mechanisms by which insulin regulates glucose metabolism in skeletal muscle is critical to understanding the etiology of insulin resistance and type 2 diabetes. Our knowledge of these mechanisms is limited by the difficulty of obtaining in vivo intracellular data. To quantitatively distinguish significant transport and metabolic mechanisms from limited experimental data, we developed a physiologically based, multiscale mathematical model of cellular metabolic dynamics in skeletal muscle. The model describes mass transport and metabolic processes including distinctive processes of the cytosol and mitochondria. The model simulated skeletal muscle metabolic responses to insulin corresponding to human hyperinsulinemic-euglycemic clamp studies. Insulin-mediated rate of glucose disposal was the primary model input. For model validation, simulations were compared with experimental data: intracellular metabolite concentrations and patterns of glucose disposal. Model variations were simulated to investigate three alternative mechanisms to explain insulin enhancements: Model 1 (M.1), simple mass action; M.2, insulin-mediated activation of key metabolic enzymes (i.e., hexokinase, glycogen synthase, pyruvate dehydrogenase); or M.3, parallel activation by a phenomenological insulin-mediated intracellular signal that modifies reaction rate coefficients. These simulations indicated that models M.1 and M.2 were not sufficient to explain the experimentally measured metabolic responses. However, by application of mechanism M.3, the model predicts metabolite concentration changes and glucose partitioning patterns consistent with experimental data. The reaction rate fluxes quantified by this detailed model of insulin/glucose metabolism provide information that can be used to evaluate the development of type 2 diabetes. PMID:20332360

  6. High resolution simulations of energy absorption in dynamically loaded cellular structures

    NASA Astrophysics Data System (ADS)

    Winter, R. E.; Cotton, M.; Harris, E. J.; Eakins, D. E.; McShane, G.

    2016-04-01

    Cellular materials have potential application as absorbers of energy generated by high velocity impact. CTH, a Sandia National Laboratories Code which allows very severe strains to be simulated, has been used to perform very high resolution simulations showing the dynamic crushing of a series of two-dimensional, stainless steel metal structures with varying architectures. The structures are positioned to provide a cushion between a solid stainless steel flyer plate with velocities ranging from 300 to 900 m/s, and an initially stationary stainless steel target. Each of the alternative architectures under consideration was formed by an array of identical cells each of which had a constant volume and a constant density. The resolution of the simulations was maximised by choosing a configuration in which one-dimensional conditions persisted for the full period over which the specimen densified, a condition which is most readily met by impacting high density specimens at high velocity. It was found that the total plastic flow and, therefore, the irreversible energy dissipated in the fully densified energy absorbing cell, increase (a) as the structure becomes more rodlike and less platelike and (b) as the impact velocity increases. Sequential CTH images of the deformation processes show that the flow of the cell material may be broadly divided into macroscopic flow perpendicular to the compression direction and jetting-type processes (microkinetic flow) which tend to predominate in rod and rodlike configurations and also tend to play an increasing role at increased strain rates. A very simple analysis of a configuration in which a solid flyer impacts a solid target provides a baseline against which to compare and explain features seen in the simulations. The work provides a basis for the development of energy absorbing structures for application in the 200-1000 m/s impact regime.

  7. Utilizing dynamic laser speckle to probe nanoscale morphology evolution in nanoporous gold thin films

    DOE PAGESBeta

    Chapman, Christopher A. R.; Ly, Sonny; Wang, Ling; Seker, Erkin; Matthews, Manyalibo J.

    2016-03-02

    Here we show the use of dynamic laser speckle autocorrelation spectroscopy in conjunction with the photothermal treatment of nanoporous gold (np-Au) thin films to probe nanoscale morphology changes during the photothermal treatment. Utilizing this spectroscopy method, backscattered speckle from the incident laser is tracked during photothermal treatment and both the characteristic feature size and annealing time of the film are determined. These results demonstrate that this method can successfully be used to monitor laser-based surface modification processes without the use of ex-situ characterization.

  8. Probing internal structure of {Lambda}(1405) in meson-baryon dynamics with chiral symmetry

    SciTech Connect

    Sekihara, Takayasu; Hyodo, Tetsuo; Jido, Daisuke

    2011-10-21

    The internal structure of the resonant {Lambda}(1405) state is investigated based on meson-baryon coupled-channels chiral dynamics, by evaluating density distributions obtained from the form factors of the {Lambda}(1405) state. The form factors are extracted from current-coupled scattering amplitudes in which the current is coupled to the constituent hadrons inside {Lambda}(1405). Using several probe interactions and channel decomposition, we find that the resonant {Lambda}(1405) state is dominantly composed of widely spread K-bar around N, with a small fraction of the escaping {pi}{Sigma} component.

  9. Critical behavior of gelation probed by the dynamics of latex spheres

    SciTech Connect

    Fadda, G. C.; Lairez, D.; Pelta, J.

    2001-06-01

    We report a quasielastic light scattering study of the dynamics of large latex probe particles (R=225nm) in gelatin solution undergoing gelation. We show that by focusing on the short-time and long-time behavior of the autocorrelation function, it is possible to simply interpret out data in terms of the divergence of the viscosity and emergence of the shear elastic modulus near the gel point. Our crude analysis allows us to grasp the critical behavior of gelation and to obtain the two critical exponents of the transport properties.

  10. Multicolor probe-based confocal laser endomicroscopy: a new world for in vivo and real-time cellular imaging

    NASA Astrophysics Data System (ADS)

    Vercauteren, Tom; Doussoux, François; Cazaux, Matthieu; Schmid, Guillaume; Linard, Nicolas; Durin, Marie-Amélie; Gharbi, Hédi; Lacombe, François

    2013-03-01

    Since its inception in the field of in vivo imaging, endomicroscopy through optical fiber bundles, or probe-based Confocal Laser Endomicroscopy (pCLE), has extensively proven the benefit of in situ and real-time examination of living tissues at the microscopic scale. By continuously increasing image quality, reducing invasiveness and improving system ergonomics, Mauna Kea Technologies has turned pCLE not only into an irreplaceable research instrument for small animal imaging, but also into an accurate clinical decision making tool with applications as diverse as gastrointestinal endoscopy, pulmonology and urology. The current implementation of pCLE relies on a single fluorescence spectral band making different sources of in vivo information challenging to distinguish. Extending the pCLE approach to multi-color endomicroscopy therefore appears as a natural plan. Coupling simultaneous multi-laser excitation with minimally invasive, microscopic resolution, thin and flexible optics, allows the fusion of complementary and valuable biological information, thus paving the way to a combination of morphological and functional imaging. This paper will detail the architecture of a new system, Cellvizio Dual Band, capable of video rate in vivo and in situ multi-spectral fluorescence imaging with a microscopic resolution. In its standard configuration, the system simultaneously operates at 488 and 660 nm, where it automatically performs the necessary spectral, photometric and geometric calibrations to provide unambiguously co-registered images in real-time. The main hardware and software features, including calibration procedures and sub-micron registration algorithms, will be presented as well as a panorama of its current applications, illustrated with recent results in the field of pre-clinical imaging.

  11. Ultrafast dynamics in helium nanodroplets probed by femtosecond time-resolved EUV photoelectron imaging

    SciTech Connect

    Kornilov, Oleg; Wang, Chia C.; Buenermann, Oliver; Healy, Andrew T.; Leonard, Mathew; Peng, Chunte; Leone, Stephen R.; Neumark, Daniel M.; Gessner, Oliver

    2010-07-09

    The dynamics of electronically excited helium nanodroplets are studied by femtosecond time-resolved photoelectron imaging. EUV excitation into a broad absorption band centered around 23.8 eV leads to an indirect photoemission process that generates ultraslow photoelectrons. A 1.58 eV probe pulse transiently depletes the indirect photoemission signal for pump-probe time delays <200 fs and enhances the signal beyond this delay. The depletion is due to suppression of the indirect ionization process by the probe photon, which generates a broad, isotropically emitted photoelectron band. Similar time scales in the decay of the high energy photoelectron signal and the enhancement of the indirect photoemission signal suggest an internal relaxation process that populates states in the range of a lower energy droplet absorption band located just below the droplet ionization potential (IP {approx} 23.0 eV). A nearly 70% enhancement of the ultraslow photoelectron signal indicates that interband relaxation plays a more dominant role for the droplet de-excitation mechanism than photoemission.

  12. Radition belt dynamics : Recent results from van Allen Probes and future observations from CeREs

    NASA Astrophysics Data System (ADS)

    Kanekal, Shrikanth; O'Brien, Paul; Baker, Daniel N.; Ogasawara, Keiichi; Fennell, Joseph; Christian, Eric; Claudepierre, Seth; Livi, Stefano; Desai, Mihir; Li, Xinlin; Jaynes, Allison; Turner, Drew; Jones, Ashley; Schiller, Quintin

    2016-07-01

    We describe recent observations of the Earth's radiation belts made by instruments on board the Van Allen Probes mission, particularly the Relativistic Electron Proton Telescope (REPT) and the Magnetic Electron Ion spectrometer (MagEIS). These observations have significantly advanced our understanding of terrestrial radiation belt dynamics. The Van Allen Probes mission comprises two identically instrumented spacecraft which were launched 31 August, 2012 into low-inclination lapping equatorial orbits. The orbit periods are about 9 hours, with perigees and apogees of of ~600 km and 5.8 RE respectively. We discuss the new scientific findings of the Van Allen Probes mission regarding the physics of energization and loss of relativistic electrons and their implications for future low-cost missions, especially CubeSats. We describe the CeREs (a Compact Radiation belt Explorer) CubeSat mission currently being built at the Goddard Space Flight Center, and carrying on board, an innovative instrument, the Miniaturized Electron Proton Telescope (MERiT). The MERiT is a compact low-mass low-power instrument measuring electrons from a few keV to tens of MeV in multiple differential channels. MERiT is optimized to measure electron microbursts with a high time resolution of a few milliseconds. We present and discuss possible future scientific contributions from CeREs.

  13. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    PubMed Central

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  14. Cellular automata approach for the dynamics of HIV infection under antiretroviral therapies: The role of the virus diffusion

    NASA Astrophysics Data System (ADS)

    González, Ramón E. R.; de Figueirêdo, Pedro Hugo; Coutinho, Sérgio

    2013-10-01

    We study a cellular automata model to test the timing of antiretroviral therapy strategies for the dynamics of infection with human immunodeficiency virus (HIV). We focus on the role of virus diffusion when its population is included in previous cellular automata model that describes the dynamics of the lymphocytes cells population during infection. This inclusion allows us to consider the spread of infection by the virus-cell interaction, beyond that which occurs by cell-cell contagion. The results show an acceleration of the infectious process in the absence of treatment, but show better efficiency in reducing the risk of the onset of AIDS when combined antiretroviral therapies are used even with drugs of low effectiveness. Comparison of results with clinical data supports the conclusions of this study.

  15. Direct Tracking of Amyloid and Tu Dynamics in Neuroblastoma Cells Using Nanoplasmonic Fiber Tip Probes.

    PubMed

    Liang, Feng; Zhang, Yiying; Hong, Wooyoung; Dong, Yuanlin; Xie, Zhongcong; Quan, Qimin

    2016-07-13

    Amyloid plaques and neurofibrillary tangles are the pathological hallmarks of Alzheimer's disease. However, there has been a long-standing discussion on the dynamic relations between Aβ and tau proteins, partially due to the lack of a tool to track protein dynamics in individual live neurons at the early stage of Aβ generation and tau phosphorylation. Here, we developed nanoplasmonic fiber tip probe (nFTP) technology to simultaneously monitor Aβ42 generation and tau phosphorylation (at serine 262) in living, single neuroblastoma cells over 12 h. We observed that Aβ42 generation, under clinically relevant anesthetic treatment, preceded tau phosphorylation, which then facilitated Aβ42 generation. This observation is also supported by measuring proteins in cell lysates using the ultrasensitive label-free photonic crystal nanosensors. nFTP therefore provides an advanced method to investigate protein expression and post-translational modification in live cells and determine outcomes of intervention of Alzheimer's disease and other neurodegenerative disorders. PMID:27266855

  16. Probing polariton dynamics in trapped ions with phase-coherent two-dimensional spectroscopy.

    PubMed

    Gessner, Manuel; Schlawin, Frank; Buchleitner, Andreas

    2015-06-01

    We devise a phase-coherent three-pulse protocol to probe the polariton dynamics in a trapped-ion quantum simulation. In contrast to conventional nonlinear signals, the presented scheme does not change the number of excitations in the system, allowing for the investigation of the dynamics within an N-excitation manifold. In the particular case of a filling factor one (N excitations in an N-ion chain), the proposed interaction induces coherent transitions between a delocalized phonon superfluid and a localized atomic insulator phase. Numerical simulations of a two-ion chain demonstrate that the resulting two-dimensional spectra allow for the unambiguous identification of the distinct phases, and the two-dimensional line shapes efficiently characterize the relevant decoherence mechanism. PMID:26049459

  17. Probing polariton dynamics in trapped ions with phase-coherent two-dimensional spectroscopy

    NASA Astrophysics Data System (ADS)

    Gessner, Manuel; Schlawin, Frank; Buchleitner, Andreas

    2015-06-01

    We devise a phase-coherent three-pulse protocol to probe the polariton dynamics in a trapped-ion quantum simulation. In contrast to conventional nonlinear signals, the presented scheme does not change the number of excitations in the system, allowing for the investigation of the dynamics within an N-excitation manifold. In the particular case of a filling factor one (N excitations in an N-ion chain), the proposed interaction induces coherent transitions between a delocalized phonon superfluid and a localized atomic insulator phase. Numerical simulations of a two-ion chain demonstrate that the resulting two-dimensional spectra allow for the unambiguous identification of the distinct phases, and the two-dimensional line shapes efficiently characterize the relevant decoherence mechanism.

  18. Rotational dynamics of colloidal spheres probed with fluorescence recovery after photobleaching.

    PubMed

    Lettinga, M P; Koenderink, G H; Kuipers, B W M; Bessels, E; Philipse, A P

    2004-03-01

    We report a polarized fluorescence recovery after photobleaching (pFRAP) method to measure the rotational dynamics of fluorescent colloids over a wide dynamic range. The method is based on the polarization anisotropy in the fluorescence intensity, generated by bleaching of fluorescently labeled particles with an intense pulse of linearly polarized laser light. The rotational mobilities of the fluorescent particles can be extracted from the relaxation kinetics of the postbleach fluorescence polarization anisotropy. Our pFRAP setup has access to correlation times over a range of time scales from tens of microseconds to tens of seconds, and is highly sensitive, so very low concentrations of labeled particles can be probed. We present a detailed description of the theoretical background of pFRAP. The performance of the equipment is demonstrated for fluorescent colloidal silica spheres, dispersed in pure solvents as well as in fd-virus suspensions. PMID:15268620

  19. Probing polariton dynamics in trapped ions with phase-coherent two-dimensional spectroscopy

    SciTech Connect

    Gessner, Manuel; Schlawin, Frank; Buchleitner, Andreas

    2015-06-07

    We devise a phase-coherent three-pulse protocol to probe the polariton dynamics in a trapped-ion quantum simulation. In contrast to conventional nonlinear signals, the presented scheme does not change the number of excitations in the system, allowing for the investigation of the dynamics within an N-excitation manifold. In the particular case of a filling factor one (N excitations in an N-ion chain), the proposed interaction induces coherent transitions between a delocalized phonon superfluid and a localized atomic insulator phase. Numerical simulations of a two-ion chain demonstrate that the resulting two-dimensional spectra allow for the unambiguous identification of the distinct phases, and the two-dimensional line shapes efficiently characterize the relevant decoherence mechanism.

  20. Low-frequency dynamics of aqueous alkali chloride solutions as probed by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Kann, Z. R.; Skinner, J. L.

    2016-06-01

    Terahertz (far infrared) spectroscopy provides a useful tool for probing both ionic motions in solution and the effect of ionic solutes on the dynamics of the solvent. In this study, we calculate terahertz spectra of aqueous alkali chloride solutions using classical but novel (the water model includes three-body interactions, the ion parameterization is non-standard, and the dipole surface is polarizable) molecular dynamics simulations. The calculated spectra compare reasonably well to experimental spectra. Decomposition of the calculated spectra is used to gain a deeper understanding of the physical phenomena underlying the spectra and the connection to, for instance, the vibrational density of states for the ions. The decomposed results are also used to explain many of the cation-dependent trends observed in the experimental spectra.

  1. Investigation of implosion dynamics and magnetic fields in 1-MA wire arrays by optical probing diagnostics

    NASA Astrophysics Data System (ADS)

    Laca, P. J.; Sarkisov, G. S.

    2005-10-01

    Multiframe optical probing diagnostics were applied for the investigation of implosion dynamics and magnetic fields in z-pinch plasma of wire arrays and x-pinches at the Nevada Terawatt Facility (NTF). Five shadow frames per shot, with a long 34-ns or short 9-ns pulse train, presents fine details of plasma evolution in the wire array. A Faraday rotation diagnostic consists of identical shadow and Faraday channels, shearing air-wedge interferometer, and schlieren channel. Evolution of the wire array z-pinch in different regimes of implosion was investigated. Fast dynamics of bubbles in plasma streams were studied in detail. A current in the plasma column of Al wire arrays and magnetic bubbles were found by the Faraday rotation diagnostic.

  2. Real time monitoring of superoxide dynamics in vivo through fluorescent proteins using a sensitive fiber probe

    NASA Astrophysics Data System (ADS)

    Chang, Yu-Chung; Ken, Chuian-Fu; Hsu, Che-Wei; Liu, Ya-Ging

    2014-03-01

    Superoxide anion is the primary oxygen free radical generated in mitochondria that causes intracellular oxidative stress. The lack of a method to directly monitor superoxide concentration in vivo in real time has severely hindered our understanding on its pathophysiology. We made transgenic zebrafish to specifically express fluorescent proteins, which are recently developed as reversible superoxide-specific indicators, in the liver. A fiber-optic fluorescent probe was used to noninvasively monitor superoxide generation in the liver in real time. The fish were placed in microfluidic channels for manipulation and reagents administration. Several superoxide-inducing and scavenging reagents were administrated onto the fish to investigate their effects on superoxide anion balancing. The biochemical dynamics of superoxide due to the application reagents were revealed in the transient behaviors of fluorescence time courses. With the ability to monitor superoxide dynamics in vivo in real time, this method can be used as an in vivo pharmaceutical screening platform.

  3. Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping

    NASA Astrophysics Data System (ADS)

    Frasinski, L. J.; Zhaunerchyk, V.; Mucke, M.; Squibb, R. J.; Siano, M.; Eland, J. H. D.; Linusson, P.; v. d. Meulen, P.; Salén, P.; Thomas, R. D.; Larsson, M.; Foucar, L.; Ullrich, J.; Motomura, K.; Mondal, S.; Ueda, K.; Osipov, T.; Fang, L.; Murphy, B. F.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Schorb, S.; Messerschmidt, M.; Glownia, J. M.; Cryan, J. P.; Coffee, R. N.; Takahashi, O.; Wada, S.; Piancastelli, M. N.; Richter, R.; Prince, K. C.; Feifel, R.

    2013-08-01

    When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called “partial covariance mapping” to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.

  4. Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane.

    PubMed

    Murugan, N Arul; Apostolov, Rossen; Rinkevicius, Zilvinas; Kongsted, Jacob; Lindahl, Erik; Ågren, Hans

    2013-09-11

    Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, N-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy. PMID:23951997

  5. Towards pump probe experiments of defect dynamics with short ion beam pulses

    SciTech Connect

    Schenkel, T.; Lidia, S.; Weis, C. D.; Waldron, W. L.; Schwartz, J.; Minor, Andrew; Hosemann, P; Kwan, J. W.

    2013-01-01

    A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 1011 ions/pulse), 0.6 to 600 ns duration pulses of 0.05 1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1 10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of 30,000 K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

  6. Towards pump-probe experiments of defect dynamics with short ion beam pulses

    NASA Astrophysics Data System (ADS)

    Schenkel, T.; Lidia, S. M.; Weis, C. D.; Waldron, W. L.; Schwartz, J.; Minor, A. M.; Hosemann, P.; Kwan, J. W.

    2013-11-01

    A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 × 1011 ions/pulse), 0.6 to ∼600 ns duration pulses of 0.05-1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1-10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of ∼30,000 °K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump-probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump-probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

  7. Probe Dependent Solvation Dynamics Study in a Microscopically Immiscible Dimethyl Sulfoxide-Glycerol Binary Solvent.

    PubMed

    Kaur, Harveen; Koley, Somnath; Ghosh, Subhadip

    2014-06-26

    Excited state dipole solvation of three coumarin dyes with different hydrophobicities was studied in DMSO-glycerol binary solvent. The solvation times obtained from the three dyes are remarkably different. The highly hydrophilic dye coumarin 343 (C343) exhibits the slowest solvation time (>12 ns) among all the dyes we used. This is in contrast to the most hydrophobic dye coumarin 153 (C153), where the solvated state is reached just within ∼104 ps. However, the moderately hydrophobic dye coumarin 480 (C480) demonstrates an intermediate (∼396 ps) solvation time. Unprecedented slowdown of solvation time of C343 is probably due to the slow diffusion of solvent molecules in the glycerol-rich first solvation shell followed by hydrogen bond rearrangements around the solute dipole. On the other hand, fast solvation of hydrophobic dye C153 is most likely caused by the fast reorganization dynamics of hydrophobic -CH3 groups of DMSO or the carbon backbone of the glycerol molecule around the solute dipole. Interestingly, a remarkable probe dependency in solvation dynamics was not observed in the case of DMSO-water binary solvent or in a neat solvent isopropanol. Probe dependent solvation in a DMSO-glycerol mixture is attributed to the microscopic phase segregation and different locations of coumarin dyes within this binary solvent. PMID:24942350

  8. Binding hotspots on K-Ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis

    PubMed Central

    Prakash, Priyanka; Hancock, John F.; Gorfe, Alemayehu A.

    2015-01-01

    We have used probe-based molecular dynamics (pMD) simulations to search for interaction hotspots on the surface of the therapeutically highly relevant oncogenic K-Ras G12D. Combining the probe-based query with an ensemble-based pocket identification scheme and an analysis of existing Ras-ligand complexes, we show that (i) pMD is a robust and cost-effective strategy for binding site identification, (ii) all four of the previously reported ligand binding sites are suitable for structure-based ligand design, and (iii) in some cases probe binding and expanded sampling of configurational space enable pocket expansion and increase the likelihood of site identification. Furthermore, by comparing the distribution of hotspots in non-pocket-like regions with known protein- and membrane-interacting interfaces, we propose that pMD has the potential to predict surface patches responsible for protein-biomolecule interactions. These observations have important implications for future drug design efforts and will facilitate the search for potential interfaces responsible for the proposed transient oligomerization or interaction of Ras with other biomolecules in the cellular milieu. PMID:25740554

  9. Probing the dynamics of highly excited toluene on the fs timescale.

    PubMed

    Papadopoulou, C C; Kaziannis, S; Kosmidis, C

    2015-12-21

    Investigation of the dynamics of toluene-h8 (C6H5CH3), toluene-d8 (C6D5CD3) and toluene-α,α,α-d3 (C6H5CD3) has been performed utilizing the VUV pump-IR probe technique on the fs timescale. Using the 5th harmonic (∼160 nm) of a Ti:sapphire laser as the pump beam, two superimposed electronic states, the valence S3 and the Rydberg 4p, were excited by one-photon absorption, followed by ionization and dissociation induced by the probe beam (800 nm). Analysis of the transient signal of the parent (P(+)) and fragment ions ([P-H](+) or [P-D](+)) implies the existence of two different relaxation processes: (i) from the Rydberg and (ii) from the S3 valence state. Using a rate equation model, the decay times have been determined and comparison between the different isotopologues has been made. Conclusions on the relaxation path, the relative displacements of the potential energy surfaces and the activation energies needed have been drawn from the decay times. The signals corresponding to the fragment ions present a small in amplitude, but nonetheless, unambiguous periodical modulation, which is attributed to out-of-plane bending oscillation, involving also the methyl group. The dynamics of the H- and D-loss channels has been investigated. Especially for the case of toluene-α,α,α-d3, where both channels are in operation, it was found that the ratio of the abundance of H/D-loss dissociation reactions decreases as the pump-probe delay time increases. PMID:26559123

  10. Proposed experimental probes of chemical reaction molecular dynamics in solution: ICN photodissociation

    NASA Astrophysics Data System (ADS)

    Benjamin, I.; Wilson, Kent R.

    1989-04-01

    Knowledge of how translational and rotational motions are influenced by the solvent during the course of a photodissociation ``half-collision'' reaction in solution is of interest in itself and can also help our understanding of how thermally activated reactions take place in solution by means of fluctuations in translational and rotational motion. With this goal, the molecular dynamics of the photodissociation of the triatomic molecule ICN are compared in the gas phase and in Xe solution. The time evolution of the trajectories (particularly with respect to interfragment distance and CN orientation) and of the energy partitioning (particularly into fragment translational recoil and into rotation of the CN) are displayed. Two types of solution experiments are proposed and simulated, both closely related to recent gas phase studies by Dantus, Rosker, and Zewail. These experiments are designed to probe the detailed dynamics of chemical reactions in solution during the time period the reaction is in progress, in particular to reveal the dramatic effects of the solvent on translational motions and energies. Both are pump-probe experiments in which the first photon dissociates the ICN and the second induces fluorescence in the CN fragment. In the first type of experiment, which is particularly sensitive to fragment translational motion, the fluorescence intensity is measured as a function of photon energy and of time delay. In the second type of experiment, which is particularly sensitive to fragment rotation, in addition the angle between the polarizations of the pump and probe photons is varied. In the calculations presented here, the effect of the absorption of the photodissociation photon is treated using the classical Frank-Condon principle. The coupling between the assumed two upper electronic surfaces is taken into account semiclassically using a generalization to the condensed phase of the classical electron model of Miller and Meyer, which was applied to ICN

  11. Transcriptome and Proteome Dynamics of the Cellular Response of Shewanella oneidensis to Chromium Stress

    SciTech Connect

    Thompson, D.K.

    2005-04-18

    The overall goal of this DOE NABIR project is to characterize the molecular basis and regulation of hexavalent chromium [Cr(VI)] stress response and reduction by Shewanella oneidensis strain MR-1. Temporal genomic profiling and mass spectrometry-based proteomic analysis were employed to characterize the dynamic molecular response of S. oneidensis MR-1 to both acute and chronic Cr(VI) exposure. The acute stress response of aerobic, mid-exponential phase cells shocked to a final concentration of 1 mM potassium chromate (K2CrO4) was examined at post-exposure time intervals of 5, 30, 60, and 90 min relative to untreated cells. The transcriptome of mid-exponential cultures was also analyzed 30 min after shock doses of 0.3, 0.5, or 1 mM K{sub 2}CrO{sub 4}. The tonB1-exbB1-exbD1 genes comprising the TonB1 iron transport system were some of the most highly induced coding sequences (CDSs) after 90 min (up to {approx}240 fold), followed by other genes involved in heme transport, sulfate transport, and sulfur assimilation pathways. In addition, transcript levels for CDSs with annotated functions in DNA repair (dinP, recX, recA, recN) and detoxification processes (so3585, so3586) were substantially increased in Cr(VI)-exposed cells compared to untreated cells. By contrast, genes predicted to encode hydrogenases (HydA, HydB), oxidoreductases (SO0902-03-04, SO1911), iron-sulfur cluster binding proteins (SO4404), decaheme cytochrome c proteins (MtrA, OmcA, OmcB), and a number of LysR or TetR family transcriptional regulators were some of the most highly repressed CDSs following the 90-min shock period. Transcriptome profiles generated from MR-1 cells adapted to 0.3 mM Cr(VI) differed significantly from those characterizing cells exposed to acute Cr(VI) stress without adaptation. Parallel proteomic characterization of soluble protein and membrane protein fractions extracted from Cr(VI)-shocked and Cr(VI)-adapted MR-1 cells was performed using multidimensional HPLC-ESI-MS/MS (both

  12. Multi-color fluorescence imaging of sub-cellular dynamics of cancer cells in live mice

    NASA Astrophysics Data System (ADS)

    Hoffman, Robert M.

    2006-02-01

    We have genetically engineered dual-color fluorescent cells with one color in the nucleus and the other in the cytoplasm that enables real-time nuclear-cytoplasmic dynamics to be visualized in living cells in the cytoplasm in vivo as well as in vitro. To obtain the dual-color cells, red fluorescent protein (RFP) was expressed of the cancer cells, and green fluorescent protein (GFP) linked to histone H2B was expressed in the nucleus. Mitotic cells were visualized by whole-body imaging after injection in the mouse ear. Common carotid artery or heart injection of dual-color cells and a reversible skin flap enabled the external visualization of the dual-color cells in microvessels in the mouse where extreme elongation of the cell body as well as the nucleus occurred. The migration velocities of the dual-color cancer cells in the capillaries were measured by capturing individual images of the dual-color fluorescent cells over time. Human HCT-116-GFP-RFP colon cancer and mouse mammary tumor (MMT)-GFP-RFP cells were injected in the portal vein of nude mice. Extensive clasmocytosis (destruction of the cytoplasm) of the HCT-116-GFP-RFP cells occurred within 6 hours. The data suggest rapid death of HCT-116-GFP-RFP cells in the portal vein. In contrast, MMT-GFP-RFP cells injected into the portal vein mostly survived and formed colonies in the liver. However, when the host mice were pretreated with cyclophosphamide, the HCT-116-GFP-RFP cells also survived and formed colonies in the liver after portal vein injection. These results suggest that a cyclophosphamide-sensitive host cellular system attacked the HCT-116-GFP-RFP cells but could not effectively kill the MMT-GFP-RFP cells. With the ability to continuously image cancer cells at the subcellular level in the live animal, our understanding of the complex steps of metastasis will significantly increase. In addition, new drugs can be developed to target these newly visible steps of metastasis.

  13. Probing nuclear dynamics and architecture using single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Jung, Yoon; Li, Junang; Fakhri, Nikta

    Chromatin is a multiscale dynamic architecture that acts as a template for many biochemical processes such as transcription and DNA replication. Recent developments such as Hi-C technology enable an identification of chromatin interactions across an entire genome. However, a single cell dynamic view of chromatin organization is far from understood. We discuss a new live cell imaging technique to probe the dynamics of the nucleus at a single cell level using single-walled carbon nanotubes (SWNTs). SWNTs are non-perturbing rigid rods (diameter of 1 nm and length of roughly 100 nm) that fluoresce in the near infrared region. Due to their high aspect ratio, they can diffuse in tight spaces and report on the architecture and dynamics of the nucleoplasm. We develop 3D imaging and tracking of SWNTs in the volume of the nucleus using double helix point spread function microscopy (DH-PSF) and discuss the capabilities of the DH-PSF for inferring the 3D orientation of nanotubes based on vectorial diffraction theory.

  14. Probing interfacial electron dynamics with time-resolved X-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Neppl, Stefan

    2015-05-01

    Time-resolved core-level spectroscopy techniques using laser pulses to initiate and short X-ray pulses to probe photo-induced processes have the potential to provide electronic state- and atomic site-specific insight into fundamental electron dynamics at complex interfaces. We describe the implementation of femto- and picosecond time-resolved photoelectron spectroscopy at the Linac Coherent Light Source (LCLS) and at the Advanced Light Source (ALS) in order to follow light-driven electron dynamics at dye-semiconductor interfaces on femto- to nanosecond timescales, and from the perspective of individual atomic sites. A distinct transient binding-energy shift of the Ru3d photoemission lines originating from the metal centers of N3 dye-molecules adsorbed on nanoporous ZnO is observed 500 fs after resonant HOMO-LUMO excitation with a visible laser pulse. This dynamical chemical shift is accompanied by a characteristic surface photo-voltage response of the semiconductor substrate. The two phenomena and their correlation will be discussed in the context of electronic bottlenecks for efficient interfacial charge-transfer and possible charge recombination and relaxation pathways leading to the neutralization of the transiently oxidized dye following ultrafast electron injection. First steps towards in operando time-resolved X-ray absorption spectroscopy techniques to monitor interfacial chemical dynamics will be presented.

  15. Analysis of dynamic nonlinearity of flow control loop through modified relay test probing

    NASA Astrophysics Data System (ADS)

    Boiko, I.; Sayedain, S.

    2010-12-01

    Most of the controller tuning methods in process control are based on linear models. Through the development of a detail model of the actuator-pneumatic valve dynamics, we show that even if the static characteristic of the valve is linear (including possible linearity of the flow dependence on the valve opening) the actuator-valve dynamics are strongly nonlinear. Therefore, tuning of the flow loop will be affected by the selection of the operating point and the amplitude of the relay in the relay feedback test (RFT) or modifications of this test. It is shown that Lyapunov linearisation around an equilibrium point fails to provide a local linear model of the system, and modified RFT probing is used for investigation of the system dynamics. The same test is used for the proportional-integral controller tuning in various operating points. It is recommended that the difference in the dynamic response of the loop for different relay amplitudes and operating points should be accounted for by larger stability margins.

  16. The In Situ Tryptophan Analogue Probes the Conformational Dynamics in Asparaginase Isozymes.

    PubMed

    Chao, Wei-Chih; Shen, Jiun-Yi; Yang, Cheng-Han; Lan, Yi-Kang; Yuan, Jui-Hung; Lin, Li-Ju; Yang, Hsiao-Ching; Lu, Jyh-Feng; Wang, Jinn-Shyan; Wee, Kevin; Chen, You-Hua; Chou, Pi-Tai

    2016-04-26

    Dynamic water solvation is crucial to protein conformational reorganization and hence to protein structure and functionality. We report here the characterization of water dynamics on the L-asparaginase structural homology isozymes L-asparaginases I (AnsA) and II (AnsB), which are shown via fluorescence spectroscopy and dynamics in combination with molecular dynamics simulation to have distinct catalytic activity. By use of the tryptophan (Trp) analog probe 2,7-diaza-tryptophan ((2,7-aza)Trp), which exhibits unique water-catalyzed proton-transfer properties, AnsA and AnsB are shown to have drastically different local water environments surrounding the single Trp. In AnsA, (2,7-aza)Trp exhibits prominent green N(7)-H emission resulting from water-catalyzed excited-state proton transfer. In stark contrast, the N(7)-H emission is virtually absent in AnsB, which supports a water-accessible and a water-scant environment in the proximity of Trp for AnsA and AnsB, respectively. In addition, careful analysis of the emission spectra and corresponding relaxation dynamics, together with the results of molecular dynamics simulations, led us to propose two structural states associated with the rearrangement of the hydrogen-bond network in the vicinity of Trp for the two Ans. The water molecules revealed in the proximity of the Trp residue have semiquantitative correlation with the observed emission spectral variations of (2,7-aza)Trp between AnsA and AnsB. Titration of aspartate, a competitive inhibitor of Ans, revealed an increase in N(7)-H emission intensity in AnsA but no obvious spectral changes in AnsB. The changes in the emission profiles reflect the modulation of structural states by locally confined environment and trapped-water collective motions. PMID:27119634

  17. Ultrafast dynamics in thiophene investigated by femtosecond pump probe photoelectron spectroscopy and theory.

    PubMed

    Weinkauf, R; Lehr, L; Schlag, E W; Salzmann, S; Marian, C M

    2008-01-21

    A hybrid of a time-of-flight mass spectrometer and a time-of-flight "magnetic-bottle type" photoelectron (PE) spectrometer is used for fs pump-probe investigations of the excited state dynamics of thiophene. A resonant two-photon ionization spectrum of the onset of the excited states has been recorded with a tunable UV laser of 190 fs pulse width. With the pump laser set to the first intense transition we find by UV probe ionization first a small time shift of the maxima in the PE spectrum and then a fast decay to a low constant intensity level. The fitted time constants are 80+/-10 fs, and 25+/-10 fs, respectively. Theoretical calculations show that upon geometry relaxation the electronic state order changes and conical intersections between excited states exist. We use the vertical state order S1, S2, S3 to define the terms S1, S2, and S3 for the characterization of the electron configuration of these states. On the basis of our theoretical result we discuss the electronic state order in the UV spectra and identify in the photoelectron spectrum the origin of the first cation excited state D1. The fast excited state dynamics agrees best with a vibrational dynamics in the photo-excited S1 (80+/-10 fs) and an ultrafast decay via a conical intersection, presumably a ring opening to the S3 state (25+/-10 fs). The subsequently observed weak constant signal is taken as an indication, that in the gas phase the ring-closure to S0 is slower than 50 ps. An ultrafast equilibrium between S1 and S2 before ring opening is not supported by our data. PMID:18174981

  18. Probing Local Ionic Dynamics in Functional Oxides: From Nanometer to Atomic Scale

    NASA Astrophysics Data System (ADS)

    Kalinin, Sergei

    2014-03-01

    Vacancy-mediated electrochemical reactions in oxides underpin multiple applications ranging from electroresistive memories, to chemical sensors to energy conversion systems such as fuel cells. Understanding the functionality in these systems requires probing reversible (oxygen reduction/evolution reaction) and irreversible (cathode degradation and activation, formation of conductive filaments) electrochemical processes. In this talk, I summarize recent advances in probing and controlling these transformations locally on nanometer level using scanning probe microscopy. The localized tip concentrates the electric field in the nanometer scale volume of material, inducing local transition. Measured simultaneously electromechanical response (piezoresponse) or current (conductive AFM) provides the information on the bias-induced changes in material. Here, I illustrate how these methods can be extended to study local electrochemical transformations, including vacancy dynamics in oxides such as titanates, LaxSr1-xCoO3, BiFeO3, and YxZr1-xO2. The formation of electromechanical hysteresis loops and their bias-, temperature- and environment dependences provide insight into local electrochemical mechanisms. In materials such as lanthanum-strontium cobaltite, mapping both reversible vacancy motion and vacancy ordering and static deformation is possible, and can be corroborated by post mortem STEM/EELS studies. In ceria, a broad gamut of electrochemical behaviors is observed as a function of temperature and humidity. The possible strategies for elucidation ionic motion at the electroactive interfaces in oxides using high-resolution electron microscopy and combined ex-situ and in-situ STEM-SPM studies are discussed. In the second part of the talk, probing electrochemical phenomena on in-situ grown surfaces with atomic resolution is illustrated. I present an approach based on the multivariate statistical analysis of the coordination spheres of individual atoms to reveal

  19. Core-shell CdSe/ZnS Quantum dots as a dual mode spatiotemporal microscopy probe for understanding cellular responses

    NASA Astrophysics Data System (ADS)

    LeDuc, Philip R.; Zhang, Ying

    2009-02-01

    Probing the spatiotemporal response of individual intracellular proteins and multi-peptide complexes is essential in understanding the integrated response of cells. Although dynamic information can be captured using optical microscopy, most conventional spatial resolutions are limited to around 200 nm, which is significantly greater than the size of molecules. One mode of microscopy that overcomes this resolution limitation is the electron microscope, which enables in situ protein labeling and allows for single or sub-nanometer resolution to be obtained. Transmission electron microscopy though is limited by the inability to capture dynamic molecular responses. Here, we have demonstrated the ability to use quantum dots for both modes of microscopy through a single labeling technology, which allows both dynamic and high resolution visualization with optical and electron microscopy. We visualized core-shell CdSe/ZnS quantum dots within Dictyostelium discoideum using both microscopy modes through a bacterial nutrient protocol, which enables the quantum dots to enter living cells without the need of an artificial transporter system for assisted internalization. Optical imaging was first used to visualize the spatiotemporal behavior of actin filaments using phalloidin conjugated quantum dots. The same cells were then imaged using a transmission electron microscope to examine the detailed intracellular distribution down to a single nanometer size scale. These results have potential applications in a variety of areas including biophysics, cell motility, cancer metastasis, and cell structure.

  20. GRIN lens rod based probe for endoscopic spectral domain optical coherence tomography with fast dynamic focus tracking

    NASA Astrophysics Data System (ADS)

    Xie, Tuqiang; Guo, Shuguang; Chen, Zhongping; Mukai, David; Brenner, Matthew

    2006-04-01

    In this manuscript, a GRIN (gradient index) lens rod based probe for endoscopic spectral domain optical coherence tomography (OCT) with dynamic focus tracking is presented. Current endoscopic OCT systems have a fixed focal plane or working distance. In contrast, the focus of this endoscopic OCT probe can dynamically be adjusted at a high speed (500 mm/s) without changing reference arm length to obtain high quality OCT images for contact or non-contact tissue applications, or for areas of difficult access for probes. The dynamic focusing range of the probe can be from 0 to 7.5 mm without moving the probe itself. The imaging depth is 2.8 mm and the lateral scanning range is up to 2.7 mm or 4.5 mm (determined by the diameter of different GRIN lens rods). Three dimensional imaging can be performed using this system over an area of tissue corresponding to the GRIN lens surface. The experimental results demonstrate that this GRIN lens rod based OCT system can perform a high quality non-contact in vivo imaging. This rigid OCT probe is solid and can be adapted to safely access internal organs, to perform front or side view imaging with an imaging speed of 8 frames per second, with all moving parts proximal to the GRIN lens, and has great potential for use in extremely compact OCT endoscopes for in vivo imaging in both biological research and clinical applications.

  1. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

    PubMed Central

    Voelz, Vincent A.; Luttmann, Edgar; Bowman, Gregory R.; Pande, Vijay S.

    2009-01-01

    Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of ~140 ± 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either DPDP-II folds at time scales longer than 240 ns, or that DPDP-II is not a well-defined three-stranded β-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another. PMID:19399235

  2. Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study

    PubMed Central

    Papadimitriou, Konstantinos I.; Stan, Guy-Bart V.; Drakakis, Emmanuel M.

    2013-01-01

    This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented. PMID:23393550

  3. Organization of inner cellular components as reported by a viscosity-sensitive fluorescent Bodipy probe suitable for phasor approach to FLIM.

    PubMed

    Ferri, Gianmarco; Nucara, Luca; Biver, Tarita; Battisti, Antonella; Signore, Giovanni; Bizzarri, Ranieri

    2016-01-01

    According to the recent developments in imaging strategies and in tailoring fluorescent molecule as probe for monitoring biological systems, we coupled a Bodipy-based molecular rotor (BoMe) with FLIM phasor approach to evaluate the viscosity in different intracellular domains. BoMe rapidly permeates cells, stains cytoplasmic as well as nuclear domains, and its optical properties make it perfectly suited for widely diffused confocal microscopy imaging setups. The capability of BoMe to report on intracellular viscosity was put to the test by using a cellular model of a morbid genetic pathology (Hutchinson-Gilford progeria syndrome, HGPS). Our results show that the nucleoplasm of HGPS cells display reduced viscosity as compared to normal cells. Since BoMe displays significant affinity towards DNA, as demonstrated by an in vitro essay, we hypothesize that genetic features of HGPS, namely the misassembly of lamin A protein within the nuclear lamina, modulates chromatin compaction. This hypothesis nicely agrees with literature data. PMID:26127025

  4. Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy

    SciTech Connect

    Lin, Ming-Fu; Neumark, Daniel M.; Gessner, Oliver; Leone, Stephen R.

    2014-02-14

    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH{sub 2}=CHBr, are probed using femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy. Strong-field ionization is initiated with an intense femtosecond, near infrared (NIR, 775 nm) laser field. Femtosecond XUV pulses covering the photon energy range of 50-72 eV probe the subsequent dynamics by measuring the time-dependent spectroscopic features associated with transitions of the Br (3d) inner-shell electrons to vacancies in molecular and atomic valence orbitals. Spectral signatures are observed for the depletion of neutral C{sub 2}H{sub 3}Br, the formation of C{sub 2}H{sub 3}Br{sup +} ions in their ground (X{sup ~}) and first excited (A{sup ~}) states, the production of C{sub 2}H{sub 3}Br{sup ++} ions, and the appearance of neutral Br ({sup 2}P{sub 3/2}) atoms by dissociative ionization. The formation of free Br ({sup 2}P{sub 3/2}) atoms occurs on a timescale of 330 ± 150 fs. The ionic A{sup ~} state exhibits a time-dependent XUV absorption energy shift of ∼0.4 eV within the time window of the atomic Br formation. The yield of Br atoms correlates with the yield of parent ions in the A{sup ~} state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C{sub 2}H{sub 3}Br{sup +} (A{sup ~}) ions undergoes intramolecular vibrational energy redistribution followed by the C–Br bond dissociation. The C{sub 2}H{sub 3}Br{sup +} (X{sup ~}) products and the majority of the C{sub 2}H{sub 3}Br{sup ++} ions are relatively stable due to a deeper potential well and a high dissociation barrier, respectively. The results offer powerful new insights about orbital-specific electronic processes in high field ionization, coupled vibrational relaxation and dissociation dynamics, and the correlation of valence hole-state location and dissociation in polyatomic molecules, all probed simultaneously by ultrafast table-top XUV spectroscopy.

  5. Novel super-resolution capable mitochondrial probe, MitoRed AIE, enables assessment of real-time molecular mitochondrial dynamics

    PubMed Central

    Lo, Camden Yeung-Wah; Chen, Sijie; Creed, Sarah Jayne; Kang, Miaomiao; Zhao, Na; Tang, Ben Zhong; Elgass, Kirstin Diana

    2016-01-01

    Mitochondria and mitochondrial dynamics play vital roles in health and disease. With the intricate nanometer-scale structure and rapid dynamics of mitochondria, super-resolution microscopy techniques possess great un-tapped potential to significantly contribute to understanding mitochondrial biology and kinetics. Here we present a novel mitochondrial probe (MitoRed AIE) suitable for live mitochondrial dynamics imaging and single particle tracking (SPT), together with a multi-dimensional data analysis approach to assess local mitochondrial (membrane) fluidity. The MitoRed AIE probe localizes primarily to mitochondrial membranes, with 95 ms fluorophore on-time delivering 106 photons/ms, characteristics which we exploit to demonstrate live cell 100 fps 3D time-lapse tracking of mitochondria. Combining our experimental and analytical approaches, we uncover mitochondrial dynamics at unprecedented time scales. This approach opens up a new regime into high spatio-temporal resolution dynamics in many areas of mitochondrial biology. PMID:27492961

  6. Novel super-resolution capable mitochondrial probe, MitoRed AIE, enables assessment of real-time molecular mitochondrial dynamics.

    PubMed

    Lo, Camden Yeung-Wah; Chen, Sijie; Creed, Sarah Jayne; Kang, Miaomiao; Zhao, Na; Tang, Ben Zhong; Elgass, Kirstin Diana

    2016-01-01

    Mitochondria and mitochondrial dynamics play vital roles in health and disease. With the intricate nanometer-scale structure and rapid dynamics of mitochondria, super-resolution microscopy techniques possess great un-tapped potential to significantly contribute to understanding mitochondrial biology and kinetics. Here we present a novel mitochondrial probe (MitoRed AIE) suitable for live mitochondrial dynamics imaging and single particle tracking (SPT), together with a multi-dimensional data analysis approach to assess local mitochondrial (membrane) fluidity. The MitoRed AIE probe localizes primarily to mitochondrial membranes, with 95 ms fluorophore on-time delivering 106 photons/ms, characteristics which we exploit to demonstrate live cell 100 fps 3D time-lapse tracking of mitochondria. Combining our experimental and analytical approaches, we uncover mitochondrial dynamics at unprecedented time scales. This approach opens up a new regime into high spatio-temporal resolution dynamics in many areas of mitochondrial biology. PMID:27492961

  7. Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

    NASA Astrophysics Data System (ADS)

    Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

    2008-12-01

    Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the

  8. Tree-grass competition in space and time: Insights from a simple cellular automata model based on ecohydrological dynamics

    NASA Astrophysics Data System (ADS)

    van Wijk, Mark T.; Rodriguez-Iturbe, Ignacio

    2002-09-01

    Water is a key resource in determining the composition and structure of savanna ecosystems. In this study we present a simple cellular automata model in which death and reproduction chances of trees and grasses are based on the dynamical description of plant water stress by a probabilistic ecohydrological point model, using the parameterization for a Texas savanna. The results show that the model behavior, despite its simplicity, can be linked to ecological reality: the model yields a dynamic tree-grass coexistence driven by the annual rainfall, and the space-time behavior shows that both random and clustered tree distributions for periods up to 100 years can be observed. Both temporal and spatial model output display fractal characteristics suggesting the possibility of a self-organized critical dynamics. Thus power law behavior is observed in both the spectral density function and the cluster size distribution. The presence of spatial fractal characteristic opens avenues for more thorough model testing.

  9. Foundations of observing dark energy dynamics with the Wilkinson Microwave Anisotropy Probe

    SciTech Connect

    Corasaniti, P.S.; Kunz, M.; Parkinson, D.; Copeland, E.J.; Bassett, B.A.

    2004-10-15

    Detecting dark energy dynamics is the main quest of current dark energy research. Addressing the issue demands a fully consistent analysis of cosmic microwave background, large-scale structure and SN-Ia data with multiparameter freedom valid for all redshifts. Here we undertake a ten parameter analysis of general dark energy confronted with the first year Wilkinson Microwave Anisotropy Probe, 2dF galaxy survey and latest SN-Ia data. Despite the huge freedom in dark energy dynamics there are no new degeneracies with standard cosmic parameters apart from a mild degeneracy between reionization and the redshift of acceleration, both of which effectively suppress small scale power. Breaking this degeneracy will help significantly in detecting dynamics, if it exists. Our best-fit model to the data has significant late-time evolution at z<1.5. Phantom models are also considered and we find that the best-fit crosses w=-1 which, if confirmed, would be a clear signal for radically new physics. Treatment of such rapidly varying models requires careful integration of the dark energy density usually not implemented in standard codes, leading to crucial errors of up to 5%. Nevertheless cosmic variance means that standard {lambda} cold dark matter models are still a very good fit to the data and evidence for dynamics is currently very weak. Independent tests of reionization or the epoch of acceleration (e.g., integrated Sachs-Wolfe-large scale structure correlations) or reduction of cosmic variance at large scales (e.g., cluster polarization at high redshift) may prove key in the hunt for dynamics.

  10. The Juno and Cassini gravity measurements: probing the interior dynamics of Jupiter and Saturn

    NASA Astrophysics Data System (ADS)

    Kaspi, Y.; Galanti, E.; Hubbard, W. B.; Davighi, J. E.

    2015-10-01

    During 2016-2017 both the Juno and Cassini spacecraft will enter into close-by polar orbits of Jupiter and Saturn, respectively. Using Doppler tracking from Earth these flybys will allow high precision gravity measurements of these planets [1]. These will include high order gravity harmonics (at least up to J10), and the yet to be measured odd gravity spectrum. As the dynamics of deep flows relate to perturbations in the density of the planets, this data can be used to probe for the first time the atmospheric and interior flows on these planets [4, 5, 8]. Particularly, this may allow addressing one of the longest-standing questions in planetary atmospheric dynamics regarding the depth of the observed strong east-west jets-streams on Jupiter and Saturn. In this talk we review different approaches to analyze the gravity measurements, discuss the proposed models relating the gravity fields to the dynamics, and the implications of the results for understanding the mechanisms governing the interiors and atmospheres of Jupiter and Saturn.

  11. Fluorescence probe of polypeptide conformational dynamics in gas phase and in solution

    NASA Astrophysics Data System (ADS)

    Iavarone, Anthony T.; Meinen, Jan; Schulze, Susanne; Parks, Joel H.

    2006-07-01

    Fluorescence measurements of polypeptides derivatized with the fluorescent dye BODIPY TMR have been used to probe the polypeptide conformational dynamics as a function of temperature and charge state. Measurements of (BODIPY TMR)-[Pro]n-Arg-Trp and (BODIPY TMR)-[Gly-Ser]m-Arg-Trp have been performed for charge states 1+ and 2+ of n = 4 and 10 and m = 2 and 5. The 2+ charge states of both of these polypeptides exhibit similar temperature dependences for equal chain lengths (n = 4, m = 2 and n = 10, m = 5) and suggest conformations dominated by Coulomb repulsion. In the absence of such Coulomb repulsion, the 1+ charge state conformations appear to be characterized by the flexibility of the polypeptide chain for which [Gly-Ser]m > [Pro]n. Comparisons of these gas phase polypeptide measurements with corresponding measurements in solution provide a direct measure of the effects of solvent on the conformational dynamics. The change in fluorescence as a function of temperature in the gas phase is two orders of magnitude greater than that in solution, a dramatic result we attribute to the restrictions on intramolecular dynamics imposed by diffusion-limited kinetics and the lack of shielding by solvent. Measurements were also made of unsolvated Pron peptides without the tryptophan (Trp) residue to isolate the interaction of the fluorescent dye with charges.

  12. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

    PubMed

    Tan, Yaw Sing; Reeks, Judith; Brown, Christopher J; Thean, Dawn; Ferrer Gago, Fernando Jose; Yuen, Tsz Ying; Goh, Eunice Tze Leng; Lee, Xue Er Cheryl; Jennings, Claire E; Joseph, Thomas L; Lakshminarayanan, Rajamani; Lane, David P; Noble, Martin E M; Verma, Chandra S

    2016-09-01

    Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design. PMID:27532490

  13. UV Pump - VUV Probe Studies of Ultrafast Dynamics in Simple Aromatic Molecules

    NASA Astrophysics Data System (ADS)

    Shivaram, Niranjan; Champenois, Elio; Cryan, James; Wright, Travis; Belkacem, Ali

    2015-05-01

    Aromatic molecules like nitro-phenols play an important role in atmospheric chemistry. They have a high absorption cross section in the ultraviolet (UV) where excitations lead to different fragmentation pathways involving internal relaxation processes. These pathways lead to elimination of the hydroxyl and nitro groups, internal re-arrangement of these groups and even formation of bonds between them. We use a high pulse energy, high repetition rate femtosecond laser system (30 mJ, 1 kHz, 780 nm, 25 fs) to generate high flux vacuum ultraviolet (VUV)/extreme ultraviolet (XUV) high order harmonics in a gas such as argon. These harmonics are then used to study femtosecond time resolved dynamics in neutral 2-Nitrophenol excited to a manifold of states around 4.75 eV and probed with higher harmonics. A velocity map imaging spectrometer is used to obtain energy/angle resolved photo-ion and photoelectron spectra as a function of pump-probe delay. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  14. Real-time Electrophysiology: Using Closed-loop Protocols to Probe Neuronal Dynamics and Beyond.

    PubMed

    Linaro, Daniele; Couto, João; Giugliano, Michele

    2015-01-01

    Experimental neuroscience is witnessing an increased interest in the development and application of novel and often complex, closed-loop protocols, where the stimulus applied depends in real-time on the response of the system. Recent applications range from the implementation of virtual reality systems for studying motor responses both in mice and in zebrafish, to control of seizures following cortical stroke using optogenetics. A key advantage of closed-loop techniques resides in the capability of probing higher dimensional properties that are not directly accessible or that depend on multiple variables, such as neuronal excitability and reliability, while at the same time maximizing the experimental throughput. In this contribution and in the context of cellular electrophysiology, we describe how to apply a variety of closed-loop protocols to the study of the response properties of pyramidal cortical neurons, recorded intracellularly with the patch clamp technique in acute brain slices from the somatosensory cortex of juvenile rats. As no commercially available or open source software provides all the features required for efficiently performing the experiments described here, a new software toolbox called LCG was developed, whose modular structure maximizes reuse of computer code and facilitates the implementation of novel experimental paradigms. Stimulation waveforms are specified using a compact meta-description and full experimental protocols are described in text-based configuration files. Additionally, LCG has a command-line interface that is suited for repetition of trials and automation of experimental protocols. PMID:26132434

  15. Non-equilibrium two-level system dynamics probed with a biased bridge resonator

    NASA Astrophysics Data System (ADS)

    Khalil, Moe; Gladchenko, Sergiy; Stoutimore, M. J. A.; Wellstood, F. C.; Osborn, K. D.

    2013-03-01

    We have designed a biased bridge resonator (BBR), which allows us to probe amorphous dielectric films by simultaneously applying a quasi-static electric bias field in addition to a microwave electric field. The BBR is made with a bridge arrangement of capacitors using superconducting aluminum electrodes and operated at millikelvin temperatures. Measurements of a universal amorphous dielectric film at high microwave amplitudes and a sufficiently fast bias field ramp reveals a non-equilibrium dielectric loss equal to its intrinsic steady state value. This phenomenon is explained by a theory which uses the dynamics of charged two-level systems undergoing Landau-Zener transitions to remain in their ground state. We will compare the experimental data to Monte Carlo simulations of the theory which allow for the separate extraction of the dipole moment and the spectral density of two-level systems.

  16. Probing how initial retinal configuration controls photochemical dynamics in retinal proteins

    NASA Astrophysics Data System (ADS)

    Wand, A.; Rozin, R.; Eliash, T.; Friedman, N.; Jung, K. H.; Sheves, M.; Ruhman, S.

    2013-03-01

    The effects of the initial retinal configuration and the active isomerization coordinate on the photochemistry of retinal proteins (RPs) are assessed by comparing photochemical dynamics of two stable retinal ground state configurations (all-trans,15-anti vs. 13-cis,15-syn), within two RPs: Bacteriorhodopsin (BR) and Anabaena Sensory Rhodopsin (ASR). Hyperspectral pump-probe spectroscopy shows that photochemistry starting from 13-cis retinal in both proteins is 3-10 times faster than when started in the all-trans state, suggesting that the hastening is ubiquitous to microbial RPs, regardless of their different biological functions and origin. This may also relate to the known disparity of photochemical rates between microbial RPs and visual pigments. Importance and possible underlying mechanisms are discussed as well.

  17. Time-Resolved X-Ray Triple-Crystal Diffractometry Probing Dynamic Strain in Semiconductors

    SciTech Connect

    Hayashi, Yujiro; Tanaka, Yoshihito; Kirimura, Tomoyuki; Ishikawa, Tetsuya; Tsukuda, Noboru; Kuramoto, Eiichi

    2007-01-19

    Intense synchrotron radiation sources have enabled us to combine time-resolved measurements and triple-crystal diffractometry. The time-resolved triple-crystal diffractometry (TRTCD) determines the time-dependent dilational and shear components of deformation tensor, separately. The TRTCD experiments have been performed at a long undulator beamline of SPring-8. The time-resolved measurement system using pump-probe technique and a fast multi-channel scaler covers a full range of milliseconds with a time-resolution of several tens of picoseconds. The TRTCD with wide time range was applied to the dynamic strain measurement for semiconductor wafers irradiated by a femtosecond pulse laser. We observed a dilational component of acoustic echo pulses to analyze the time-varying pulse shape due to propagation. The lattice motion in the successively induced flexural standing wave has also been observed through a shear component.

  18. Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies.

    PubMed

    García-Beltrán, Olimpo; Yañez, Osvaldo; Caballero, Julio; Galdámez, Antonio; Mena, Natalia; Nuñez, Marco T; Cassels, Bruce K

    2014-04-01

    Three coumarin-derived fluorescent probes, 3-acetyl-7-[(6-bromohexyl)oxy]-2H-chromen-2-one (FM1), 7-[(6-bromohexyl)oxy]-4-methyl-2H-chromen-2-one (FM2) and ethyl 2-{7-[(6-bromohexyl)oxy]-2-oxo-2H-chromen-4-yl}acetate (FM3), are described, with their photophysical constants. The compounds were tested in preliminary studies employing epifluorescence microscopy demonstrating that they allow the imaging of human neuroblastoma SH-SY5Y cell membranes. The structure of FM3 was confirmed by X-ray crystallographic analysis. Molecular dynamics (MD) simulations were used to characterize the localization and interactions of the studied compounds with a lipid bilayer model of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). PMID:24576613

  19. Tethered Spectroscopic Probes Estimate Dynamic Distances with Subnanometer Resolution in Voltage-Dependent Potassium Channels

    PubMed Central

    Jarecki, Brian W.; Zheng, Suqing; Zhang, Leili; Li, Xiaoxun; Zhou, Xin; Cui, Qiang; Tang, Weiping; Chanda, Baron

    2013-01-01

    Measurements of inter- and intramolecular distances are important for monitoring structural changes and understanding protein interaction networks. Fluorescence resonance energy transfer and functionalized chemical spacers are the two predominantly used strategies to map short-range distances in living cells. Here, we describe the development of a hybrid approach that combines the key advantages of spectroscopic and chemical methods to estimate dynamic distance information from labeled proteins. Bifunctional spectroscopic probes were designed to make use of adaptable-anchor and length-varied spacers to estimate molecular distances by exploiting short-range collisional electron transfer. The spacers were calibrated using labeled polyproline peptides of defined lengths and validated by molecular simulations. This approach was extended to estimate distance restraints that enable us to evaluate the resting-state model of the Shaker potassium channel. PMID:24359744

  20. Ring current electron dynamics during geomagnetic storms based on the Van Allen Probes measurements

    NASA Astrophysics Data System (ADS)

    Zhao, H.; Li, X.; Baker, D. N.; Claudepierre, S. G.; Fennell, J. F.; Blake, J. B.; Larsen, B. A.; Skoug, R. M.; Funsten, H. O.; Friedel, R. H. W.; Reeves, G. D.; Spence, H. E.; Mitchell, D. G.; Lanzerotti, L. J.

    2016-04-01

    Based on comprehensive measurements from Helium, Oxygen, Proton, and Electron Mass Spectrometer Ion Spectrometer, Relativistic Electron-Proton Telescope, and Radiation Belt Storm Probes Ion Composition Experiment instruments on the Van Allen Probes, comparative studies of ring current electrons and ions are performed and the role of energetic electrons in the ring current dynamics is investigated. The deep injections of tens to hundreds of keV electrons and tens of keV protons into the inner magnetosphere occur frequently; after the injections the electrons decay slowly in the inner belt but protons in the low L region decay very fast. Intriguing similarities between lower energy protons and higher-energy electrons are also found. The evolution of ring current electron and ion energy densities and energy content are examined in detail during two geomagnetic storms, one moderate and one intense. The results show that the contribution of ring current electrons to the ring current energy content is much smaller than that of ring current ions (up to ~12% for the moderate storm and ~7% for the intense storm), and <35 keV electrons dominate the ring current electron energy content at the storm main phases. Though the electron energy content is usually much smaller than that of ions, the enhancement of ring current electron energy content during the moderate storm can get to ~30% of that of ring current ions, indicating a more dynamic feature of ring current electrons and important role of electrons in the ring current buildup. The ring current electron energy density is also shown to be higher at midnight and dawn while lower at noon and dusk.

  1. Functional network macroscopes for probing past and present Earth system dynamics (Invited)

    NASA Astrophysics Data System (ADS)

    Donges, J. F.

    2013-12-01

    probing past and present Earth system dynamics: Complex hierarchical interactions, tipping points, and beyond" by J.F. Donges, Humboldt University, Berlin, Germany, 2012. URL: http://nbn-resolving.de/urn:nbn:de:kobv:11-100207126.

  2. Probing the Biexponential Dynamics of Ring-Opening in 7-Dehydrocholesterol.

    PubMed

    Smith, Broc D; Spears, Kenneth G; Sension, Roseanne J

    2016-08-25

    Our prior discovery of a novel biexponential photochemical ring-opening in 7-dehydrocholesterol (DHC) to previtamin D3 [ Tang J. Chem. Phys. 2011 , 134 , 104503 ] is further explored with ultrafast transient absorption spectroscopy, and the results are compared with recently reported high-level theoretical calculations. Three types of experiments are reported. First, variation of the excitation wavelength from 297 to 266 nm leaves the excited state dynamics unaffected. The biexponential decay of the excited state absorption is independent of excitation wavelength with time constants of 0.57 ± 0.06 and 1.88 ± 0.09 ps, in excellent agreement with the results reported earlier (0.56 ± 0.06 and 1.81 ± 0.15 ps) following excitation at 266 nm. Second, variation of the chirp of the excitation pulse influences the relative amplitude of the fast and slow decay components but has no influence on the photoproduct yield. Third, a 545 nm pulse delayed by 0.64 ps with respect to the initial 266 nm pulse was used to perturb the "slow" population and probe the influence of additional electronic or vibrational energy on the reaction process. The results show ultrafast internal conversion Sn → S1 on a ca. 150 fs time scale but no subsequent effect on the reaction dynamics. The experiments reported here are consistent with the recent state averaged complete active space self-consistent field ab initio multiple spawning (SA-CASSCF-AIMS) calculations of Snyder et al. [ J. Phys. Chem. Lett. 2016 , 7 , 2444 ] that assign the biexponential decay to nonequilibrium dynamics related to the opening and closing motion of the cyclohexadiene ring moiety on the excited state surface. These new experiments support the model prediction that the biexponential dynamics does not involve multiple minima and demonstrate the direction for new experimental designs to manipulate the product yields and pathways. PMID:27529502

  3. Calibrating floor field cellular automaton models for pedestrian dynamics by using likelihood function optimization

    NASA Astrophysics Data System (ADS)

    Lovreglio, Ruggiero; Ronchi, Enrico; Nilsson, Daniel

    2015-11-01

    The formulation of pedestrian floor field cellular automaton models is generally based on hypothetical assumptions to represent reality. This paper proposes a novel methodology to calibrate these models using experimental trajectories. The methodology is based on likelihood function optimization and allows verifying whether the parameters defining a model statistically affect pedestrian navigation. Moreover, it allows comparing different model specifications or the parameters of the same model estimated using different data collection techniques, e.g. virtual reality experiment, real data, etc. The methodology is here implemented using navigation data collected in a Virtual Reality tunnel evacuation experiment including 96 participants. A trajectory dataset in the proximity of an emergency exit is used to test and compare different metrics, i.e. Euclidean and modified Euclidean distance, for the static floor field. In the present case study, modified Euclidean metrics provide better fitting with the data. A new formulation using random parameters for pedestrian cellular automaton models is also defined and tested.

  4. Pressure Probe Designs for Dynamic Pressure Measurements in a Supersonic Flow Field. [conducted in the Glenn Supersonic Wind Tunnel (SWT)

    NASA Technical Reports Server (NTRS)

    Porro, A. Robert

    2001-01-01

    A series of dynamic flow field pressure probes were developed for use in large-scale supersonic wind tunnels at NASA Glenn Research Center. These flow field probes include pitot, static, and five-hole conical pressure probes that are capable of capturing fast acting flow field pressure transients that occur on a millisecond time scale. The pitot and static probes can be used to determine local Mach number time histories during a transient event. The five-hole conical pressure probes are used primarily to determine local flow angularity, but can also determine local Mach number. These probes were designed, developed, and tested at the NASA Glenn Research Center. They were also used in a NASA Glenn 10- by 10-Foot Supersonic Wind Tunnel (SWT) test program where they successfully acquired flow field pressure data in the vicinity of a propulsion system during an engine compressor stall and inlet unstart transient event. Details of the design, development, and subsequent use of these probes are discussed in this report.

  5. Investigation on Dynamic Calibration for an Optical-Fiber Solids Concentration Probe in Gas-Solid Two-Phase Flows

    PubMed Central

    Xu, Guiling; Liang, Cai; Chen, Xiaoping; Liu, Daoyin; Xu, Pan; Shen, Liu; Zhao, Changsui

    2013-01-01

    This paper presents a review and analysis of the research that has been carried out on dynamic calibration for optical-fiber solids concentration probes. An introduction to the optical-fiber solids concentration probe was given. Different calibration methods of optical-fiber solids concentration probes reported in the literature were reviewed. In addition, a reflection-type optical-fiber solids concentration probe was uniquely calibrated at nearly full range of the solids concentration from 0 to packed bed concentration. The effects of particle properties (particle size, sphericity and color) on the calibration results were comprehensively investigated. The results show that the output voltage has a tendency to increase with the decreasing particle size, and the effect of particle color on calibration result is more predominant than that of sphericity. PMID:23867745

  6. Simple and Flexible Self-Reproducing Structures in Asynchronous Cellular Automata and Their Dynamics

    NASA Astrophysics Data System (ADS)

    Huang, Xin; Lee, Jia; Yang, Rui-Long; Zhu, Qing-Sheng

    2013-03-01

    Self-reproduction on asynchronous cellular automata (ACAs) has attracted wide attention due to the evident artifacts induced by synchronous updating. Asynchronous updating, which allows cells to undergo transitions independently at random times, might be more compatible with the natural processes occurring at micro-scale, but the dark side of the coin is the increment in the complexity of an ACA in order to accomplish stable self-reproduction. This paper proposes a novel model of self-timed cellular automata (STCAs), a special type of ACAs, where unsheathed loops are able to duplicate themselves reliably in parallel. The removal of sheath cannot only allow various loops with more flexible and compact structures to replicate themselves, but also reduce the number of cell states of the STCA as compared to the previous model adopting sheathed loops [Y. Takada, T. Isokawa, F. Peper and N. Matsui, Physica D227, 26 (2007)]. The lack of sheath, on the other hand, often tends to cause much more complicated interactions among loops, when all of them struggle independently to stretch out their constructing arms at the same time. In particular, such intense collisions may even cause the emergence of a mess of twisted constructing arms in the cellular space. By using a simple and natural method, our self-reproducing loops (SRLs) are able to retract their arms successively, thereby disentangling from the mess successfully.

  7. Bases for time-resolved probing of transient carrier dynamics by optical pump-probe scanning tunneling microscopy

    NASA Astrophysics Data System (ADS)

    Yokota, Munenori; Yoshida, Shoji; Mera, Yutaka; Takeuchi, Osamu; Oigawa, Haruhiro; Shigekawa, Hidemi

    2013-09-01

    The tangled mechanism that produces optical pump-probe scanning tunneling microscopy spectra from semiconductors was analyzed by comparing model simulation data with experimental data. The nonlinearities reflected in the spectra, namely, the excitations generated by paired laser pulses with a delay time, the logarithmic relationship between carrier density and surface photovoltage (SPV), and the effect of the change in tunneling barrier height depending on SPV, were examined along with the delay-time-dependent integration process used in measurement. The optimum conditions required to realize reliable measurement, as well as the validity of the microscopy technique, were demonstrated for the first time.

  8. Probing Physical and Chemical Properties of Laser Shocked Materials using Ultrafast Dynamic Ellipsometry and Spectroscopies

    NASA Astrophysics Data System (ADS)

    Dang, Nhan

    2013-06-01

    Ultrafast laser techniques allow resolution of shock induced physics and chemistry picoseconds behind the shock front. In this presentation, the 350 ps sustained laser-generated shocks will be shown to combine with ultrafast dynamic ellipsometry to measure the shock state and transient absorption to measure the molecular electronic response to shock loading. Experimental data will be presented on shocked explosive crystals and liquids. Ultrafast dynamic ellipsometry was used to measure the shock and particle velocity as well as the shocked refractive index. Transient absorption spectra of RDX and simple molecular liquids in the spectral region from 440 to 780 nm were measured to map out shock reactivity during the first 350 ps, over shock stress states from 7 to 20 GPa. Additionally, nonlinear spectroscopic probes will be demonstrated to offer the potential to measure even more details of the molecular shock response, such as evolution of chemical species and vibrational temperature. Preliminary results of shocked phenylacetylene obtained using vibrational coherent anti-Stokes Raman spectroscopy (CARS) and the capability of femtosecond stimulated Raman scattering (FSRS) data to measure the nonequilibrium time evolution of mode specific vibrational temperatures on picosecond time scales will be discussed.

  9. Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics.

    PubMed

    Fenwick, R Bryn; Oyen, David; Wright, Peter E

    2016-02-17

    Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are a valuable tool for the characterization of structural transitions on the micro-millisecond timescale. While the measurement of (15)N relaxation dispersion is now routine, the measurements with alternative nuclei remain limited. Here we report (15)N as well as (1)H R2 relaxation dispersion measurements of the N23PP/S148A "dynamic knockout" mutant of dihydrofolate reductase. The (1)H dispersion measurements are complementary to (15)N data as many additional residues are observed to have dispersive behavior for the (1)H nucleus. Simultaneous fitting of the dispersion profiles for the two nuclei increases the accuracy of exchange parameters determined for individual residues and clustered groups of residues. The different sensitivity of the two nuclei to changes in backbone torsional angles, ring currents, and hydrogen bonding effects provides important insights into the nature of the structural changes that take place during the exchange process. We observe clear evidence of direct and indirect hydrogen bond effects for the (15)N and (1)H chemical shift changes in the active-site, modulation of ring current shielding in the CD-loop and backbone torsional changes in a cluster of residues associated with the C-terminus. This work demonstrates the power of combined (1)H and (15)N probes for the study of backbone dynamics on the micro-millisecond timescale though the analysis of chemical shift changes. PMID:26426424

  10. Prediction of Liquefaction Potential of Dredge Fill Sand by DCP and Dynamic Probing

    NASA Astrophysics Data System (ADS)

    Alam, Md. Jahangir; Azad, Abul Kalam; Rahman, Ziaur

    2008-07-01

    From many research it is proved that liquefaction potential of sand is function of mainly relative density and confining pressure. During routine site investigations, high-quality sampling and laboratory testing of sands are not feasible because of inevitable sample disturbance effects and budgetary constraints. On the other hand quality control of sand fill can be done by determining in situ density of sand in layer by layer which is expensive and time consuming. In this paper TRL DCP (Transportation Research Laboratory Dynamic Cone Penetration) and DPL (Dynamic Probing Light) are calibrated to predict the relative density of sand deposit. For this purpose sand of known relative density is prepared in a calibration chamber which is a mild steel cylinder with diameter 0.5 m and height 1.0 m. Relative density of sand is varied by controlling height of fall and diameter of hole of sand discharge bowl. After filling, every time DPL and DCP tests are performed and for every blow the penetration of cone is recorded. N10 is then calculated from penetration records. Thus a database is compiled where N10 and relative densities are known. A correlation is made between N10 and relative density for two types of sand. A good correlation of N10 and relative density is found.

  11. Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?

    SciTech Connect

    Makarov, Dmitrii E.

    2014-12-28

    In single-molecule pulling experiments, the molecule of interest is attached to a much larger object such as an atomic force microscope tip or a micrometer sized bead. The measured dynamics of molecular transitions is therefore affected by the hydrodynamic drag on the pulling instrument itself. By considering the transitions within the combined system (the molecule and the instrument), it is shown here that two distinct physical regimes exist: when the intrinsic stiffness of the molecule is greater than that of the linker connecting the molecule to the pulling setup then the pulling experiment probes the intrinsic dynamics of the molecule with only relatively small (and quantifiable) corrections resulting from the pulling setup. In contrast, when the stiffness of the linker exceeds that of the molecule, the molecular transition in question involves concerted motion of the molecule and the pulling setup and the hydrodynamic drag on the pulling instrument becomes the dominant source of friction along the molecular reaction coordinate. An analytical formula interpolating between these two cases is further derived. These results explain recent conflicting observations where some single-molecule pulling measurements report anomalously low diffusion coefficients along molecular reaction coordinates while others do not.

  12. Probing dynamics of a spin ensemble of P1 centers in diamond using a superconducting resonator

    NASA Astrophysics Data System (ADS)

    de Lange, Gijs; Ranjan, Vishal; Schutjens, Ron; Debelhoir, Thibault; Groen, Joost; Szombati, Daniel; Thoen, David; Klapwijk, Teun; Hanson, Ronald; Dicarlo, Leonardo

    2013-03-01

    Solid-state spin ensembles are promising candidates for realizing a quantum memory for superconducting circuits. Understanding the dynamics of such ensembles is a necessary step towards achieving this goal. Here, we investigate the dynamics of an ensemble of nitrogen impurities (P1 centers) in diamond using magnetic-field controlled coupling to the first two modes of a superconducting (NbTiN) coplanar waveguide resonator. Three hyperfine-split spin sub-ensembles are clearly resolved in the 0.25-1.2 K temperature range, with a collective coupling strength extrapolating to 23 MHz at full polarization. The coupling to multiple modes allows us to distinguish the contributions of dipolar broadening and magnetic field inhomogeneity to the spin linewidth. We find the spin polarization recovery rate to be temperature independent below 1 K and conclude that spin out-diffusion across the resonator mode volume provides the mechanism for spin relaxation of the ensemble. Furthermore, by pumping spins in one sub-ensemble and probing the spins in the other sub-ensembles, we observe fast steady-state cross-relaxation (compared to spin repolarization) across the hyperfine transitions. These observations have important implications for using the three sub-ensembles as independent quantum memories. Research supported by NWO, FOM, and EU Project SOLID

  13. Prediction of Liquefaction Potential of Dredge Fill Sand by DCP and Dynamic Probing

    SciTech Connect

    Alam, Md. Jahangir; Azad, Abul Kalam; Rahman, Ziaur

    2008-07-08

    From many research it is proved that liquefaction potential of sand is function of mainly relative density and confining pressure. During routine site investigations, high-quality sampling and laboratory testing of sands are not feasible because of inevitable sample disturbance effects and budgetary constraints. On the other hand quality control of sand fill can be done by determining in situ density of sand in layer by layer which is expensive and time consuming. In this paper TRL DCP (Transportation Research Laboratory Dynamic Cone Penetration) and DPL (Dynamic Probing Light) are calibrated to predict the relative density of sand deposit. For this purpose sand of known relative density is prepared in a calibration chamber which is a mild steel cylinder with diameter 0.5 m and height 1.0 m. Relative density of sand is varied by controlling height of fall and diameter of hole of sand discharge bowl. After filling, every time DPL and DCP tests are performed and for every blow the penetration of cone is recorded. N10 is then calculated from penetration records. Thus a database is compiled where N10 and relative densities are known. A correlation is made between N{sub 10} and relative density for two types of sand. A good correlation of N{sub 10} and relative density is found.

  14. Initial dynamics of the Norrish Type I reaction in acetone: probing wave packet motion.

    PubMed

    Brogaard, Rasmus Y; Sølling, Theis I; Møller, Klaus B

    2011-02-10

    The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results. PMID:21229990

  15. Application of Universal Stress Proteins in Probing the Dynamics of Potent Degraders in Complex Terephthalate Metagenome

    PubMed Central

    Mbah, Andreas N.; Isokpehi, Raphael D.

    2013-01-01

    The culture-independent strategies to study microbial diversity and function have led to a revolution in environmental genomics, enabling fundamental questions about the distribution of microbes and their influence on bioremediation to be addressed. In this research we used the expression of universal stress proteins as a probe to determine the changes in degrading microbial population from a highly toxic terephthalate wastewater to a less toxic activated sludge bioreactor. The impact of relative toxicities was significantly elaborated at the levels of genus and species. The results indicated that 23 similar prokaryotic phyla were represented in both metagenomes irrespective of their relative abundance. Furthermore, the following bacteria taxa Micromonosporaceae, Streptomyces, Cyanothece sp. PCC 7822, Alicyclobacillus acidocaldarius, Bacillus halodurans, Leuconostoc mesenteroides, Lactococcus garvieae, Brucellaceae, Ralstonia solanacearum, Verminephrobacter eiseniae, Azoarcus, Acidithiobacillus ferrooxidans, Francisella tularensis, Methanothermus fervidus, and Methanocorpusculum labreanum were represented only in the activated sludge bioreactor. These highly dynamic microbes could serve as taxonomic biomarkers for toxic thresholds related to terephthalate and its derivatives. This paper, highlights the application of universal stress proteins in metagenomics analysis. Dynamics of microbial consortium of this nature can have future in biotechnological applications in bioremediation of toxic chemicals and radionuclides. PMID:24151583

  16. Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?

    NASA Astrophysics Data System (ADS)

    Makarov, Dmitrii E.

    2014-12-01

    In single-molecule pulling experiments, the molecule of interest is attached to a much larger object such as an atomic force microscope tip or a micrometer sized bead. The measured dynamics of molecular transitions is therefore affected by the hydrodynamic drag on the pulling instrument itself. By considering the transitions within the combined system (the molecule and the instrument), it is shown here that two distinct physical regimes exist: when the intrinsic stiffness of the molecule is greater than that of the linker connecting the molecule to the pulling setup then the pulling experiment probes the intrinsic dynamics of the molecule with only relatively small (and quantifiable) corrections resulting from the pulling setup. In contrast, when the stiffness of the linker exceeds that of the molecule, the molecular transition in question involves concerted motion of the molecule and the pulling setup and the hydrodynamic drag on the pulling instrument becomes the dominant source of friction along the molecular reaction coordinate. An analytical formula interpolating between these two cases is further derived. These results explain recent conflicting observations where some single-molecule pulling measurements report anomalously low diffusion coefficients along molecular reaction coordinates while others do not.

  17. Data set for comparison of cellular dynamics between human AAVS1 locus-modified and wild-type cells

    PubMed Central

    Mizutani, Takeomi; Haga, Hisashi; Kawabata, Kazushige

    2016-01-01

    This data article describes cellular dynamics, such as migration speed and mobility of the cytoskeletal protein, of wild-type human fibroblast cells and cells with a modified adeno-associated virus integration site 1 (AAVS1) locus on human chromosome 19. Insertion of exogenous gene into the AAVS1 locus has been conducted in recent biological researches. Previously, our data showed that the AAVS1-modification changes cellular contractile force (Mizutani et al., 2015 [1]). To assess if this AAVS1-modification affects cell migration, we compared cellular migration speed and turnover of cytoskeletal protein in human fibroblasts and fibroblasts with a green fluorescent protein gene knocked-in at the AAVS1 locus in this data article. Cell nuclei were stained and changes in their position attributable to cell migration were analyzed. Fluorescence recovery was observed after photobleaching for the fluorescent protein-tagged myosin regulatory light chain. Data here are related to the research article “Transgene Integration into the Human AAVS1 Locus Enhances Myosin II-Dependent Contractile Force by Reducing Expression of Myosin Binding Subunit 85” [1]. PMID:26937449

  18. Data set for comparison of cellular dynamics between human AAVS1 locus-modified and wild-type cells.

    PubMed

    Mizutani, Takeomi; Haga, Hisashi; Kawabata, Kazushige

    2016-03-01

    This data article describes cellular dynamics, such as migration speed and mobility of the cytoskeletal protein, of wild-type human fibroblast cells and cells with a modified adeno-associated virus integration site 1 (AAVS1) locus on human chromosome 19. Insertion of exogenous gene into the AAVS1 locus has been conducted in recent biological researches. Previously, our data showed that the AAVS1-modification changes cellular contractile force (Mizutani et al., 2015 [1]). To assess if this AAVS1-modification affects cell migration, we compared cellular migration speed and turnover of cytoskeletal protein in human fibroblasts and fibroblasts with a green fluorescent protein gene knocked-in at the AAVS1 locus in this data article. Cell nuclei were stained and changes in their position attributable to cell migration were analyzed. Fluorescence recovery was observed after photobleaching for the fluorescent protein-tagged myosin regulatory light chain. Data here are related to the research article "Transgene Integration into the Human AAVS1 Locus Enhances Myosin II-Dependent Contractile Force by Reducing Expression of Myosin Binding Subunit 85" [1]. PMID:26937449

  19. Probing Reaction Dynamics of Transition-Metal Complexes in Solution via Time-Resolved Soft X-ray Spectroscopy

    SciTech Connect

    Huse, Nils; Kim, Tae Kyu; Khalil, Munira; Jamula, Lindsey; McCusker, James K.; Schoenlein, Robert W.

    2010-05-02

    We report the first time-resolved soft x-ray measurements of solvated transition-metal complexes. L-edge spectroscopy directly probes dynamic changes in ligand-field splitting of 3d orbitals associated with the spin transition, and mediated by changes in ligand-bonding.

  20. Investigation of electronically excited indole relaxation dynamics via photoionization and fragmentation pump-probe spectroscopy

    SciTech Connect

    Godfrey, T. J.; Yu, Hui; Ullrich, Susanne

    2014-07-28

    The studies herein investigate the involvement of the low-lying {sup 1}L{sub a} and {sup 1}L{sub b} states with {sup 1}ππ{sup *} character and the {sup 1}πσ{sup *} state in the deactivation process of indole following photoexcitation at 201 nm. Three gas-phase, pump-probe spectroscopic techniques are employed: (1) Time-resolved photoelectron spectroscopy (TR-PES), (2) hydrogen atom (H-atom) time-resolved kinetic energy release (TR-KER), and (3) time-resolved ion yield (TR-IY). Each technique provides complementary information specific to the photophysical processes in the indole molecule. In conjunction, a thorough examination of the electronically excited states in the relaxation process, with particular focus on the involvement of the {sup 1}πσ{sup *} state, is afforded. Through an extensive analysis of the TR-PES data presented here, it is deduced that the initial excitation of the {sup 1}B{sub b} state decays to the {sup 1}L{sub a} state on a timescale beyond the resolution of the current experimental setup. Relaxation proceeds on the {sup 1}L{sub a} state with an ultrafast decay constant (<100 femtoseconds (fs)) to the lower-lying {sup 1}L{sub b} state, which is found to possess a relatively long lifetime of 23 ± 5 picoseconds (ps) before regressing to the ground state. These studies also manifest an additional component with a relaxation time of 405 ± 76 fs, which is correlated with activity along the {sup 1}πσ{sup *} state. TR-KER and TR-IY experiments, both specifically probing {sup 1}πσ{sup *} dynamics, exhibit similar decay constants, further validating these observations.

  1. Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: N-tridecane

    NASA Astrophysics Data System (ADS)

    Lukešová, M.; Zgardzinska, B.; Švajdlenková, H.; Zaleski, R.; Charmas, B.; Bartoš, J.

    2015-11-01

    A joint external probe ESR and PALS study on n-tridecane (n-TRD) using stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) or ortho-positronium (o-Ps), respectively, is presented. In contrast to n-hexadecane (n-HXD) [Physica B 430, 99 (2013)], five crossovers in the spin probe TEMPO mobility coinciding with those in the o-Ps probe annihilation parameters at the characteristic ESR and PALS temperatures in the solid phase were revealed: 1) acceleration within the slow regime at TX1slow in accordance with the changes in both o-Ps lifetime, τ3, and relative o-Ps intensity, I3, at Tb1 cr * in the rigid crystalline solid are related to very local end methyl group dynamics, 2) slow to fast regime transition at T50G<probe TEMPO dynamics in the expanding interlamellar gap due to the molecular probe deformation induced enhanced end-chain mobility close to the rigid to soft crystalline solid transition at Tb1cr being connected also with the starting dominance of electron detrapping over positron mobility, 3) the first change within the fast regime at TX1fast coinciding with reduction of I3 at Tb2 cr * * is related to strong electron detrapping due to longitudinal disordering and 4) the next one at TX2 fast * is related to the soft to plastic crystalline solid phase transition at Tb2 cr * =TssDSC =0.95TmDSC . Finally, similarly as for n-HXD the highest T crossover at TX2fast ≅TmPALS is related with the collective chain dynamics of the melting transition TmDSC . The underlying structural-dynamic processes behind the observed ESR and PALS crossover coincidencies are discussed in the light of the present thermodynamic DSC and reported dynamic NMR, QENS and IR data.

  2. Excited state dynamics of metastable phthalocyanine-tetrasulfonate tetra-anions probed by pump/probe photoelectron spectroscopy

    SciTech Connect

    Ehrler, Oli T.; Yang Jiping; Sugiharto, Albert B.; Unterreiner, Andreas N.; Kappes, Manfred M.

    2007-11-14

    Femtosecond time-resolved pump-probe photoelectron spectroscopy was used to study elementary relaxation processes occurring in isolated phthalocyanine-tetrasulfonate tetra-anions ([MPc(SO{sub 3}){sub 4}]{sup 4-}, M=Cu,Ni, and ''free-base'' [H{sub 2}Pc(SO{sub 3}){sub 4}]{sup 4-}) following Q band excitation by one-photon absorption at 775 nm. Whereas the Cu and Ni systems decay rapidly by means of internal conversion without electron loss, the free-base phthalocyanine primarily undergoes excited state tunneling electron emission. This reflects less efficient coupling to lower lying states within the corresponding spin manifold. Results are interpreted in terms of (time-dependent) density functional theory calculations of ground and electronically excited states and kinetically modeled to yield the associated rates.

  3. Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response

    PubMed Central

    Kirkconnell, Killeen S.; Paulsen, Michelle T.; Magnuson, Brian; Bedi, Karan

    2016-01-01

    ABSTRACT Dynamic regulation of gene expression via signal transduction pathways is of fundamental importance during many biological processes such as cell state transitioning, cell cycle progression and stress responses. In this study we used serum stimulation as a cell response paradigm to apply the nascent RNA Bru-seq technique in order to capture early dynamic changes in the nascent transcriptome. Our data provides an unprecedented view of the dynamics of genome-wide transcription during the first two hours of serum stimulation in human fibroblasts. While some genes showed sustained induction or repression, other genes showed transient or delayed responses. Surprisingly, the dynamic patterns of induction and suppression of response genes showed a high degree of similarity, suggesting that these opposite outcomes are triggered by a common set of signals. As expected, early response genes such as those encoding components of the AP-1 transcription factor and those involved in the circadian clock were immediately but transiently induced. Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed. We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not. These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome. PMID:27230646

  4. Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response.

    PubMed

    Kirkconnell, Killeen S; Paulsen, Michelle T; Magnuson, Brian; Bedi, Karan; Ljungman, Mats

    2016-01-01

    Dynamic regulation of gene expression via signal transduction pathways is of fundamental importance during many biological processes such as cell state transitioning, cell cycle progression and stress responses. In this study we used serum stimulation as a cell response paradigm to apply the nascent RNA Bru-seq technique in order to capture early dynamic changes in the nascent transcriptome. Our data provides an unprecedented view of the dynamics of genome-wide transcription during the first two hours of serum stimulation in human fibroblasts. While some genes showed sustained induction or repression, other genes showed transient or delayed responses. Surprisingly, the dynamic patterns of induction and suppression of response genes showed a high degree of similarity, suggesting that these opposite outcomes are triggered by a common set of signals. As expected, early response genes such as those encoding components of the AP-1 transcription factor and those involved in the circadian clock were immediately but transiently induced. Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed. We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not. These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome. PMID:27230646

  5. Investigations of ultrafast charge dynamics in laser-irradiated targets by a self probing technique employing laser driven protons

    NASA Astrophysics Data System (ADS)

    Ahmed, H.; Kar, S.; Cantono, G.; Nersisyan, G.; Brauckmann, S.; Doria, D.; Gwynne, D.; Macchi, A.; Naughton, K.; Willi, O.; Lewis, C. L. S.; Borghesi, M.

    2016-09-01

    The divergent and broadband proton beams produced by the target normal sheath acceleration mechanism provide the unique opportunity to probe, in a point-projection imaging scheme, the dynamics of the transient electric and magnetic fields produced during laser-plasma interactions. Commonly such experimental setup entails two intense laser beams, where the interaction produced by one beam is probed with the protons produced by the second. We present here experimental studies of the ultra-fast charge dynamics along a wire connected to laser irradiated target carried out by employing a 'self' proton probing arrangement - i.e. by connecting the wire to the target generating the probe protons. The experimental data shows that an electromagnetic pulse carrying a significant amount of charge is launched along the wire, which travels as a unified pulse of 10s of ps duration with a velocity close to speed of light. The experimental capabilities and the analysis procedure of this specific type of proton probing technique are discussed.

  6. Sensitive probes of protein structure and dynamics in well-controlled environments: combining mass spectrometry with fluorescence spectroscopy.

    PubMed

    Czar, Martin F; Jockusch, Rebecca A

    2015-10-01

    Combining the selectivity of mass spectrometry (MS) with laser-induced fluorescence (LIF) presents a promising route to probe the intrinsic conformation, stability and dynamics of biological macromolecules. However, applications to proteins are in their infancy. Recent advances include the realization of Förster (fluorescence) resonance energy transfer (FRET) to provide nm-range distance constraints in de-solvated proteins, and measurement of dynamic fluorescence quenching rates to assess shorter-range interactions in peptides and Trp-cage. Temperature-dependent experiments employing FRET and dynamic quenching as conformational probes enable determination of enthalpy and entropy of conformational change in de-solvated biomolecules. These developments show the feasibility of using MS-LIF to dissect complex molecular interactions. For example, MS-LIF of protein-ligand complexes and partially hydrated proteins will better elucidate the energetics of specific binding interactions and the role of the solvent in protein structure and folding. PMID:26490336

  7. Molecular probe dynamics and free volume in organic glass-formers and their relationships to structural relaxation: 1-propanol

    NASA Astrophysics Data System (ADS)

    Bartoš, J.; Švajdlenková, H.; Šauša, O.; Lukešová, M.; Ehlers, D.; Michl, M.; Lunkenheimer, P.; Loidl, A.

    2016-01-01

    A joint study of the rotational dynamics and free volume in amorphous 1-propanol (1-PrOH) as a prototypical monohydroxy alcohol by electron spin resonance (ESR) or positron annihilation lifetime spectroscopy (PALS), respectively, is reported. The dynamic parameters of the molecular spin probe 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and the annihilation ones of the atomic ortho-positronium (o-Ps) probe as a function of temperature are compared. A number of coincidences between various effects in the ESR and PALS responses at the corresponding characteristic ESR and PALS temperatures were found suggesting a common origin of the underlying dynamic processes that were identified using viscosity (VISC) in terms of the two-order parameter (TOP) model and broadband dielectric spectroscopy (BDS) data.

  8. Two-dimensional near ultraviolet (2DNUV) spectroscopic probe of structural-dependent exciton dynamics in a protein.

    PubMed

    Li, Jun; Deng, Mingsen; Voronine, Dmitri V; Mukamel, Shaul; Jiang, Jun

    2015-01-29

    Understanding the exciton dynamics in biological systems is crucial for the manipulation of their function. We present a combined quantum mechanics (QM) and molecular dynamics (MD) simulation study that demonstrates how coherent two-dimensional near-ultraviolet (2DNUV) spectra can be used to probe the exciton dynamics in a mini-protein, Trp-cage. The 2DNUV signals originate from aromatic transitions that are significantly affected by the couplings between residues, which determine exciton transport and energy relaxation. The temporal evolution of 2DNUV features captures important protein structural information, including geometric details and peptide orientations. PMID:25544569

  9. Quantum Nuclear Dynamics Pumped and Probed by Ultrafast Polarization Controlled Steering of a Coherent Electronic State in LiH.

    PubMed

    Nikodem, Astrid; Levine, R D; Remacle, F

    2016-05-19

    The quantum wave packet dynamics following a coherent electronic excitation of LiH by an ultrashort, polarized, strong one-cycle infrared optical pulse is computed on several electronic states using a grid method. The coupling to the strong field of the pump and the probe pulses is included in the Hamiltonian used to solve the time-dependent Schrodinger equation. The polarization of the pump pulse allows us to control the localization in time and in space of the nonequilibrium coherent electronic motion and the subsequent nuclear dynamics. We show that transient absorption, resulting from the interaction of the total molecular dipole with the electric fields of the pump and the probe, is a very versatile probe of the different time scales of the vibronic dynamics. It allows probing both the ultrashort, femtosecond time scale of the electronic coherences as well as the longer dozens of femtoseconds time scales of the nuclear motion on the excited electronic states. The ultrafast beatings of the electronic coherences in space and in time are shown to be modulated by the different periods of the nuclear motion. PMID:26928262

  10. Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes

    PubMed Central

    Shim, Sang-Hee; Xia, Chenglong; Zhong, Guisheng; Babcock, Hazen P.; Vaughan, Joshua C.; Huang, Bo; Wang, Xun; Xu, Cheng; Bi, Guo-Qiang; Zhuang, Xiaowei

    2012-01-01

    Imaging membranes in live cells with nanometer-scale resolution promises to reveal ultrastructural dynamics of organelles that are essential for cellular functions. In this work, we identified photoswitchable membrane probes and obtained super-resolution fluorescence images of cellular membranes. We demonstrated the photoswitching capabilities of eight commonly used membrane probes, each specific to the plasma membrane, mitochondria, the endoplasmic recticulum (ER) or lysosomes. These small-molecule probes readily label live cells with high probe densities. Using these probes, we achieved dynamic imaging of specific membrane structures in living cells with 30–60 nm spatial resolution at temporal resolutions down to 1–2 s. Moreover, by using spectrally distinguishable probes, we obtained two-color super-resolution images of mitochondria and the ER. We observed previously obscured details of morphological dynamics of mitochondrial fusion/fission and ER remodeling, as well as heterogeneous membrane diffusivity on neuronal processes. PMID:22891300

  11. Perspectives of Deuteron Field-Cycling NMR Relaxometry for Probing Molecular Dynamics in Soft Matter.

    PubMed

    Flämig, M; Becher, M; Hofmann, M; Körber, T; Kresse, B; Privalov, A F; Willner, L; Kruk, D; Fujara, F; Rössler, E A

    2016-08-11

    Due to the single-particle character of the quadrupolar interaction in molecular systems, (2)H NMR poses a unique method for probing reorientational dynamics. Spin-lattice relaxation gives access to the spectral density, and its frequency dependency can be monitored by field-cycling (FC) techniques. However, most FC NMR studies employ (1)H; the use of (2)H is still rare. We report on the application of (2)H FC NMR for investigating the dynamics in molecular liquids and polymers. Commercial as well as home-built relaxometers are employed accessing a frequency range from 30 Hz to 6 MHz. Due to low gyromagnetic ratio, high coupling constants, and finite FC switching times, current (2)H FC NMR does not reach the dispersion region in liquids (toluene and glycerol), yet good agreement with the results from conventional high-field (HF) relaxation studies is demonstrated. The pronounced difference at low frequencies between (2)H and (1)H FC NMR data shows the relevance of intermolecular relaxation in the case of (1)H NMR. In the case of the polymers polybutadiene and poly(ethylene-alt-propylene), very similar relaxation dispersion is observed and attributed to Rouse and entanglement dynamics. Combination with HF (2)H relaxation data via applying frequency-temperature superposition allows the reconstruction of the full spectral density reflecting both polymer as well as glassy dynamics. Transformation into the time domain yields the reorientational correlation function C2(t) extending over nine decades in time with a long-time power law, C2(t) ∝ t(-0.45±0.05), which does not conform to the prediction of the tube-reptation model, for which ∝ t(-0.25) is expected. Entanglement sets in below C2(t = τe) ≅ S(2) = 0.001, where τe is the entanglement time and S the corresponding order parameter. Finally, we discuss the future prospects of the (2)H FC NMR technique. PMID:27420118

  12. Dynamical and critical behavior of a simple discrete model of the cellular immune system

    NASA Astrophysics Data System (ADS)

    Brass, A.; Bancroft, A. J.; Clamp, M. E.; Grencis, R. K.; Else, K. J.

    1994-08-01

    A simple cellular automata model has been constructed to investigate the interactions between the two T-helper subset cell types (TH1 and TH2) in a lymph node during chronic parasitic infection. The model exhibits behavior similar to a phase transition as a function of the antigenic burden placed on the host. At low antigen density the behavior of the model resembles that of a ``paramagnetic'' phase in which both T-helper cell subset cells can coexist. Above a threshold antigen density then one or other of the TH subset cells becomes dominant and forms a single, connected, infinite cluster (equivalent to a ``ferromagnetic'' phase). Much of the phenomenological behavior of the model is seen to be in good agreement with that observed in animal models of parasitic infection.

  13. The integrin alphav beta3 increases cellular stiffness and cytoskeletal remodeling dynamics to facilitate cancer cell invasion

    NASA Astrophysics Data System (ADS)

    Mierke, Claudia Tanja

    2013-01-01

    The process of cancer cell invasion through the extracellular matrix (ECM) of connective tissue plays a prominent role in tumor progression and is based fundamentally on biomechanics. Cancer cell invasion usually requires cell adhesion to the ECM through the cell-matrix adhesion receptors integrins. The expression of the αvβ3 integrin is increased in several tumor types and is consistently associated with increased metastasis formation in patients. The hypothesis was that the αvβ3 integrin expression increases the invasiveness of cancer cells through increased cellular stiffness, and increased cytoskeletal remodeling dynamics. Here, the invasion of cancer cells with different αvβ3 integrin expression levels into dense three-dimensional (3D) ECMs has been studied. Using a cell sorter, two subcell lines expressing either high or low amounts of αvβ3 integrins (αvβ3high or αvβ3low cells, respectively) have been isolated from parental MDA-MB-231 breast cancer cells. αvβ3high cells showed a threefold increased cell invasion compared to αvβ3low cells. Similar results were obtained for A375 melanoma, 786-O kidney and T24 bladder carcinoma cells, and cells in which the β3 integrin subunit was knocked down using specific siRNA. To investigate whether contractile forces are essential for αvβ3 integrin-mediated increased cellular stiffness and subsequently enhanced cancer cell invasion, invasion assays were performed in the presence of myosin light chain kinase inhibitor ML-7 and Rho kinase inhibitor Y27632. Indeed, cancer cell invasiveness was reduced after addition of ML-7 and Y27632 in αvβ3high cells but not in αvβ3low cells. Moreover, after addition of the contractility enhancer calyculin A, an increase in pre-stress in αvβ3low cells was observed, which enhanced cellular invasiveness. In addition, inhibition of the Src kinase, STAT3 or Rac1 strongly reduced the invasiveness of αvβ3high cells, whereas the invasiveness of β3 specific knock

  14. Probing collagen/enzyme mechanochemistry in native tissue with dynamic, enzyme-induced creep.

    PubMed

    Zareian, Ramin; Church, Kelli P; Saeidi, Nima; Flynn, Brendan P; Beale, John W; Ruberti, Jeffrey W

    2010-06-15

    Mechanical strain or stretch of collagen has been shown to be protective of fibrils against both thermal and enzymatic degradation. The details of this mechanochemical relationship could change our understanding of load-bearing tissue formation, growth, maintenance, and disease in vertebrate animals. However, extracting a quantitative relationship between strain and the rate of enzymatic degradation is extremely difficult in bulk tissue due to confounding diffusion effects. In this investigation, we develop a dynamic, enzyme-induced creep assay and diffusion/reaction rate scaling arguments to extract a lower bound on the relationship between strain and the cutting rate of bacterial collagenase (BC) at low strains. The assay method permits continuous, forced probing of enzyme-induced strain which is very sensitive to degradation rate differences between specimens at low initial strain. The results, obtained on uniaxially loaded strips of bovine corneal tissue (0.1, 0.25, or 0.5 N), demonstrate that small differences in strain alter the enzymatic cutting rate of the BC substantially. It was estimated that a change in tissue elongation of only 1.5% (at approximately 5% strain) reduces the maximum cutting rate of the enzyme by more than half. Estimation of the average load per monomer in the tissue strips indicates that this protective "cutoff" occurs when the collagen monomers are transitioning from an entropic to an energetic mechanical regime. The continuous tracking of the enzymatic cleavage rate as a function of strain during the initial creep response indicates that the decrease in the cleavage rate of the BC is nonlinear (initially steep between 4.5 and 6.5% and then flattens out from 6.5 to 9.5%). The high sensitivity to strain at low strain implies that even lightly loaded collagenous tissue may exhibit significant strain protection. The dynamic, enzyme-induced creep assay described herein has the potential to permit the rapid characterization of collagen

  15. Probing charge transfer and hot carrier dynamics in organic solar cells with terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Cunningham, Paul D.; Lane, Paul A.; Melinger, Joseph S.; Esenturk, Okan; Heilweil, Edwin J.

    2016-04-01

    Time-resolved terahertz spectroscopy (TRTS) was used to explore charge generation, transfer, and the role of hot carriers in organic solar cell materials. Two model molecular photovoltaic systems were investigated: with zinc phthalocyanine (ZnPc) or alpha-sexathiophene (α-6T) as the electron donors and buckminsterfullerene (C60) as the electron acceptor. TRTS provides charge carrier conductivity dynamics comprised of changes in both population and mobility. By using time-resolved optical spectroscopy in conjunction with TRTS, these two contributions can be disentangled. The sub-picosecond photo-induced conductivity decay dynamics of C60 were revealed to be caused by auto-ionization: the intrinsic process by which charge is generated in molecular solids. In donor-acceptor blends, the long-lived photo-induced conductivity is used for weight fraction optimization of the constituents. In nanoscale multilayer films, the photo-induced conductivity identifies optimal layer thicknesses. In films of ZnPc/C60, electron transfer from ZnPc yields hot charges that localize and become less mobile as they thermalize. Excitation of high-lying Franck Condon states in C60 followed by hole-transfer to ZnPc similarly produces hot charge carriers that self-localize; charge transfer clearly precedes carrier cooling. This picture is contrasted to charge transfer in α-6T/C60, where hole transfer takes place from a thermalized state and produces equilibrium carriers that do not show characteristic signs of cooling and self-localization. These results illustrate the value of terahertz spectroscopic methods for probing charge transfer reactions.

  16. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    DOE PAGESBeta

    Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen; Collins, Liam; Belianinov, Alex; Somnath, Suhas

    2016-08-12

    Kelvin probe force microscopy (KPFM) has provided deep insights into the role local electronic, ionic and electrochemical processes play on the global functionality of materials and devices, even down to the atomic scale. Conventional KPFM utilizes heterodyne detection and bias feedback to measure the contact potential difference (CPD) between tip and sample. This measurement paradigm, however, permits only partial recovery of the information encoded in bias- and time-dependent electrostatic interactions between the tip and sample and effectively down-samples the cantilever response to a single measurement of CPD per pixel. This level of detail is insufficient for electroactive materials, devices, ormore » solid-liquid interfaces, where non-linear dielectrics are present or spurious electrostatic events are possible. Here, we simulate and experimentally validate a novel approach for spatially resolved KPFM capable of a full information transfer of the dynamic electric processes occurring between tip and sample. General acquisition mode, or G-Mode, adopts a big data approach utilising high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates (> 4 MHz), providing a permanent record of the tip trajectory. We develop a range of methodologies for analysing the resultant large multidimensional datasets involving classical, physics-based and information-based approaches. Physics-based analysis of G-Mode KPFM data recovers the parabolic bias dependence of the electrostatic force for each cycle of the excitation voltage, leading to a multidimensional dataset containing spatial and temporal dependence of the CPD and capacitance channels. We use multivariate statistical methods to reduce data volume and separate the complex multidimensional data sets into statistically significant components that can then be mapped onto separate physical mechanisms. Overall, G-Mode KPFM offers a new paradigm to study

  17. Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling.

    PubMed

    Zheng, Wenjun

    2016-08-01

    Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc. PMID:27090373

  18. Interface dynamics of immiscible two-phase lattice-gas cellular automata: A model with random dynamic scatterers and quenched disorder in two dimensions

    NASA Astrophysics Data System (ADS)

    Azevedo, R. M.; Montenegro-Filho, R. R.; Coutinho-Filho, M. D.

    2013-09-01

    We use a lattice gas cellular automata model in the presence of random dynamic scattering sites and quenched disorder in the two-phase immiscible model with the aim of producing an interface dynamics similar to that observed in Hele-Shaw cells. The dynamics of the interface is studied as one fluid displaces the other in a clean lattice and in a lattice with quenched disorder. For the clean system, if the fluid with a lower viscosity displaces the other, we show that the model exhibits the Saffman-Taylor instability phenomenon, whose features are in very good agreement with those observed in real (viscous) fluids. In the system with quenched disorder, we obtain estimates for the growth and roughening exponents of the interface width in two cases: viscosity-matched fluids and the case of unstable interface. The first case is shown to be in the same universality class of the random deposition model with surface relaxation. Moreover, while the early-time dynamics of the interface behaves similarly, viscous fingers develop in the second case with the subsequent production of bubbles in the context of a complex dynamics. We also identify the Hurst exponent of the subdiffusive fractional Brownian motion associated with the interface, from which we derive its fractal dimension and the universality classes related to a percolation process.

  19. The dynamic and geometric phase transition in the cellular network of pancreatic islet

    NASA Astrophysics Data System (ADS)

    Wang, Xujing

    2013-03-01

    The pancreatic islet is a micro-organ that contains several thousands of endocrine cells, majority of which being the insulin releasing β - cells . - cellsareexcitablecells , andarecoupledtoeachother through gap junctional channels. Here, using percolation theory, we investigate the role of network structure in determining the dynamics of the β-cell network. We show that the β-cell synchronization depends on network connectivity. More specifically, as the site occupancy is reducing, initially the β-cell synchronization is barely affected, until it reaches around a critical value, where the synchronization exhibit a sudden rapid decline, followed by an slow exponential tail. This critical value coincides with the critical site open probability for percolation transition. The dependence over bond strength is similar, exhibiting critical-behavior like dependence around a certain value of bond strength. These results suggest that the β-cell network undergoes a dynamic phase transition when the network is percolated. We further apply the findings to study diabetes. During the development of diabetes, the β - cellnetworkconnectivitydecreases . Siteoccupancyreducesfromthe reducing β-cell mass, and the bond strength is increasingly impaired from β-cell stress and chronic hyperglycemia. We demonstrate that the network dynamics around the percolation transition explain the disease dynamics around onset, including a long time mystery in diabetes, the honeymoon phenomenon.

  20. Probing of field-induced structures and their dynamics in ferrofluids using oscillatory rheology.

    PubMed

    Felicia, Leona J; Philip, John

    2014-10-21

    We probe field-induced structures and their dynamics in ferrofluids using oscillatory rheology. The magnetic field dependence of the relaxation time and crossover modulus showed two distinct regions, indicating the different microstructures in those regions. The observed relaxation at various magnetic field strengths indicates that side chains are attached to the pinned single-sphere-width chains between the rheometer plates. Our results suggest that the ferrofluid under a magnetic field exhibits a soft solidlike behavior whose relaxation is governed by the imposed strain rate and the magnetic field. Using the scaling factors obtained from the frequency and modulus at the crossover point in the oscillatory rheological measurements, the constant strain-rate frequency sweep data is superimposed onto a single master curve. The frequency scaling factor increases with the strain rate as a power law with an exponent close to unity, whereas the amplitude scaling factor is almost strain-rate-independent at high magnetic field strengths. These findings are useful for a better understanding of field-induced ordering of nanoparticles in fluids and their optimization for practical applications. PMID:25268053

  1. Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions

    NASA Astrophysics Data System (ADS)

    Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle

    2015-03-01

    Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.

  2. Probing initial-stages of ALD growth with dynamic in situ spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Muneshwar, Triratna; Cadien, Ken

    2015-02-01

    The initial stages of ALD surface reactions are probed using dynamic in situ spectroscopic ellipsometry (d-iSE) technique during plasma-enhanced ALD of zirconium nitride (ZrN) thin films in spectral range of 0.73-6.4 eV. The measured change in the ellipsometry parameter Δ, with every precursor (TDMAZr) and reactant (forming gas plasma) exposure is interpreted as the combined effect of film growth and change in surface chemistry during ALD. We present application of Bruggeman's effective-medium approximation (B-EMA) in the analysis of d-iSE data to determine fractional surface coverage (θ) of ALD grown film at the end of every deposition cycle. During the deposition of first few ZrN monolayers, d-iSE datasets are analyzed on the basis of surface diffusion enhanced ALD growth, where the surface adsorbed precursor molecules can diffuse over substrate surface to occupy energetically favorable surface sites. The determined surface coverage of ZrN films highlights the effects of substrate enhanced ALD growth.

  3. Chemical Lectinology: Tools for Probing the Ligands and Dynamics of Mammalian Lectins In Vivo

    PubMed Central

    Belardi, Brian; Bertozzi, Carolyn R.

    2015-01-01

    Summary The importance and complexity associated with the totality of glycan structures, i.e. the glycome, has garnered significant attention from chemists and biologists alike. However, what is lacking from this biochemical picture is how cells, tissues, and organisms interpret glycan patterns and translate this information into appropriate responses. Lectins, glycan-binding proteins, are thought to bridge this gap by decoding the glycome and dictating cell fate based on the underlying chemical identities and properties of the glycome. Yet, our understanding of the in vivo ligands and function for most lectins is still incomplete. This review focuses on recent advances in chemical tools to study the specificity and dynamics of mammalian lectins in live cells. A picture emerges of lectin function that is highly sensitive to its organization, which in turn drastically shapes immunity and cancer progression. We hope this review will inspire biologists to make use of these new techniques and stimulate chemists to continue developing innovative approaches to probe lectin biology in vivo. PMID:26256477

  4. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    PubMed Central

    Collins, Liam; Belianinov, Alex; Somnath, Suhas; Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen

    2016-01-01

    Kelvin probe force microscopy (KPFM) has provided deep insights into the local electronic, ionic and electrochemical functionalities in a broad range of materials and devices. In classical KPFM, which utilizes heterodyne detection and closed loop bias feedback, the cantilever response is down-sampled to a single measurement of the contact potential difference (CPD) per pixel. This level of detail, however, is insufficient for materials and devices involving bias and time dependent electrochemical events; or at solid-liquid interfaces, where non-linear or lossy dielectrics are present. Here, we demonstrate direct recovery of the bias dependence of the electrostatic force at high temporal resolution using General acquisition Mode (G-Mode) KPFM. G-Mode KPFM utilizes high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates. We show how G-Mode KPFM can be used to capture nanoscale CPD and capacitance information with a temporal resolution much faster than the cantilever bandwidth, determined by the modulation frequency of the AC voltage. In this way, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as a promising route to extend KPFM to the solid-liquid interface. PMID:27514987

  5. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  6. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space.

    PubMed

    Collins, Liam; Belianinov, Alex; Somnath, Suhas; Balke, Nina; Kalinin, Sergei V; Jesse, Stephen

    2016-01-01

    Kelvin probe force microscopy (KPFM) has provided deep insights into the local electronic, ionic and electrochemical functionalities in a broad range of materials and devices. In classical KPFM, which utilizes heterodyne detection and closed loop bias feedback, the cantilever response is down-sampled to a single measurement of the contact potential difference (CPD) per pixel. This level of detail, however, is insufficient for materials and devices involving bias and time dependent electrochemical events; or at solid-liquid interfaces, where non-linear or lossy dielectrics are present. Here, we demonstrate direct recovery of the bias dependence of the electrostatic force at high temporal resolution using General acquisition Mode (G-Mode) KPFM. G-Mode KPFM utilizes high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates. We show how G-Mode KPFM can be used to capture nanoscale CPD and capacitance information with a temporal resolution much faster than the cantilever bandwidth, determined by the modulation frequency of the AC voltage. In this way, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as a promising route to extend KPFM to the solid-liquid interface. PMID:27514987

  7. Probing and characterizing the early stages of cavitation in glassy polymers in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Estevez, R.; Long, D.

    2011-06-01

    This work focuses on a specific aspect of polymer fracture: the onset of cavitation during deformation. Failure in polymers involves plastic deformation by shear yielding and crazing. The competition between these two mechanisms is thought to govern the ductile versus brittle response of the material. The present molecular dynamics (MD) analysis shows that at a small scale, cavitation results from a transition between a homogeneous to a highly heterogeneous deformation field during loading. We characterize here these two regimes thanks to a scalar non-affine displacement probe, which displays a sharp transition at the onset of cavitation. Close scrutiny of cavitation allows for defining a stress-based cavitation criterion, the validity of which is checked for two temperatures in the glassy state. A mapping between the MD results and the corresponding estimates at the continuum scale indicates that the onset of cavitation at high deformation rates corresponds to a noticeably larger stress level as compared with that at low and intermediate loading rates. Since cavitation precedes failure in glassy polymers, this effect could be responsible for the marked increase in toughness reported experimentally under impact conditions.

  8. Hydrated fractions of cellulosics probed by infrared spectroscopy coupled with dynamics of deuterium exchange.

    PubMed

    Driemeier, Carlos; Mendes, Fernanda M; Ling, Liu Yi

    2015-08-20

    This article presents a novel method to selectively probe the non-crystalline, hydrated fractions of cellulosic biomass. The method is based on time-resolved infrared spectra analyzed to provide information on spectral and dynamical features of deuterium exchange (OH → OD) in D2O atmosphere. We assign deuterium exchange spectral regions (700-3800 cm(-1)) and explore changes due to relative humidity, different cellulosic samples, and infrared polarization. Here, two results are highlighted. First, a wide range of celluloses isolated from plants show remarkable spectral similarities whatever the relative amounts of cellulose and xylan. This result supports an inherent type of hydrated disorder which is mostly insensitive to the molecular identities of the associated polysaccharides. Second, polarized infrared analysis of cotton reveals hydrated cellulose having chains preferentially aligned with those of crystals, while the hydroxyls of hydrated cellulose present much more randomized orientation. Our results provide new insights on molecular and group orientation and on hydrogen bonding in hydrated fractions of cellulosic biomass. PMID:25965468

  9. Probing the geometric constraints of RNA binding via dynamic covalent chemistry.

    PubMed

    McAnany, John D; Reichert, John P; Miller, Benjamin L

    2016-09-01

    Dynamic Combinatorial Chemistry (DCC) has proven to be a reliable method for identifying hit compounds for target nucleic acid (DNA and RNA) sequences. Typically, these hit compounds are subjected to a lengthy process of optimization via traditional medicinal chemistry. Here, we examine the potential of DCC to also generate and test variations on a hit compound as a method for probing the binding site of an RNA-targeted compound. Specifically, we demonstrate that addition of linker dithiols to a disulfide library containing a known binder to the HIV-1 frameshift-stimulatory RNA (a critical regulator of the HIV life cycle) can yield a mixture of new bridged structures incorporating the dithiol, depending on dithiol structure. Equilibration of this library with the HIV FSS RNA resulted in selection of the original disulfide in preference to bridged structures, suggesting incorporation of the bridge is not compatible with this particular binding site. Application of this strategy to other RNA targets should allow for rapidly profiling the affinity of modified compounds. PMID:26935941

  10. Femtosecond isomerization dynamics in the ethylene cation measured in an EUV-pump NIR-probe configuration

    SciTech Connect

    van Tilborg, Jeroen; Allison, Tom; Wright, Travis; Hertlein, Marc; Falcone, Roger; Liu, Yanwei; Merdji, Hamed; Belkacem, Ali

    2009-03-17

    Dynamics in the excited ethylene cation C{sub 2}H{sub 4}{sup +} lead to isomerization to the ethylidene configuration (HC-CH{sub 3}){sup +}, which is predicted to be a transient configuration for electronic relaxation. With an intense femtosecond EUV (extreme ultraviolet) pump pulse to populate the excited state, and an NIR (near infrared) probe pulse to produce the fragments CH{sup +} and CH{sub 3}{sup +} (which provides a direct signature of ethylidene), we measure optimum fragment yields at a probe delay of 80 fs. Also, an H{sub 2}-stretch transient configuration, yielding H{sub 2}{sup +} upon probing, is found to succeed the ethylidene configuration. We find that a simple single- or double-decay model does not match the data, and we present a modified model (introduction of an isomerization delay of 50 {+-} 25 fs) that does provide agreement.

  11. Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

    PubMed Central

    Giordano, Nils; Mairet, Francis; Gouzé, Jean-Luc

    2016-01-01

    Microbial physiology exhibits growth laws that relate the macromolecular composition of the cell to the growth rate. Recent work has shown that these empirical regularities can be derived from coarse-grained models of resource allocation. While these studies focus on steady-state growth, such conditions are rarely found in natural habitats, where microorganisms are continually challenged by environmental fluctuations. The aim of this paper is to extend the study of microbial growth strategies to dynamical environments, using a self-replicator model. We formulate dynamical growth maximization as an optimal control problem that can be solved using Pontryagin’s Maximum Principle. We compare this theoretical gold standard with different possible implementations of growth control in bacterial cells. We find that simple control strategies enabling growth-rate maximization at steady state are suboptimal for transitions from one growth regime to another, for example when shifting bacterial cells to a medium supporting a higher growth rate. A near-optimal control strategy in dynamical conditions is shown to require information on several, rather than a single physiological variable. Interestingly, this strategy has structural analogies with the regulation of ribosomal protein synthesis by ppGpp in the enterobacterium Escherichia coli. It involves sensing a mismatch between precursor and ribosome concentrations, as well as the adjustment of ribosome synthesis in a switch-like manner. Our results show how the capability of regulatory systems to integrate information about several physiological variables is critical for optimizing growth in a changing environment. PMID:26958858

  12. VolRoverN: Enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function

    PubMed Central

    Edwards, John; Daniel, Eric; Kinney, Justin; Bartol, Tom; Sejnowski, Terrence; Johnston, Daniel; Harris, Kristen; Bajaj, Chandrajit

    2014-01-01

    Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type (including glia) and are used here on complex spiny dendrites and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models. PMID:24100964

  13. Dynamic cellular and molecular modulations of diabetes mediated head and neck carcinogenesis

    PubMed Central

    Chen, Chang-Yi; Sun, Fang-Ju; Cheng, Hui-Wen; Chen, Tsai-Ying; Lin, Shu-Chun; Li, Wan-Chun

    2015-01-01

    Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent neoplasms worldwide. While numerous potent dietary insults were considered as oncogenic players for HNSCC development, the impact of metabolic imbalance was less emphasized during HNSCC carcinogenesis. Previous preclinical and epidemiological investigations showed that DM could possibly be correlated with greater incidence and poorer prognosis in HNSCC patients; however, the outcomes from different groups are contradictive and underlying mechanisms remains elusive. In the present study, the changes of cellular malignancy in response to prolonged glucose incubation in HNSCC cells were examined. The results demonstrated that hyperglycemia enhanced HNSCC cell malignancy over time through suppression of cell differentiation, promotion of cell motility, increased resistance to cisplatin, and up-regulation of the nutrient-sensing Akt/AMPK-mTORC1 pathway. Further analysis showed that a more aggressive tongue neoplastic progression was found under DM conditions compared to non-DM state whereas DM pathology led to a higher percentage of cervical lymph node metastasis and poorer prognosis in HNSCC patients. Taken together, the present study confirms that hyperglycemia and DM could enhance HNSCC malignancy and the outcomes are of great benefit in providing better anti-cancer treatment strategy for DM patients with HNSCC. PMID:26337468

  14. ECM signaling regulates collective cellular dynamics to control pancreas branching morphogenesis

    PubMed Central

    Shih, Hung Ping; Panlasigui, Devin; Cirulli, Vincenzo; Sander, Maike

    2015-01-01

    Summary During pancreas development, epithelial buds undergo branching morphogenesis to form an exocrine and endocrine gland. Proper morphogenesis is necessary for correct lineage allocation of pancreatic progenitors; however, the cellular events underlying pancreas morphogenesis are unknown. Here, we employed time-lapse microscopy and fluorescent labeling of cells to analyze cell behaviors associated with pancreas morphogenesis. We observed that outer bud cells adjacent to the basement membrane are pleomorphic and rearrange frequently; as well, they largely remain in the outer cell compartment even after mitosis. These cell behaviors and pancreas branching depend on cell contacts with the basement membrane, which induce actomyosin cytoskeleton remodeling via integrin-mediated activation of FAK/Src signaling. We show that integrin signaling reduces E-cadherin-mediated cell-cell adhesion in outer cells, and provide genetic evidence that this regulation is necessary for initiation of branching. Our study suggests that regulation of cell motility and adhesion by local niche cues initiates pancreas branching morphogenesis. PMID:26748698

  15. Study of cellular dynamics on polarized CoCrMo alloy using time-lapse live-cell imaging.

    PubMed

    Haeri, Morteza; Gilbert, Jeremy L

    2013-11-01

    The physico-chemical processes and phenomena occurring at the interface of metallic biomedical implants and the body dictate their successful integration in vivo. Changes in the surface potential and the associated redox reactions at metallic implants can significantly influence several aspects of biomaterial/cell interactions such as cell adhesion and survival in vitro. Accordingly, there is a voltage viability range (voltages which do not compromise cellular viability of the cells cultured on the polarized metal) for metallic implants. We report on cellular dynamics (size, polarity, movement) and temporal changes in the number and total area of focal adhesion complexes in transiently transfected MC3T3-E1 pre-osteoblasts cultured on CoCrMo alloy surfaces polarized at the cathodic and anodic edges of its voltage viability range (-400 and +500 mV (Ag/AgCl), respectively). Nucleus dynamics (size, circularity, movement) and the release of reactive oxygen species (ROS) were also studied on the polarized metal at -1000, -400 and +500 mV (Ag/AgCl). Our results show that at -400 mV, where reduction reactions dominate, a gradual loss of adhesion occurs over 24 h while cells shrink in size during this time. At +500 mV, where oxidation reactions dominate (i.e. metal ions form, including Cr6+), cells become non-viable after 5h without showing any significant changes in adhesion behavior right before cell death. Nucleus size of cells at -1000 mV decreased sharply within 15 min after polarization, which rendered the cells completely non-viable. No significant amount of ROS release by cells was detected on the polarized CoCrMo at any of these voltages. PMID:23831720

  16. Nonlinear cellular dynamics of keratinocytes in normal and psoriatic epidermis under action of UV radiation

    NASA Astrophysics Data System (ADS)

    Stolnitz, Mikhail M.; Medvedev, Boris A.; Gribko, Tatyana V.

    2004-05-01

    The semi-phenomenological model of epidermal cell dynamics is submitted. The model takes into account three types of basal layer keratinocytes (stem, transient amplifying, terminally differentiated), distribution of first two types cells on mitotic cycle stages and resting states, keratinocytes-lymphocytes interactions that provide a positive feedback loop, influence of more differentiated cells on their progenitors that provide a negative feedback loop. Simplified model are developed and its stationary solutions are received. The opportunity of interpretation of some received modes as corresponding to various stages of psoriasis is discussed. Influence of UV-radiation on transitions between various modes of epidermis functioning is qualitatively analyzed.

  17. Use of indium-111-labeled cells in measurement of cellular dynamics of experimental cardiac allograft rejection

    SciTech Connect

    Oluwole, S.; Wang, T.; Fawwaz, R.; Satake, K.; Nowygrod, R.; Reemtsma, K.; Hardy, M.A.

    1981-01-01

    This study evaluates the kinetics and utility of infused indium-111-labeled cells in detecting rejection in ACI to Lewis rat heart allografts. Syngeneic leukocytes, lymph node lymphocytes, and platelets were isolated and labeled with indium-111 (/sup 111/In) oxine, respectively, and were infused i.v. into Lewis rats carrying beating ACI or syngeneic hearts from post-transplant days 0 to 6. Recipients were imaged serially at 24 hr after infusion of labeled cells followed by excision of both native and transplanted hearts for direct isotope count. Labeled leukocytes accumulative progressively in the allograft with the scan becoming positive by post-transplant day 4. The ratio of allograft to native heart isotope counts rose from 1.25 on day 1 to 10.07 (P less than 0.0001) on day 7. The Lewis recipients infused with labeled lymphocytes showed a positive scan on days 6 and 7 whereas the allograft to native heart isotope count ratio rose from 0.97 on day 1 to 5.33 (P less than 0.001) on day 7. Recipients infused with /sup 111/In-labeled platelets showed a positive scan on days 5 to 7 and the allograft to native heart isotope count ratio rose sharply from 2.56 on day 4 to 16.98 (P less than 0.005) on day 7. Syngeneic heart grafts failed to demonstrate significant accumulation of any of the labeled cell population. These studies confirm the importance of nonlymphocytic cells in cellular rejection, evaluate the kinetics of graft invasion by the various cell types, and suggest that the techniques used afford a method for a safe and an early detection of allograft rejection.

  18. Analysis of the local organization and dynamics of cellular actin networks

    PubMed Central

    Luo, Weiwei; Yu, Cheng-han; Lieu, Zi Zhao; Allard, Jun; Mogilner, Alex; Sheetz, Michael P.

    2013-01-01

    A ctin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm. PMID:24081490

  19. Role of Junctin Protein Interactions in Cellular Dynamics of Calsequestrin Polymer upon Calcium Perturbation*

    PubMed Central

    Lee, Keun Woo; Maeng, Jin-Soo; Choi, Jeong Yi; Lee, Yu Ran; Hwang, Chae Young; Park, Sung Sup; Park, Hyun Kyu; Chung, Bong Hyun; Lee, Seung-Goo; Kim, Yeon-Soo; Jeon, Hyesung; Eom, Soo Hyun; Kang, ChulHee; Kim, Do Han; Kwon, Ki-Sun

    2012-01-01

    Calsequestrin (CSQ), the major intrasarcoplasmic reticulum calcium storage protein, undergoes dynamic polymerization and depolymerization in a Ca2+-dependent manner. However, no direct evidence of CSQ depolymerization in vivo with physiological relevance has been obtained. In the present study, live cell imaging analysis facilitated characterization of the in vivo dynamics of the macromolecular CSQ structure. CSQ2 appeared as speckles in the presence of normal sarcoplasmic reticulum (SR) Ca2+ that were decondensed upon Ca2+ depletion. Moreover, CSQ2 decondensation occurred only in the stoichiometric presence of junctin (JNT). When expressed alone, CSQ2 speckles remained unchanged, even after Ca2+ depletion. FRET analysis revealed constant interactions between CSQ2 and JNT, regardless of the SR Ca2+ concentration, implying that JNT is an essential component of the CSQ scaffold. In vitro solubility assay, electron microscopy, and atomic force microscopy studies using purified recombinant proteins confirmed Ca2+ and JNT-dependent disassembly of the CSQ2 polymer. Accordingly, we conclude that reversible polymerization and depolymerization of CSQ are critical in SR Ca2+ homeostasis. PMID:22123818

  20. Imaging the impact of chemically inducible proteins on cellular dynamics in vivo.

    PubMed

    Leong, Hon S; Lizardo, Michael M; Ablack, Amber; McPherson, Victor A; Wandless, Thomas J; Chambers, Ann F; Lewis, John D

    2012-01-01

    The analysis of dynamic events in the tumor microenvironment during cancer progression is limited by the complexity of current in vivo imaging models. This is coupled with an inability to rapidly modulate and visualize protein activity in real time and to understand the consequence of these perturbations in vivo. We developed an intravital imaging approach that allows the rapid induction and subsequent depletion of target protein levels within human cancer xenografts while assessing the impact on cell behavior and morphology in real time. A conditionally stabilized fluorescent E-cadherin chimera was expressed in metastatic breast cancer cells, and the impact of E-cadherin induction and depletion was visualized using real-time confocal microscopy in a xenograft avian embryo model. We demonstrate the assessment of protein localization, cell morphology and migration in cells undergoing epithelial-mesenchymal and mesenchymal-epithelial transitions in breast tumors. This technique allows for precise control over protein activity in vivo while permitting the temporal analysis of dynamic biophysical parameters. PMID:22276156

  1. Analysis of the local organization and dynamics of cellular actin networks.

    PubMed

    Luo, Weiwei; Yu, Cheng-han; Lieu, Zi Zhao; Allard, Jun; Mogilner, Alex; Sheetz, Michael P; Bershadsky, Alexander D

    2013-09-30

    Actin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm. PMID:24081490

  2. Tissue architecture and function: dynamic reciprocity via extra- and intra-cellular matrices

    PubMed Central

    Boudreau, Aaron

    2009-01-01

    Mammary gland development, functional differentiation, and homeostasis are orchestrated and sustained by a balance of biochemical and biophysical cues from the organ’s microenvironment. The three-dimensional microenvironment of the mammary gland, predominantly ‘encoded’ by a collaboration between the extracellular matrix (ECM), hormones, and growth factors, sends signals from ECM receptors through the cytoskeletal intracellular matrix to nuclear and chromatin structures resulting in gene expression; the ECM in turn is regulated and remodeled by signals from the nucleus. In this chapter, we discuss how coordinated ECM deposition and remodeling is necessary for mammary gland development, how the ECM provides structural and biochemical cues necessary for tissue-specific function, and the role of the cytoskeleton in mediating the extra—to intracellular dialogue occurring between the nucleus and the microenvironment. When operating normally, the cytoskeletal-mediated dynamic and reciprocal integration of tissue architecture and function directs mammary gland development, tissue polarity, and ultimately, tissue-specific gene expression. Cancer occurs when these dynamic inter-actions go awry for an extended time. PMID:19160017

  3. Tissue architecture and function: dynamic reciprocity via extra- and intra-cellular matrices

    SciTech Connect

    Xu, Ren; Boudreau, Aaron; Bissell, Mina J

    2008-12-23

    Mammary gland development, functional differentiation, and homeostasis are orchestrated and sustained by a balance of biochemical and biophysical cues from the organ's microenvironment. The three-dimensional microenvironment of the mammary gland, predominantly 'encoded' by a collaboration between the extracellular matrix (ECM), hormones, and growth factors, sends signals from ECM receptors through the cytoskeletal intracellular matrix to nuclear and chromatin structures resulting in gene expression; the ECM in turn is regulated and remodeled by signals from the nucleus. In this chapter, we discuss how coordinated ECM deposition and remodeling is necessary for mammary gland development, how the ECM provides structural and biochemical cues necessary for tissue-specific function, and the role of the cytoskeleton in mediating the extra - to intracellular dialogue occurring between the nucleus and the microenvironment. When operating normally, the cytoskeletal-mediated dynamic and reciprocal integration of tissue architecture and function directs mammary gland development, tissue polarity, and ultimately, tissue-specific gene expression. Cancer occurs when these dynamic interactions go awry for an extended time.

  4. Microwave field distribution in a magic angle spinning dynamic nuclear polarization NMR probe

    NASA Astrophysics Data System (ADS)

    Nanni, Emilio A.; Barnes, Alexander B.; Matsuki, Yoh; Woskov, Paul P.; Corzilius, Björn; Griffin, Robert G.; Temkin, Richard J.

    2011-05-01

    We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B 1 S) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4 mm diameter sapphire rotor containing the sample. The predicted average B 1 S field is 13 μT/W 1/2, where S denotes the electron spin. For a routinely achievable input power of 5 W the corresponding value is γSB 1 S = 0.84 MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement ( ɛ) vs. ω1 S/(2 π) for a sample of 13C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment.

  5. ReAsH as a Quantitative Probe of In-Cell Protein Dynamics.

    PubMed

    Gelman, Hannah; Wirth, Anna Jean; Gruebele, Martin

    2016-04-01

    The tetracysteine (tc) tag/biarsenical dye system (FlAsH or ReAsH) promises to combine the flexibility of fluorescent protein tags with the small size of dye labels, allowing in-cell study of target proteins that are perturbed by large protein tags. Quantitative thermodynamic and kinetic studies in-cell using FlAsH and ReAsH have been hampered by methodological complexities presented by the fluorescence properties of the tag-dye complex probed by either Förster resonance energy transfer (FRET) or direct excitation. We label the model protein phosphoglycerate kinase (PGK) with AcGFP1 and ReAsH for direct comparison with AcGFP1/mCherry-labeled PGK. We find that fast relaxation imaging (FReI), combining millisecond temperature jump kinetics with fluorescence microscopy detection, circumvents many of the difficulties encountered working with the ReAsH system, allowing us to obtain quantitative FRET measurements of protein stability and kinetics both in vitro and in cells. We also demonstrate the to us surprising result that fluorescence from directly excited, unburied ReAsH at the C-terminus of the model protein also reports on folding in vitro and in cells. Comparing the ReAsH-labeled protein to a construct labeled with two fluorescent protein tags allows us to evaluate how a bulkier protein tag affects protein dynamics in cells and in vitro. We find that the average folding rate in the cell is closer to the in vitro rate with the smaller tag, highlighting the effect of tags on quantitative in-cell measurements. PMID:26959408

  6. Microwave field distribution in a magic angle spinning dynamic nuclear polarization NMR probe.

    PubMed

    Nanni, Emilio A; Barnes, Alexander B; Matsuki, Yoh; Woskov, Paul P; Corzilius, Björn; Griffin, Robert G; Temkin, Richard J

    2011-05-01

    We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B(1S)) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4mm diameter sapphire rotor containing the sample. The predicted average B(1S) field is 13μT/W(1/2), where S denotes the electron spin. For a routinely achievable input power of 5W the corresponding value is γ(S)B(1S)=0.84MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement (ϵ) vs. ω(1S)/(2π) for a sample of (13)C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment. PMID:21382733

  7. Microwave Field Distribution in a Magic Angle Spinning Dynamic Nuclear Polarization NMR Probe

    PubMed Central

    Nanni, Emilio A.; Barnes, Alexander B.; Matsuki, Yoh; Woskov, Paul P.; Corzilius, Björn; Griffin, Robert G.; Temkin, Richard J.

    2011-01-01

    We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B1S) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4 mm diameter sapphire rotor containing the sample. The predicted average B1S field is 13µT/W1/2, where S denotes the electron spin. For a routinely achievable input power of 5 W the corresponding value is γ SB1S = 0.84 MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement (ε) vs. ω1S/(2π) for a sample of 13C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment. PMID:21382733

  8. Slingshot dynamics for self-replicating probes and the effect on exploration timescales

    NASA Astrophysics Data System (ADS)

    Nicholson, Arwen; Forgan, Duncan

    2013-10-01

    Interstellar probes can carry out slingshot manoeuvres around the stars they visit, gaining a boost in velocity by extracting energy from the star's motion around the Galactic Centre. These manoeuvres carry little to no extra energy cost, and in previous work it has been shown that a single Voyager-like probe exploring the Galaxy does so 100 times faster when carrying out these slingshots than when navigating purely by powered flight (Forgan et al. 2012). We expand on these results by repeating the experiment with self-replicating probes. The probes explore a box of stars representative of the local Solar neighbourhood, to investigate how self-replication affects exploration timescales when compared with a single non-replicating probe. We explore three different scenarios of probe behaviour: (i) standard powered flight to the nearest unvisited star (no slingshot techniques used), (ii) flight to the nearest unvisited star using slingshot techniques and (iii) flight to the next unvisited star that will give the maximum velocity boost under a slingshot trajectory. In all three scenarios, we find that as expected, using self-replicating probes greatly reduces the exploration time, by up to three orders of magnitude for scenarios (i) and (iii) and two orders of magnitude for (ii). The second case (i.e. nearest-star slingshots) remains the most time effective way to explore a population of stars. As the decision-making algorithms for the fleet are simple, unanticipated `race conditions' among probes are set up, causing the exploration time of the final stars to become much longer than necessary. From the scaling of the probes' performance with star number, we conclude that a fleet of self-replicating probes can indeed explore the Galaxy in a sufficiently short time to warrant the existence of the Fermi Paradox.

  9. Dynamical studies of model membrane and cellular response to nanosecond, high-intensity pulsed electric fields

    NASA Astrophysics Data System (ADS)

    Hu, Qin

    The dynamics of electroporation of biological cells subjected to nanosecond, high intensity pulses are studied based on a coupled scheme involving the current continuity and Smoluchowski equations. The improved pore formation energy model includes a dependence on pore population and density. It also allows for variable surface tension and incorporates the effects of finite conductivity on the electrostatic correction term, which was not considered by the simple energy models in the literature. It is shown that E(r) becomes self-adjusting with variations in its magnitude and profile. The whole scheme is self-consistent and dynamic. An electromechanical analysis based on thin-shell theory is presented to analyze cell shape changes in response to external electric fields. The calculations demonstrate that at large fields, the spherical cell geometry can be modified, and even ellipsoidal forms may not be appropriate to account for the resulting shape. It is shown that, in keeping with reports in the literature, the final shape depends on membrane thickness. This has direct implications for tissues in which significant molecular restructuring can occur. This study is also focused on obtaining qualitative predictions of pulse width dependence to apoptotic cell irreversibility that has been observed experimentally. The analysis couples a distributed electrical model for current flow with the Smoluchowski equation to provide self-consistent, time-dependent transmembrane voltages. The model captures the essence of the experimentally observed pulse-width dependence, and provides a possible physical picture that depends only on the electrical trigger. Different cell responses of normal and malignant (Farage) tonsillar B-cell are also compared and discussed. It is shown that subjecting a cell to an ultrashort, high-intensity electric pulse is the optimum way for reversible intracellular manipulation. Finally, a simple but physical atomistic model is presented for molecular

  10. Probing protein dynamics and function under native and mildly denaturing conditions with hydrogen exchange and mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kaltashov, Igor A.

    2005-02-01

    A combination of hydrogen exchange and mass spectrometry emerged in recent years as a powerful experimental tool capable of probing both structural and dynamic features of proteins. Although its concept is very simple, the interpretation of experimental data is not always straightforward, as a combination of chemical reactions (isotope exchange) and dynamic processes within protein molecules give rise to convoluted exchange patterns. This paper provides a historical background of this technique, candid assessment of its current state and limitations and a discussion of promising recent developments that can result in tremendous improvements and a dramatic expansion of the scope of its applications.

  11. Tethered Dynamics Explorer and Tethered Atmospheric Probe - A low-cost, low-risk tethered satellite program

    NASA Technical Reports Server (NTRS)

    Deloach, R.; Wood, G.; Crumbly, K.; Rupp, C.; Harrison, J.

    1989-01-01

    A tethered satellite flight program to test theoretical studies of tether concepts is proposed. The program consists of multiple flights of an ELV such as the Delta II, using the Small Expendable Deployment System (SEDS) to deploy two instrumented satellite payloads, the Tethered Dynamics Explorer (TDE) and the Tethered Atmospheric Probe (TAP). The applications and characteristics of the TDE and the TAP are described, including verification of the SEDS, the validation of the dynamics and control model for low-tension deployment and the force and moment instrumentation, the demonstration of tether initiated reentry, the collection of in-situ atmospheric and aerothermodynamic data, and the study of long-term tether exposure.

  12. Tip cells act as dynamic cellular anchors in the morphogenesis of looped renal tubules in Drosophila.

    PubMed

    Weavers, Helen; Skaer, Helen

    2013-11-11

    Tissue morphogenesis involves both the sculpting of tissue shape and the positioning of tissues relative to one another in the body. Using the renal tubules of Drosophila, we show that a specific distal tubule cell regulates both tissue architecture and position in the body cavity. Focusing on the anterior tubules, we demonstrate that tip cells make transient contacts with alary muscles at abdominal segment boundaries, moving progressively forward as convergent extension movements lengthen the tubule. Tip cell anchorage antagonizes forward-directed, TGF-β-guided tubule elongation, thereby ensuring the looped morphology characteristic of renal tubules from worms to humans. Distinctive tip cell exploratory behavior, adhesion, and basement membrane clearing underlie target recognition and dynamic interactions. Defects in these features obliterate tip cell anchorage, producing misshapen and misplaced tubules with impaired physiological function. PMID:24229645

  13. Water protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions

    SciTech Connect

    Mamontov, Eugene; Chu, Xiang-Qiang

    2012-01-01

    Both the structure and dynamics of biomolecules are known to be essential for their biological function. In the dehydrated state, the function of biomolecules, such as proteins, is severely impeded, so hydration is required for bioactivity. The dynamics of the hydrated biomolecules and their hydration water are related - but how closely? The problem involves several layers of complexity. Even for water in the bulk state, the contribution from various dynamic components to the overall dynamics is not fully understood. In biological systems, the effects of confinement on the hydration water further complicate the picture. Even if the various components of the hydration water dynamics are properly understood, which of them are coupled to the protein dynamics, and how? The studies of protein dynamics over the wide temperature range, from physiological to low temperatures, provide some answers to these question. At low temperatures, both the protein and its hydration water behave as solids, with only vibrational degrees of freedom. As the temperature is increased, non-vibrational dynamic components start contributing to the measurable dynamics and eventually become dominant at physiological temperatures. Thus, the temperature dependence of the dynamics of protein and its hydration water may allow probing various dynamic components separately. In order to suppress the water freezing, the low-temperature studies of protein rely on either low-hydrated samples (essentially, hydrated protein powders), or cryo-protective solutions. Both approaches introduce the hydration environments not characteristic of the protein environments in living systems, which are typically aqueous protein solutions of various concentrations. In this paper, we discuss the coupling between the dynamic components of the protein and its hydration water by critical examining of the existing literature, and then propose that proteins can be studied in an aqueous solution that is remarkably similar in

  14. A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis

    NASA Astrophysics Data System (ADS)

    Kumar, Mohit; Brocorens, Patrick; Tonnelé, Claire; Beljonne, David; Surin, Mathieu; George, Subi J.

    2014-12-01

    Design of artificial systems, which can respond to fluctuations in concentration of adenosine phosphates (APs), can be useful in understanding various biological processes. Helical assemblies of chromophores, which dynamically respond to such changes, can provide real-time chiroptical readout of various chemical transformations. Towards this concept, here we present a supramolecular helix of achiral chromophores, which shows chiral APs responsive tunable handedness along with dynamically switchable helicity. This system, composing of naphthalenediimides with phosphate recognition unit, shows opposite handedness on binding with ATP compared with ADP or AMP, which is comprehensively analysed with molecular dynamic simulations. Such differential signalling along with stimuli-dependent fast stereomutations have been capitalized to probe the reaction kinetics of enzymatic ATP hydrolysis. Detailed chiroptical analyses provide mechanistic insights into the enzymatic hydrolysis and various intermediate steps. Thus, a unique dynamic helical assembly to monitor the real-time reaction processes via its stimuli-responsive chiroptical signalling is conceptualized.

  15. A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis.

    PubMed

    Kumar, Mohit; Brocorens, Patrick; Tonnelé, Claire; Beljonne, David; Surin, Mathieu; George, Subi J

    2014-01-01

    Design of artificial systems, which can respond to fluctuations in concentration of adenosine phosphates (APs), can be useful in understanding various biological processes. Helical assemblies of chromophores, which dynamically respond to such changes, can provide real-time chiroptical readout of various chemical transformations. Towards this concept, here we present a supramolecular helix of achiral chromophores, which shows chiral APs responsive tunable handedness along with dynamically switchable helicity. This system, composing of naphthalenediimides with phosphate recognition unit, shows opposite handedness on binding with ATP compared with ADP or AMP, which is comprehensively analysed with molecular dynamic simulations. Such differential signalling along with stimuli-dependent fast stereomutations have been capitalized to probe the reaction kinetics of enzymatic ATP hydrolysis. Detailed chiroptical analyses provide mechanistic insights into the enzymatic hydrolysis and various intermediate steps. Thus, a unique dynamic helical assembly to monitor the real-time reaction processes via its stimuli-responsive chiroptical signalling is conceptualized. PMID:25511998

  16. A dynamic and non-invasive technique for space cellular effects research based on the SPR principle

    NASA Astrophysics Data System (ADS)

    Wang, C. Y.; Li, Y. H.; Xiong, J. H.; Tan, Y. J.; Yu, J. R.; Nie, J. L.

    Space cell and molecular biology research has shown that space environment can affect the cellular morphology and function induce physiological and biochemical disorders The effect mechanism of space factors on the intracellular molecular events involved in signal transduction cytoskeleton reorganization and protein expression Surface plasmon resonance SPR is a promising tool for monitoring and studying the spatio-temporal and dynamic characteristic of the intricate biochemical reactions inside living cells For its advantages such as high sensitivity fast determination safety anti-jamming and long distance transmission it might be used in the space environment for studying the dynamic characteristic of intracellular molecular events In this paper a prototype of portable SPR based cytosensor SBCS was constructed for cell culture and SPR signal record and on the basis of it the corresponding technique was also established and utilized to study the possible involvement of actin cytoskeleton in the glutamate Glu uptake activity in C6 cells Firstly SBCS was used for monitoring the depolymerization of actin cytoskeleton in C6 cells at real-time After cytochalasin D CD was injected into the flow cell to disrupt actin cytoskeleton the SPR sensorgram declined gradually in a time- and dose-dependent manner Then the sensorgrams induced by Glu on C6 cells with or without CD preincubation were monitored The SPR signals induced by Glu were significant depressed by CD pretreatment which indicated that actin cytoskeleton played a crucial

  17. Deriving urban dynamic evolution rules from self-adaptive cellular automata with multi-temporal remote sensing images

    NASA Astrophysics Data System (ADS)

    He, Yingqing; Ai, Bin; Yao, Yao; Zhong, Fajun

    2015-06-01

    Cellular automata (CA) have proven to be very effective for simulating and predicting the spatio-temporal evolution of complex geographical phenomena. Traditional methods generally pose problems in determining the structure and parameters of CA for a large, complex region or a long-term simulation. This study presents a self-adaptive CA model integrated with an artificial immune system to discover dynamic transition rules automatically. The model's parameters are allowed to be self-modified with the application of multi-temporal remote sensing images: that is, the CA can adapt itself to the changed and complex environment. Therefore, urban dynamic evolution rules over time can be efficiently retrieved by using this integrated model. The proposed AIS-based CA model was then used to simulate the rural-urban land conversion of Guangzhou city, located in the core of China's Pearl River Delta. The initial urban land was directly classified from TM satellite image in the year 1990. Urban land in the years 1995, 2000, 2005, 2009 and 2012 was correspondingly used as the observed data to calibrate the model's parameters. With the quantitative index figure of merit (FoM) and pattern similarity, the comparison was further performed between the AIS-based model and a Logistic CA model. The results indicate that the AIS-based CA model can perform better and with higher precision in simulating urban evolution, and the simulated spatial pattern is closer to the actual development situation.

  18. Expression of plasmid DNA in the salivary gland epithelium: novel approaches to study dynamic cellular processes in live animals

    PubMed Central

    Sramkova, Monika; Masedunskas, Andrius; Parente, Laura; Molinolo, Alfredo

    2009-01-01

    The ability to dynamically image cellular and subcellular structures in a live animal and to target genes to a specific cell population in a living tissue provides a unique tool to address many biological questions in the proper physiological context. Here, we describe a powerful approach that is based on the use of rat submandibular salivary glands, which offer the possibility to easily perform intravital imaging and deliver molecules from the oral cavity, and plasmid DNA, which offers the advantage of rapid manipulations. We show that, under different experimental conditions, a reporter molecule can be rapidly expressed in specific compartments of the glands: 1) in the intercalated ducts, when plasmid DNA is administered alone, and 2) in granular ducts, striated ducts, and, to a lesser extent, acini, when plasmid DNA is mixed with replication-deficient adenovirus subtype 5 particles. Remarkably, we also found that gene expression can be directed to acinar cells when plasmid DNA is administered during isoproterenol-stimulated exocytosis, suggesting a novel mechanism of plasmid internalization regulated by compensatory endocytosis. Finally, as a practical application of these strategies, we show how the expression of fluorescently tagged molecules enables the study of the dynamics of various organelles in live animals at a resolution comparable to that achieved in cell cultures. PMID:19794147

  19. Algorithms for the automated analysis of cellular dynamics within living fungal colonies.

    PubMed

    Angarita-Jaimes, N C; Roca, M G M; Towers, C E; Read, N D; Towers, D P

    2009-09-01

    We present robust and efficient algorithms to automate the measurement of nuclear movement and germ tube extension rates in living fungal networks. The aim is to facilitate the understanding of the dynamics and regulation of nuclear migration in growing fungal colonies. The proposed methodology combines a cascade correlation filter to identify nuclear centers from which 2D nuclear velocities are determined and a level set algorithm for centerline extraction to monitor spore (conidial) germling growth. We show how the proposed cascaded filter improves spatial resolution in the presence of noise and is robust when fluorescently labeled nuclei with different intensities are in close proximity to each other. The performance of the filter is evaluated by simulation in comparison to the well known Rayleigh and Sparrow criteria, and experimental evidence is given from clusters of nuclei and nuclei undergoing mitotic division. The capabilities developed have enabled the robust and objective analysis of 10's of Gigabytes of image data that is being exploited by biological scientists. PMID:19504570

  20. Cellular Dynamics Drives the Emergence of Supracellular Structure in the Cyanobacterium, Phormidium sp. KS

    PubMed Central

    Sato, Naoki; Katsumata, Yutaro; Sato, Kaoru; Tajima, Naoyuki

    2014-01-01

    Motile filamentous cyanobacteria, such as Oscillatoria, Phormidium and Arthrospira, are ubiquitous in terrestrial and aquatic environments. As noted by Nägeli in 1860, many of them form complex three-dimensional or two-dimensional structures, such as biofilm, weed-like thalli, bundles of filaments and spirals, which we call supracellular structures. In all of these structures, individual filaments incessantly move back and forth. The structures are, therefore, macroscopic, dynamic structures that are continuously changing their microscopic arrangement of filaments. In the present study, we analyzed quantitatively the movement of individual filaments of Phormidium sp. KS grown on agar plates. Junctional pores, which have been proposed to drive cell movement by mucilage/slime secretion, were found to align on both sides of each septum. The velocity of movement was highest just after the reversal of direction and, then, attenuated exponentially to a final value before the next reversal of direction. This kinetics is compatible with the “slime gun” model. A higher agar concentration restricts the movement more severely and, thus, resulted in more spiral formation. The spiral is a robust form compatible with non-homogeneous movements of different parts of a long filament. We propose a model of spiral formation based on the microscopic movement of filaments. PMID:25460162

  1. Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas

    PubMed Central

    Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D; Kropat, Janette; Dodani, Sheel C; Chan, Jefferson; Barupala, Dulmini; Domaille, Dylan W; Shirasaki, Dyna I; Loo, Joseph A; Weber, Peter K; Pett-Ridge, Jennifer; Stemmler, Timothy L; Chang, Christopher J; Merchant, Sabeeha S

    2014-01-01

    We identified a Cu accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulated Cu, dependent on the nutritional Cu sensor CRR1, but was functionally Cu-deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. NanoSIMS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy (XAS) was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bio-available for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mis-metallation during Zn deficiency and enabling efficient cuproprotein (re)-metallation upon Zn resupply. PMID:25344811

  2. A Dynamic Programming Approach for Base Station Sleeping in Cellular Networks

    NASA Astrophysics Data System (ADS)

    Gong, Jie; Zhou, Sheng; Niu, Zhisheng

    The energy consumption of the information and communication technology (ICT) industry, which has become a serious problem, is mostly due to the network infrastructure rather than the mobile terminals. In this paper, we focus on reducing the energy consumption of base stations (BSs) by adjusting their working modes (active or sleep). Specifically, the objective is to minimize the energy consumption while satisfying quality of service (QoS, e.g., blocking probability) requirement and, at the same time, avoiding frequent mode switching to reduce signaling and delay overhead. The problem is modeled as a dynamic programming (DP) problem, which is NP-hard in general. Based on cooperation among neighboring BSs, a low-complexity algorithm is proposed to reduce the size of state space as well as that of action space. Simulations demonstrate that, with the proposed algorithm, the active BS pattern well meets the time variation and the non-uniform spatial distribution of system traffic. Moreover, the tradeoff between the energy saving from BS sleeping and the cost of switching is well balanced by the proposed scheme.

  3. Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems

    PubMed Central

    2013-01-01

    Background Model development is a key task in systems biology, which typically starts from an initial model candidate and, involving an iterative cycle of hypotheses-driven model modifications, leads to new experimentation and subsequent model identification steps. The final product of this cycle is a satisfactory refined model of the biological phenomena under study. During such iterative model development, researchers frequently propose a set of model candidates from which the best alternative must be selected. Here we consider this problem of model selection and formulate it as a simultaneous model selection and parameter identification problem. More precisely, we consider a general mixed-integer nonlinear programming (MINLP) formulation for model selection and identification, with emphasis on dynamic models consisting of sets of either ODEs (ordinary differential equations) or DAEs (differential algebraic equations). Results We solved the MINLP formulation for model selection and identification using an algorithm based on Scatter Search (SS). We illustrate the capabilities and efficiency of the proposed strategy with a case study considering the KdpD/KdpE system regulating potassium homeostasis in Escherichia coli. The proposed approach resulted in a final model that presents a better fit to the in silico generated experimental data. Conclusions The presented MINLP-based optimization approach for nested-model selection and identification is a powerful methodology for model development in systems biology. This strategy can be used to perform model selection and parameter estimation in one single step, thus greatly reducing the number of experiments and computations of traditional modeling approaches. PMID:23938131

  4. An automated programmable platform enabling multiplex dynamic stimuli delivery and cellular response monitoring for high-throughput suspension single-cell signaling studies.

    PubMed

    He, Luye; Kniss, Ariel; San-Miguel, Adriana; Rouse, Tel; Kemp, Melissa L; Lu, Hang

    2015-03-21

    Cell signaling events are orchestrated by dynamic external biochemical cues. By rapidly perturbing cells with dynamic inputs and examining the output from these systems, one could study the structure and dynamic properties of a cellular signaling network. Conventional experimental techniques limit the implementation of these systematic approaches due to the lack of sophistication in manipulating individual cells and the fluid microenvironment around them; existing microfluidic technologies thus far are mainly targeting adherent cells. In this paper we present an automated platform to interrogate suspension cells with dynamic stimuli while simultaneously monitoring cellular responses in a high-throughput manner at single-cell resolution. We demonstrate the use of this platform in an experiment to measure Jurkat T cells in response to distinct dynamic patterns of stimuli; we find cells exhibit highly heterogeneous responses under each stimulation condition. More interestingly, these cells act as low-pass filters, only entrained to the low frequency stimulus signals. We also demonstrate that this platform can be easily programmed to actively generate arbitrary dynamic signals. We envision our platform to be useful in other contexts to study cellular signaling dynamics, which may be difficult using conventional experimental methods. PMID:25609410

  5. Titanium dioxide nanoparticles alter cellular morphology via disturbing the microtubule dynamics

    NASA Astrophysics Data System (ADS)

    Mao, Zhilei; Xu, Bo; Ji, Xiaoli; Zhou, Kun; Zhang, Xuemei; Chen, Minjian; Han, Xiumei; Tang, Qiusha; Wang, Xinru; Xia, Yankai

    2015-04-01

    Titanium dioxide (TiO2) nanoparticles (NPs) have been widely used in our daily lives, for example, in the areas of sunscreens, cosmetics, toothpastes, food products, and nanomedical reagents. Recently, increasing concern has been raised about their neurotoxicity, but the mechanisms underlying such toxic effects are still unknown. In this work, we employed a human neuroblastoma cell line (SH-SY5Y) to study the effects of TiO2 NPs on neurological systems. Our results showed that TiO2 NPs did not affect cell viability but induced noticeable morphological changes until 100 μg ml-1. Immunofluorescence detection showed disorder, disruption, retraction, and decreased intensity of the microtubules after TiO2 NPs treatment. Both α and β tubule expressions did not change in the TiO2 NP-treated group, but the percentage of soluble tubules was increased. A microtubule dynamic study in living cells indicated that TiO2 NPs caused a lower growth rate and a higher shortening rate of microtubules as well as shortened lifetimes of de novo microtubules. TiO2 NPs did not cause changes in the expression and phosphorylation state of tau proteins, but a tau-TiO2 NP interaction was observed. TiO2 NPs could interact with tubule heterodimers, microtubules and tau proteins, which led to the instability of microtubules, thus contributing to the neurotoxicity of TiO2 NPs.Titanium dioxide (TiO2) nanoparticles (NPs) have been widely used in our daily lives, for example, in the areas of sunscreens, cosmetics, toothpastes, food products, and nanomedical reagents. Recently, increasing concern has been raised about their neurotoxicity, but the mechanisms underlying such toxic effects are still unknown. In this work, we employed a human neuroblastoma cell line (SH-SY5Y) to study the effects of TiO2 NPs on neurological systems. Our results showed that TiO2 NPs did not affect cell viability but induced noticeable morphological changes until 100 μg ml-1. Immunofluorescence detection showed disorder

  6. Exciton dynamics in pentacene and tetracene studied using optical pump-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Thorsmølle, V. K.; Averitt, R. D.; Demsar, J.; Chi, X.; Smith, D. L.; Ramirez, A. P.; Taylor, A. J.

    We present room temperature photoinduced reflection and transmission measurements in pentacene and tetracene single crystals using optical pump-probe spectroscopy. Singlet exciton recombination, singlet-triplet fission, excited singlet, and triplet state absorption is observed.

  7. Exciton dynamics in pentacene and tetracene studied using optical pump-probe spectroscopy

    SciTech Connect

    Thorsmølle, V. K.; Averitt, R. D.; Demsar, J.; Chi, X.; Smith, D. L.; Ramirez, A. P.; Taylor, Antoinette J.,

    2004-01-01

    We present room temperature photoinduced reflection and transmission measurements in pentacene and tetracene single crystals using optical pump-probe spectroscopy. Singlet exciton recombination, singlet-triplet fission, excited singlet, and triplet state absorption is observed.

  8. Probing in Space and Time the Nuclear Motion Driven by Nonequilibrium Electronic Dynamics in Ultrafast Pumped N2.

    PubMed

    Ajay, J; Šmydke, J; Remacle, F; Levine, R D

    2016-05-19

    An ultrafast electronic excitation of N2 in the vacuum ultraviolet creates a nonstationary coherent linear superposition of interacting valence and Rydberg states resulting in a net oscillating dipole moment. There is therefore a linear response to an electrical field that can be queried by varying the time delay between the pump and a second optical probe pulse. Both the pump and probe pulses are included in our computation as part of the Hamiltonian, and the time-dependent wave function for both electronic and nuclear dynamics is computed using a grid representation for the internuclear coordinate. Even on an ultrafast time scale there are several processes that can be discerned beyond the expected coherence oscillations. In particular, the coupling between the excited valence and Rydberg states of the same symmetry is very evident and can be directly probed by varying the delay between pulse and probe. For quite a number of vibrations the nuclear motion does not dephase the electronic disequilibrium. However, the nuclear motion does modulate the dipolar response by taking the wave packet in and out of the Franck-Condon region and by its strong influence on the coupling of the Rydberg and valence states. A distinct isotope effect arises from the dependence of the interstate coupling on the nuclear mass. PMID:26937745

  9. Labeling Cytosolic Targets in Live Cells with Blinking Probes

    PubMed Central

    Xu, Jianmin; Chang, Jason; Yan, Qi; Dertinger, Thomas; Bruchez, Marcel; Weiss, Shimon

    2013-01-01

    With the advent of superresolution imaging methods, fast dynamic imaging of biological processes in live cells remains a challenge. A subset of these methods requires the cellular targets to be labeled with spontaneously blinking probes. The delivery and specific targeting of cytosolic targets and the control of the probes’ blinking properties are reviewed for three types of blinking probes: quantum dots, synthetic dyes, and fluorescent proteins. PMID:23930154

  10. On the synthesis of a bio-inspired dual-cellular fluidic flexible matrix composite adaptive structure based on a non-dimensional dynamics model

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2013-01-01

    A recent study investigated the dynamic characteristics of an adaptive structure concept featuring dual fluidic flexible matrix composite (F2MC) cells inspired by the configuration of plant cells and cell walls. This novel bio-inspired system consists of two F2MC cells with different fiber angles connected through internal fluid circuits. It was discovered that the dual F2MC cellular structure can be characterized as a two degree of freedom damped mass-spring oscillator, and can be utilized as a vibration absorber or an enhanced actuator under different operation conditions. These results demonstrated that the concept is promising and further investigations are needed to develop methodologies for synthesizing future multi-cellular F2MC structural systems. While interesting, the previous study focused on specific case studies and analysis. That is, the outcome did not provide insight that could be generalized, or tools for synthesizing a multiple F2MC cellular structure. This paper attempts to address this important issue by developing a non-dimensional dynamic model, which reveals good physical insights as well as identifying crucial constitutive parameters for F2MC cellular design. Working with these parameters, rather than physical variables, can greatly simplify the mathematics involved in the study. A synthesis tool is then developed for the dual-cellular structure, and it is found that for each set of achievable target poles and zero, there exist multiple F2MC cellular designs, forming a design space. The presented physical insights and synthesis tool for the dual-cellular structure will be the building blocks for future investigation on cellular structures with a larger number of cells.

  11. Spin probe dynamics in relation to free volume in crystalline organics by means of ESR and PALS: n-Hexadecane

    NASA Astrophysics Data System (ADS)

    Bartoš, J.; Švajdlenková, H.; Zaleski, R.; Edelmann, M.; Lukešová, M.

    2013-12-01

    We report on a combined study of the guest dynamics and free volume in n-hexadecane (n-HXD) using two external microscopic probes: stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and ortho-positronium (o-Ps) by means of ESR or PALS, respectively. Dynamic behavior of the molecular TEMPO probe and annihilation properties of the atomistic o-Ps one as a function of temperature are compared. Two coincidencies between the crossover effects at the characteristic ESR and PALS temperatures T50 G and Tb1cr below and TX2fast and TmPALS at the melting point TmDSC of n-HXD from macroscopic DSC scan were found. First, the slow to fast regime transition is ascribed to the spin probe TEMPO localization in the expanding interlamellar gap due to the induced enhanced end-chain mobility. Second, the high-temperature crossover within the fast regime is directly connected to the collective chain movements at the melting which takes place under the similar free volume fluctuation condition as revealed recently for a series of amorphous small molecular and polymer glass-formers.

  12. TIRFM and pH-sensitive GFP-probes to evaluate neurotransmitter vesicle dynamics in SH-SY5Y neuroblastoma cells: cell imaging and data analysis.

    PubMed

    Daniele, Federica; Di Cairano, Eliana S; Moretti, Stefania; Piccoli, Giovanni; Perego, Carla

    2015-01-01

    Synaptic vesicles release neurotransmitters at chemical synapses through a dynamic cycle of fusion and retrieval. Monitoring synaptic activity in real time and dissecting the different steps of exo-endocytosis at the single-vesicle level are crucial for understanding synaptic functions in health and disease. Genetically-encoded pH-sensitive probes directly targeted to synaptic vesicles and Total Internal Reflection Fluorescence Microscopy (TIRFM) provide the spatio-temporal resolution necessary to follow vesicle dynamics. The evanescent field generated by total internal reflection can only excite fluorophores placed in a thin layer (<150 nm) above the glass cover on which cells adhere, exactly where the processes of exo-endocytosis take place. The resulting high-contrast images are ideally suited for vesicles tracking and quantitative analysis of fusion events. In this protocol, SH-SY5Y human neuroblastoma cells are proposed as a valuable model for studying neurotransmitter release at the single-vesicle level by TIRFM, because of their flat surface and the presence of dispersed vesicles. The methods for growing SH-SY5Y as adherent cells and for transfecting them with synapto-pHluorin are provided, as well as the technique to perform TIRFM and imaging. Finally, a strategy aiming to select, count, and analyze fusion events at whole-cell and single-vesicle levels is presented. To validate the imaging procedure and data analysis approach, the dynamics of pHluorin-tagged vesicles are analyzed under resting and stimulated (depolarizing potassium concentrations) conditions. Membrane depolarization increases the frequency of fusion events and causes a parallel raise of the net fluorescence signal recorded in whole cell. Single-vesicle analysis reveals modifications of fusion-event behavior (increased peak height and width). These data suggest that potassium depolarization not only induces a massive neurotransmitter release but also modifies the mechanism of vesicle

  13. Evolving a three-dimensional cellular automata dynamic system constituted of cells-charges for modelling real earthquake activity

    NASA Astrophysics Data System (ADS)

    Sirakoulis, G. Ch.

    2009-04-01

    Greece is referred as the most active seismically region of Europe and one of the top active lands in the world. However, the complexity of the available seismicity information calls for the development of ever more powerful and more reliable computational tools to tackle complex problems associated with proper interpretation of the obtained geophysical information. Cellular Automata (CAs) were showed to be a promising model for earthquake modelling, because certain aspects of the earthquake dynamics, function and evolution can be simulated using several mathematical tools introduced through the use of CAs. In this study, a three-dimensional (3-d) CA dynamic system constituted of cell-charges and taking into account the recorded focal depth, able to simulate real earthquake activity is presented. The whole simulation process of the earthquake activity is evolved with an LC analogue CA model in correspondence to well known earthquake models. The parameterisation of the CA model in terms of potential threshold and geophysical area characteristics is succeeded by applying a standard genetic algorithm (GA) which would extend the model ability to study various hypotheses concerning the seismicity of the region under consideration. As a result, the proposed model optimizes the simulation results, which are compared with the Gutenberg - Richter (GR) scaling relations derived by the use of real data, as well as it expands its validity in broader and different regions of increased hazard. Finally, the hardware implementation of the proposed model is also examined. The FPGA realisation of the proposed 3-d CA based earthquake simulation model will exhibit distinct features that facilitate its utilisation, meaning low-cost, high-speed, compactness and portability. The development and manufacture of the dedicated processor aims at its effective incorporation into an efficient seismographic system. As a result, the dedicated processor could realize the first stage of a

  14. Real-Time In Vivo Imaging of Butterfly Wing Development: Revealing the Cellular Dynamics of the Pupal Wing Tissue

    PubMed Central

    Iwata, Masaki; Ohno, Yoshikazu; Otaki, Joji M.

    2014-01-01

    Butterfly wings are covered with regularly arranged single-colored scales that are formed at the pupal stage. Understanding pupal wing development is therefore crucial to understand wing color pattern formation. Here, we successfully employed real-time in vivo imaging techniques to observe pupal hindwing development over time in the blue pansy butterfly, Junonia orithya. A transparent sheet of epithelial cells that were not yet regularly arranged was observed immediately after pupation. Bright-field imaging and autofluorescent imaging revealed free-moving hemocytes and tracheal branches of a crinoid-like structure underneath the epithelium. The wing tissue gradually became gray-white, epithelial cells were arranged regularly, and hemocytes disappeared, except in the bordering lacuna, after which scales grew. The dynamics of the epithelial cells and scale growth were also confirmed by fluorescent imaging. Fluorescent in vivo staining further revealed that these cells harbored many mitochondria at the surface of the epithelium. Organizing centers for the border symmetry system were apparent immediately after pupation, exhibiting a relatively dark optical character following treatment with fluorescent dyes, as well as in autofluorescent images. The wing tissue exhibited slow and low-frequency contraction pulses with a cycle of approximately 10 to 20 minutes, mainly occurring at 2 to 3 days postpupation. The pulses gradually became slower and weaker and eventually stopped. The wing tissue area became larger after contraction, which also coincided with an increase in the autofluorescence intensity that might have been caused by scale growth. Examination of the pattern of color development revealed that the black pigment was first deposited in patches in the central areas of an eyespot black ring and a parafocal element. These results of live in vivo imaging that covered wide wing area for a long time can serve as a foundation for studying the cellular dynamics of living

  15. Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells

    NASA Astrophysics Data System (ADS)

    Ohta, Yoshihiro; Kodama, Tatsuhiko; Ihara, Sigeo

    2011-10-01

    RNA polymerase II (RNAPII) is the responsible motor protein for transcription. Here we report the formulation and results of a cellular automaton model of the RNAPII dynamics of gene transcription that takes account the effect of the velocity change according to the gene position, such as occurs in introns and exons. We describe RNAPII dynamics in terms of the properties in the time domain, such as elapsed time, residence time, and time intervals. We found that the RNAPII molecules move as a free-flow state, though regions of reduced velocity do exist such as exons, as far as the time interval between nearest RNAPII molecules is larger than the time required for an RNAPII passing the exclusion length in the velocity reduction region. On the other hand, if the reduction is strong enough to reach a certain threshold, at the maximally reductive velocity region, a transition occurs from the RNAPII free-flow state to the states with congested and repetitive flows. We analytically obtained the conditions for these flow states and the transition threshold. From simulations of high-density RNAPII in the SAMD4A gene with the strong blockade, we confirmed the transition from free flow to the repetitive and congested flows, suggesting that the transition may serve as a regulatory mechanism of gene expression. By fitting the experimentally observed RNAPII density profile of the SAMD4A gene during the course of transcription of the normal and altered gene (in knock-down cells) with or without roadblock, we found that the RNAPII density flow is a free state. However, even in this free state, there is a long-range correlation between RNAPII molecules, ranging from 1 to 20 min, with the corresponding distance from 3 to 80 kbp, during transcription in normal cells. This long-range correlation probably relates to the higher-order DNA loop structure.

  16. AUTOFLUORESCENCE IN PRIMARY RAINBOW TROUT HEPATOCYTES INTERFERES WITH MEASUREMENT OF OXIDATIVE ACTIVITY VIA THE EXOGENOUS PROBE, DCF, BUT PROVIDES INTRINSIC MEASURE OF CELLULAR OXIDATIVE STATE

    EPA Science Inventory

    The compound 2', 7'-dichlorodihydrofluoroscein diacetate is a probe commonly used to detect oxidative activity in live cells. Studies were undertaken to measure reactive oxygen species generated in freshly isolated rainbow trout hepatocytes exposed to a variety of redox cycling c...

  17. In vivo quantifying molecular specificity of Cy5.5-labeled cyclic 9-mer peptide probe with dynamic fluorescence imaging.

    PubMed

    Dai, Yunpeng; Yin, Jipeng; Huang, Yu; Chen, Xueli; Wang, Guodong; Liu, Yajun; Zhang, Xianghan; Nie, Yongzhan; Wu, Kaichun; Liang, Jimin

    2016-04-01

    We quantified molecular specificity of Cy5.5-GX1 in vivo with dynamic fluorescence imaging to better understand its kinetic properties. According to whether or not free GX1 was injected and when it was injected, twelve of BGC-823 xenografted mice were randomly divided into three groups and underwent a 60 minute dynamic fluorescence scanning. Combined with a principal-component analysis, the binding potential (Bp) of the probe was determined by both Logan graphical analysis with reference tissue model (GARTM) and Lammertsma simplified reference tissue model (SRTM). The sum of the pharmacokinetic rate constants (SKRC) was quantified by the Gurfinkel exponential model (GEXPM). Cy5.5-GX1 specifically targeted tumor both in vitro and in vivo. We obtained similar quantification results of Bp (GARTM Bp = 0.582 ± 0.2655, SRTM Bp = 0.618 ± 0.2923), and obtained a good linear relation between the Bp value and the SKRC value. Our results indicate that the SKRC value is more suitable for an early-stage kinetic data analysis, and the Bp value depicts kinetic characteristics under the equilibrium state. Dynamic fluorescence imaging in conjunction with various kinetic models are optimal tools to quantify molecular specificity of the Cy5.5-GX1 probe in vivo. PMID:27446643

  18. In vivo quantifying molecular specificity of Cy5.5-labeled cyclic 9-mer peptide probe with dynamic fluorescence imaging

    PubMed Central

    Dai, Yunpeng; Yin, Jipeng; Huang, Yu; Chen, Xueli; Wang, Guodong; Liu, Yajun; Zhang, Xianghan; Nie, Yongzhan; Wu, Kaichun; Liang, Jimin

    2016-01-01

    We quantified molecular specificity of Cy5.5-GX1 in vivo with dynamic fluorescence imaging to better understand its kinetic properties. According to whether or not free GX1 was injected and when it was injected, twelve of BGC-823 xenografted mice were randomly divided into three groups and underwent a 60 minute dynamic fluorescence scanning. Combined with a principal-component analysis, the binding potential (Bp) of the probe was determined by both Logan graphical analysis with reference tissue model (GARTM) and Lammertsma simplified reference tissue model (SRTM). The sum of the pharmacokinetic rate constants (SKRC) was quantified by the Gurfinkel exponential model (GEXPM). Cy5.5-GX1 specifically targeted tumor both in vitro and in vivo. We obtained similar quantification results of Bp (GARTM Bp = 0.582 ± 0.2655, SRTM Bp = 0.618 ± 0.2923), and obtained a good linear relation between the Bp value and the SKRC value. Our results indicate that the SKRC value is more suitable for an early-stage kinetic data analysis, and the Bp value depicts kinetic characteristics under the equilibrium state. Dynamic fluorescence imaging in conjunction with various kinetic models are optimal tools to quantify molecular specificity of the Cy5.5-GX1 probe in vivo. PMID:27446643

  19. Production of HIV Particles Is Regulated by Altering Sub-Cellular Localization and Dynamics of Rev Induced by Double-Strand RNA Binding Protein

    PubMed Central

    Urcuqui-Inchima, Silvio; Patiño, Claudia; Zapata, Ximena; García, María Patricia; Arteaga, José; Chamot, Christophe; Kumar, Ajit; Hernandez-Verdun, Danièle

    2011-01-01

    Human immunodeficiency virus (HIV)-1 encoded Rev is essential for export from the nucleus to the cytoplasm, of unspliced and singly spliced transcripts coding for structural and nonstructural viral proteins. This process is spatially and temporally coordinated resulting from the interactions between cellular and viral proteins. Here we examined the effects of the sub-cellular localization and dynamics of Rev on the efficiency of nucleocytoplasmic transport of HIV-1 Gag transcripts and virus particle production. Using confocal microscopy and fluorescence recovery after bleaching (FRAP), we report that NF90ctv, a cellular protein involved in Rev function, alters both the sub-cellular localization and dynamics of Rev in vivo, which drastically affects the accumulation of the viral protein p24. The CRM1–dependent nuclear export of Gag mRNA linked to the Rev Response Element (RRE) is dependent on specific domains of the NF90ctv protein. Taken together, our results demonstrate that the appropriate intracellular localization and dynamics of Rev could regulate Gag assembly and HIV-1 replication. PMID:21364984

  20. Cellular dynamics of regeneration reveals role of two distinct Pax7 stem cell populations in larval zebrafish muscle repair

    PubMed Central

    Pipalia, Tapan G.; Koth, Jana; Roy, Shukolpa D.; Hammond, Christina L.; Kawakami, Koichi

    2016-01-01

    ABSTRACT Heterogeneity of stem cells or their niches is likely to influence tissue regeneration. Here we reveal stem/precursor cell diversity during wound repair in larval zebrafish somitic body muscle using time-lapse 3D confocal microscopy on reporter lines. Skeletal muscle with incision wounds rapidly regenerates both slow and fast muscle fibre types. A swift immune response is followed by an increase in cells at the wound site, many of which express the muscle stem cell marker Pax7. Pax7+ cells proliferate and then undergo terminal differentiation involving Myogenin accumulation and subsequent loss of Pax7 followed by elongation and fusion to repair fast muscle fibres. Analysis of pax7a and pax7b transgenic reporter fish reveals that cells expressing each of the duplicated pax7 genes are distinctly localised in uninjured larvae. Cells marked by pax7a only or by both pax7a and pax7b enter the wound rapidly and contribute to muscle wound repair, but each behaves differently. Low numbers of pax7a-only cells form nascent fibres. Time-lapse microscopy revealed that the more numerous pax7b-marked cells frequently fuse to pre-existing fibres, contributing more strongly than pax7a-only cells to repair of damaged fibres. pax7b-marked cells are more often present in rows of aligned cells that are observed to fuse into a single fibre, but more rarely contribute to nascent regenerated fibres. Ablation of a substantial portion of nitroreductase-expressing pax7b cells with metronidazole prior to wounding triggered rapid pax7a-only cell accumulation, but this neither inhibited nor augmented pax7a-only cell-derived myogenesis and thus altered the cellular repair dynamics during wound healing. Moreover, pax7a-only cells did not regenerate pax7b cells, suggesting a lineage distinction. We propose a modified founder cell and fusion-competent cell model in which pax7a-only cells initiate fibre formation and pax7b cells contribute to fibre growth. This newly discovered cellular

  1. Molecular Probe Dynamics Reveals Suppression of Ice-Like Regions in Strongly Confined Supercooled Water

    PubMed Central

    Banerjee, Debamalya; Bhat, Shrivalli N.; Bhat, Subray V.; Leporini, Dino

    2012-01-01

    The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice [Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448–11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed. PMID:23049747

  2. Ophthalmic diagnostics using a new dynamic light scattering fiber optic probe

    NASA Astrophysics Data System (ADS)

    Ansari, Rafat R.; Suh, Kwang I.; Dellavecchia, Michael A.; Dubin, Stephen

    1995-11-01

    A new fiber optic probe is developed to study different parts of the eye. The probe positioned in front of an eye, delivers a low power light from a laser diode into the eye and guides the light which is back scattered by different components (aqueous humor, lens, and vitreous humor) of the eye through a receiving optical fiber to a photo detector. The probe provides rapid determination of macromolecular diffusivities and their respective size distributions in the eye lens and the gel-like material in the vitreous humor. We report alpha-crystalline size distributions, as a function of penetration depth, inside the lens and hyaluronic acid molecular size distribution in the vitreous body. In a clinical setting, the probe can be mounted on a slit-lamp apparatus simply by using a H-ruby lens holder. The capability of detecting cataracts, both nuclear and peripheral, in their early stages of formation, in a non invasive and quantitative fashion, has the potential in patient monitoring and in developing and testing new drugs or diet therapies to 'dissolve' or slow down the cataract formation before surgery is necessary. The ability to detect biochemical and macromolecular changes in the vitreous structure can be very useful in identifying certain diseases of the posterior chamber, e.g., posterior vitreous detachment.

  3. Ophthalmic diagnostics using a new dynamic light scattering fiber optic probe

    NASA Astrophysics Data System (ADS)

    Ansari, Rafat R.; Suh, Kwang I.; DellaVecchia, Michael A.; Dubin, Stephen

    1996-01-01

    A new fiber optic probe is developed to study different parts of the eye. The probe positioned in front of an eye, delivers a low power light from a laser diode into the eye and guides the light which is back scattered by different components (aqueous humor, lens, and vitreous humor) of the eye through a receiving optical fiber to a photo detector. The probe provides rapid determination of macromolecular diffusivities and their respective size distributions in the eye lens and the gel-like material in the vitreous humor. We report alpha-crystalline size distributions, as a function of penetration depth, inside the lens and hyaluronic acid molecular size distribution in the vitreous body. In a clinical setting, the probe can be mounted on a slit- lamp apparatus simply by using a H-ruby lens holder. The capability of detecting cataracts, both nuclear and peripheral, in their early stages of formation, in a non invasive and quantitative fashion, has the potential in patient monitoring and in developing and testing new drugs or diet therapies to 'dissolve' or slow down the cataract formation before surgery is necessary. The ability to detect biochemical and macromolecular changes in the vitreous structure can be very useful in identifying certain diseases of the posterior chamber, e.g., posterior vitreous detachment.

  4. Investigations of laser plasmas dynamics by means of real and virtual Langmuir probes

    SciTech Connect

    Gambino, N.; Mascali, D.; Tudisco, S.; Anzalone, A.; Gammino, S.; Musumeci, F.; Spitaleri, A.

    2011-07-01

    In this paper we propose a novel technique for LPP-Laser Produced Plasmas investigation, combining high time resolved measurements using compact Langmuir Probes with the output of a theoretical model called HYBLAS developed on purpose, which is able to simulate the charged particles collected by a so-called virtual probe. It will be shown that with an appropriate experimental set-up and with the use of a Matlab software able to accurately analyze the experimental I-V curves, laser plasmas can be investigated properly even if the probe is placed very close to the target surface. This permits not only to study the plume expansion with a high temporal resolution, but also to estimate correctly the self-generated coulomb electric field inside the plume and to detect the inner structure of the the first upcoming expanding plasma. HYBLAS is able to predict and describe the plume expansion at relatively low power densities and is a powerful method to compare directly the experimental current signals with the numerical results if the initial conditions are settled properly. A direct comparison of the theoretical data with the experimental ones realized on different metal targets shows that our method is able to predict properly the overall plasma expansion in the nanosecond laser pulse duration regime. The virtual probe method was moreover tested by comparing the numerical results with another numerical code called MULTI, which simulate the expansion by combining the hydrodynamics equations to a multigroup method in order to include the radiation transport. (authors)

  5. Ophthalmic Diagnostics Using a New Dynamic Light Scattering Fiber Optic Probe

    NASA Technical Reports Server (NTRS)

    Ansari, Rafat R.; Suh, Kwang I.; Dellavecchia, Michael A.; Dubin, Stephen

    1995-01-01

    A new fiber optic probe is developed to study different parts of the eye. The probe positioned in front of an eye, delivers a low power light from a laser diode into the eye and guides the light which is back scattered by different components (aqueous humor, lens, and vitreous humor) of the eye through a receiving optical fiber to a photo detector. The probe provides rapid determination of macromolecular diffusivities and their respective size distributions in the eye lens and the gel-like material in the vitreous humor. We report alpha-crystalline size distributions, as a function of penetration depth, inside the lens and hyaluronic acid molecular size distribution in the vitreous body. In a clinical setting, the probe can be mounted on a slit-lamp apparatus simply by using a H-ruby lens holder. The capability of detecting cataracts, both nuclear and peripheral, in their early stages of formation, in a non invasive and quantitative fashion, has the potential in patient monitoring and in developing and testing new drugs or diet therapies to 'dissolve' or slow down the cataract formation before surgery is necessary. The ability to detect biochemical and macromolecular changes in the vitreous structure can be very useful in identifying certain diseases of the posterior chamber, e.g., posterior vitreous detachment.

  6. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  7. Location, dynamics and solvent relaxation of a Nile Red-based phase-sensitive fluorescent membrane probe.

    PubMed

    Saxena, Roopali; Shrivastava, Sandeep; Haldar, Sourav; Klymchenko, Andrey S; Chattopadhyay, Amitabha

    2014-10-01

    Fluorescent membrane probes offer the advantage of high sensitivity, suitable time resolution, and multiplicity of measurable parameters, and provide useful information on model and cell membranes. In this paper, we have explored the location, dynamics, and solvent relaxation characteristics of a novel Nile Red-based phase-sensitive probe (NR12S). Unlike Nile Red, NR12S enjoys unique orientation and location in the membrane, and is localized exclusively in the outer leaflet of the membrane bilayer. By analysis of membrane depth using the parallax approach, we show that the fluorescent group in NR12S is localized at the membrane interface, a region characterized by slow solvent relaxation. Our results show that NR12S exhibits REES (red edge excitation shift), consistent with its interfacial localization. More interestingly, REES of NR12S displays sensitivity to the membrane phase. In addition, fluorescence emission maximum, anisotropy, and lifetime of NR12S are dependent on the membrane phase. We envision that NR12S may prove to be a useful probe in future studies of complex natural membranes. PMID:24802972

  8. Time-Resolved UV-Pump (4.8eV) and Vacuum-UV (8eV) Probe Experiments of Neutral Excited State Dynamics

    NASA Astrophysics Data System (ADS)

    Horton, Spencer; Liu, Yusong; Matsika, Spiridoula; Weinacht, Thomas

    2016-05-01

    Excited state dynamics in polyatomic molecules involve a rich mixture of internal conversion, intersystem crossing, isomerization, and dissociation. Probing these dynamics with ultrafast laser pulses poses a number of challenges, in terms of both the execution of the measurements and their interpretation. We have developed an apparatus for probing excited state dynamics using a 260nm UV-pump pulse and a 156nm Vacuum-UV (VUV) probe pulse. For many systems of interest, an 8eV probe pulse can ionize the molecule from essentially any position along the excited state potential, while not having a background ionization yield from the ground state. Furthermore, given the perturbative interaction of each pulse with the molecule, it is possible interpret and model the experimental results with greater ease and confidence than more complicated probe interactions such as strong field ionization. We compare UV-IR strong-field ionization pump-probe experiments previously conducted directly with our 8eV probing and explore the differences between the two.

  9. Using NV centers to probe magnetization dynamics in normal metal/magnetic insulator hybrid system at the nanoscale

    NASA Astrophysics Data System (ADS)

    Zhang, Huiliang; Ku, Mark J. H.; Han, Minyong; Casola, Francesco; van der Sar, Toeno; Yacoby, Amir; Walsworth, Ronald L.

    2016-05-01

    Understanding magnetization dynamics induced by electric current is of great interest for both fundamental and practical reasons. Great endeavor has been dedicated to spin-orbit torques (SOT) in metallic structures, while quantitative study of analogous phenomena in magnetic insulators remains challenging where transport measurements are not feasible. Recently we have developed techniques using nitrogen vacancy (NV) centers in diamond to probe few-nanometre-scale correlated-electron magnetic excitations (i.e., spin waves). Here we demonstrate how this powerful tool can be implemented to study magnetization dynamics inside ferromagnetic insulator, Yttrium iron garnet (YIG) with spin injection from electrical current through normal metal (Platinum in our case). Particularly our work will focus on NV magnetic detection, imaging, and spectroscopy of coherent auto-oscillations in Pt/YIG microdisc. Magnetic fluctuations and local temperature measurements, both with nearby NV centers, will also be interesting topics relevant to SOT physics in Pt/YIG hybrid system.

  10. Community Structure and Dynamics of Small Eukaryotes Targeted by New Oligonucleotide Probes: New Insight into the Lacustrine Microbial Food Web▿

    PubMed Central

    Mangot, Jean-François; Lepère, Cécile; Bouvier, Christophe; Debroas, Didier; Domaizon, Isabelle

    2009-01-01

    The seasonal dynamics of the small eukaryotic fraction (cell diameter, 0.2 to 5 μm) was investigated in a mesotrophic lake by tyramide signal amplification-fluorescence in situ hybridization targeting seven different phylogenetic groups: Chlorophyceae, Chrysophyceae, Cryptophyceae, Cercozoa, LKM11, Perkinsozoa (two clades), and Fungi. The abundance of small eukaryotes ranged from 1,692 to 10,782 cells ml−1. The dominant groups were the Chrysophyceae and the Chlorophyceae, which represented 19.6% and 17.9% of small eukaryotes, respectively. The results also confirmed the quantitative importance of putative parasites, Fungi and Perkinsozoa, in the small heterotrophic eukaryotic assemblage. The relative abundances recorded for the Perkinsozoa group reached as much as 31.6% of total targeted eukaryotes during the summer. The dynamics of Perkinsozoa clade 1 coincided with abundance variations in Peridinium and Ceratium spp. (Dinoflagellates), while the dynamics of Perkinsozoa clade 2 was linked to the presence of Dinobryon spp. (Chrysophyceae). Fungi, represented by chytrids, reached maximal abundance in December (569 cells ml−1) and were mainly correlated with the dynamics of diatoms, especially Melosira varians. A further new finding of this study is the recurrent presence of Cercozoa (6.2%) and LKM11 (4.5%) cells. This quantitative approach based on newly designed probes offers a promising means of in-depth analysis of microbial food webs in lakes, especially by revealing the phylogenetic composition of the small heterotrophic flagellate assemblage, for which an important fraction of cells are generally unidentified by classical microscopy (on average, 96.8% of the small heterotrophic flagellates were identified by the specific probes we used in this study). PMID:19666727

  11. Time-Resolved X-Ray Magnetic Circular Dichroism - A Selective Probe of Magnetization Dynamics on Nanosecond Timescales

    NASA Astrophysics Data System (ADS)

    Pizzini, Stefania; Vogel, Jan; Bonfim, Marlio; Fontaine, Alain

    Many synchrotron radiation techniques have been developed in the last 15 years for studying the magnetic properties of thin-film materials. The most attractive properties of synchrotron radiation are its energy tunability and its time structure. The first property allows measurements in resonant conditions at an absorption edge of each of the magnetic elements constituting the probed sample, and the latter allows time-resolved measurements on subnanosecond timescales. In this review, we introduce some of the synchrotron-based techniques used for magnetic investigations. We then describe in detail X-ray magnetic circular dichroism (XMCD) and how time-resolved XMCD studies can be carried out in the pump-probe mode. Finally, we illustrate some applications to magnetization reversal dynamics in spin valves and tunnel junctions, using fast magnetic field pulses applied along the easy magnetization axis of the samples. Thanks to the element-selectivity of X-ray absorption spectroscopy, the magnetization dynamics of the soft (Permalloy) and the hard (cobalt) layers can be studied independently. In the case of spin valves, this allowed us to show that two magnetic layers that are strongly coupled in a static regime can become uncoupled on nanosecond timescales.Present address: Universidade Federal do Paraná, Centro Politécnico CP 19011, Curitiba - PR CEP 81531-990, Brazil

  12. Dynamical instability of a spin spiral in an interacting Fermi gas as a probe of the Stoner transition

    SciTech Connect

    Conduit, G. J.; Altman, E.

    2010-10-15

    We propose an experiment to probe ferromagnetic phenomena in an ultracold Fermi gas, while alleviating the sensitivity to three-body loss and competing many-body instabilities. The system is initialized in a small pitch spin spiral, which becomes unstable in the presence of repulsive interactions. To linear order the exponentially growing collective modes exhibit critical slowing down close to the Stoner transition point. Also, to this order, the dynamics are identical on the paramagnetic and ferromagnetic sides of the transition. However, we show that scattering off the exponentially growing modes qualitatively alters the collective mode structure. The critical slowing down is eliminated and in its place a new unstable branch develops at large wave vectors. Furthermore, long-wavelength instabilities are quenched on the paramagnetic side of the transition. We study the experimental observation of the instabilities, specifically addressing the trapping geometry and how phase-contrast imaging will reveal the emerging domain structure. These probes of the dynamical phenomena could allow experiments to detect the transition point and distinguish between the paramagnetic and ferromagnetic regimes.

  13. Probing reaction dynamics of transition-metal complexes in solution via time-resolved soft x-ray spectroscopy

    SciTech Connect

    Huse, N.; Kim, T.-K.; Khalil, M.; Jamula, L.; McCusker, J.K.; Schoenlein, R.W.

    2008-08-01

    We report the first time-resolved soft x-ray measurements of solvated transition-metal complexes. L-edge spectroscopy directly probes dynamic changes in ligand-field splitting of 3d orbitals associated with the spin transition, and mediated by changes in ligand-bonding. We report the first time-resolved soft x-ray spectroscopy of solution-phase molecular dynamics. Changes in ligand-field splitting and spin-state populations in 3d orbitals of the Fe{sup II} complex are directly probed via transient absorption changes of the Fe L{sub 2} and L{sub 3} edges following photo-induced metal-to-ligand charge transfer. With the emergence of high-flux ultrafast soft x-ray sources, details on interplay between atomic structure, electronic states, and spin contributions will be revealed. Our experimental approach opens the door to femtosecond soft x-ray investigations of liquid phase chemistry that have previously been inaccessible.

  14. Gas clouds as dynamical probes of the accretion flow around SgrA*

    NASA Astrophysics Data System (ADS)

    Madigan, Ann-Marie

    2016-05-01

    Sgr A* is our closest example of an accreting supermassive black hole. Important aspects of how the gas makes its way to the black hole, and why its so radiatively inefficient, remain unknown however. In this talk, I will discuss how we can use the change in orbital parameters of the G1 and G2 gas clouds as they move through the accretion flow to probe the gas at a critical range of radii.

  15. Exciton and Trion Valley dynamics in WSe2 measured by two-color pump-probe

    NASA Astrophysics Data System (ADS)

    Singh, Akshay; Tran, Kha; Seifert, Joe; Wang, Yiping; Scott, Marie; Pleskot, Dennis; Gabor, Nathaniel; Yan, Jiaqiang; Mandrus, David; Xu, Xiaodong; Li, Xiaoqin

    Monolayer transition metal dichalcogenides are semiconducting materials demonstrating spin-valley coupling as well as quasiparticles with large binding energies. These quasiparticles, excitons and trions (charged excitons), have quite different spin polarization properties, with the trion having larger spin lifetimes than excitons. Photoluminescence and time resolved Kerr rotation techniques have been used earlier to measure spin lifetimes. However, most of these early optical measurements have relied on non-resonant excitation conditions which tend to mask the intrinsic valley (spin) scattering properties. Here, we use circularly polarized two-color pump probe spectroscopy to measure valley (spin) polarization in monolayer WSe2 at low temperatures. We utilize quasi-resonant excitation with pump 1 meV (0.5 nm) spectrally separated from the probe, thus resulting in very efficient valley initialization. We present polarization resolved measurements on resonantly excited excitons and trions, which suggest that trions have larger spin lifetimes. Further, we probe spin polarization of trions when pumping at exciton energies, and vice-versa. We discuss the relative importance of different scattering mechanism at play. We acknowledge support from ARO and AFOSR.

  16. Direct Observation of Coupling between Structural Fluctuation and Ultrafast Hydration Dynamics of Fluorescent Probes in Anionic Micelles.

    PubMed

    Choudhury, Susobhan; Mondal, Prasanna Kumar; Sharma, V K; Mitra, S; Sakai, V Garcia; Mukhopadhyay, R; Pal, Samir Kumar

    2015-08-27

    The coupling of structural fluctuation and the dynamics of associated water molecules of biological macromolecules is vital for various biological activities. Although a number of molecular dynamics (MD) studies on proteins/DNA predicted the importance of such coupling, experimental evidence of variation of hydration dynamics with controlled structural fluctuation even in model macromolecule is sparse and raised controversies in the contemporary literature. Here, we have investigated dynamics of hydration at the surfaces of two similar anionic micelles sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) as model macromolecules using coumarin 500 (C500) as spectroscopic probe with femtosecond to picosecond time resolution up to 20 ns time window. The constituting surfactants SDS and SDBS are structurally similar except one benzene moiety in the SDBS may offer additional rigidity to the SDBS micelles through π-stacking and added bulkiness. The structural integrity of the micelles in the aqueous medium is confirmed in dynamic light scattering (DLS) studies. A variety of studies including polarization gated fluorescence spectroscopy and quasielastic neutron scattering (QENS) have been used to confirm differential structural fluctuation of SDS and SDBS micelles. We have also employed femtosecond-resolved Förster resonance energy transfer (FRET) in order to study binding of a cationic organic ligand ethidium bromide (EtBr) salt at the micellar surfaces. The distance distribution of the donor (C500)-acceptor (EtBr) in the micellar media reveals the manifestation of the structural flexibility of the micelles. Our studies on dynamical coupling of the structural flexibility with surface hydration in the nanoscopic micellar media may find the relevance in the "master-slave" type water dynamics in biologically relevant macromolecules. PMID:25874585

  17. Fluorescent pH probes, fluorescent proteins, and intrinsic cellular fluorochromes are tools to study cytosolic pH (pHcyt) in mammalian cells.

    NASA Astrophysics Data System (ADS)

    Martinez, Gloria M.; Gollahon, Lauren S.; Shafer, Keri; Oomman, Sowmini K.; Busch, Christian; Martinez-Zaguilan, Raul

    2001-07-01

    Our understanding of intracellular pH homeostatis in eukaryotic systems has been enhanced since the introduction of carboxyfluorescein diacetate as a useful pH probe more than 20 years ago. BCECF, a derivative of this earlier fluoroprobe has dominated the field. In the past 10 years, SNARF-1 has emerged as an alternative pH probe. Recently, a novel derivative of BCECF, BCPCF has been developed. Green Fluorescent Proteins (GFPs) have also been used recently to monitor pH in a non invasive manner in several cell types. Here, we report that human mammary epithelial cells can be transfected with the gene encoding for cyan (CFP), green (GFP), and yellow (YFP), to study cytosolic pH. The novel red fluorescent protein (DsRed) is not sensitive to pH. Multidrug resistance (MDR) has been associated with altered cytosolic pH homeostasis. We show that experimental maneuvers that decrease pHin enhance the efficacy of chemotherapeutic drugs. We also show that short pulses of UV-B light elicited acidosis in cells, as evaluated by ratio ion cell imaging, and confocal/spectral imaging microscopy. During the course of these experiments we noticed that cells exhibit intrinsic fluorochromes that can be used to monitor pH in living cells.

  18. Impact of Hydrophilic Surfaces on Interfacial Water Dynamics Probed with NMR Spectroscopy

    PubMed Central

    Yoo, Hyok; Paranji, Rajan

    2011-01-01

    In suspensions of Nafion beads and of cationic gel beads, NMR spectroscopy showed two water–proton resonances, one representing intimate water layers next to the polymer surface, the other corresponding to water lying beyond. Both resonances show notably shorter spin–lattice relaxation times (T1) and smaller self-diffusion coefficients (D) indicating slower dynamics than bulk water. These findings confirm the existence of highly restricted water layers adsorbed onto hydrophilic surfaces and dynamically stable water beyond the first hydration layers. Thus, aqueous regions on the order of micrometers are dynamically different from bulk water. PMID:22003430

  19. Exciton dynamics in pentacene thin films studied by pump-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Jundt, C.; Klein, G.; Sipp, B.; Le Moigne, J.; Joucla, M.; Villaeys, A. A.

    1995-07-01

    Pentacene microcrystalline thin films have been investigated by pump-probe spectroscopy in the femtosecond regime. The competition between induced absorption in the singlet S 1 → S n and triplet T1 → T n excited electronic configurations and bleaching of the S 0 → S 1 transition has been observed. A theoretical description is proposed to explain the experimental results. The importance of the different contributions associated with the various competing processes are stressed. A very fast triplet exciton creation with rate constant 1.3 × 10 13 s -1 is attributed to a fission process from one S 1 exciton to a pair of lowest triplet T 1 excitons.

  20. E917 experiment: Probing the dynamics of HI collisions + searching for the QGP

    SciTech Connect

    Ogilvie, C.A.; E917 Collaboration

    1996-12-31

    Experiment E917 has two main goals: to understand and probe the detailed mechanism of hadronic rescattering in HI collisions and to systematically search for a small volume of QGP. Correlated, discrete changes in sensitive QGP signatures as a function of both centrality and beam energy could indicate the presence of new physics. A precursor to the QGP is the possible change of hadronic properties in a dense medium. We will measure the {phi} and K{sup *} effective mass as a function of centrality to search for any change in the width or mass of these particles.