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Sample records for probing cellular dynamics

  1. Stiffening hydrogels to probe short- and long-term cellular responses to dynamic mechanics

    NASA Astrophysics Data System (ADS)

    Guvendiren, Murat; Burdick, Jason A.

    2012-04-01

    Biological processes are dynamic in nature, and growing evidence suggests that matrix stiffening is particularly decisive during development, wound healing and disease; yet, nearly all in vitro models are static. Here we introduce a step-wise approach, addition then light-mediated crosslinking, to fabricate hydrogels that stiffen (for example, ~3-30 kPa) in the presence of cells, and investigated the short-term (minutes-to-hours) and long-term (days-to-weeks) cell response to dynamic stiffening. When substrates are stiffened, adhered human mesenchymal stem cells increase their area from ~500 to 3,000 μm2 and exhibit greater traction from ~1 to 10 kPa over a timescale of hours. For longer cultures up to 14 days, human mesenchymal stem cells selectively differentiate based on the period of culture, before or after stiffening, such that adipogenic differentiation is favoured for later stiffening, whereas osteogenic differentiation is favoured for earlier stiffening.

  2. Probing the Dynamic Interaction between Damaged DNA and a Cellular Responsive Protein Using a Piezoelectric Mass Biosensor.

    PubMed

    Jin, Yulong; Xie, Yunfeng; Wu, Kui; Huang, Yanyan; Wang, Fuyi; Zhao, Rui

    2017-03-15

    The binding events between damaged DNA and recognition biomolecules are of great interest for understanding the activity of DNA-damaging drugs and the related DNA repair networks. Herein, a simple and sensitive sensor system was tailored for real-time probing of the dynamic molecular recognition between cisplatin-damaged-DNA (cisPt-DNA) and a cellular responsive protein, high-mobility-group box 1 (HMGB1). By integration of flow injection analysis (FIA) with quartz crystal microbalance (QCM), the interaction time-course of cisPt-DNA and HMGB1 domain A (HMGB1a) was investigated. The highly specific sensing interface was carefully designed and fabricated using cisPt-DNA as recognition element. A hybrid self-assembled monolayer consisting of cysteamine and mercaptohexanol was introduced to resist nonspecific adsorption. The calculated kinetic parameters (kass and kdiss) and the dissociation constant (KD) demonstrated the rapid recognition and tight binding of HMGB1a toward cisPt-DNA. Molecular docking was employed to simulate the complex formed by cisPt-DNA and HMGB1a. The tight binding of such a DNA-damage responsive complex is appealing for the downstream molecular recognition event related to the resistance to DNA repair. This continuous-flow QCM biosensor is an ideal tool for studying specific interactions between drug-damaged-DNAs and their recognition proteins in a physiological-relevant environment, and will provide a potential sensor platform for rapid screening and evaluating metal anticancer drugs.

  3. 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…

  4. Phosphatidylserine dynamics in cellular membranes.

    PubMed

    Kay, Jason G; Koivusalo, Mirkka; Ma, Xiaoxiao; Wohland, Thorsten; Grinstein, Sergio

    2012-06-01

    Much has been learned about the role of exofacial phosphatidylserine (PS) in apoptosis and blood clotting using annexin V. However, because annexins are impermeant and unable to bind PS at low calcium concentration, they are unsuitable for intracellular use. Thus little is known about the topology and dynamics of PS in the endomembranes of normal cells. We used two new probes-green fluorescent protein (GFP)-LactC2, a genetically encoded fluorescent PS biosensor, and 1-palmitoyl-2-(dipyrrometheneboron difluoride)undecanoyl-sn-glycero-3-phospho-L-serine (TopFluor-PS), a synthetic fluorescent PS analogue-to examine PS distribution and dynamics inside live cells. The mobility of PS was assessed by a combination of advanced optical methods, including single-particle tracking and fluorescence correlation spectroscopy. Our results reveal the existence of a sizable fraction of PS with limited mobility, with cortical actin contributing to the confinement of PS in the plasma membrane. We were also able to measure the dynamics of PS in endomembrane organelles. By targeting GFP-LactC2 to the secretory pathway, we detected the presence of PS in the luminal leaflet of the endoplasmic reticulum. Our data provide new insights into properties of PS inside cells and suggest mechanisms to account for the subcellular distribution and function of this phospholipid.

  5. 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.

  6. Cellular dynamics and embryonic morphogenesis

    NASA Astrophysics Data System (ADS)

    Zallen, Jennifer

    2007-11-01

    The elongated body axis is a characteristic feature of many multicellular animals. Axis elongation occurs largely through cell rearrangements that are coordinated across a large cell population and driven by an asymmetric distribution of cytoskeletal and junctional proteins [1]. To visualize cellular dynamics during this process, we performed time-lapse confocal imaging of cell behavior in the Drosophila embryo. These studies revealed that rearranging cells display a steady increase in topological disorder that is accompanied by the formation of transient structures where 5-11 cells meet [2,3]. These multicellular rosettes form and resolve in a directional fashion to produce a local change in the aspect ratio of the cellular assembly, contributing to an overall change in tissue structure. We propose that higher-order rosette structures link local cell interactions to global tissue reorganization during morphogenesis. [1] J. Zallen and E. Wieschaus, Developmental Cell 6, 343 (2004). [2] J. Zallen and R. Zallen, J. Phys.: Condens. Matter 16, S5073 (2004). [3] J. Blankenship et al., Developmental Cell 11, 459 (2006).

  7. Instrumentation and probes for molecular and cellular imaging.

    PubMed

    Lecchi, M; Ottobrini, L; Martelli, C; Del Sole, A; Lucignani, G

    2007-06-01

    Molecular and cellular imaging is a branch of biomedical sciences that combines the use of imaging instrumentation and biotechnology to characterize molecular and cellular processes in living organisms in normal and pathologic conditions. The two merging areas of research behind molecular and cellular imaging are detection technology, i.e. scanners and imaging devices, and development of tracers, contrast agents and reporter probes that make imaging with scanners and devices possible. Several in vivo imaging instruments currently used in human studies, such as computer tomography, ultrasound, magnetic resonance, positron emission tomography and single photon emission computed tomography, have been rescaled for small animal studies, while other methods initially used for in vitro evaluation, such as bioluminescence and fluorescence, have been refined for in vivo imaging. Conventional imaging relies on the use of non specific contrast agents and classical probes; however, newly developed targeted contrast agents and activable ''smart'' imaging probes for so-called ''targeted imaging'' have demonstrated high specificity and high signal to noise ratio in small animal studies. This review focuses on basic recent findings in the technical aspects of molecular and cellular imaging modalities (equipment, targeted probe and contrast agents and applied combinations of instrumentation and probe) with particular attention to the choice of the future: the multimodal imaging approach.

  8. Micro-thermocouple probe for measurement of cellular thermal responses.

    PubMed

    Watanabe, M; Kakuta, N; Mabuchi, K; Yamada, Y

    2005-01-01

    We have produced micro-thermocouple probes for the measurement of cellular thermal responses. Cells generate heat with their metabolisms and more heat with reactions to a certain physical or chemical stimulation. Therefore, the analysis of the cellular thermal responses would provide new physiological information. However, a real-time thermal measurement technique on a target of a single cell has not been established. In this study, glass micropipettes, which are widely used in bioengineering and medicine, are used for the base of the thermocouple probes. Using microfabrication techniques, the junction of two different metal films is formed at the micropipette tip with a diameter of 1 μm. This probe can inject a chemical substance into a cell and to detect its subsequent temperature changes simultaneously.

  9. 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).

  10. Doped semiconductor nanocrystal based fluorescent cellular imaging probes.

    PubMed

    Maity, Amit Ranjan; Palmal, Sharbari; Basiruddin, S K; Karan, Niladri Sekhar; Sarkar, Suresh; Pradhan, Narayan; Jana, Nikhil R

    2013-06-21

    Doped semiconductor nanocrystals such as Mn doped ZnS, Mn doped ZnSe and Cu doped InZnS, are considered as new classes of fluorescent biological probes with low toxicity. Although the synthesis in high quality of such nanomaterials is now well established, transforming them into functional fluorescent probes remains a challenge. Here we report a fluorescent cellular imaging probe made of high quality doped semiconductor nanocrystals. We have identified two different coating approaches suitable for transforming the as synthesized hydrophobic doped semiconductor nanocrystals into water-soluble functional nanoparticles. Following these approaches we have synthesized TAT-peptide- and folate-functionalized nanoparticles of 10-80 nm hydrodynamic diameter and used them as a fluorescent cell label. The results shows that doped semiconductor nanocrystals can be an attractive alternative for conventional cadmium based quantum dots with low toxicity.

  11. Doped semiconductor nanocrystal based fluorescent cellular imaging probes

    NASA Astrophysics Data System (ADS)

    Maity, Amit Ranjan; Palmal, Sharbari; Basiruddin, Sk; Karan, Niladri Sekhar; Sarkar, Suresh; Pradhan, Narayan; Jana, Nikhil R.

    2013-05-01

    Doped semiconductor nanocrystals such as Mn doped ZnS, Mn doped ZnSe and Cu doped InZnS, are considered as new classes of fluorescent biological probes with low toxicity. Although the synthesis in high quality of such nanomaterials is now well established, transforming them into functional fluorescent probes remains a challenge. Here we report a fluorescent cellular imaging probe made of high quality doped semiconductor nanocrystals. We have identified two different coating approaches suitable for transforming the as synthesized hydrophobic doped semiconductor nanocrystals into water-soluble functional nanoparticles. Following these approaches we have synthesized TAT-peptide- and folate-functionalized nanoparticles of 10-80 nm hydrodynamic diameter and used them as a fluorescent cell label. The results shows that doped semiconductor nanocrystals can be an attractive alternative for conventional cadmium based quantum dots with low toxicity.Doped semiconductor nanocrystals such as Mn doped ZnS, Mn doped ZnSe and Cu doped InZnS, are considered as new classes of fluorescent biological probes with low toxicity. Although the synthesis in high quality of such nanomaterials is now well established, transforming them into functional fluorescent probes remains a challenge. Here we report a fluorescent cellular imaging probe made of high quality doped semiconductor nanocrystals. We have identified two different coating approaches suitable for transforming the as synthesized hydrophobic doped semiconductor nanocrystals into water-soluble functional nanoparticles. Following these approaches we have synthesized TAT-peptide- and folate-functionalized nanoparticles of 10-80 nm hydrodynamic diameter and used them as a fluorescent cell label. The results shows that doped semiconductor nanocrystals can be an attractive alternative for conventional cadmium based quantum dots with low toxicity. Electronic supplementary information available: Characterization details of coating and

  12. Complexity, dynamic cellular network, and tumorigenesis.

    PubMed

    Waliszewski, P

    1997-01-01

    A holistic approach to tumorigenesis is proposed. The main element of the model is the existence of dynamic cellular network. This network comprises a molecular and an energetistic structure of a cell connected through the multidirectional flow of information. The interactions within dynamic cellular network are complex, stochastic, nonlinear, and also involve quantum effects. From this non-reductionist perspective, neither tumorigenesis can be limited to the genetic aspect, nor the initial event must be of molecular nature, nor mutations and epigenetic factors are mutually exclusive, nor a link between cause and effect can be established. Due to complexity, an unstable stationary state of dynamic cellular network rather than a group of unrelated genes determines the phenotype of normal and transformed cells. This implies relativity of tumor suppressor genes and oncogenes. A bifurcation point is defined as an unstable state of dynamic cellular network leading to the other phenotype-stationary state. In particular, the bifurcation point may be determined by a change of expression of a single gene. Then, the gene is called bifurcation point gene. The unstable stationary state facilitates the chaotic dynamics. This may result in a fractal dimension of both normal and tumor tissues. The co-existence of chaotic dynamics and complexity is the essence of cellular processes and shapes differentiation, morphogenesis, and tumorigenesis. In consequence, tumorigenesis is a complex, unpredictable process driven by the interplay between self-organisation and selection.

  13. Optimal temporal patterns for dynamical cellular signaling

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yoshihiko

    2016-11-01

    Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information. Here, we use optimal control theory to obtain the dynamical signal patterns for the optimal transmission of information, in terms of efficiency (low energy) and reliability (low uncertainty). Adopting an activation-deactivation decoding network, we reproduce several dynamical patterns found in actual signals, such as steep, gradual, and overshooting dynamics. Notably, when minimizing the energy of the input signal, the optimal signals exhibit overshooting, which is a biphasic pattern with transient and steady phases; this pattern is prevalent in actual dynamical patterns. We also identify conditions in which these three patterns (steep, gradual, and overshooting) confer advantages. Our study shows that cellular signal transduction is governed by the principle of minimizing free energy dissipation and uncertainty; these constraints serve as selective pressures when designing dynamical signaling patterns.

  14. Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations

    PubMed Central

    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

  15. 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

  16. Dynamical Response of Continuum Regime Langmuir Probe

    NASA Astrophysics Data System (ADS)

    Rappaport, H. L.

    2009-11-01

    Probe dynamic response is sometimes used as a way to increase the amount of information obtained from Langmuir probes [1]. In this poster, the effects of frequency dependent probe capacitance and coupling of probe fields to damped Langmuir waves and damped ion acoustic waves are considered. In the continuum regime, with small Debye length to spherical probe radius ratio, the probe DC current vs. voltage characteristic displays a hard saturation at sufficiently large probe potential [2]. In this regime, the sheath thickness varies little with the applied voltage although the plasma response can still be measured. A goal of the present investigation is to show that the probe dynamical response is richer as a result of modulation of sheath thickness or shielding particularly in the larger Debye length to probe radius ratio regime. Inertia inhibits ion response at sufficiently high frequency and deviation from the DC characteristic is shown.[4pt] [1] D. N. Walker, R.F. Fernsler, D.D. Blackwell, and W.E. Amatucci, Phys. Plasmas 15, 123506 (2008).[0pt] [2] E. Baum and R.L. Chapkis, AIAA J. 8, 1073 (1970).

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Conditional measurements as probes of quantum dynamics

    SciTech Connect

    Siddiqui, Shabnam; Erenso, Daniel; Vyas, Reeta; Singh, Surendra

    2003-06-01

    We discuss conditional measurements as probes of quantum dynamics and show that they provide different ways to characterize quantum fluctuations. We illustrate this by considering the light from a subthreshold degenerate parametric oscillator. Analytic results and curves are presented to illustrate the behavior.

  2. Chiral hexagonal cellular sandwich structures: dynamic response

    NASA Astrophysics Data System (ADS)

    Spadoni, A.; Ruzzene, M.; Scarpa, F.

    2005-05-01

    Periodic cellular configurations with negative Poisson's ratio have attracted the attention of several researchers because of their superior dynamic characteristics. Among the geometries featuring a negative Poisson's ratio, the chiral topology possesses a geometric complexity that guarantees unique deformed configurations when excited at one of its natural frequencies. Specifically, localized deformations have been observed even at relatively low excitation frequencies. This is of particular importance as resonance can be exploited to minimize the power required for the appearance of localized deformations, thus giving practicality to the concept. The particular nature of these deformed configurations and the authority provided by the chiral geometry, suggest the application of the proposed structural configuration for the design of innovative lifting bodies, such as helicopter rotor blades or airplane wings. The dynamic characteristics of chiral structures are here investigated through a numerical model and experimental investigations. The numerical formulation uses dynamic shape functions to accurately describe the behavior of the considered structural assembly over a wide frequency range. The model is used to predict frequency response functions, and to investigate the occurrence of localized deformations. Experimental tests are also performed to demonstrate the accuracy of the model and to illustrate the peculiarities of the behavior of the considered chiral structures.

  3. Fluorescent cyanine probe for DNA detection and cellular imaging

    NASA Astrophysics Data System (ADS)

    Zheng, Yong-Chao; Zheng, Mei-Ling; Zhao, Zhen-Sheng; Duan, Xuan-Ming

    2014-03-01

    In our study, two carbazole-based cyanines, 3,6-bis[2-(1-methylpyridinium)vinyl]-9-methyl carbazole diiodide (A) and 6,6'-bis[2-(1-methylpyridinium)vinyl]-bis(9-methyl-carbazol-3yl)methane diiodide (B) were synthesized and employed as light-up probes for DNA and cell imaging. Both of the cyanine probes possess a symmetric structure and bis-cationic center. The obvious induced circular dichroism signals in circular dichroism spectra reveal that the molecules can specifically interact with DNA. Strong fluorescence enhancement is observed when these two cyanines are bound to DNA. These cyanine probes show high binding affinity to oligonucleotides but different binding preferences to various secondary structures. Confocal microscopy images of fixed cell stained by the probes exhibit strong brightness and high contrast in nucleus with a very low cytoplasmic background.

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

    PubMed Central

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

    2015-01-01

    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

  5. 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.

  6. Mechanical properties of interphase nuclei probed by cellular strain application.

    PubMed

    Lammerding, Jan; Lee, Richard T

    2009-01-01

    The mechanical properties of the interphase nucleus have important implications for cellular function and can reflect changes in nuclear envelope structure and/or chromatin organization. Mutations in the nuclear envelope proteins lamin A and C cause several human diseases, such as Emery-Dreifuss muscular dystrophy, and dramatic changes in nuclear stiffness have been reported in cells from lamin A/C-deficient mice. We have developed a cellular strain technique to measure nuclear stiffness in intact, adherent cells and have applied this experimental method to fibroblasts from mouse models of Emery-Dreifuss muscular dystrophy and to skin fibroblasts from laminopathy patients and healthy control subjects. The experimental protocol is based on measuring induced nuclear deformations in cells plated on a flexible silicone substrate; the nuclear stiffness can subsequently be inferred from the ratio of induced nuclear strain to the applied membrane strain. These experiments reveal that lamins A and C are important determinants of nuclear stiffness and that lamin mutations associated with muscular dystrophies and other laminopathies often result in disturbed nuclear stiffness that could contribute to the tissue-specific disease phenotypes.

  7. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

    PubMed Central

    González-Vera, Juan A.; Morris, May C.

    2015-01-01

    Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes. PMID:28248276

  8. 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.

  9. Bioimage informatics for understanding spatiotemporal dynamics of cellular processes.

    PubMed

    Yang, Ge

    2013-01-01

    The inner environment of the cell is highly dynamic and heterogeneous yet exquisitely organized. Successful completion of cellular processes within this environment depends on the right molecules or molecular complexes to function at the right place at the right time. Understanding spatiotemporal behaviors of cellular processes is therefore essential to understanding their molecular mechanisms at the systems level. These behaviors are usually visualized and recorded using imaging techniques. However, to infer from them systems-level molecular mechanisms, computational analysis and understanding of recorded image data is crucial, not only for acquiring quantitative behavior measurements but also for comprehending complex interactions among the molecules or molecular complexes involved. The technology of computational analysis and understanding of biological images is often referred to simply as bioimage informatics. This article introduces fundamentals of bioimage informatics for understanding spatiotemporal dynamics of cellular processes and reviews recent advances on this topic. Basic bioimage informatics concepts and techniques for characterizing spatiotemporal cell dynamics are introduced first. Studies on specific cellular processes such as cell migration and signal transduction are then used as examples to analyze and summarize recent advances, with the focus on transforming quantitative measurements of spatiotemporal cellular behaviors into knowledge of underlying molecular mechanisms. Despite the advances made, substantial technological challenges remain, especially in representation of spatiotemporal cellular behaviors and inference of systems-level molecular mechanisms. These challenges are briefly discussed. Overall, understanding spatiotemporal cell dynamics will provide critical insights into how specific cellular processes as well as the entire inner cellular environment are dynamically organized and regulated.

  10. Supramolecular polymers as dynamic multicomponent cellular uptake carriers.

    PubMed

    Petkau-Milroy, Katja; Sonntag, Michael H; van Onzen, Arthur H A M; Brunsveld, Luc

    2012-05-16

    Supramolecular synthesis represents a flexible approach to the generation of dynamic multicomponent materials with tunable properties. Here, cellular uptake systems based on dynamic supramolecular copolymers have been developed using a combination of differently functionalized discotic molecules. Discotics featuring peripheral amine functionalities that endow the supramolecular polymer with cellular uptake capabilities were readily synthesized. This enabled the uptake of otherwise cell-impermeable discotics via cotransport as a function of supramolecular coassembly. Dynamic multicomponent and multifunctional supramolecular polymers represent a novel and unique platform for modular cellular uptake systems.

  11. Cellular automaton formulation of passive scalar dynamics

    NASA Technical Reports Server (NTRS)

    Chen, Hudong; Matthaeus, William H.

    1987-01-01

    Cellular automata modeling of the advection of a passive scalar in a two-dimensional flow is examined in the context of discrete lattice kinetic theory. It is shown that if the passive scalar is represented by tagging or 'coloring' automation particles a passive advection-diffusion equation emerges without use of perturbation expansions. For the specific case of the hydrodynamic lattice gas model of Frisch et al. (1986), the diffusion coefficient is calculated by perturbation.

  12. Dynamic Probing for Intrusion Detection under Resource Constraints

    DTIC Science & Technology

    2013-06-01

    performance measure of regret, defined as the performance loss compared to that of a genie who knows the entire attack processes a priori and probes...performance as that of the omniscient genie . Index Terms—Intrusion detection, dynamic probing, non- stochastic multi-armed bandit, regret. I...dynamic probing strategy under the performance measure of regret, de ned as the performance loss compared to that of a genie who knows the entire attack

  13. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity.

    PubMed

    Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

    2017-01-01

    Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying

  14. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity

    PubMed Central

    Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

    2017-01-01

    Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying

  15. 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

  16. 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.

  17. Quantitatively mapping cellular viscosity with detailed organelle information via a designed PET fluorescent probe.

    PubMed

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

    2014-06-24

    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.

  18. 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.

  19. Real-Time Bioluminescent Tracking of Cellular Population Dynamics

    PubMed Central

    Close, Dan; Xu, Tingling; Ripp, Steven; Sayler, Gary

    2015-01-01

    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. PMID:24166372

  20. 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).

  1. A "distorted-BODIPY"-based fluorescent probe for imaging of cellular viscosity in live cells.

    PubMed

    Zhu, Hao; Fan, Jiangli; Li, Miao; Cao, Jianfang; Wang, Jingyun; Peng, Xiaojun

    2014-04-14

    Cellular viscosity is a critical factor in governing diffusion-mediated cellular processes and is linked to a number of diseases and pathologies. Fluorescent molecular rotors (FMRs) have recently been developed to determine viscosity in solutions or biological fluid. Herein, we report a "distorted-BODIPY"-based probe BV-1 for cellular viscosity, which is different from the conventional "pure rotors". In BV-1, the internal steric hindrance between the meso-CHO group and the 1,7-dimethyl group forced the boron-dipyrrin framework to be distorted, which mainly caused nonradiative deactivation in low-viscosity environment. BV-1 gave high sensitivity (x=0.62) together with stringent selectivity to viscosity, thus enabling viscosity mapping in live cells. Significantly, the increase of cytoplasmic viscosity during apoptosis was observed by BV-1 in real time.

  2. Probing intracellular dynamics in living cells with near-field optics.

    PubMed

    Bui, J D; Zelles, T; Lou, H J; Gallion, V L; Phillips, M I; Tan, W

    1999-07-01

    Near-field optics (NFO) overcomes the diffraction limit of light microscopes and permits visualization of single molecules. However, despite numerous applications of NFO in the physical sciences, there is still a paucity of applications in the neurosciences. In this work, the authors have developed NFO probes to image intracellular dynamic processes in living cells. This is the first time a NFO probe has been inserted inside a living cell to deliver light to a spatially controlled region for optical measurements and to record cellular responses to external stimuli. Two different optical detection systems (CCD camera and avalanche photon detection) were developed to monitor cellular responses to drug administration in two different cell types. NG108-15 neuroblastoma cells and vascular smooth muscle cells (VSMC) were penetrated with NFO probes. Intracellular Ca2+ increases post drug stimulation were detected by NFO probes. The cells were loaded with either fura-2/AM or fluo-3/AM calcium dyes. VSMC were stimulated with angiotensin II, resulting in a precise area of intracellular Ca2+ increase. Different response profiles of Ca2+ increases were observed after ionomycin and bradykinin administration in NG108-15 cells. Responsive heterogeneities due to ionomycin among different cells of the same type were recorded. The results show that NFO probes make possible real-time visualization of intracellular events. With refinement, intracellular NFO probes offer the potential of probing cell function with fast temporal and excellent spatial resolutions.

  3. 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

  4. 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

  5. Synthesis, metal coordination, and cellular internalization of a siderophore-bearing NIR fluorescent carbocyanine probe

    NASA Astrophysics Data System (ADS)

    Ye, Yunpeng; Xu, Baogang; Bloch, Sharon; Achilefu, Samuel

    2006-02-01

    In order to explore novel NIR fluorescent probes for optical imaging in biomedicines, one desferrioxamine (DFO)-bearing NIR fluorescent probe was designed and synthesized based on a dicarboxylic acid-containing carbocyanine (Cypate). Similar to the free DFO, the resulting conjugate Cypate-DFO showed high binding affinity with Fe(III) and Ga(III) as identified by ES-MS. Nevertheless, the iron binding was found to quench its fluorescent emission significantly, suggesting that the siderophore moiety might perturb the spectroscopic properties of the attached carbocyanine fluorophore through metal binding. As observed by fluorescence microscopy, Cypate-DFO showed significant cellular internalization in A549 cells in vitro. Further studies on novel Cypate-DFO derivatives of this type may reveal some exciting properties and biological activities.

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

    PubMed Central

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

    2017-01-01

    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

  7. HSP90: the Rosetta stone for cellular protein dynamics?

    PubMed

    Dezwaan, Diane C; Freeman, Brian C

    2008-04-15

    The Hsp90 proteomic network is expansive and includes a variety of cell processes operating within the cytoplasm and nucleoplasm. Though the functional significance of the extensive interactions has not been defined, we suggest that the Hsp90 molecular chaperone machinery promotes dynamic behaviors for client proteins that is critical to achieve homeostasis. A general rapid action by cell factors would permit both proper assembly of biological complexes and efficient transitions between distinct structures. Here, we describe why the properties that are inherent to molecular chaperones place these proteins in a unique position to drive the dynamic cellular environment.

  8. 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.

  9. Criticality of environmental information obtainable by dynamically controlled quantum probes

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    A universal approach to decoherence control combined with quantum estimation theory reveals a critical behavior, akin to a phase transition, of the information obtainable by a qubit probe concerning the memory time of environmental fluctuations of generalized Ornstein-Uhlenbeck processes. The criticality is intrinsic to the environmental fluctuations but emerges only when the probe is subject to suitable dynamical control aimed at inferring the memory time. A sharp transition is anticipated between two dynamical phases characterized by either a short or long memory time compared to the probing time. This phase transition of the environmental information is a fundamental feature that characterizes open quantum-system dynamics and is important for attaining the highest estimation precision of the environment memory time under experimental limitations.

  10. Dynamic Force Sensing Using an Optically Trapped Probing System

    PubMed Central

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

    2013-01-01

    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

  11. Towards local electromechanical probing of cellular and biomolecular systems in a liquid environment.

    PubMed

    Kalinin, Sergei V; Rodriguez, Brian J; Jesse, Stephen; Seal, Katyayani; Proksch, Roger; Hohlbauch, Sophia; Revenko, Irene; Thompson, Gary Lee; Vertegel, Alexey A

    2007-10-24

    Electromechanical coupling is ubiquitous in biological systems, with examples ranging from simple piezoelectricity in calcified and connective tissues to voltage-gated ion channels, energy storage in mitochondria, and electromechanical activity in cardiac myocytes and outer hair cell stereocilia. Piezoresponse force microscopy (PFM) originally emerged as a technique to study electromechanical phenomena in ferroelectric materials, and in recent years has been employed to study a broad range of non-ferroelectric polar materials, including piezoelectric biomaterials. At the same time, the technique has been extended from ambient to liquid imaging on model ferroelectric systems. Here, we present results on local electromechanical probing of several model cellular and biomolecular systems, including insulin and lysozyme amyloid fibrils, breast adenocarcinoma cells, and bacteriorhodopsin in a liquid environment. The specific features of PFM operation in liquid are delineated and bottlenecks on the route towards nanometre-resolution electromechanical imaging of biological systems are identified.

  12. 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.

  13. Experimental design for dynamics identification of cellular processes.

    PubMed

    Dinh, Vu; Rundell, Ann E; Buzzard, Gregery T

    2014-03-01

    We address the problem of using nonlinear models to design experiments to characterize the dynamics of cellular processes by using the approach of the Maximally Informative Next Experiment (MINE), which was introduced in W. Dong et al. (PLoS ONE 3(8):e3105, 2008) and independently in M.M. Donahue et al. (IET Syst. Biol. 4:249-262, 2010). In this approach, existing data is used to define a probability distribution on the parameters; the next measurement point is the one that yields the largest model output variance with this distribution. Building upon this approach, we introduce the Expected Dynamics Estimator (EDE), which is the expected value using this distribution of the output as a function of time. We prove the consistency of this estimator (uniform convergence to true dynamics) even when the chosen experiments cluster in a finite set of points. We extend this proof of consistency to various practical assumptions on noisy data and moderate levels of model mismatch. Through the derivation and proof, we develop a relaxed version of MINE that is more computationally tractable and robust than the original formulation. The results are illustrated with numerical examples on two nonlinear ordinary differential equation models of biomolecular and cellular processes.

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

    PubMed

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

    2012-12-24

    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.

  15. 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

  16. Probing Stellar Dynamics With Space Photometry

    NASA Astrophysics Data System (ADS)

    García, Rafael A.; Salabert, D.; Ballot, J.; Beck, P. G.; Bigot, L.; Corsaro, E.; Creevey, O.; Egeland, R.; Jiménez, A.; Mathur, S.; Metcalfe, T.; do Nascimento, J.; Pallé, P. L.; Pérez Hernández, F.; Regulo, C.

    2016-08-01

    The surface magnetic field has substantial influence on various stellar properties that can be probed through various techniques. With the advent of new space-borne facilities such as CoRoT and Kepler, uninterrupted long high-precision photometry is available for hundred of thousand of stars. This number will substantially grow through the forthcoming TESS and PLATO missions. The unique Kepler observations -covering up to 4 years with a 30-min cadence- allows studying stellar variability with different origins such as pulsations, convection, surface rotation, or magnetism at several time scales from hours to years. We study the photospheric magnetic activity of solar-like stars by means of the variability induced in the observed signal by starspots crossing the visible disk. We constructed a solar photometric magnetic activity proxy, Sph from SPM/VIRGO/SoHO, as if the Sun was a distant star and we compare it with several solar well-known magnetic proxies. The results validate this approach. Thus, we compute the Sph proxy for a set of CoRoT and Kepler solar-like stars for which pulsations were already detected. After characterizing the rotation and the magnetic properties of 300 solar-like stars, we use their seismic properties to characterize 18 solar analogs for which we study their magnetism. This allows us to put the Sun into context of its siblings.

  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. Reassessing cellular glutathione homoeostasis: novel insights revealed by genetically encoded redox probes.

    PubMed

    Morgan, Bruce

    2014-08-01

    Glutathione is the most abundant small molecule thiol in nearly all eukaryotes. Whole-cell levels of oxidized (GSSG) and reduced (GSH) glutathione are variable and responsive to genetic and chemical manipulations, which has led to their relative levels being widely used as a marker of the 'cellular redox state' and to indicate the level of 'oxidative stress' experienced by cells, tissues and organisms. However, the applicability of glutathione as a marker for a generalized 'cellular redox state' is questionable, especially in the light of recent observations in yeast cells. In yeast, whole-cell GSSG changes are almost completely dependent upon the activity of an ABC-C (ATP-binding cassette-C) transporter, Ycf1 (yeast cadmium factor 1), which mediates sequestration of GSSG to the vacuole. In the absence of Ycf1 whole-cell GSSG content is strongly decreased and extremely robust to perturbation. These observations are consistent with highly specific redox-sensitive GFP probe-based measurements of the cytosolic glutathione pool and indicate that cytosolic GSSG reductive systems are easily able to reduce nearly all GSSG formed, even following treatment with large concentrations of oxidant. In the present paper, I discuss the consequences of these new findings for our understanding of glutathione homoeostasis in the eukaryotic cell.

  19. 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.

  20. Cellular contact guidance through dynamic sensing of nanotopography.

    PubMed

    Driscoll, Meghan K; Sun, Xiaoyu; Guven, Can; Fourkas, John T; Losert, Wolfgang

    2014-04-22

    We investigate the effects of surface nanotopography on the migration and cell shape dynamics of the amoeba Dictyostelium discoideum. Multiple prior studies have implicated the patterning of focal adhesions in contact guidance. However, we observe significant contact guidance of Dictyostelium along surfaces with nanoscale ridges or grooves, even though this organism lacks integrin-based adhesions. Cells that move parallel to nanoridges are faster, more protrusive at their fronts, and more elongated than are cells that move perpendicular to nanoridges. Quantitative studies show that nanoridges spaced 1.5 μm apart exhibit the greatest contact guidance efficiency. Because Dictyostelium cells exhibit oscillatory shape dynamics, we model contact guidance as a process in which stochastic cellular harmonic oscillators couple to the periodicity of the nanoridges. In support of this connection, we find that nanoridges nucleate actin polymerization waves of nanoscale width that propagate parallel to the nanoridges.

  1. 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

  2. A dynamic cellular vertex model of growing epithelial tissues

    NASA Astrophysics Data System (ADS)

    Lin, Shao-Zhen; Li, Bo; Feng, Xi-Qiao

    2017-03-01

    Intercellular interactions play a significant role in a wide range of biological functions and processes at both the cellular and tissue scales, for example, embryogenesis, organogenesis, and cancer invasion. In this paper, a dynamic cellular vertex model is presented to study the morphomechanics of a growing epithelial monolayer. The regulating role of stresses in soft tissue growth is revealed. It is found that the cells originating from the same parent cell in the monolayer can orchestrate into clustering patterns as the tissue grows. Collective cell migration exhibits a feature of spatial correlation across multiple cells. Dynamic intercellular interactions can engender a variety of distinct tissue behaviors in a social context. Uniform cell proliferation may render high and heterogeneous residual compressive stresses, while stress-regulated proliferation can effectively release the stresses, reducing the stress heterogeneity in the tissue. The results highlight the critical role of mechanical factors in the growth and morphogenesis of epithelial tissues and help understand the development and invasion of epithelial tumors.

  3. 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."

  4. 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'.

  5. Microfluidics-integrated time-lapse imaging for analysis of cellular dynamics.

    PubMed

    Albrecht, Dirk R; Underhill, Gregory H; Resnikoff, Joshua; Mendelson, Avital; Bhatia, Sangeeta N; Shah, Jagesh V

    2010-06-01

    An understanding of the mechanisms regulating cellular responses has recently been augmented by innovations enabling the observation of phenotypes at high spatio-temporal resolution. Technologies such as microfluidics have sought to expand the throughput of these methods, although assimilation with advanced imaging strategies has been limited. Here, we describe the pairing of high resolution time-lapse imaging with microfluidic multiplexing for the analysis of cellular dynamics, utilizing a design selected for facile fabrication and operation, and integration with microscopy instrumentation. This modular, medium-throughput platform enables the long-term imaging of living cells at high numerical aperture (via oil immersion) by using a conserved 96-well, approximately 6 x 5 mm(2) imaging area with a variable input/output channel design chosen for the number of cell types and microenvironments under investigation. In the validation of this system, we examined fundamental features of cell cycle progression, including mitotic kinetics and spindle orientation dynamics, through the high-resolution parallel analysis of model cell lines subjected to anti-mitotic agents. We additionally explored the self-renewal kinetics of mouse embryonic stem cells, and demonstrate the ability to dynamically assess and manipulate stem cell proliferation, detect rare cell events, and measure extended time-scale correlations. We achieved an experimental throughput of >900 cells/experiment, each observed at >40x magnification for up to 120 h. Overall, these studies illustrate the capacity to probe cellular functions and yield dynamic information in time and space through the integration of a simple, modular, microfluidics-based imaging platform.

  6. Fluorescence-based Broad Dynamic Range Viscosity Probes.

    PubMed

    Dragan, Anatoliy; Graham, August E; Geddes, Chris D

    2014-03-01

    We introduce two new fluorescent viscosity probes, SYBR Green (SG) and PicoGreen (PG), that we have studied over a broad range of viscosity and in collagen solutions. In water, both dyes have low quantum yields and excited state lifetimes, while in viscous solvents or in complex with DNA both parameters dramatically (300-1000-fold) increase. We show that in log-log scale the dependence of the dyes' quantum yield vs. viscosity is linear, the slope of which is sensitive to temperature. Application of SG and PG, as a fluorescence-based broad dynamic range viscosity probes, to the life sciences is discussed.

  7. Lanthanum Probe Studies of Cellular Pathophysiology Induced by Hypoxia in Isolated Cardiac Muscle

    PubMed Central

    Burton, Karen P.; Hagler, Herbert K.; Templeton, Gordon H.; Willerson, James T.; Buja, L. Maximilian

    1977-01-01

    This study was undertaken to evaluate directly the relationship between evolution of irreversible myocardial injury induced by hypoxia in an isolated papillary muscle preparation and the development of pathophysiological alterations related to severely impaired membrane function. An ionic lanthanum probe technique was employed as a cytochemical marker to monitor the progression of cellular injury, and data from this cytologic technique were correlated with ultrastructure and measurements of contractile parameters in a total of 67 muscles subjected to control conditions or to graded intervals of hypoxia with or without reoxygenation. Marked depression of developed tension and rate of tension development occurred after 30 min of hypoxia. Contractile function showed significant recovery with reoxygenation after 1 h and 15 min of hypoxia but remained depressed when reoxygenation was provided after 2 or 3 h of hypoxia. Examination by transmission and analytical electron microscopy (energy dispersive X-ray microanalysis) revealed lanthanum deposition only in extracellular regions of control muscles and muscles subjected to 30 min of hypoxia. After hypoxic intervals of over 1 h, abnormal intracytoplasmic and intramitochondrial localization of lanthanum were detected. After 1 h and 15 min of hypoxia, abnormal intracellular lanthanum accumulation was associated with only minimal ultrastructural evidence of injury; muscle provided reoxygenation after 1 h and 15 min of hypoxia showed improved ultrastructure and did not exhibit intracellular lanthanum deposits upon exposure to lanthanum during the reoxygenation period. After 2 to 3 h of hypoxia, abnormal intracellular lanthanum accumulation was associated with ultrastructural evidence of severe muscle injury which persisted after reoxygenation. Thus, the data support the conclusion that cellular and membrane alterations responsible for abnormal intracellular lanthanum deposition precede the development of irreversible injury

  8. FRAP, FLIM, and FRET: Detection and analysis of cellular dynamics on a molecular scale using fluorescence microscopy

    PubMed Central

    De Los Santos, Carla; Chang, Ching-Wei; Mycek, Mary-Ann; Cardullo, Richard A.

    2015-01-01

    The combination of fluorescent-probe technology plus modern optical microscopes allows investigators to monitor dynamic events in living cells with exquisite temporal and spatial resolution. Fluorescence recovery after photobleaching (FRAP), for example, has long been used to monitor molecular dynamics both within cells and on cellular surfaces. Although bound by the diffraction limit imposed on all optical microscopes, the combination of digital cameras and the application of fluorescence intensity information on large-pixel arrays have allowed such dynamic information to be monitored and quantified. Fluorescence lifetime imaging microscopy (FLIM), on the other hand, utilizes the information from an ensemble of fluorophores to probe changes in the local environment. Using either fluorescence-intensity or lifetime approaches, fluorescence resonance energy transfer (FRET) microscopy provides information about molecular interactions, with Ångstrom resolution. In this review, we summarize the theoretical framework underlying these methods and illustrate their utility in addressing important problems in reproductive and developmental systems. PMID:26010322

  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. Cellular Automaton Simulation of Vegetated Dune Field Dynamics

    NASA Astrophysics Data System (ADS)

    Nield, J. M.; Baas, A. C.

    2007-12-01

    Vegetated aeolian dune fields develop through non-linear interactions between physical geomorphic processes and ecological vegetation growth and response into complex ecogeomorphic systems that are sensitive to both climatic and environmental variations. We present a Discrete Ecogeomorphic Aeolian Landscape (DECAL) cellular automaton model that replicates the self-organisation of vegetated dune systems and enables the investigation of conditions necessary for long-walled (hairpin) parabolic dune and nebkha formation in coastal and semi-arid environments over various temporal and spatial scales. The algorithm utilises simple transport rules and mutual feedback between geomorphic and ecological components to investigate vegetation pattern formation and how and why this influences dune dynamics. We examine ecogeomorphic interactions both by exploring system mechanics via dune mobility and by more descriptive numerical state variables, facilitating the investigation of trajectories and potential attractors as a function of environmental parameters and system perturbations and leading to the identification of possible system sensitivities and thresholds. The model simulations elucidate possible dune field responses to anthropogenic impacts and palaeo and future climate variations and highlight the ability of vegetation to impart a characteristic length-scale on a landscape. This simple vegetated dune model illustrates the power and versatility of a cellular automaton approach for exploring ecological and geomorphic interactions in complex earth surface systems.

  11. Dynamic modeling of cellular populations within iBioSim.

    PubMed

    Stevens, Jason T; Myers, Chris J

    2013-05-17

    As the complexity of synthetic genetic circuits increases, modeling is becoming a necessary first step to inform subsequent experimental efforts. In recent years, the design automation community has developed a wealth of computational tools for assisting experimentalists in designing and analyzing new genetic circuits at several scales. However, existing software primarily caters to either the DNA- or single-cell level, with little support for the multicellular level. To address this need, the iBioSim software package has been enhanced to provide support for modeling, simulating, and visualizing dynamic cellular populations in a two-dimensional space. This capacity is fully integrated into the software, capitalizing on iBioSim's strengths in modeling, simulating, and analyzing single-celled systems.

  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. Probing dynamics at interfaces: resonance enhanced dynamic light scattering.

    PubMed

    Plum, Markus A; Steffen, Werner; Fytas, George; Knoll, Wolfgang; Menges, Bernhard

    2009-06-08

    Experiments addressing supramolecular dynamics at interfaces are of paramount importance for the understanding of the dynamic behaviour of polymers, particles, or cells at interfaces, transport phenomena to and from surfaces, thin films or membranes. However, there are only few reports in the literature due to the paucity of experimental methods that offer the required spatial and time resolution. Evanescent wave dynamic light scattering originally developed to meet these needs has limited sensitivity and is restricted to glass substrates. Here we report the first experimental realization of a dynamic light scattering experiment close to an interface using surface plasmon polaritons as light source offering a strong increase in the signal to noise ratio and allowing for the use of metallic interfaces. As a proof of concept, we consider the diffusion of particles with radii down to 10nm in dilute dispersions close to a gold surface.

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

    DOE PAGES

    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.

  15. 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.

  16. Stochastic cellular automata model for stock market dynamics

    NASA Astrophysics Data System (ADS)

    Bartolozzi, M.; Thomas, A. W.

    2004-04-01

    In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two-dimensional grid. Active traders are characterized by the decision to buy, σi (t)=+1 , or sell, σi (t)=-1 , a stock at a certain discrete time step. The remaining cells are inactive, σi (t)=0 . The trading dynamics is then determined by the stochastic interaction between traders belonging to the same cluster. Extreme, intermittent events, such as crashes or bubbles, are triggered by a phase transition in the state of the bigger clusters present on the grid, where almost all the active traders come to share the same spin orientation. Most of the stylized aspects of the financial market time series, including multifractal proprieties, are reproduced by the model. A direct comparison is made with the daily closures of the S&P500 index.

  17. 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.

  18. 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.

  19. Stochastic cellular automata model for stock market dynamics.

    PubMed

    Bartolozzi, M; Thomas, A W

    2004-04-01

    In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two-dimensional grid. Active traders are characterized by the decision to buy, sigma(i) (t)=+1, or sell, sigma(i) (t)=-1, a stock at a certain discrete time step. The remaining cells are inactive, sigma(i) (t)=0. The trading dynamics is then determined by the stochastic interaction between traders belonging to the same cluster. Extreme, intermittent events, such as crashes or bubbles, are triggered by a phase transition in the state of the bigger clusters present on the grid, where almost all the active traders come to share the same spin orientation. Most of the stylized aspects of the financial market time series, including multifractal proprieties, are reproduced by the model. A direct comparison is made with the daily closures of the S&P 500 index.

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

    PubMed

    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."

  1. Cellular uptake and dynamics of unlabeled freestanding silicon nanowires

    PubMed Central

    Zimmerman, John F.; Parameswaran, Ramya; Murray, Graeme; Wang, Yucai; Burke, Michael; Tian, Bozhi

    2016-01-01

    The ability to seamlessly merge electronic devices with biological systems at the cellular length scale is an exciting prospect for exploring new fundamental cell biology and in designing next-generation therapeutic devices. Semiconductor nanowires are well suited for achieving this goal because of their intrinsic size and wide range of possible configurations. However, current studies have focused primarily on delivering substrate-bound nanowire devices through mechanical abrasion or electroporation, with these bulkier substrates negating many of the inherent benefits of using nanoscale materials. To improve on this, an important next step is learning how to distribute these devices in a drug-like fashion, where cells can naturally uptake and incorporate these electronic components, allowing for truly noninvasive device integration. We show that silicon nanowires (SiNWs) can potentially be used as such a system, demonstrating that label-free SiNWs can be internalized in multiple cell lines (96% uptake rate), undergoing an active “burst-like” transport process. Our results show that, rather than through exogenous manipulation, SiNWs are internalized primarily through an endogenous phagocytosis pathway, allowing cellular integration of these materials. To study this behavior, we have developed a robust set of methodologies for quantitatively examining high–aspect ratio nanowire-cell interactions in a time-dependent manner on both single-cell and ensemble levels. This approach represents one of the first dynamic studies of semiconductor nanowire internalization and offers valuable insight into designing devices for biomolecule delivery, intracellular sensing, and photoresponsive therapies. PMID:28028534

  2. 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

  3. 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).

  4. Dynamics and Control Modeling for Gravity Probe B

    NASA Astrophysics Data System (ADS)

    Pelivan, Ivanka

    2010-03-01

    A generic drag-free simulator has been developed to aid in the design, on-orbit and post-mission data analysis phases of increasingly complex future missions such as Gaia and STEP. Adaptation to the recent science mission Gravity Probe B (GP-B) has been carried out for a first simulator verification with actual flight data. Lessons learned from GP-B have shown that the controls simulator, developed concurrently with GP-B, has been invaluable to test flight control design and furthermore to resolve on-orbit anomalies in a time-saving manner. A complete mission software simulator including controls, full-body dynamics and comprehensive spacecraft environment disturbances has been established for Gravity Probe B. This simulator provides a reference and development platform for future mission design. The importance of this effort lies in the challenge to meet rising science requirements for future missions in the area of maximum disturbance rejection.

  5. 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.

  6. Ultrafast Molecular Dynamics probed by Vacuum Ultraviolet Pulses

    NASA Astrophysics Data System (ADS)

    Cryan, James; Champenois, Elio; Shivaram, Niranjan; Wright, Travis; Yang, Chan-Shan; Falcone, Roger; Belkacem, Ali

    2014-05-01

    We present time-resolved measurements of the relaxation dynamics in small molecular systems (CO2 and C2H4) following ultraviolet (UV) photo-excitation. We probe these excitations through photoionization and velocity map imaging (VMI) spectroscopy. Vacuum and extreme ultraviolet (VUV/XUV) pump and probe pulses are created by exploiting strong-field high harmonic generation (HHG) from our state-of-the-art 30 mJ, 1 kHz laser system. Three dimensional photoelectron and photoion momentum images recorded with our VMI spectrometer reveal non-Born Oppenheimer dynamics in the vicinity of a conical intersection, and allow us track the state of the system as a function of time. We also present initial experiments with the goal of controlling the dynamics near a conical intersection using a strong-field IR pulse. Finally, we will show progress towards measurements of time-resolved molecular frame photoelectron angular distributions (TRMFPADs) by applying our VUV/XUV pulse sequence to an aligned molecular ensemble. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  7. Measuring lipid packing of model and cellular membranes with environment sensitive probes.

    PubMed

    Sezgin, Erdinc; Sadowski, Tomasz; Simons, Kai

    2014-07-15

    The extent of lipid packing is one of the key physicochemical features of biological membranes and is involved in many membrane processes. Polarity sensitive fluorescent probes are commonly used tools to measure membrane lipid packing in both artificial and biological membranes. In this paper, we have systematically compared eight different probes to measure membrane lipid ordering. We investigated how these probes behave in small unilamellar liposomes, phase-separated giant unilamellar vesicles, cell-derived giant plasma membrane vesicles, and live cells. We have tested the order sensitivity of a variety of measurable parameters, including generalized polarization, peak shift, or intensity shift. We also investigated internalization and photostability of the probes to assess probe potential for time-lapse live cell imaging. These results provide a catalogue of properties to facilitate the choice of probe according to need.

  8. Pump probe spectroscopy of quasiparticle dynamics in cuprate superconductors

    SciTech Connect

    Segre, Gino P.

    2001-01-01

    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.

  9. Probing peroxisome dynamics and biogenesis by fluorescence imaging.

    PubMed

    Jauregui, Miluska; Kim, Peter K

    2014-03-03

    Peroxisomes are the most recently discovered classical organelles, and only lately have their diverse functions been truly recognized. Peroxisomes are highly dynamic structures, changing both morphologically and in number in response to both extracellular and intracellular signals. This metabolic organelle came to prominence due to the many genetic disorders caused by defects in its biogenesis or enzymatic functions. There is now growing evidence that suggests peroxisomes are involved in lipid biosynthesis, innate immunity, redox homeostasis, and metabolite scavenging, among other functions. Therefore, it is important to have available suitable methods and techniques to visualize and quantify peroxisomes in response to various cellular signals. This unit includes a number of protocols that will enable researchers to image, qualify, and quantify peroxisome numbers and morphology-with both steady-state and time-lapse imaging using mammalian cells. The use of photoactivatable fluorescent proteins to detect and measure peroxisome biogenesis is also described. Altogether, the protocols described here will facilitate understanding of the dynamic changes that peroxisomes undergo in response to various cellular signals.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Probing Electron Dynamics in Simple Molecules with Attosecond Pulses

    NASA Astrophysics Data System (ADS)

    Rivière, Paula; Palacios, Alicia; Pérez-Torres, Jhon Fredy; Martín, Fernando

    Attosecond pulses are an ideal tool to explore electron and nuclear dynamics in atoms and molecules. Either as single attosecond pulses (SAP), in attosecond pulse trains (APT), or in combination with infrared (IR) pulses, these pulses, with frequencies in the VUV-XUV regime, have been widely used to probe ionization, electron tunneling, or autoionization in atoms. More recently, similar processes have been studied in molecules. A correct theoretical description of such processes in molecules often requires a fully dimensional treatment due to the important role of nuclear motion and electron correlation. This restricts ab initio calculations to the simplest molecules. In this chapter, we discuss single ionization of hydrogen molecules (H2 and D2) induced by time-delayed SAP+IR and APT+IR schemes. Ab initio time-dependent theoretical calculations are compared with existing experiments.

  16. Integrated fiber optic probe for dynamic light scattering

    NASA Technical Reports Server (NTRS)

    Dhadwal, Harbans S.; Khan, Romel R.; Suh, Kwang

    1993-01-01

    An integrated fiber optic probe, comprising a monomode optical fiber fusion spliced to a short length of a graded-index multimode fiber, is fabricated for use as a coherent receiver in dynamic light scattering. The multimode fiber is cleaved to provide a gradient-index fiber lens with a focal length of 125 microns and an f-number close to unity. An integrated fiber receiver is used to measure the intensity-intensity autocorrelation data from a 0.05 percent by weight concentration of an aqueous suspension of polystyrene latex spheres. Analysis of 100 independent data sets indicates that the particle size can be recovered with an accuracy of +/- 1 percent.

  17. In vivo cellular-resolution retinal imaging in infants and children using an ultracompact handheld probe

    NASA Astrophysics Data System (ADS)

    Larocca, Francesco; Nankivil, Derek; Dubose, Theodore; Toth, Cynthia A.; Farsiu, Sina; Izatt, Joseph A.

    2016-09-01

    Enabled by adaptive optics, retinal photoreceptor cell imaging is changing our understanding of retinal structure and function, as well as the pathogenesis of numerous ocular diseases. To date, use of this technology has been limited to cooperative adult subjects due to the size, weight and inconvenience of the equipment, thus excluding study of retinal maturation during human development. Here, we report the design and operation of a handheld probe that can perform both scanning laser ophthalmoscopy and optical coherence tomography of the parafoveal photoreceptor structure in infants and children without the need for adaptive optics. The probe, featuring a compact optical design weighing only 94 g, was able to quantify packing densities of parafoveal cone photoreceptors and visualize cross-sectional photoreceptor substructure in children with ages ranging from 14 months to 12 years. The probe will benefit paediatric research by improving the understanding of retinal development, maldevelopment and early onset of disease during human growth.

  18. Cellular-based modeling of oscillatory dynamics in brain networks.

    PubMed

    Skinner, Frances K

    2012-08-01

    Oscillatory, population activities have long been known to occur in our brains during different behavioral states. We know that many different cell types exist and that they contribute in distinct ways to the generation of these activities. I review recent papers that involve cellular-based models of brain networks, most of which include theta, gamma and sharp wave-ripple activities. To help organize the modeling work, I present it from a perspective of three different types of cellular-based modeling: 'Generic', 'Biophysical' and 'Linking'. Cellular-based modeling is taken to encompass the four features of experiment, model development, theory/analyses, and model usage/computation. The three modeling types are shown to include these features and interactions in different ways.

  19. Pathogen virulence factors as molecular probes of basic plant cellular functions

    PubMed Central

    Speth, Elena Bray; Lee, Young Nam; He, Sheng Yang

    2007-01-01

    Summary To successfully colonize plants, pathogens have evolved a myriad of virulence factors that allow them to manipulate host cellular pathways in order to gain entry into, multiply and move within, and eventually exit the host for a new infection cycle. In the past few years, substantial progress has been made in characterizing the host targets of viral and bacterial virulence factors, providing unique insights into basic plant cellular processes such as gene silencing, vesicle trafficking, hormone signaling, and innate immunity. Identification of the host targets of additional pathogen virulence factors promises to continue shedding light on fundamental cellular mechanisms in plants, thus enhancing our understanding of plant signaling, metabolism and cell biology. PMID:17884715

  20. 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.

  1. Probing scale interaction in brain dynamics through synchronization.

    PubMed

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

    2014-10-05

    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.

  2. 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

    2016-08-08

    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.

  3. 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

  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. Spectral representations and global maps of cellular automata dynamics

    NASA Astrophysics Data System (ADS)

    Raptis, Theophanes E.

    2016-10-01

    We present a spectral representation of any computation performed by a Cellular Automaton (CA) of arbitrary topology and dimensionality via an appropriate coding scheme in Fourier space that can be implemented in an analog machine ideally circumventing part of the overall waste heat production. We explore further consequences of this encoding and we provide a simple example based on the Game-of-Life where we find global maps for small lattices indicating an interesting underlying recursive structure.

  6. 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.

  7. A Novel Water-Soluble Fluorescence Probe with Wash-Free Cellular Imaging Capacity Based on AIE Characteristics.

    PubMed

    Qian, Yunxia; Liu, Hongmei; Tan, Haijian; Yang, Qingmin; Zhang, Shuchen; Han, Lingui; Yi, Xuegang; Huo, Li; Zhao, Hongchi; Wu, Yonggang; Bai, Libin; Ba, Xinwu

    2017-03-21

    A potential real-time imaging water-soluble fluorescent polymer (P3) is facilely prepared via one-pot method. For P3, tetraphenylethene unit serves as the fluorescent unit, poly(acryloyl ethylene diamine) (a kind of polyelectrolyte) with specific degree of polymerization acts as water-soluble part. (1) H-NMR, gel permeation chromatography (GPC), UV-vis spectroscopy, photoluminescence (PL), and confocal laser scanning microscopy are undertaken to characterize the structure and property of P3. The results of wash-free cellular imaging show that the signal-to-noise ratio is high as the concentration of P3 is 50 μg mL(-1) . In addition, the pH-responsive and Cd(2+) -responsive are also investigated in this paper. The results coming from pH-responsive show that P3 solution displays significant fluorescence under near neutral. And the result from the cellular imaging shows that intracellular fluorescence intensity enhances with the augment of concentration of Cd(2+) , which reveals that P3 can give a hint to resolve the dilemma of traditional fluorescent dyes used as living cellular fluorescent probe.

  8. Direct high-resolution label-free imaging of cellular nanostructure dynamics in living cells

    NASA Astrophysics Data System (ADS)

    Heo, Chaejeong; Lee, Sohee; Lee, Si Young; Jeong, Mun Seok; Lee, Young Hee; Suh, Minah

    2013-06-01

    We report the application of an optical microscope equipped with a high-resolution dark-field condenser for detecting dynamic responses of cellular nanostructures in real time. Our system provides an easy-to-use technique to visualize biological specimens without any staining. This system can visualize the dynamic behavior of nanospheres and nanofibers, such as F-actin, at the leading edges of adjacent neuronal cells. We confirmed that the nanofibers imaged with this high-resolution optical microscopic technique are F-actin by using fluorescence microscopy after immunostaining the F-actin of fixed cells. Furthermore, cellular dynamics are enhanced by applying noncontact electric field stimulation through a transparent graphene electric field stimulator. High-resolution label-free optical microscopy enables the visualization of nanofiber dynamics initiated by filopodial nanofiber contacts. In conclusion, our optical microscopy system allows the visualization of nanoscale cellular dynamics under various external stimuli in real time without specific staining.

  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.

  10. Spectroscopic probing of location and dynamics of an environment-sensitive intramolecular charge transfer probe within liposome membranes.

    PubMed

    Paul, Bijan Kumar; Guchhait, Nikhil

    2011-11-15

    The present work demonstrates the interaction of an intramolecular charge transfer (ICT) probe 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid methyl ester (DPDAME) with liposome membranes of dimyristoyl-L-α-phosphatidylcholine (DMPC) and dimyristoyl-L-α-phosphatidylglycerol (DMPG) studied by steady-state absorption, emission and time-resolved emission techniques. A huge hypsochromic shift together with remarkable enhancement of fluorescence quantum yield of the polarity sensitive ICT emission of DPDAME upon interaction with the lipids has been rationalized in terms of incorporation of the probe into hydrophobic interior of the lipids. Compelling evidences for penetration of the probe into the hydrocarbon interior of the lipids have been deduced from intertwining different experimental results e.g., micropolarity in the immediate vicinity of the probe in lipid environments, steady-state anisotropy, red-edge excitation shift (REES), fluorescence quenching experiments and time-resolved measurements. The rotational relaxation dynamics study of the membrane-bound probe unveils the impartation of high degree of motional rigidity. Wavelength-selective emission behaviour paves way for monitoring of solvent-relaxation in the membranes. Overall, the ICT probe DPDAME displays its commendable sensitivity in deciphering the microheterogeneous environments of liposomal membranes of DMPC and DMPG and promises a new membrane-polarity sensitizing probe.

  11. 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.

  12. Ultrafast X-ray Auger probing of photoexcited molecular dynamics

    DOE PAGES

    McFarland, B. K.; Farrell, J. P.; Miyabe, S.; ...

    2014-06-23

    Here, molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation—X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towardsmore » high kinetic energies, resulting from a particular C–O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.« less

  13. Frequency modulated spectroscopy as a probe of molecular collision dynamics.

    PubMed

    Alagappan, Azhagammai; Costen, Matthew L; McKendrick, Kenneth G

    2006-04-01

    We describe the application of frequency modulated spectroscopy (FMS) with an external cavity tuneable diode laser to the study of the scalar and vector properties of inelastic collisions. CN X(2)Sigma(+) radicals are produced by polarized photodissociation of ICN at 266 nm, with a sharp velocity and rotational angular momentum distribution. The collisional evolution of the distribution is observed via sub-Doppler FMS on the A(2)Pi-X(2)Sigma(+) (2,0) band. He, Ar, N(2), O(2) and CO(2) were studied as collider gases. Doppler profiles were acquired in different experimental geometries of photolysis and probe laser propagation and polarization, and on different spectroscopic branches. These were combined to give composite Doppler profiles from which the speed distributions and specific speed-dependent vector correlations could be determined. The angular scattering dynamics with species other than He are found to be very similar, dominated by backward scattering which accompanies transfer of energy between rotation and translation. The kinematics of collisions with He are not conducive to the determination of differential scattering and angular momentum polarization correlations. Angular momentum correlations show interesting differences between reactive and non-reactive colliders. We propose that this reflects differences in the potential energy surfaces, in particular, the nature and depth of attractive potential wells.

  14. Ultrafast X-ray Auger probing of photoexcited molecular dynamics

    SciTech Connect

    McFarland, B. K.; Farrell, J. P.; Miyabe, S.; Tarantelli, F.; Aguilar, A.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Castagna, J. C.; Coffee, R. N.; Cryan, J. P.; Fang, L.; Feifel, R.; Gaffney, K. J.; Glownia, J. M.; Martinez, T. J.; Mucke, M.; Murphy, B.; Natan, A.; Osipov, T.; Petrović, V. S.; Schorb, S.; Schultz, Th.; Spector, L. S.; Swiggers, M.; Tenney, I.; Wang, S.; White, J. L.; White, W.; Gühr, M.

    2014-06-23

    Here, molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation—X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C–O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.

  15. Optical biosensors for probing at the cellular level: a review of recent progress and future prospects.

    PubMed

    Velasco-Garcia, M N

    2009-02-01

    New approaches are required to understand the complex processes taking place in the smallest unit of life. Recent years have seen an increasing activity in the use of optical devices and techniques for the investigation of the properties of single cells and also populations of cells including cell to cell communication. This article reviews relevant optical technologies to date as well as new advances in biosensor development, and goes on to explore reported applications in detection of biotargets and cellular signalling pathways inside individual living cells.

  16. Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon.

    PubMed

    Chen, Lizhen; Chao, Jie; Qu, Xiangmeng; Zhang, Hongbo; Zhu, Dan; Su, Shao; Aldalbahi, Ali; Wang, Lianhui; Pei, Hao

    2017-03-08

    Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications.

  17. 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.

  18. A fluorescent probe for detection of histidine in cellular homogenate and ovalbumin based on the strategy of click chemistry.

    PubMed

    Qiu, Suyan; Miao, Miao; Wang, Tianxi; Lin, Zhenyu; Guo, Longhua; Qiu, Bin; Chen, Guonan

    2013-04-15

    A sensitive and selective fluorescent probe for histidine has been designed by taking the advantages of the click chemistry reaction (copper(I)-catalyzed azides and alkynes cycloaddition) and the inhibition of copper(II)-induced ascorbate oxidation by histidine. The fluorescence intensity decreases with the increasing of histidine concentration, and the value of F₀/F shows a good linear relationship with the concentration of histidine over the range of 0.5-100 μM with a detection limit of 76 nM, which is lower than those of many other fluorescent sensors. Moreover, the sensor has high specificity for histidine compared to some potential interferents, such as other amino acids and metal ions. In addition, the proposed sensor has been applied to determine histidine in cellular homogenate and ovalbumin samples with satisfactory results. The preferable simplicity, sensitivity and specificity for the detection of histidine indicate that the proposed sensor have potential prospect in environmental and biomedical analysis.

  19. 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.

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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.

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

    SciTech Connect

    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 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. 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.

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

    DOE PAGES

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; ...

    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

  4. Micro-connectomics: probing the organization of neuronal networks at the cellular scale.

    PubMed

    Schröter, Manuel; Paulsen, Ole; Bullmore, Edward T

    2017-03-01

    Defining the organizational principles of neuronal networks at the cellular scale, or micro-connectomics, is a key challenge of modern neuroscience. In this Review, we focus on graph theoretical parameters of micro-connectome topology, often informed by economical principles that conceptually originated with Ramón y Cajal's conservation laws. First, we summarize results from studies in intact small organisms and in samples from larger nervous systems. We then evaluate the evidence for an economical trade-off between biological cost and functional value in the organization of neuronal networks. Various results suggest that many aspects of neuronal network organization are indeed the outcome of competition between these two fundamental selection pressures.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. A cysteine-selective fluorescent probe for the cellular detection of cysteine.

    PubMed

    Jung, Hyo Sung; Han, Ji Hye; Pradhan, Tuhin; Kim, Sooyeon; Lee, Seok Won; Sessler, Jonathan L; Kim, Tae Woo; Kang, Chulhun; Kim, Jong Seung

    2012-01-01

    A series of coumarin fluorophores (1-3), each bearing a double bond conjugated quinoline unit that can undergo a Michael-type reaction with thiol-containing compounds, is reported. These systems, designed to provide so-called turn-on changes in fluorescence response when exposed to thiols, act as fluorescent chemical sensors for cysteine (Cys), homocysteine (Hcy), and glutathione (GSH). In the case of 1, selectivity for Cys over Hcy and GSH is observed, both in terms of analyte-induced signal enhancement and response time. On the basis of fluorescence spectroscopic analyses, DFT calculations, and pH dependent studies this substrate selectivity is ascribed to steric interactions between the substituents on the quinolone units present in 1 and the targeted thiols, as well as to the comparatively lower pK(a) value of Cys relative to Hcy and GSH. In aqueous solution, probe 1 was found capable of detecting Cys with a detection limit of 10(-7) m. This system was successfully applied to the fluorescence imaging of intracellular Cys in HepG2 cells.

  10. Cell adhesion: integrating cytoskeletal dynamics and cellular tension

    PubMed Central

    Parsons, J. Thomas; Horwitz, Alan Rick; Schwartz, Martin A.

    2010-01-01

    Cell migration affects all morphogenetic processes and contributes to numerous diseases, including cancer and cardiovascular disease. For most cells in most environments, movement begins with protrusion of the cell membrane followed by the formation of new adhesions at the cell front that link the actin cytoskeleton to the substratum, generation of traction forces that move the cell forwards and disassembly of adhesions at the cell rear. Adhesion formation and disassembly drive the migration cycle by activating Rho GTPases, which in turn regulate actin polymerization and myosin II activity, and therefore adhesion dynamics. PMID:20729930

  11. Cell-surface sensors for real-time probing of cellular environments

    NASA Astrophysics Data System (ADS)

    Zhao, Weian; Schafer, Sebastian; Choi, Jonghoon; Yamanaka, Yvonne J.; Lombardi, Maria L.; Bose, Suman; Carlson, Alicia L.; Phillips, Joseph A.; Teo, Weisuong; Droujinine, Ilia A.; Cui, Cheryl H.; Jain, Rakesh K.; Lammerding, Jan; Love, J. Christopher; Lin, Charles P.; Sarkar, Debanjan; Karnik, Rohit; Karp, Jeffrey M.

    2011-08-01

    The ability to explore cell signalling and cell-to-cell communication is essential for understanding cell biology and developing effective therapeutics. However, it is not yet possible to monitor the interaction of cells with their environments in real time. Here, we show that a fluorescent sensor attached to a cell membrane can detect signalling molecules in the cellular environment. The sensor is an aptamer (a short length of single-stranded DNA) that binds to platelet-derived growth factor (PDGF) and contains a pair of fluorescent dyes. When bound to PDGF, the aptamer changes conformation and the dyes come closer to each other, producing a signal. The sensor, which is covalently attached to the membranes of mesenchymal stem cells, can quantitatively detect with high spatial and temporal resolution PDGF that is added in cell culture medium or secreted by neighbouring cells. The engineered stem cells retain their ability to find their way to the bone marrow and can be monitored in vivo at the single-cell level using intravital microscopy.

  12. 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.

  13. 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.

  14. Cell-surface sensors for real-time probing of cellular environments

    PubMed Central

    Zhao, Weian; Schafer, Sebastian; Choi, Jonghoon; Yamanaka, Yvonne J.; Lombardi, Maria L.; Bose, Suman; Carlson, Alicia L.; Phillips, Joseph A.; Teo, Weisuong; Droujinine, Ilia A.; Cui, Cheryl H.; Jain, Rakesh K.; Lammerding, Jan; Love, J. Christopher; Lin, Charles P.; Sarkar, Debanjan; Karnik, Rohit; Karp, Jeffrey M.

    2011-01-01

    The ability to explore cell signalling and cell-to-cell communication is essential for understanding cell biology and developing effective therapeutics. However, it is not yet possible to monitor the interaction of cells with their environments in real time. Here, we show that a fluorescent sensor attached to a cell membrane can detect signalling molecules in the cellular environment. The sensor is an aptamer (a short length of single-stranded DNA) that binds to platelet-derived growth factor (PDGF) and contains a pair of fluorescent dyes. When bound to PDGF, the aptamer changes conformation and the dyes come closer to each other, producing a signal. The sensor, which is covalently attached to the membranes of mesenchymal stem cells, can quantitatively detect with high spatial and temporal resolution PDGF that is added in cell culture medium or secreted by neighbouring cells. The engineered stem cells retain their ability to find their way to the bone marrow and can be monitored in vivo at the single-cell level using intravital microscopy. PMID:21765401

  15. Cellular Transport and Membrane Dynamics of the Glycine Receptor

    PubMed Central

    Dumoulin, Andrea; Triller, Antoine; Kneussel, Matthias

    2009-01-01

    Regulation of synaptic transmission is essential to tune individual-to-network neuronal activity. One way to modulate synaptic strength is to regulate neurotransmitter receptor numbers at postsynaptic sites. This can be achieved either through plasma membrane insertion of receptors derived from intracellular vesicle pools, a process depending on active cytoskeleton transport, or through surface membrane removal via endocytosis. In parallel, lateral diffusion events along the plasma membrane allow the exchange of receptor molecules between synaptic and extrasynaptic compartments, contributing to synaptic strength regulation. In recent years, results obtained from several groups studying glycine receptor (GlyR) trafficking and dynamics shed light on the regulation of synaptic GlyR density. Here, we review (i) proteins and mechanisms involved in GlyR cytoskeletal transport, (ii) the diffusion dynamics of GlyR and of its scaffolding protein gephyrin that control receptor numbers, and its relationship with synaptic plasticity, and (iii) adaptative changes in GlyR diffusion in response to global activity modifications, as a homeostatic mechanism. PMID:20161805

  16. 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.

  17. 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

  18. Simultaneous optical and mechanical probes to investigate complex cellular responses to physical cues

    NASA Astrophysics Data System (ADS)

    Haase, Kristina; Al-Rekabi, Zeinab; Guolla, Louise; Hickey, Ryan; Tremblay, Dominique; Pelling, Andrew E.

    2015-03-01

    Living cells possess an exquisite ability to sense and respond to physical information in their microenvironment. This ability plays a key role in many fundamentally important physiological and pathological processes. We will describe our work utilizing a variety of biophysical tools to investigate the dynamic responses of cells to mechanical stimuli and how physical cues can be employed to re-purpose and manipulate biological processes. These responses to physical cues are not simply a side-product of biology but are key components of biological and physical feedback loops that govern the life of a cell.

  19. 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

  20. Metal Chelation as a Powerful Strategy to Probe Cellular Circuitry Governing Fungal Drug Resistance and Morphogenesis

    PubMed Central

    Averette, Anna F.; Lee, Soo Chan; Kim, Taeyup; Bahn, Yong-Sun; Robbins, Nicole; Heitman, Joseph; Cowen, Leah E.

    2016-01-01

    Fungal pathogens have evolved diverse strategies to sense host-relevant cues and coordinate cellular responses, which enable virulence and drug resistance. Defining circuitry controlling these traits opens new opportunities for chemical diversity in therapeutics, as the cognate inhibitors are rarely explored by conventional screening approaches. This has great potential to address the pressing need for new therapeutic strategies for invasive fungal infections, which have a staggering impact on human health. To explore this approach, we focused on a leading human fungal pathogen, Candida albicans, and screened 1,280 pharmacologically active compounds to identify those that potentiate the activity of echinocandins, which are front-line therapeutics that target fungal cell wall synthesis. We identified 19 compounds that enhance activity of the echinocandin caspofungin against an echinocandin-resistant clinical isolate, with the broad-spectrum chelator DTPA demonstrating the greatest synergistic activity. We found that DTPA increases susceptibility to echinocandins via chelation of magnesium. Whole genome sequencing of mutants resistant to the combination of DTPA and caspofungin identified mutations in the histidine kinase gene NIK1 that confer resistance to the combination. Functional analyses demonstrated that DTPA activates the mitogen-activated protein kinase Hog1, and that NIK1 mutations block Hog1 activation in response to both caspofungin and DTPA. The combination has therapeutic relevance as DTPA enhanced the efficacy of caspofungin in a mouse model of echinocandin-resistant candidiasis. We found that DTPA not only reduces drug resistance but also modulates morphogenesis, a key virulence trait that is normally regulated by environmental cues. DTPA induced filamentation via depletion of zinc, in a manner that is contingent upon Ras1-PKA signaling, as well as the transcription factors Brg1 and Rob1. Thus, we establish a new mechanism by which metal chelation

  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. 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

  3. 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.

  4. Cellular dynamics of the negative transcription elongation factor NELF

    SciTech Connect

    Yung, Tetsu M.C.; Narita, Takashi; Komori, Toshiharu; Yamaguchi, Yuki; Handa, Hiroshi

    2009-06-10

    Negative Elongation Factor (NELF) is a transcription factor discovered based on its biochemical activity to suppress transcription elongation, and has since been implicated in various diseases ranging from neurological disorders to cancer. Besides its role in promoter-proximal pausing of RNA polymerase II during early stages of transcription, recently we found that it also plays important roles in the 3'-end processing of histone mRNA. Furthermore, NELF has been found to form a distinct subnuclear structure, which we named NELF bodies. These recent developments point to a wide range of potential functions for NELF, and, as most studies on NELF thus far had been carried out in vitro, here, we prepared a complete set of fusion protein constructs of NELF subunits and carried out a general cell biological study of the intracellular dynamics of NELF. Our data show that NELF subunits exhibit highly specific subcellular localizations, such as in NELF bodies or in midbodies, and some shuttle actively between the nucleus and cytoplasm. We further show that loss of NELF from cells can lead to enlarged and/or multiple nuclei. This work serves as a foundation and starting point for further cell biological investigations of NELF in the future.

  5. Rational design of reversible fluorescent probes for live-cell imaging and quantification of fast glutathione dynamics

    NASA Astrophysics Data System (ADS)

    Umezawa, Keitaro; Yoshida, Masafumi; Kamiya, Mako; Yamasoba, Tatsuya; Urano, Yasuteru

    2016-11-01

    Alterations in glutathione (GSH) homeostasis are associated with a variety of diseases and cellular functions, and therefore, real-time live-cell imaging and quantification of GSH dynamics are important for understanding pathophysiological processes. However, existing fluorescent probes are unsuitable for these purposes due to their irreversible fluorogenic mechanisms or slow reaction rates. In this work, we have successfully overcome these problems by establishing a design strategy inspired by Mayr's work on nucleophilic reaction kinetics. The synthesized probes exhibit concentration-dependent, reversible and rapid absorption/fluorescence changes (t1/2 = 620 ms at [GSH] = 1 mM), as well as appropriate Kd values (1-10 mM: within the range of intracellular GSH concentrations). We also developed FRET-based ratiometric probes, and demonstrated that they are useful for quantifying GSH concentration in various cell types and also for real-time live-cell imaging of GSH dynamics with temporal resolution of seconds.

  6. Imaging Cellular Dynamics with Spectral Relaxation Imaging Microscopy: Distinct Spectral Dynamics in Golgi Membranes of Living Cells

    PubMed Central

    Lajevardipour, Alireza; Chon, James W. M.; Chattopadhyay, Amitabha; Clayton, Andrew H. A.

    2016-01-01

    Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics. PMID:27872481

  7. Imaging Cellular Dynamics with Spectral Relaxation Imaging Microscopy: Distinct Spectral Dynamics in Golgi Membranes of Living Cells

    NASA Astrophysics Data System (ADS)

    Lajevardipour, Alireza; Chon, James W. M.; Chattopadhyay, Amitabha; Clayton, Andrew H. A.

    2016-11-01

    Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics.

  8. 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.

  9. 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

  10. Dynamic interactions between 14-3-3 proteins and phosphoproteins regulate diverse cellular processes

    PubMed Central

    2004-01-01

    14-3-3 proteins exert an extraordinarily widespread influence on cellular processes in all eukaryotes. They operate by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. In these ways, 14-3-3s ‘finish the job’ when phosphorylation alone lacks the power to drive changes in the activities of intracellular proteins. By interacting dynamically with phosphorylated proteins, 14-3-3s often trigger events that promote cell survival – in situations from preventing metabolic imbalances caused by sudden darkness in leaves to mammalian cell-survival responses to growth factors. Recent work linking specific 14-3-3 isoforms to genetic disorders and cancers, and the cellular effects of 14-3-3 agonists and antagonists, indicate that the cellular complement of 14-3-3 proteins may integrate the specificity and strength of signalling through to different cellular responses. PMID:15167810

  11. 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.

  12. Temporal and mechanistic tracking of cellular uptake dynamics with novel surface fluorophore-bound nanodiamonds.

    PubMed

    Schrand, Amanda M; Lin, Jonathan B; Hens, Suzanne Ciftan; Hussain, Saber M

    2011-02-01

    Nanoparticles (NPs) offer promise for a multitude of biological applications including cellular probes at the bio-interface for targeted delivery of anticancer substances, Raman and fluorescent-based imaging and directed cell growth. Nanodiamonds (NDs), in particular, have several advantages compared to other carbon-based nanomaterials - including a rich surface chemistry useful for chemical conjugation, high biocompatibility with little reactive oxygen species (ROS) generation, physical and chemical stability that affords sterilization, high surface area to volume ratio, transparency and a high index of refraction. The visualization of ND internalization into cells is possible via photoluminescence, which is produced by direct dye conjugation or high energy irradiation that creates nitrogen vacancy centers. Here, we explore the kinetics and mechanisms involved in the intracellular uptake and localization of novel, highly-stable, fluorophore-conjugated NDs. Examination in a neuronal cell line (N2A) shows ND localization to early endosomes and lysosomes with eventual release into the cytoplasm. The addition of endocytosis and exocytosis inhibitors allows for diminished uptake and increased accumulation, respectively, which further corroborates cellular behavior in response to NDs. Ultimately, the ability of the NDs to travel throughout cellular compartments of varying pH without degradation of the surface-conjugated fluorophore or alteration of cell viability over extended periods of time is promising for their use in biomedical applications as stable, biocompatible, fluorescent probes.

  13. 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

  14. 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...

  15. Dynamic stress-strain states for metal foams using a 3D cellular model

    NASA Astrophysics Data System (ADS)

    Zheng, Zhijun; Wang, Changfeng; Yu, Jilin; Reid, Stephen R.; Harrigan, John J.

    2014-12-01

    Dynamic uniaxial impact behaviour of metal foams using a 3D cell-based finite element model is examined. At sufficiently high loading rates, these materials respond by forming ‘shock or consolidation waves' (Tan et al., 2005a, 2005b). However, the existing dynamic experimental methods have limitations in fully informing this behaviour, particularly for solving boundary/initial value problems. Recently, the problem of the shock-like response of an open-cell foam has been examined by Barnes et al. (2014) using the Hugoniot-curve representations. The present study is somewhat complementary to that approach and additionally aims to provide insight into the ‘rate sensitivity' mechanism applicable to cellular materials. To assist our understanding of the ‘loading rate sensitivity' behaviour of cellular materials, a virtual ‘test' method based on the direct impact technique is explored. Following a continuum representation of the response, the strain field calculation method is employed to determine the local strains ahead of and behind the resulting ‘shock front'. The dynamic stress-strain states in the densification stage are found to be different from the quasi-static ones. It is evident that the constitutive behaviour of the cellular material is deformation-mode dependent. The nature of the ‘rate sensitivity' revealed for cellular materials in this paper is different from the strain-rate sensitivity of dense metals. It is shown that the dynamic stress-strain states behind a shock front of the cellular material lie on a unique curve and each point on the curve corresponds to a particular ‘impact velocity', referred as the velocity upstream of the shock in this study. The dynamic stress-strain curve is related to a layer-wise collapse mode, whilst the equivalent quasi-static curve is related to a random shear band collapse mode. The findings herein are aimed at improving the experimental test techniques used to characterise the rate-sensitivity behaviour

  16. Dynamics of the Multiplicity of Cellular Infection in a Plant Virus

    PubMed Central

    Gutiérrez, Serafín; Monsion, Baptiste; Michalakis, Yannis; Blanc, Stéphane

    2010-01-01

    Recombination, complementation and competition profoundly influence virus evolution and epidemiology. Since viruses are intracellular parasites, the basic parameter determining the potential for such interactions is the multiplicity of cellular infection (cellular MOI), i.e. the number of viral genome units that effectively infect a cell. The cellular MOI values that prevail in host organisms have rarely been investigated, and whether they remain constant or change widely during host invasion is totally unknown. Here, we fill this experimental gap by presenting the first detailed analysis of the dynamics of the cellular MOI during colonization of a host plant by a virus. Our results reveal ample variations between different leaf levels during the course of infection, with values starting close to 2 and increasing up to 13 before decreasing to initial levels in the latest infection stages. By revealing wide dynamic changes throughout a single infection, we here illustrate the existence of complex scenarios where the opportunity for recombination, complementation and competition among viral genomes changes greatly at different infection phases and at different locations within a multi-cellular host. PMID:20862320

  17. 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

  18. 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.

  19. A mathematical model to study the dynamics of epithelial cellular networks.

    PubMed

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

    2012-01-01

    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).

  20. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Sliozberg, Yelena R.; Chantawansri, Tanya L.

    2016-05-01

    To elucidate the mechanism of ion transport through a transmembrane pore, all-atom molecular dynamics simulations were employed. A model membrane where a pore connects the intra- and extra-cellular compartment was considered. Pores with radii of 1.5 nm or less exhibited resealing over the course of 135 ns simulations, and ionic disturbance is minimal. Ion transport through a larger pore (2 nm radius) leads to a substantial change in the intra- and extra-cellular ionic concentrations. The influx of Na+ and Cl- ions down their concentration gradients is greater than the efflux of K+ leading to an osmotic influx of water.

  1. 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.

  2. 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

  3. 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…

  4. Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation

    PubMed Central

    Niessen, Carien M.; Leckband, Deborah; Yap, Alpha S.

    2013-01-01

    This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains; the regulation of cadherin expression at the cell surface; cooperation between cadherins and the actin cytoskeleton; and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields. PMID:21527735

  5. 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.

  6. 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.

  7. Dynamic Simulation of 1D Cellular Automata in the Active aTAM.

    PubMed

    Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

    2015-07-01

    The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location.

  8. Dynamic Simulation of 1D Cellular Automata in the Active aTAM

    PubMed Central

    Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

    2016-01-01

    The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location. PMID:27789918

  9. 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.

  10. Subtle dynamics of holo glutamine binding protein revealed with a rigid paramagnetic probe.

    PubMed

    Liu, Zhu; Gong, Zhou; Guo, Da-Chuan; Zhang, Wei-Ping; Tang, Chun

    2014-03-11

    Bacterial periplasmic binding proteins (PBPs) are involved in the translocation of small molecules in the periplasm. To unload, the two domains of a PBP open up, allowing the ligand to exit. However, it is not clear whether there are dynamics near the binding site which can facilitate the rapid dissociation of a ligand. To visualize such dynamics, we utilized paramagnetic relaxation enhancement (PRE) NMR and introduced a rigid paramagnetic probe to a PBP, glutamine-binding protein (QBP) with its cognate ligand bound. A paramagnetic Cu(II) ion is sandwiched between an engineered di-histidine motif at a helix and an NTA capping molecule. The afforded paramagnetic probe is so rigid that PRE values calculated from a single structure of holo QBP largely agree with the observed values. The remaining PRE discrepancies, however, manifest dynamics of a loop in the opposite domain from the paramagnetic probe. This loop packs against the glutamine ligand in the holo QBP and undergoes fluctuations upon ligand dissociation, as assessed by steered molecular dynamics simulations. As such, the loop dynamics, occurring for a small population in nanosecond to microsecond time scale, may be related to the ligand dissociation process. The rigid paramagnetic probe described herein can be grafted to other protein systems for structure and dynamics studies.

  11. Stochastic modeling for dynamics of HIV-1 infection using cellular automata: A review.

    PubMed

    Precharattana, Monamorn

    2016-02-01

    Recently, the description of immune response by discrete models has emerged to play an important role to study the problems in the area of human immunodeficiency virus type 1 (HIV-1) infection, leading to AIDS. As infection of target immune cells by HIV-1 mainly takes place in the lymphoid tissue, cellular automata (CA) models thus represent a significant step in understanding when the infected population is dispersed. Motivated by these, the studies of the dynamics of HIV-1 infection using CA in memory have been presented to recognize how CA have been developed for HIV-1 dynamics, which issues have been studied already and which issues still are objectives in future studies.

  12. 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

  13. Optical probing of sodium dynamics in neurons and astrocytes.

    PubMed

    Lamy, Christophe M; Chatton, Jean-Yves

    2011-09-15

    Changes in intracellular Na(+) concentration underlie essential neurobiological processes, but few reliable tools exist for their measurement. Here we characterize a new synthetic Na(+)-sensitive fluorescent dye, Asante Natrium Green (ANG), with unique properties. This indicator was excitable in the visible spectrum and by two-photon illumination, suffered little photobleaching and located to the cytosol were it remained for long durations without noticeable unwanted effects on basic cell properties. When used in brain tissue, ANG yielded a bright fluorescent signal during physiological Na(+) responses both in neurons and astrocytes. Synchronous electrophysiological and fluorometric recordings showed that ANG produced accurate Na(+) measurement in situ. This new Na(+) indicator opens innovative ways of probing neuronal circuits.

  14. Fluorescence probes of spectroscopic and dynamical aspects of molecular photoionization

    NASA Astrophysics Data System (ADS)

    Poliakoff, Erwin D.

    1988-11-01

    Studies were made of vibrationally resolved aspects of shape resonant excitation in the photoionization of N(2)0. This experiment was performed by generating dispersed fluorescence spectra from electronically excited photoions. These results are the first vibrationally resolved results on a polyatomic shape resonance. In vibrationally resolved measurements, different internuclear configurations are probed by sampling alternative vibrational levels of the ion. As a result, the continuum electron behavior can be mapped out most clearly, and the qualitative aspects of the electron ejection can be understood clearly. A central motivation for studying polyatomic shape resonances is that alternative vibrational modes may be explored, revealing facets that are nonexistent for diatomic systems, which are the only systems that have been characterized previously.

  15. Probing dynamic protein ensembles with atomic proximity measures.

    PubMed

    Gáspári, Zoltán; Angyán, Annamária F; Dhir, Somdutta; Franklin, Dino; Perczel, András; Pintar, Alessandro; Pongor, Sándor

    2010-11-01

    The emerging role of internal dynamics in protein fold and function requires new avenues of structure analysis. We analyzed the dynamically restrained conformational ensemble of ubiquitin generated from residual dipolar coupling data, in terms of protruding and buried atoms as well as interatomic distances, using four proximity-based algorithms, CX, DPX, PRIDE and PRIDE-NMR (http://hydra.icgeb.trieste.it/protein/). We found that Ubiquitin, this relatively rigid molecule has a highly diverse dynamic ensemble. The environment of protruding atoms is highly variable across conformers, on the other hand, only a part of buried atoms tends to fluctuate. The variability of the ensemble cautions against the use of single conformers when explaining functional phenomena. We also give a detailed evaluation of PRIDE-NMR on a wide dataset and discuss its usage in the light of the features of available NMR distance restraint sets in public databases.

  16. 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

  17. CO2 exploding cluster dynamics probed by XUV fluorescence

    NASA Astrophysics Data System (ADS)

    Negro, M.; Ruf, H.; Fabre, B.; Dorchies, F.; Devetta, M.; Staedter, D.; Vozzi, C.; Mairesse, Y.; Stagira, S.

    2014-07-01

    Clusters excited by intense laser pulses are a unique source of warm dense matter, that has been the subject of intensive experimental studies. The majority of these investigations concern atomic clusters, whereas the evolution of molecular clusters excited by intense laser pulses is less explored. In this work we trace the dynamics of C{{O}_{2}} clusters triggered by a few-cycle 1.45\\;\\mu m driving pulse through the detection of XUV fluorescence induced by a delayed 800 nm ignition pulse. Striking differences among fluorescence dynamics from different ionic species are observed.

  18. 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

  19. Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

    DTIC Science & Technology

    2008-07-17

    Medical Research and Materiel Command, Fort Detrick, Maryland #Department of Cell Biology and Biochemistry , U.S. Army Medical Research Institute of...Molecular dynamics of n- alkanes ," J. Comput. Phys., vol. 23, pp. 327-341, 1977. [24] S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M

  20. 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.

  1. 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.

  2. Anderson Mobility Gap Probed by Dynamic Coherent Backscattering.

    PubMed

    Cobus, L A; Skipetrov, S E; Aubry, A; van Tiggelen, B A; Derode, A; Page, J H

    2016-05-13

    We use dynamic coherent backscattering to study one of the Anderson mobility gaps in the vibrational spectrum of strongly disordered three-dimensional mesoglasses. Comparison of experimental results with the self-consistent theory of localization allows us to estimate the localization (correlation) length as a function of frequency in a wide spectral range covering bands of diffuse transport and a mobility gap delimited by two mobility edges. The results are corroborated by transmission measurements on one of our samples.

  3. 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.

  4. 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.

  5. Probing Molecular Organization and Electronic Dynamics at Buried Organic Interfaces

    NASA Astrophysics Data System (ADS)

    Roberts, Sean

    2015-03-01

    Organic semiconductors are a promising class of materials due to their ability to meld the charge transport capabilities of semiconductors with many of the processing advantages of plastics. In thin film organic devices, interfacial charge transfer often comprises a crucial step in device operation. As molecular materials, the density of states within organic semiconductors often reflect their intermolecular organization. Truncation of the bulk structure of an organic semiconductor at an interface with another material can lead to substantial changes in the density of states near the interface that can significantly impact rates for interfacial charge and energy transfer. Here, we will present the results of experiments that utilize electronic sum frequency generation (ESFG) to probe buried interfaces in these materials. Within the electric dipole approximation, ESFG is only sensitive to regions of a sample that experience a breakage of symmetry, which occurs naturally at material interfaces. Through modeling of signals measured for thin organic films using a transfer matrix-based formalism, signals from buried interfaces between two materials can be isolated and used to uncover the interfacial density of states.

  6. 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.

  7. Nuclear magnetic resonance probes of membrane biophysics: Structure and dynamics

    NASA Astrophysics Data System (ADS)

    Leftin, Avigdor

    The phospholipid membrane is a self-assembled, dynamic molecular system that may exist alone in association with only water, or in complex systems comprised of multiple lipid types and proteins. In this dissertation the intra- and inter-molecular forces responsible for the atomistic, molecular and collective equilibrium structure and dynamics are studied by nuclear magnetic resonance spectroscopy (NMR). The multinuclear NMR measurements and various experimental techniques are able to provide data that enable the characterization of the hierarchical spatio-temporal organization of the phospholipid membrane. The experimental and theoretical studies conducted target membrane interactions ranging from model systems composed of only water and lipids, to multiple component domain forming membranes that are in association with peripheral and trans-membrane proteins. These measurements consisit of frequency spectrum lineshapes and nuclear-spin relaxation rates obtained using 2H NMR, 13C NMR, 31P NMR and 1H NMR. The changes of these experimental observables are interpreted within a statistical thermodynamic framework that allows the membrane structure, activation energies, and correlation times of motion to be determined. The cases presented demonstrate how fundamental principles of NMR spectroscopy may be applied to a host of membranes, leading to the biophysical characterization of membrane structure and dynamics.

  8. Yielding and post-yield behaviour of closed-cell cellular materials under multiaxial dynamic loading

    NASA Astrophysics Data System (ADS)

    Vesenjak, Matej; Ren, Zoran

    2016-05-01

    The paper focuses on characterisation of yielding and post-yield behaviour of metals with closed-cell cellular structure when subjected to multiaxial dynamic loading, considering the influence of the relative density, base material, strain rate and pore gas pressure. Research was conducted by extensive parametric fully-coupled computational simulations using the finite element code LS-DYNA. Results have shown that the macroscopic yield stress of cellular material rises with increase of the relative density, while its dependence on the hydrostatic stress decreases. The yield limit also rises with increase of the strain rate, while the hydrostatic stress influence remains more or less the same at different strain-rates. The macroscopic yield limit of the cellular material is also strongly influenced by the choice of base material since the base materials with higher yield limit contribute also to higher macroscopic yield limit of the cellular material. By increasing the pore gas filler pressure the dependence on hydrostatic stress increases while at the same time the yield surface shifts along the hydrostatic axis in the negative direction. This means that yielding at compression is delayed due to influence of the initial pore pressure and occurs at higher compressive loading, while the opposite is true for tensile loading.

  9. A general formalism for tissue morphogenesis based on cellular dynamics and control system interactions.

    PubMed

    Forest, Loïc; Demongeot, Jacques

    2008-06-01

    Morphogenesis is a key process in developmental biology. An important issue is the understanding of the generation of shape and cellular organisation in tissues. Despite of their great diversity, morphogenetic processes share common features. This work is an attempt to describe this diversity using the same formalism based on a cellular description. Tissue is seen as a multi-cellular system whose behaviour is the result of all constitutive cells dynamics. Morphogenesis is then considered as a spatiotemporal organization of cells activities. We show how this formalism relies on Reaction-Diffusion/Positional Information approach and how it permits to generalize its modelling possibilities. Three quite different applications for concrete morphogenetic processes are presented. The first one is a model for epithelial invagination, the second is a model of cellular differentiation by local cell-cell signalling. The last example is the secondary radial growth of conifer trees. From the mathematical point of view, different modelling tools are used according to the specificity of each process.

  10. Regeneration in Macrostomum lignano (Platyhelminthes): cellular dynamics in the neoblast stem cell system.

    PubMed

    Nimeth, Katharina Theresia; Egger, Bernhard; Rieger, Reinhard; Salvenmoser, Willi; Peter, Roland; Gschwentner, Robert

    2007-03-01

    Neoblasts are potentially totipotent stem cells and the only proliferating cells in adult Platyhelminthes. We have examined the cellular dynamics of neoblasts during the posterior regeneration of Macrostomum lignano. Double-labeling of neoblasts with bromodeoxyuridine and the anti-phospho histone H3 mitosis marker has revealed a complex cellular response in the first 48 h after amputation; this response is different from that known to occur during regeneration in triclad platyhelminths and in starvation/feeding experiments in M. lignano. Mitotic activity is reduced during the first 8 h of regeneration but, at 48 h after amputation, reaches almost twice the value of control animals. The total number of S-phase cells significantly increases after 1 day of regeneration. A subpopulation of fast-cycling neoblasts surprisingly shows the same dynamics during regeneration as those in control animals. Wound healing and regeneration are accompanied by the formation of a distinct blastema. These results present new insights, at the cellular level, into the early regeneration of rhabditophoran Platyhelminthes.

  11. 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.

  12. 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.

  13. Reduced Humidity Effects on Probe Nano-Oxidation Investigated Using Dynamic Force Microscope

    NASA Astrophysics Data System (ADS)

    Kuramochi, Hiromi; Ando, Kazunori; Tokizaki, Takashi; Yokoyama, Hiroshi

    2006-03-01

    Humidity effects on nano-oxidation are investigated using a dynamic force microscope in the humidity range of 30-60%. Oxide size and detected faradaic current increased with relative humidity and applied voltage. The aspect ratios of fabricated oxides at various humidities are approximately of the same magnitude. Scanning probe microscope nano-oxidation in the dynamic mode is less subject to the relative humidity than that in the contact mode.

  14. Probing the dynamics of photosynthetic membranes with fluorescence recovery after photobleaching.

    PubMed

    Mullineaux, Conrad W; Sarcina, Mary

    2002-06-01

    In the past few years, there has been remarkable progress in knowledge of the structures and organization of the protein complexes of photosynthetic membranes. However, static structures do not tell the whole story. Photosynthetic membranes, like other biological membranes, are dynamic systems. Recent technological advances are making it increasingly easy to probe the dynamics of photosynthetic membranes using fluorescence recovery after photobleaching. Here we explain the potential and the limitations of the technique.

  15. On Diversity of Configurations Generated by Excitable Cellular Automata with Dynamical Excitation Intervals

    NASA Astrophysics Data System (ADS)

    Adamatzky, Andrew

    2012-11-01

    Excitable cellular automata with dynamical excitation interval exhibit a wide range of space-time dynamics based on an interplay between propagating excitation patterns which modify excitability of the automaton cells. Such interactions leads to formation of standing domains of excitation, stationary waves and localized excitations. We analyzed morphological and generative diversities of the functions studied and characterized the functions with highest values of the diversities. Amongst other intriguing discoveries we found that upper boundary of excitation interval more significantly affects morphological diversity of configurations generated than lower boundary of the interval does and there is no match between functions which produce configurations of excitation with highest morphological diversity and configurations of interval boundaries with highest morphological diversity. Potential directions of future studies of excitable media with dynamically changing excitability may focus on relations of the automaton model with living excitable media, e.g. neural tissue and muscles, novel materials with memristive properties and networks of conductive polymers.

  16. 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.

  17. Studying complex fluids and crystal formation using Dynamic Light Scattering and Optical Probe Diffusion

    NASA Astrophysics Data System (ADS)

    Streletzky, Kiril A.

    2004-10-01

    Dynamic light scattering (DLS) spectroscopy provides non-destructive analytic technique for probing structure and dynamics of polymer solutions, colloids, micellar systems, liquid crystals, and, in some cases, observation of nucleation and crystal growth. The method of optical probe diffusion uses DLS to measure transport of dilute mesoscopic probes in a complex fluid solution. If tracer particles are the dominant scatterers in solution, their diffusion provides important information for inferring physical properties of the complex fluid. In situ nature of DLS allows non-invasive studies of different chemical and physical processes such as polymer and colloidal diffusion, gelation, micellar aggregation and dynamics. DLS is also useful for studying critical behavior of liquid crystals and for observing crystallization from clear solutions. The highlights of our results obtained using DLS and optical probe diffusion are presented. These examples include: a) research on polymer dynamics in dilute and concentrated solutions of a neutral HPC polymer; b) project on aggregation and transport of spherical Tx-100 micelles; c) study of crystallization of molecular sieve zeolite NaA.

  18. Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics.

    PubMed

    Ho, Mon-Shu; Huang, Chih-Pong; Tsai, Jyun-Hwei; Chou, Che-Fu; Lee, Wen-Jay

    2016-09-28

    This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors. Molecular dynamics (MD) method with semi-empirical potential can be used to study the nanoindentation of C84-embedded Si substrate. A detailed description for performing MD simulation is presented here. Details for a comprehensive study on mechanical analysis of MD simulation such as indentation force, Young's modulus, surface stiffness, atomic stress, and atomic strain are included. The atomic stress and von-Mises strain distributions of the indentation model can be calculated to monitor deformation mechanism with time evaluation in atomistic level.

  19. 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.

  20. Generation and precise control of dynamic biochemical gradients for cellular assays

    NASA Astrophysics Data System (ADS)

    Saka, Yasushi; MacPherson, Murray; Giuraniuc, Claudiu V.

    2017-03-01

    Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusion-based gradient generation for cellular assays. A unique channel design of the device eliminates cross-flow between the source and sink channels, thereby stabilizing gradients by passive diffusion. The platform also enables quick and flexible control of chemical concentration that makes highly dynamic gradients in diffusion chambers. A model with the first approximation of diffusion and surface adsorption of molecules recapitulates the experimentally observed gradients. Budding yeast cells cultured in a gradient of a chemical inducer expressed a reporter fluorescence protein in a concentration-dependent manner. This microfluidic platform serves as a versatile prototype applicable to a broad range of biomedical investigations.

  1. 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.

  2. 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.

  3. 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.

  4. State-resolved probes of methane dissociation dynamics

    NASA Astrophysics Data System (ADS)

    Juurlink, L. B. F.; Killelea, D. R.; Utz, A. L.

    2009-04-01

    A new generation of experimental techniques quantifies the gas-surface reactivity of polyatomic reactants prepared in a single quantum state. These experiments eliminate internal state averaging and permit reactivity measurements on molecules with well-defined internal and translational energy. Varying the identity of the selected vibrational and rotational state and the molecule’s translational energy reveals how energy in specific energetic coordinates promotes reaction. When applied to methane’s dissociative chemisorption, which is rate-limiting in the industrial steam reforming reaction, these experiments reveal the molecular basis for activation, and they provide detailed insight into energy flow dynamics prior to reaction. This review will focus on experiments that quantify the reactivity of methane prepared in select rovibrational quantum states via optical excitation in a supersonic molecular beam. An overview will provide context, and a survey of experimental methods will emphasize features unique to these experiments. A presentation and discussion of state-resolved beam-surface scattering studies of methane activation on Ni(1 1 1), Ni(1 0 0), and Pt(1 1 1) will highlight the mechanistic and dynamical insights that such studies can provide. For example, while C-H stretching excitation best promotes transition state access on Ni(1 1 1) and Ni(1 0 0), bending excitation also activates dissociation, suggesting that many different energetic coordinates contribute to reactivity. Among those states studied, non-statistical behavior, including vibrational mode-specific and even bond-selective chemistry, is widespread, which indicates that the assumptions underlying statistical rate theories do not apply to this reaction. We examine the relevant timescales for energy exchange and reaction to provide a plausible explanation for the observation of non-statistical behavior. Finally, we suggest how these methods, and the results they have produced, might guide

  5. 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

  6. 3D Probed Lipid Dynamics in Small Unilamellar Vesicles.

    PubMed

    Chao, Meng-Hsuan; Lin, Yen-Ting; Dhenadhayalan, Namasivayam; Lee, Hsin-Lung; Lee, Hsin-Yen; Lin, King-Chuen

    2017-04-01

    Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane. First, the isomerization feasibility may be restricted by the addition of cholesterols, which form structure conjugation with DiD chromophore. Second, the oxygen transport is prevented from the ultrasmall cluster and cholesterol-rich regions, whereas it can pass through the membrane region with liquid-disordered phase (Ld ) and defects. Third, by analyzing 2D spectra correlating the lipid diffusion coefficient and triplet-state lifetime, the heterogeneity in lipid bilayer can be precisely visualized such as lipid domain with different phases, the defects of lipid packing, and DiD-induced "bouquet" ultrasmall clusters.

  7. 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.

  8. Directly probing spin dynamics in insulating antiferromagnets using ultrashort terahertz pulses

    SciTech Connect

    Bowlan, Pamela Renee; Trugman, Stuart Alan; Wang, X.; Dai, Yaomin; Cheong, S.-W.; Bauer, Eric Dietzgen; Taylor, Antoinette Jane; Yarotski, Dmitry Anatolievitch; Prasankumar, Rohit Prativadi

    2016-11-22

    We investigate spin dynamics in the antiferromagnetic (AFM) multiferroic TbMnO3 using opticalpump, terahertz (THz)-probe spectroscopy. Photoexcitation results in a broadband THz transmission change, with an onset time of 25 ps at 6 K that becomes faster at higher temperatures. We attribute this time constant to spin-lattice thermalization. The excellent agreement between our measurements and previous ultrafast resonant x-ray diffraction measurements on the same material confirms that our THz pulse directly probes spin order. We suggest that this could be the case in general for insulating AFM materials, if the origin of the static absorption in the THz spectral range is magnetic.

  9. Measuring and modeling cellular contact guidance through dynamic sensing of nanotopography

    NASA Astrophysics Data System (ADS)

    Guven, Can; Driscoll, Meghan; Sun, Xiaoyu; Fourkas, John; Losert, Wolfgang

    2013-03-01

    We investigate the shape dynamics of the amoeba Dictyostelium discoideum on nanotopographical gratings. Multiple studies have previously implicated the patterning of focal adhesion complexes (FACs) in contact guidance. However, we observe significant contact guidance of Dictyostelium along ridge-shaped nano- and microtopographic surface features, even though Dictyostelium lacks FACs. We measure the surface contact guidance efficiency, which we calculate from the statistics of cell orientations, as a function of the distance between parallel ridges. Ridges with a spacing of about 1.5 μm lead to the greatest contact guidance efficiency. We previously observed that Dictyostelium cells exhibit oscillatory shape dynamics. Therefore, we model contact guidance as a resonance between the cell oscillations and the nanogratings. In particular, we model cells as stochastic cellular harmonic oscillators that couple to the periodicity of the ridges. The spatial and temporal scales of the oscillations that best couple to the surface are consistent with those of protrusive dynamics. Our results suggest that the coupling of protrusive dynamics, which are governed by actin dynamics, to surface topography is one possible mechanism for contact guidance.

  10. 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

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

    SciTech Connect

    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.

    2016-05-23

    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 ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.

  12. 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

    2016-05-23

    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. 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.

  13. Nano-oxidation and in situ faradaic current detection using dynamic carbon nanotube probes

    NASA Astrophysics Data System (ADS)

    Kuramochi, H.; Ando, K.; Shikakura, Y.; Yasutake, M.; Tokizaki, T.; Yokoyama, H.

    2004-09-01

    Carbon nanotube-attached atomic force microscope probes were successfully used without nanotube bending to make simultaneous precision nano-oxidation and faradaic current measurements in the dynamic mode. Probe oxidation on H-passivated Si(001) surfaces was carried out by two methods involving vector-scan and raster-scan with a much higher resolution and precision compared to the nanofabrication by standard cantilevers. Faradaic current of the order of a sub-picoampere was detected during nano-oxidation using a carbon nanotube probe, accurately reflecting the subtle difference in the oxidation reaction. The minute current detection through the AFM tip is sensitive enough for the detection of very thin oxides and small-sized features. The dimension of the meniscus during nano-oxidation, which is indispensable for establishing the mechanism model, was evaluated, based on the in situ faradaic current detection and edge broadening.

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

    DOE PAGES

    Picón, A.; Lehmann, C. S.; Bostedt, C.; ...

    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

  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

    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.

  17. Applying Attractor Dynamics to Infer Gene Regulatory Interactions Involved in Cellular Differentiation.

    PubMed

    Ghaffarizadeh, Ahmadreza; Podgorski, Gregory J; Flann, Nicholas S

    2017-02-27

    The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort. This work presents a novel approach to discovering biologically plausible gene regulatory interactions that control cellular differentiation. This method integrates known cell type expression data, genetic interactions, and knowledge of the effects of gene knockouts to determine likely GRN regulatory functions. We employ a genetic algorithm to search for candidate GRNs that use a set of transcription factors that control differentiation within a lineage. Nested canalyzing functions are used to constrain the search space to biologically plausible networks. The method identifies an ensemble of GRNs whose dynamics reproduce the gene expression pattern for each cell type within a particular lineage. The method's effectiveness was tested by inferring consensus GRNs for myeloid and pancreatic cell differentiation and comparing the predicted gene regulatory interactions to manually derived interactions. We identified many regulatory interactions reported in the literature and also found differences from published reports. These discrepancies suggest areas for biological studies of myeloid and pancreatic differentiation. We also performed a study that used defined synthetic networks to evaluate the accuracy of the automated search method and found that the search algorithm was able to discover the regulatory interactions in these defined networks with high accuracy. We suggest that the GRN functions derived from the methods described here can be used to fill

  18. 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.

  19. Cyclosporin-A-induced prion protein aggresomes are dynamic quality-control cellular compartments.

    PubMed

    Ben-Gedalya, Tziona; Lyakhovetsky, Roman; Yedidia, Yifat; Bejerano-Sagie, Michal; Kogan, Natalya M; Karpuj, Marcela Viviana; Kaganovich, Daniel; Cohen, Ehud

    2011-06-01

    Despite the activity of cellular quality-control mechanisms, subsets of mature and newly synthesized polypeptides fail to fold properly and form insoluble aggregates. In some cases, protein aggregation leads to the development of human neurodegenerative maladies, including Alzheimer's and prion diseases. Aggregates of misfolded prion protein (PrP), which appear in cells after exposure to the drug cyclosporin A (CsA), and disease-linked PrP mutants have been found to accumulate in juxtanuclear deposition sites termed 'aggresomes'. Recently, it was shown that cells can contain at least two types of deposition sites for misfolded proteins: a dynamic quality-control compartment, which was termed 'JUNQ', and a site for terminally aggregated proteins called 'IPOD'. Here, we show that CsA-induced PrP aggresomes are dynamic structures that form despite intact proteasome activity, recruit chaperones and dynamically exchange PrP molecules with the cytosol. These findings define the CsA-PrP aggresome as a JUNQ-like dynamic quality-control compartment that mediates the refolding or degradation of misfolded proteins. Together, our data suggest that the formation of PrP aggresomes protects cells from proteotoxic stress.

  20. 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.

  1. 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

  2. Dynamic metabolic flux analysis--tools for probing transient states of metabolic networks.

    PubMed

    Antoniewicz, Maciek R

    2013-12-01

    Computational approaches for analyzing dynamic states of metabolic networks provide a practical framework for design, control, and optimization of biotechnological processes. In recent years, two promising modeling approaches have emerged for characterizing transients in cellular metabolism, dynamic metabolic flux analysis (DMFA), and dynamic flux balance analysis (DFBA). Both approaches combine metabolic network analysis based on pseudo steady-state (PSS) assumption for intracellular metabolism with dynamic models for extracellular environment. One strategy to capture dynamics is by combining network analysis with a kinetic model. Predictive models are thus established that can be used to optimize bioprocessing conditions and identify useful genetic manipulations. Alternatively, by combining network analysis with methods for analyzing extracellular time-series data, transients in intracellular metabolic fluxes can be determined and applied for process monitoring and control.

  3. 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

  4. Probing the dynamics of Andreev states in a coherent normal/superconducting ring.

    PubMed

    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.

  5. 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

  6. 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.

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

    DOE PAGES

    Li, Y.; Zakharov, D.; Zhao, S.; ...

    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

  8. 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.

  9. Dynamical changes of ion current distribution for a Penning discharge source using a Langmuir probe arraya)

    NASA Astrophysics Data System (ADS)

    Li, M.; Xiang, W.; Xiao, K. X.; Chen, L.

    2012-02-01

    A paralleled plate electrode and a 9-tip Langmuir probe array located 1 mm behind the extraction exit of a cold cathode Penning ion source are employed to measure the total current and the dynamical changes of the ion current in the 2D profile, respectively. Operation of the ion source by 500 V DC power supply, the paralleled plate electrode and the Langmuir probe array are driven by a bias voltage ranging from -200 V to 200 V. The dependence of the total current and the dynamical changes of the ion current in the 2D profile are presented at the different bias voltage. The experimental results show that the distribution of ion current is axial symmetry and approximate a unimodal distribution.

  10. Ultrafast internal conversion dynamics of highly excited pyrrole studied with VUV/UV pump probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Horton, Spencer L.; Liu, Yusong; Chakraborty, Pratip; Matsika, Spiridoula; Weinacht, Thomas

    2017-02-01

    We study the relaxation dynamics of pyrrole after excitation with an 8 eV pump pulse to a state just 0.2 eV below the ionization potential using vacuum ultraviolet/ultraviolet pump probe spectroscopy. Our measurements in conjunction with electronic structure calculations indicate that pyrrole undergoes rapid internal conversion to the ground state in less than 300 fs. We find that internal conversion to the ground state dominates over dissociation.

  11. 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.

  12. Ultrafast dynamics in solids probed by femtosecond time-resolved broadband electronic sum frequency generation

    NASA Astrophysics Data System (ADS)

    Foglia, Laura; Wolf, Martin; Stähler, Julia

    2016-11-01

    Time-resolved sum frequency generation is an established tool to investigate the ultrafast vibrational dynamics with surface and interface specificity, which can be extended to the regime of electronic transitions using a white light continuum as demonstrated previously by studies of liquid interfaces. We expand this technique to the investigation of solid single crystal samples. In particular, we demonstrate the potential of electronic sum frequency generation by probing the non-equilibrium dynamics at excitonic resonances in ZnO with a sensitivity as small as 0.6% and with a time resolution of 160 fs.

  13. Probe conformational dynamics of proteins in aqueous solutions by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Vinh, Nguyen Q.

    2016-10-01

    Proteins solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz frequencies, that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamic correlations among solvent water and proteins. The dynamics play an important role in enzymatic activities of proteins, but obtaining an accurate and quantitative pictures of these activities, however, is challenging due to the strong absorption of water. In response, we have developed the world's highest precision, highest sensitivity terahertz-frequency domain spectrometer and a standard terahertz-time domain system to probe the collective dynamics of proteins in aqueous solutions. Operating over the frequency range from 5 GHz up to 3 THz, our spectrometers provide an unparalleled ability to probe directly such questions as the hydration level, the dynamics of water and hydrated proteins over the 100 fs to 1 ns timescale. Employing an effective medium approximation to describe the complex dielectric response of the solvated proteins in solution we find that proteins are surrounded by a loosely and tightly held layers of water molecules that behave as if they are an integral part of the protein. The number of water molecules in the protein hydration shells varies with proteins, which can tell us the average surface structure of proteins. These measurements shed light on the macromolecular motions of proteins in their biologically relevant environment.

  14. Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

    PubMed

    Liang, Jie; Qian, Hong

    2010-01-01

    Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

  15. Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

    PubMed Central

    Liang, Jie; Qian, Hong

    2010-01-01

    Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297

  16. Impact of time delay on the dynamics of SEIR epidemic model using cellular automata

    NASA Astrophysics Data System (ADS)

    Sharma, Natasha; Gupta, Arvind Kumar

    2017-04-01

    The delay of an infectious disease is significant when aiming to predict its strength and spreading patterns. In this paper the SEIR ​(susceptible-exposed-infected-recovered) epidemic spread with time delay is analyzed through a two-dimensional cellular automata model. The time delay corresponding to the infectious span, predominantly, includes death during the latency period in due course of infection. The advancement of whole system is described by SEIR transition function complemented with crucial factors like inhomogeneous population distribution, birth and disease independent mortality. Moreover, to reflect more realistic population dynamics some stochastic parameters like population movement and connections at local level are also considered. The existence and stability of disease free equilibrium is investigated. Two prime behavioral patterns of disease dynamics is found depending on delay. The critical value of delay, beyond which there are notable variations in spread patterns, is computed. The influence of important parameters affecting the disease dynamics on basic reproduction number is also examined. The results obtained show that delay plays an affirmative role to control disease progression in an infected host.

  17. 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.

  18. Within-host spatiotemporal dynamics of plant virus infection at the cellular level.

    PubMed

    Tromas, Nicolas; Zwart, Mark P; Lafforgue, Guillaume; Elena, Santiago F

    2014-02-01

    A multicellular organism is not a monolayer of cells in a flask; it is a complex, spatially structured environment, offering both challenges and opportunities for viruses to thrive. Whereas virus infection dynamics at the host and within-cell levels have been documented, the intermediate between-cell level remains poorly understood. Here, we used flow cytometry to measure the infection status of thousands of individual cells in virus-infected plants. This approach allowed us to determine accurately the number of cells infected by two virus variants in the same host, over space and time as the virus colonizes the host. We found a low overall frequency of cellular infection (<0.3), and few cells were coinfected by both virus variants (<0.1). We then estimated the cellular contagion rate (R), the number of secondary infections per infected cell per day. R ranged from 2.43 to values not significantly different from zero, and generally decreased over time. Estimates of the cellular multiplicity of infection (MOI), the number of virions infecting a cell, were low (<1.5). Variance of virus-genotype frequencies increased strongly from leaf to cell levels, in agreement with a low MOI. Finally, there were leaf-dependent differences in the ease with which a leaf could be colonized, and the number of virions effectively colonizing a leaf. The modeling of infection patterns suggests that the aggregation of virus-infected cells plays a key role in limiting spread; matching the observation that cell-to-cell movement of plant viruses can result in patches of infection. Our results show that virus expansion at the between-cell level is restricted, probably due to the host environment and virus infection itself.

  19. Within-Host Spatiotemporal Dynamics of Plant Virus Infection at the Cellular Level

    PubMed Central

    Lafforgue, Guillaume; Elena, Santiago F.

    2014-01-01

    A multicellular organism is not a monolayer of cells in a flask; it is a complex, spatially structured environment, offering both challenges and opportunities for viruses to thrive. Whereas virus infection dynamics at the host and within-cell levels have been documented, the intermediate between-cell level remains poorly understood. Here, we used flow cytometry to measure the infection status of thousands of individual cells in virus-infected plants. This approach allowed us to determine accurately the number of cells infected by two virus variants in the same host, over space and time as the virus colonizes the host. We found a low overall frequency of cellular infection (<0.3), and few cells were coinfected by both virus variants (<0.1). We then estimated the cellular contagion rate (R), the number of secondary infections per infected cell per day. R ranged from 2.43 to values not significantly different from zero, and generally decreased over time. Estimates of the cellular multiplicity of infection (MOI), the number of virions infecting a cell, were low (<1.5). Variance of virus-genotype frequencies increased strongly from leaf to cell levels, in agreement with a low MOI. Finally, there were leaf-dependent differences in the ease with which a leaf could be colonized, and the number of virions effectively colonizing a leaf. The modeling of infection patterns suggests that the aggregation of virus-infected cells plays a key role in limiting spread; matching the observation that cell-to-cell movement of plant viruses can result in patches of infection. Our results show that virus expansion at the between-cell level is restricted, probably due to the host environment and virus infection itself. PMID:24586207

  20. Analysis of cellular behavior and cytoskeletal dynamics reveal a constriction mechanism driving optic cup morphogenesis

    PubMed Central

    Nicolás-Pérez, María; Kuchling, Franz; Letelier, Joaquín; Polvillo, Rocío; Wittbrodt, Jochen; Martínez-Morales, Juan R

    2016-01-01

    Contractile actomyosin networks have been shown to power tissue morphogenesis. Although the basic cellular machinery generating mechanical tension appears largely conserved, tensions propagate in unique ways within each tissue. Here we use the vertebrate eye as a paradigm to investigate how tensions are generated and transmitted during the folding of a neuroepithelial layer. We record membrane pulsatile behavior and actomyosin dynamics during zebrafish optic cup morphogenesis by live imaging. We show that retinal neuroblasts undergo fast oscillations and that myosin condensation correlates with episodic contractions that progressively reduce basal feet area. Interference with lamc1 function impairs basal contractility and optic cup folding. Mapping of tensile forces by laser cutting uncover a developmental window in which local ablations trigger the displacement of the entire tissue. Our work shows that optic cup morphogenesis is driven by a constriction mechanism and indicates that supra-cellular transmission of mechanical tension depends on ECM attachment. DOI: http://dx.doi.org/10.7554/eLife.15797.001 PMID:27797321

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Under lock and key: Spatiotemporal regulation of WASP family proteins coordinates separate dynamic cellular processes

    PubMed Central

    Burianek, Lauren E.; Soderling, Scott H.

    2013-01-01

    WASP family proteins are nucleation promoting factors that bind to and activate the Arp2/3 complex in order to stimulate nucleation of branched actin filaments. The WASP family consists of WASP, N-WASP, WAVE1-3, WASH, and the novel family members WHAMM and JMY. Each of the family members contains a C-terminus responsible for their nucleation promoting activity and unique N-termini that allow for them to be regulated in a spatiotemporal manner. Upon activation they reorganize the cytoskeleton for different cellular functions depending on their subcellular localization and regulatory protein interactions. Emerging evidence indicates that WASH, WHAMM, and JMY have functions that require the coordination of both actin polymerization and microtubule dynamics. Here, we review the mechanisms of regulation for each family member and their associated in vivo functions including cell migration, vesicle trafficking, and neuronal development. PMID:23291261

  6. 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.

  7. 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.

  8. Nanobodies as Probes for Protein Dynamics in Vitro and in Cells*

    PubMed Central

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

    2016-01-01

    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

  9. 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.

  10. 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.

  11. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies

    NASA Astrophysics Data System (ADS)

    Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

    2016-09-01

    Dynamics of the hydration structure around small vibrational probes have been extensively studied over the past few decades. However, we need to gain insight into how vibrational dynamics is affected by the molecular nature of the probe molecules in water. In this study, 2-nitro-5-thiocyanate benzoic acid (NTBA), which has an SCN group attached to an aromatic ring, and thiocyanate ion (SCN-) were used to investigate the vibrational dynamics of two vibrational probes, including vibrational frequency fluctuations and rotational relaxation. By performing two-dimensional infrared spectroscopic measurements, the vibrational frequency fluctuations of the SCN anti-stretching modes of these solutes were compared. The frequency-frequency time correlation function (FFTCF) of these solutes can be modeled by a delta function plus an exponential function and a constant. The FFTCF of NTBA was characterized by a time constant of 1.1 ps, which is similar to that of SCN-. Moreover, no component was longer than this constant. Consequently, the loss of the correlation in frequency fluctuations of the SCN anti-stretching mode of NTBA may be controlled by a mechanism similar to that of the ionic probe, which involves the hydrogen bonding dynamics of water. Polarization-controlled IR pump-probe measurements were performed for these vibrational probes in water to study the vibrational energy relaxation (VER) and reorientational relaxation processes. The VER rate of NTBA is much smaller than that of SCN-, which indicates that the intramolecular relaxation process is significant for VER of NTBA. Based on the rotational relaxation time of NTBA being shorter than that of SCN-, the internal rotational motion of the SCN group around the Cphenyl-S bond axis, where Cphenyl denotes a carbon atom of the aromatic ring to which the SCN group is attached, may play an important role in the anisotropic decay of NTBA in H2O.

  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. Ultrafast Electrons and X-rays as Probe of Biomolecular Dynamics

    NASA Astrophysics Data System (ADS)

    Subramanian, Ganesh

    The structure-function relation in Biology suggests that every biological molecule has evolved its structure to carry out a specific function. However, for many of these processes (such as those with catalytic activity) the structure of the biomolecule changes during the course of a reaction. Understanding the structure-function relation thus becomes a question of understanding biomolecular dynamics that span a variety of timescales (from electronic rearrangements in the femtoseconds to side-chain alteration in the microseconds and more). This dissertation deals with the study of biomolecular dynamics in the ultrafast timescales (fs-ns) using electron and X-ray probes in both time and frequency domains. It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument's capability are provided. Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump--X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.

  14. 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

  15. 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.

  16. Reduced-gravity Testing of The Huygens Probe Ssp Tiltmeter and Hasi Accelerometer Sensors and Their Role In Reconstruction of The Probe Descent Dynamics

    NASA Astrophysics Data System (ADS)

    Ghafoor, N.; Zarnecki, J.

    When the ESA Huygens Probe arrives at Titan in 2005, measurements taken during and after the descent through the atmosphere are likely to revolutionise our under- standing of SaturnSs most enigmatic moon. The accurate atmospheric profiling of Titan from these measurements will require knowledge of the probe descent trajectory and in some cases attitude history, whilst certain atmospheric information (e.g. wind speeds) may be inferred directly from the probe dynamics during descent. Two of the instruments identified as contributing valuable information for the reconstruction of the probeSs parachute descent dynamics are the Surface Science Package Tilt sensor (SSP-TIL) and the Huygens Atmospheric Structure Instrument servo accelerometer (HASI-ACC). This presentation provides an overview of these sensors and their static calibration before describing an investigation into their real-life dynamic performance under simulated Titan-gravity conditions via a low-cost parabolic flight opportunity. The combined use of SSP-TIL and HASI-ACC in characterising the aircraft dynam- ics is also demonstrated and some important challenges are highlighted. Results from some simple spin tests are also presented. Finally, having validated the performance of the sensors under simulated Titan conditions, estimates are made as to the output of SSP-TIL and HASI-ACC under a variety of probe dynamics, ranging from verti- cal descent with spin to a simple 3 degree-of-freedom parachute descent model with horizontal gusting. It is shown how careful consideration must be given to the instru- mentsS principles of operation in each case, and also the impact of the sampling rates and resolutions as selected for the Huygens mission. The presentation concludes with a discussion of ongoing work on more advanced descent modelling and surface dy- namics modelling, and also of a proposal for the testing of the sensors on a sea-surface.

  17. 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.

  18. 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

  19. GC-based dynamic QoS priority handoff scheme in multimedia cellular systems

    NASA Astrophysics Data System (ADS)

    Chen, Huan; Kumar, Sunil; Kuo, C.-C. Jay

    2001-03-01

    A dynamic call admission control (CAC) and its associated resource reservation (RR) schemes are proposed in this research based on the guard channel (GC) concept for a wireless cellular system supporting multiple QoS classes. A comprehensive service model is developed, which includes not only mobile terminals' bandwidth requirements but also their different levels of priorities, rate adaptivity and mobility. The proposed CAC policy selects the resource access thresold according to the estimated number of incoming call requests of different QoS classes. The amount of resources to be reserved is dynamically adjusted by considering neighboring-cell higher-priority calls which are likely to handoff. The handoff interaction between adjacent cells is estimated by using radio propagation in terms of the signal-to-noise ratio (SNR) and the distance of each active call in neighboring cells. Experiments are conducted by using the OPNET simulator to study the performance of the proposed scheme under various traffic conditions. It is shown that better QoS guarantees can be provided by the proposed CAC and RR schemes.

  20. 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

  1. 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.

  2. Directly probing spin dynamics in insulating antiferromagnets using ultrashort terahertz pulses

    DOE PAGES

    Bowlan, Pamela Renee; Trugman, Stuart Alan; Wang, X.; ...

    2016-11-22

    We investigate spin dynamics in the antiferromagnetic (AFM) multiferroic TbMnO3 using opticalpump, terahertz (THz)-probe spectroscopy. Photoexcitation results in a broadband THz transmission change, with an onset time of 25 ps at 6 K that becomes faster at higher temperatures. We attribute this time constant to spin-lattice thermalization. The excellent agreement between our measurements and previous ultrafast resonant x-ray diffraction measurements on the same material confirms that our THz pulse directly probes spin order. We suggest that this could be the case in general for insulating AFM materials, if the origin of the static absorption in the THz spectral range ismore » magnetic.« less

  3. Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy.

    PubMed

    Guo, Jing; Bian, Ke; Lin, Zeren; Jiang, Ying

    2016-10-28

    The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.

  4. Probing the Dynamics of a Superradiant Quantum Phase Transition with a Single Trapped Ion.

    PubMed

    Puebla, Ricardo; Hwang, Myung-Joong; Casanova, Jorge; Plenio, Martin B

    2017-02-17

    We demonstrate that the quantum phase transition (QPT) of the Rabi model and critical dynamics near the QPT can be probed in the setup of a single trapped ion. We first demonstrate that there exists equilibrium and nonequilibrium scaling functions of the Rabi model by finding a proper rescaling of the system parameters and observables, and show that those scaling functions are representative of the universality class to which the Rabi model belongs. We then propose a scheme that can faithfully realize the Rabi model in the limit of a large ratio of the effective atomic transition frequency to the oscillator frequency using a single trapped ion and, therefore, the QPT. It is demonstrated that the predicted universal functions can indeed be observed based on our scheme. Finally, the effects of realistic noise sources on probing the universal functions in experiments are examined.

  5. Probing the Dynamics of a Superradiant Quantum Phase Transition with a Single Trapped Ion

    NASA Astrophysics Data System (ADS)

    Puebla, Ricardo; Hwang, Myung-Joong; Casanova, Jorge; Plenio, Martin B.

    2017-02-01

    We demonstrate that the quantum phase transition (QPT) of the Rabi model and critical dynamics near the QPT can be probed in the setup of a single trapped ion. We first demonstrate that there exists equilibrium and nonequilibrium scaling functions of the Rabi model by finding a proper rescaling of the system parameters and observables, and show that those scaling functions are representative of the universality class to which the Rabi model belongs. We then propose a scheme that can faithfully realize the Rabi model in the limit of a large ratio of the effective atomic transition frequency to the oscillator frequency using a single trapped ion and, therefore, the QPT. It is demonstrated that the predicted universal functions can indeed be observed based on our scheme. Finally, the effects of realistic noise sources on probing the universal functions in experiments are examined.

  6. Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    Guo, Jing; Bian, Ke; Lin, Zeren; Jiang, Ying

    2016-10-01

    The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.

  7. Human mitochondria and mitochondrial genome function as a single dynamic cellular unit

    PubMed Central

    1994-01-01

    rho 0 HeLa cells entirely lacking mitochondrial DNA (mtDNA) and mitochondrial transfection techniques were used to examine intermitochondrial interactions between mitochondria with and without mtDNA, and also between those with wild-type (wt) and mutant-type mtDNA in living human cells. First, unambiguous evidence was obtained that the DNA-binding dyes ethidium bromide (EtBr) and 4',6-diamidino-2- phenylindole (DAPI) exclusively stained mitochondria containing mtDNA in living human cells. Then, using EtBr or DAPI fluorescence as a probe, mtDNA was shown to spread rapidly to all rho 0 HeLa mitochondria when EtBr- or DAPI-stained HeLa mitochondria were introduced into rho 0 HeLa cells. Moreover, coexisting wt-mtDNA and mutant mtDNA with a large deletion (delta-mtDNA) were shown to mix homogeneously throughout mitochondria, not to remain segregated by use of electron microscopic analysis of cytochrome c oxidase activities of individual mitochondria as a probe to identify mitochondria with predominantly wt- or delta- mtDNA in single cells. This rapid diffusion of mtDNA and the resultant homogeneous distribution of the heteroplasmic wt- and delta-mtDNA molecules throughout mitochondria in a cell suggest that the mitochondria in living human cells have lost their individuality. Thus, the actual number of mitochondria per cell is not of crucial importance, and mitochondria in a cell should be considered as a virtually single dynamic unit. PMID:8138574

  8. 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

  9. Dynamics of nanoscopic water: vibrational echo and infrared pump-probe studies of reverse micelles.

    PubMed

    Piletic, Ivan R; Tan, Howe-Siang; Fayer, M D

    2005-11-17

    The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H2O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, approximately 1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is approximately 10 times longer than the dynamics in bulk water. The vibrational echo

  10. Spin-labeled psoralen probes for the study of DNA dynamics

    SciTech Connect

    Spielmann, H.P.; Chi, D.Y.; Hunt, N.G.

    1995-11-14

    Six nitroxide spin-labeled psoralen derivatives have been synthesized and evaluated as probes for structural and dynamic studies. Sequence specific photoaddition of these derivatives to DNA oligonucleotides resulted in site-specifically cross-linked and spin-labeled oligomers. Comparison of the general line shape features of the observed electron paramagnetic resonance (EPR) spectra of several duplexes ranging in size from 8 to 46 base pairs with simulated EPR spectra indicate that the nitroxide spin-labeled probe reports the global tumbling motion of the oligomers. While there is no apparent large amplitude motion of the psoralen other than the overall tumbling of DNA on the time scales investigated, there are no indications of bending and other residual motions. The (A)BC excinuclease DNA repair system detects structural or dynamic features of the DNA that distinguish between damaged and undamaged DNA and are independent of the intrinsic structure of the lesion. NMR studies have shown that psoralen-cross-linked DNA has altered backbone dynamics and conformational populations in the immediate vicinity of the adduct. We suggested that the signal for recognition of a lesion to be repaired is in the sugar-phosphate backbone and not in the damaged base(s). 71 refs., 11 figs., 1 tab.

  11. Probing ultrafast dynamics of 5f electrons in crystalline UO2

    SciTech Connect

    An, Yong Q; Taylor, Antoinette J; Durakiewicz, Tomasz; Rodriguez, George

    2010-01-01

    The electronic structure and ultrafast dynamics of photoexcited carriers of Mott insulators attracts considerable attention in modern condensed matter physics. Cubic structured UO{sub 2} is a model system for understanding the physics of strongly correlated electrons in Mott insulators. Its 5f electrons may produce special electronic states and dynamics because of their complex nature. It shows an anti ferromagnetic transition at T{sub N} = 30.8 K. Several recent theoretical works have predicted the ground states and Mott characteristics of crystalline UO{sub 2}. It is believed that the band gap of UO{sub 2} is on the order of {approx} 2 eV and excitations across the gap are of the f-f character. We have performed ultrafast optical studies of carrier dynamics related to the Mott gap and its Hubbard bands with femtosecond pump-probe transient reflection measurements. From pump-probe reflectance measurements, we find the lifetimes of photoexcited 5f electrons in crystalline UO{sub 2}, {approx} 1.2 ns for midgap states and {approx} 2 {mu}s for upper Hubbard band states at low temperatures, and identify magnetic transitions.

  12. Ultrafast excited-state dynamics at interfaces: fluorescent DNA probes at the dodecane/water interface

    NASA Astrophysics Data System (ADS)

    Licari, Giuseppe; Vauthey, Eric

    2015-08-01

    Although the interfaces between two isotropic media are of primary importance in many areas of science and technology, their properties are only partially understood. Our strategy to obtain an insight into these properties is to investigate the ultrafast excited-state dynamics of environment-sensitive molecular probes at liquid interfaces using time-resolved surface second harmonic generation, and to compare it with the dynamics of the same molecules in bulk solutions. Additionally, this approach gives rich information on how the chemical reactivity may change when going from the bulk phase to the interface. This is illustrated by an investigation performed with a series of fluorescent DNA probes at the dodecane/water interface without and with the presence of DNA in the aqueous phase. Substantial differences in the conformation of these cyanine dyes (aggregated or not) and in the excited-state dynamics are observed when going from bulk solutions to the interface. Moreover, the presence of double-stranded DNA in the aqueous phase induces some chirality at the interface.

  13. Electron Dynamics at Dye-Semiconductor Interfaces probed with Picosecond Time-Resolved XPS

    NASA Astrophysics Data System (ADS)

    Neppl, Stefan; Shavorskiy, Andrey; Zegkinoglou, Ioannis; Fraund, Matthew; Salmeron, Miquel; Guo, Jinghua; Bluhm, Hendrik; Gessner, Oliver

    2014-05-01

    Picosecond time-resolved core-level spectroscopy using laser pulses to initiate and short X-ray pulses to probe photo-induced processes have the unique potential to provide electronic state- and atomic site-specific insight into fundamental electron dynamics in complex systems. Up to now, however, most of these experiments have concentrated on the electronic and structural dynamics in isolated or solvated molecules. Here we report preliminary results of a time-resolved X-ray photoelectron spectroscopy (TRXPS) study with the goal to follow the light-driven electron dynamics of N3 dye molecules adsorbed on a nano-structured ZnO semiconductor substrate - a technologically pertinent system for dye-sensitized solar cells - on the pico- to nanosecond time scale from the perspective of individual atomic sites at this complex interface. A distinct evolution of the molecular C1s photoemission line shape is observed as a function of time delay between a visible (532 nm) laser pump pulse (resonant with the N3 HOMO-LUMO gap) and the X-ray probe pulses. The observed changes in the C1s TRXPS spectra will be discussed in the context of possible charge recombination and relaxation processes leading to the neutralization of the transiently oxidized dye following ultrafast photo-induced electron injection.

  14. Probing of the assembly structure and dynamics within nanoparticles during interaction with blood proteins.

    PubMed

    Li, Yuanpei; Budamagunta, Madhu S; Luo, Juntao; Xiao, Wenwu; Voss, John C; Lam, Kit S

    2012-11-27

    Fully understanding the influence of blood proteins on the assembly structure and dynamics within nanoparticles is difficult because of the complexity of the system and the difficulty in probing the diverse elements and milieus involved. Here we show the use of site-specific labeling with spin probes and fluorophores combined with electron paramagnetic resonance (EPR) spectroscopy and fluorescence resonance energy transfer (FRET) measurements to provide insights into the molecular architecture and dynamics within nanoparticles. These tools are especially useful for determining nanoparticle stability in the context of blood proteins and lipoproteins and have allowed us to quantitatively analyze the dynamic changes in assembly structure, local stability, and cargo diffusion of a class of novel telodendrimer-based micellar nanoparticles. When combined with human plasma and individual plasma components, we find that non-cross-linked nanoparticles immediately lose their original assembly structure and release their payload upon interaction with lipoproteins. In contrast, serum albumins and immunoglobulin gamma have moderate affects on the integrity of the nanoparticles. Disulfide cross-linked nanoparticles show minimal interaction with lipoproteins and can better retain their assembly structure and payload in vitro and in vivo. We further demonstrate how the enhanced stability and release property of disulfide cross-linked nanoparticles can be reversed in reductive conditions. These findings identify factors that are crucial to the performance of nanomedicines and provide design modes to control their interplay with blood factors.

  15. 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.

  16. 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

  17. Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy.

    PubMed

    Lin, Ming-Fu; Neumark, Daniel M; Gessner, Oliver; Leone, Stephen R

    2014-02-14

    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH2=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 C2H3Br, the formation of C2H3Br(+) ions in their ground (X̃) and first excited (Ã) states, the production of C2H3Br(++) ions, and the appearance of neutral Br ((2)P3/2) atoms by dissociative ionization. The formation of free Br ((2)P3/2) atoms occurs on a timescale of 330 ± 150 fs. The ionic à 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 à state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C2H3Br(+) (Ã) ions undergoes intramolecular vibrational energy redistribution followed by the C-Br bond dissociation. The C2H3Br(+) (X̃) products and the majority of the C2H3Br(++) 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.

  18. 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.

  19. In situ detection of faradaic current in probe oxidation using a dynamic force microscope

    NASA Astrophysics Data System (ADS)

    Kuramochi, Hiromi; Ando, Kazunori; Tokizaki, Takashi; Yokoyama, Hiroshi

    2004-05-01

    A faradaic current on the order of a sub-pico-ampere was detected while fabricating two-dimensional oxide nanostructures on H-passivated Si(001) surfaces. The detected faradaic current has been shown to faithfully reflect the degree of probe oxidation with a clear dependence on the variation of voltage and the tip speed. The faradaic current in dynamic mode can serve as a sensitive monitor of the nano-oxidation reaction for implementing precise closed-loop control of the oxide growth.

  20. Multifragment azimuthal correlation functions: Probes for reaction dynamics in collisions of intermediate energy heavy ions

    SciTech Connect

    Lacey, R.A.; Elmaani, A.; Lauret, J.; Li, T.; Bauer, W.; Craig, D.; Cronqvist, M.; Gualtieri, E.; Hannuschke, S.; Reposeur, T.; Vander Molen, A.; Westfall, G.D.; Wilson, W.K.; Winfield, J.S.; Yee, J.; Yennello, S.; Nadasen, A.; Tickle, R.S.; Norbeck, E. National Superconducting Cyclotron Laboratory Department of Physics, Michigan State University, East Lansing, Michigan 48824-1321 Department of Physics, University of Michigan at Dearborn, Dearborn, Michigan 48128 Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1120 Department of Physics, University of Iowa, Iowa City, Iowa 52242 )

    1993-03-01

    Multifragment azimuthal correlation functions have been measured as a function of beam energy and impact parameter for the Ar+Sc system ([ital E]/[ital A]=35 to 115 MeV). The observed azimuthal correlation functions---which do not require corrections for dispersion of the reaction plane---exhibit strong asymmetries which are dependent on impact parameter and beam energy. Rotational collective motion and flow seem to dominate the correlation functions at low beam energies. It is proposed that multifragment azimuthal correlation functions can provide a useful probe for intermediate energy heavy ion reaction dynamics.

  1. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-04

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  2. 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.

  3. 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

  4. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization.

    PubMed

    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

    2009-06-01

    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 100K which shows 30 Hz linewidths.

  5. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2016-10-01

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  6. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics.

    PubMed

    Neville, Simon P; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S

    2016-10-14

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L(2) method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  7. 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

  8. Cellular bias on the microscale: probing the effects of digital microfluidic actuation on mammalian cell health, fitness and phenotype.

    PubMed

    Au, Sam H; Fobel, Ryan; Desai, Salil P; Voldman, Joel; Wheeler, Aaron R

    2013-08-01

    The potential benefits of using new technologies such as microfluidics for life science applications are exciting, but it is critical to understand and document potential biases imposed by these technologies on the observed results. Here, we report the first study of genome-level effects on cells manipulated by digital microfluidics. These effects were evaluated using a broad suite of tools: cell-based stress sensors for heat shock activation, single-cell COMET assays to probe changes in DNA integrity, and DNA microarrays and qPCR to evaluate changes in genetic expression. The results lead to two key observations. First, most DMF operating conditions tested, including those that are commonly used in the literature, result in negligible cell-stress or genome-level effects. Second, for DMF devices operated at high driving frequency (18 kHz) and with large driving electrodes (10 mm × 10 mm), there are significant damage to DNA integrity and differential genomic regulation. We hypothesize that these effects are caused by droplet heating. We recommend that for DMF applications involving mammalian cells that driving frequencies be kept low (≤ 10 kHz) and electrode sizes be kept small (≤ 5 mm) to avoid detrimental effects.

  9. Differential dynamic microscopy: probing wave vector dependent dynamics with a microscope.

    PubMed

    Cerbino, Roberto; Trappe, Veronique

    2008-05-09

    We demonstrate the use of an ordinary white-light microscope for the study of the q-dependent dynamics of colloidal dispersions. Time series of digital video images are acquired in bright field with a fast camera, and image differences are Fourier analyzed as a function of the time delay between them. This allows for the characterization of the particle dynamics independent of whether or not they can be resolved individually. The characteristic times are measured in a wide range of wave vectors and the results are found to be in good agreement with the theoretically expected values for Brownian motion in a viscous medium.

  10. Soft X-ray probes of ultrafast dynamics for heterogeneous catalysis

    NASA Astrophysics Data System (ADS)

    Beye, M.; Föhlisch, A.

    2013-03-01

    Soft X-ray spectroscopy is one of the best tools to directly address the electronic structure, the driving force of chemical reactions. It enables selective studies on sample surfaces to single out reaction centers in heterogeneous catalytic reactions. With core-hole clock methods, specific dynamics are related to the femtosecond life time of a core-hole. Typically, this method is used with photoemission spectroscopy, but advancements in soft X-ray emission techniques render more specific studies possible. With the advent of bright femtosecond pulsed soft X-ray sources, highly selective pump-probe X-ray emission studies are enabled with temporal resolutions down to tens of femtoseconds. This finally allows to study dynamics in the electronic structure of adsorbed reaction centers on the whole range of relevant time scales - closing the gap between kinetic soft X-ray studies and the atto- to femtosecond core-hole clock techniques.

  11. 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.

  12. 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

  13. 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

  14. Integrating the system dynamic and cellular automata models to predict land use and land cover change

    NASA Astrophysics Data System (ADS)

    Xu, Xiaoming; Du, Ziqiang; Zhang, Hong

    2016-10-01

    Land use and land cover change (LULCC) is a widely researched topic in related studies. A number of models have been established to simulate LULCC patterns. However, the integration of the system dynamic (SD) and the cellular automata (CA) model have been rarely employed in LULCC simulations, although it allows for combining the advantages of each approach and therefore improving the simulation accuracy. In this study, we integrated an SD model and a CA model to predict LULCC under three future development scenarios in Northern Shanxi province of China, a typical agro-pastoral transitional zone. The results indicated that our integrated approach represented the impacts of natural and socioeconomic factors on LULCC well, and could accurately simulate the magnitude and spatial pattern of LULCC. The modeling scenarios illustrated that different development pathways would lead to various LULCC patterns. This study demonstrated the advantages of the integration approach for simulating LULCC and suggests that LULCC is affected to a large degree by natural and socioeconomic factors.

  15. A refined and dynamic cellular automaton model for pedestrian-vehicle mixed traffic flow

    NASA Astrophysics Data System (ADS)

    Liu, Mianfang; Xiong, Shengwu

    2016-12-01

    Mixed traffic flow sharing the “same lane” and having no discipline on road is a common phenomenon in the developing countries. For example, motorized vehicles (m-vehicles) and nonmotorized vehicles (nm-vehicles) may share the m-vehicle lane or nm-vehicle lane and pedestrians may share the nm-vehicle lane. Simulating pedestrian-vehicle mixed traffic flow consisting of three kinds of traffic objects: m-vehicles, nm-vehicles and pedestrians, can be a challenge because there are some erratic drivers or pedestrians who fail to follow the lane disciplines. In the paper, we investigate various moving and interactive behavior associated with mixed traffic flow, such as lateral drift including illegal lane-changing and transverse crossing different lanes, overtaking and forward movement, and propose some new moving and interactive rules for pedestrian-vehicle mixed traffic flow based on a refined and dynamic cellular automaton (CA) model. Simulation results indicate that the proposed model can be used to investigate the traffic flow characteristic in a mixed traffic flow system and corresponding complicated traffic problems, such as, the moving characteristics of different traffic objects, interaction phenomenon between different traffic objects, traffic jam, traffic conflict, etc., which are consistent with the actual mixed traffic system. Therefore, the proposed model provides a solid foundation for the management, planning and evacuation of the mixed traffic flow.

  16. Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness to stress

    PubMed Central

    Escusa-Toret, Stéphanie; Vonk, Willianne I. M.; Frydman, Judith

    2014-01-01

    The extensive links between proteotoxic stress, protein aggregation and pathologies ranging from aging to neurodegeneration underscore the importance of understanding how cells manage protein misfolding. Using live-cell imaging, we here determine the fate of stress-induced misfolded proteins from their initial appearance until their elimination. Upon denaturation, misfolded proteins are sequestered from the bulk cytoplasm into dynamic ER-associated puncta that move and coalesce into larger structures in an energy-dependent but cytoskeleton-independent manner. These puncta, which we name Q-bodies, concentrate different misfolded and stress-denatured proteins en-route to degradation, but do not contain amyloid aggregates, which localize instead to the IPOD. Q-body formation and clearance depends on an intact cortical ER and a complex chaperone network that is affected by rapamycin and impaired during chronological aging. Importantly, Q-body formation enhances cellular fitness during stress. We conclude that spatial sequestration of misfolded proteins in Q-bodies is an early quality control strategy occurring synchronously with degradation to clear the cytoplasm from potentially toxic species. PMID:24036477

  17. 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.

  18. 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.

  19. 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.

  20. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modeling.

    PubMed

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

    2014-11-10

    Following partial hepatectomy, the liver initiates a regenerative program involving hepatocyte priming and replication driven by coordinated cytokine and growth factor actions. 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 IL-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. This article is protected by copyright. All rights reserved.

  1. 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.

  2. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks.

    PubMed

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-22

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  3. 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.

  4. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    NASA Astrophysics Data System (ADS)

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  5. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    PubMed Central

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-01-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability. PMID:27874024

  6. 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

  7. Van Allen Probes observations of electromagnetic ion cyclotron waves triggered by enhanced solar wind dynamic pressure

    NASA Astrophysics Data System (ADS)

    Cho, J.-H.; Lee, D.-Y.; Noh, S.-J.; Shin, D.-K.; Hwang, J.; Kim, K.-C.; Lee, J. J.; Choi, C. R.; Thaller, S.; Skoug, R.

    2016-10-01

    Magnetospheric compression due to impact of enhanced solar wind dynamic pressure Pdyn has long been considered as one of the generation mechanisms of electromagnetic ion cyclotron (EMIC) waves. With the Van Allen Probe-A observations, we identify three EMIC wave events that are triggered by Pdyn enhancements under prolonged northward interplanetary magnetic field (IMF) quiet time preconditions. They are in contrast to one another in a few aspects. Event 1 occurs in the middle of continuously increasing Pdyn while Van Allen Probe-A is located outside the plasmapause at postmidnight and near the equator (magnetic latitude (MLAT) -3°). Event 2 occurs by a sharp Pdyn pulse impact while Van Allen Probe-A is located inside the plasmapause in the dawn sector and rather away from the equator (MLAT 12°). Event 3 is characterized by amplification of a preexisting EMIC wave by a sharp Pdyn pulse impact while Van Allen Probe-A is located outside the plasmapause at noon and rather away from the equator (MLAT -15°). These three events represent various situations where EMIC waves can be triggered by Pdyn increases. Several common features are also found among the three events. (i) The strongest wave is found just above the He+ gyrofrequency. (ii) The waves are nearly linearly polarized with a rather oblique propagation direction ( 28° to 39° on average). (iii) The proton fluxes increase in immediate response to the Pdyn impact, most significantly in tens of keV energy, corresponding to the proton resonant energy. (iv) The temperature anisotropy with T⊥ > T|| is seen in the resonant energy for all the events, although its increase by the Pdyn impact is not necessarily always significant. The last two points (iii) and (iv) may imply that in addition to the temperature anisotropy, the increase of the resonant protons must have played a critical role in triggering the EMIC waves by the enhanced Pdyn impact.

  8. 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.

  9. 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.

  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. 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.

  12. Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis.

    PubMed

    Prakash, Priyanka; Hancock, John F; Gorfe, Alemayehu A

    2015-05-01

    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 nonpocket-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.

  13. 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

  14. Liquid microjunction surface sampling probe fluid dynamics: computational and experimental analysis of coaxial intercapillary positioning effects on sample manipulation.

    PubMed

    Elnaggar, Mariam S; Barbier, Charlotte; Van Berkel, Gary J

    2011-07-01

    A coaxial geometry liquid microjunction surface sampling probe (LMJ-SSP) enables direct extraction of analytes from surfaces for subsequent analysis by techniques like mass spectrometry. Solution dynamics at the probe-to-sample surface interface in the LMJ-SSP has been suspected to influence sampling efficiency and dispersion but has not been rigorously investigated. The effect on flow dynamics and analyte transport to the mass spectrometer caused by coaxial retraction of the inner and outer capillaries from each other and the surface during sampling with a LMJ-SSP was investigated using computational fluid dynamics and experimentation. A transparent LMJ-SSP was constructed to provide the means for visual observation of the dynamics of the surface sampling process. Visual observation, computational fluid dynamics (CFD) analysis, and experimental results revealed that inner capillary axial retraction from the flush position relative to the outer capillary transitioned the probe from a continuous sampling and injection mode through an intermediate regime to sample plug formation mode caused by eddy currents at the sampling end of the probe. The potential for analytical implementation of these newly discovered probe operational modes is discussed.

  15. Liquid Microjunction Surface Sampling Probe Fluid Dynamics: Computational and Experimental Analysis of Coaxial Intercapillary Positioning Effects on Sample Manipulation

    NASA Astrophysics Data System (ADS)

    ElNaggar, Mariam S.; Barbier, Charlotte; Van Berkel, Gary J.

    2011-07-01

    A coaxial geometry liquid microjunction surface sampling probe (LMJ-SSP) enables direct extraction of analytes from surfaces for subsequent analysis by techniques like mass spectrometry. Solution dynamics at the probe-to-sample surface interface in the LMJ-SSP has been suspected to influence sampling efficiency and dispersion but has not been rigorously investigated. The effect on flow dynamics and analyte transport to the mass spectrometer caused by coaxial retraction of the inner and outer capillaries from each other and the surface during sampling with a LMJ-SSP was investigated using computational fluid dynamics and experimentation. A transparent LMJ-SSP was constructed to provide the means for visual observation of the dynamics of the surface sampling process. Visual observation, computational fluid dynamics (CFD) analysis, and experimental results revealed that inner capillary axial retraction from the flush position relative to the outer capillary transitioned the probe from a continuous sampling and injection mode through an intermediate regime to sample plug formation mode caused by eddy currents at the sampling end of the probe. The potential for analytical implementation of these newly discovered probe operational modes is discussed.

  16. Probing the dynamics of high-viscosity entangled polymers under shear using Neutron Spin Echo spectroscopy

    NASA Astrophysics Data System (ADS)

    Kawecki, M.; Gutfreund, P.; Adlmann, F. A.; Lindholm, E.; Longeville, S.; Lapp, A.; Wolff, M.

    2016-09-01

    Neutron Spin Echo spectroscopy provides unique insight into molecular and submolecular dynamics as well as intra- and inter-molecular interactions in soft matter. These dynamics may change drastically under shear flow. In particular in polymer physics a stress plateau is observed, which might be explained by an entanglement-disentanglement transition. However, such a transition is difficult to identify directly by experiments. Neutron Spin Echo has been proven to provide information about entanglement length and degree by probing the local dynamics of the polymer chains. Combining shear experiments and neutron spin echo is challenging since, first the beam polarisation has to be preserved during scattering and second, Doppler scattered neutrons may cause inelastic scattering. In this paper we present a new shear device adapted for these needs. We demonstrate that a high beam polarisation can be preserved and present first data on an entangled polymer solution under shear. To complement the experiments on the dynamics we present novel SANS data revealing shear- induced conformational changes in highly entangled polymers.

  17. Temporal and spatial valley dynamics in two-dimensional semiconductors probed via Kerr rotation

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    Monolayer transition metal dichalcogenides (TMDCs) offer a tantalizing platform for control of both spin and valley degrees of freedom, which may enable future optoelectronic devices with enhanced and novel functionalities. Here, we investigate the valley dynamics of two prototypical members of TMDCs, namely Mo S2 and WS e2 , using time-resolved Kerr rotation (TRKR) at temperatures from 10 K to 300 K. This pump-probe technique enables sub-picosecond temporal resolution, providing insight into ultrafast valley dynamics, which is inaccessible by polarized and time-resolved photoluminescence spectroscopy. Bi-exponential decay dynamics were observed for both materials at low temperatures, and the fast decay component indicated a rapid exciton valley depolarization time (<10 ps ) due to strong Coulomb exchange interactions between the K valleys. However, the slow decay components (several tens of picoseconds) were attributed to different origins in the two materials, which were further elucidated by temperature-dependent TRKR measurements. Moreover, the spatial dependence of the TRKR intensity across Mo S2 monolayer flakes indicated a weaker valley polarization near the edges, which is likely associated with quenched excitons near the grain boundaries or a disordered edge region in chemical vapor deposition-grown monolayers. These temporal and spatial TRKR measurements reveal insight into the complex dynamics of valley excitonic states, which will be critical for valleytronic applications of monolayer TMDCs.

  18. 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.

  19. Organization and dynamics of membrane probes and proteins utilizing the red edge excitation shift.

    PubMed

    Haldar, Sourav; Chaudhuri, Arunima; Chattopadhyay, Amitabha

    2011-05-19

    Dynamics of confined water has interesting implications in the organization and function of molecular assemblies such as membranes. A direct consequence of this type of organization is the restriction imposed on the mobility of the constituent structural units. Interestingly, this restriction (confinement) of mobility couples the motion of solvent (water) molecules with the slow moving molecules in the assembly. It is in this context that the red edge excitation shift (REES) represents a sensitive approach to monitor the environment and dynamics around a fluorophore in such organized assemblies. A shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of the absorption band, is termed REES. REES relies on slow solvent reorientation in the excited state of a fluorophore that can be used to monitor the environment and dynamics around a fluorophore in a host assembly. In this article, we focus on the application of REES to monitor organization and dynamics of membrane probes and proteins.

  20. 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.

  1. Submicrosecond phospholipid dynamics using a long-lived fluorescence emission anisotropy probe.

    PubMed Central

    Davenport, L; Targowski, P

    1996-01-01

    The use of the long-lived fluorescence probe coronene (mean value of tau(FL) approximately 200 ns) is described for investigating submicrosecond lipid dynamics in DPPC model bilayer systems occurring below the lipid phase transition. Time-resolved fluorescence emission anisotropy decay profiles, measures as a function of increasing temperature toward the lipid-phase transition temperature (T(C)), for coronene-labeled DPPC small unilamellar vesicles (SUVs), are best described in most cases by three rotational decay components (phi(i = 3)). We have interpreted these data using two dynamic lipid bilayer models. In the first, a compartmental model, the long correlation time (phi(N)) is assigned to immobilized coronene molecules located in "gel-like" or highly ordered lipid phases (S-->1) of the bilayer, whereas a second fast rotational time (phi(F) approximately 2-5 ns) is associated with probes residing in more "fluid-like" regions (with corresponding lower ordering, S-->0). Interests here have focused on the origins of an intermediate correlation time (50-100 ns), the associated amplitude (beta(G)) of which increases with increasing temperature. Such behavior suggests a changing rotational environment surrounding the coronene molecules, arising from fluidization of gel lipid. The observed effective correlation time (phi(EFF)) thus reflects a discrete gel-fluid lipid exchange rate (k(FG)). A refinement of the compartmental model invokes a distribution of gel-fluid exchange rates (d(S,T)) corresponding to a distribution of lipid order parameters and is based on an adapted Landau expression for describing "gated" packing fluctuations. A total of seven parameters (five thermodynamic quantities, defined by the free energy versus temperature expansion; one gating parameter (gamma) defining a cooperative "melting" requirement; one limiting diffusion rate (or frequency factor: d(infinity))) suffice to predict complete anisotropy decay curves measured for coronene at several

  2. Probing Dynamics and Structure from Within with VUV and Ultrafast X-rays

    NASA Astrophysics Data System (ADS)

    Berrah, Nora

    2014-05-01

    VUV and X-rays produced at synchrotron facilities or free electron lasers (FELs) have energies and intensities sufficient to access core and inner-shell electrons producing, unlike visible optical lasers, inside-out photoionization to probe matter. The element-specificity of x-ray absorption, i.e., the ability to target specific atoms within molecules and select specific shells in those atoms (by tuning with high resolution the photon energy to specific spectral regions) has been used to investigate the dynamics and structure of atoms, molecules, clusters and their ions. The new class of x-ray lasers, the intense-femtosecond FELs, has opened up new opportunities to study AMO physics with atomic spatial resolution and femtosecond temporal resolution. The understanding of physical and chemical changes at an atomic spatial scale and on the time scale of atomic motion is crucial not only for AMO physics but also for a broad range of other scientific fields. We will report on experimental investigations coupled with a quantitative understanding of dynamical effects due to VUV or x-ray exposure. We will also describe newly-built instrumentation already applied to x-ray pump-x-ray probe experiments to map out time-dependent processes to interrogate molecular dynamics in order to advance our fundamental understanding of the interaction of matter with x-rays. This work is supported by the Department of Energy, Office of Science, Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences under grant No. DE-FG02-92ER14299.A002.

  3. 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

  4. 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

  5. Closed-form stochastic solutions for non-equilibrium dynamics and inheritance of cellular components over many cell divisions.

    PubMed

    Johnston, Iain G; Jones, Nick S

    2015-08-08

    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.

  6. 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

  7. 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.

  8. 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.

    2017-03-01

    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.

  9. 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.

  10. Sticholysin II: a pore-forming toxin as a probe to recognize sphingomyelin in artificial and cellular membranes.

    PubMed

    Garcia, Paloma Sanchez; Chieppa, Gabriele; Desideri, Alessandro; Cannata, Stefano; Romano, Elena; Luly, Paolo; Rufini, Stefano

    2012-10-01

    Sphingomyelin is a major component of membrane rafts, and also is a precursor of many bioactive molecules. The sphingomyelin plays important biological roles and alterations of its metabolism are the basis of some genetic disorders such as the Niemann Pick disease. A complete understanding of its biological role is frustrated by the lack of efficient tools for its recognition in the cell. Sticholysin II (StnII) is a 20 kDa protein from the sea-anemone Stichodactyla helianthus which shows a cytotoxic activity by forming oligomeric aqueous pores in the cell plasma membrane. A recent NMR analysis indicates that the sticholysin II binds specifically to sphingomyelin by two domains that recognize respectively the hydrophilic (i.e. phosphorylcholine) and the hydrophobic (i.e. ceramide) moieties of the molecule. Aim of our research has been to verify the possible employ of an antibody against the StnII to investigate the localization and the dynamics of sphingomyelin in cell membranes. For this purpose, we developed a monoclonal antibody (named A10) against the toxin and we tested its ability to bind StnII after binding to sphingomyelin. A10 antibody is able to recognize the sticholysin II both in its native form and after SDS treatment, being the protein still suitable for many analytic techniques such as ELISA, western blotting and immunofluorescence. The high affinity of the toxin for the sphingomyelin in cell membranes has been demonstrated by microscopic immuno-localization and western blot analysis; both methods confirmed that sphingomyelin is the molecular acceptor for StnII also in cell membranes. Finally, we studied the specificity of the toxin for sphingomyelin by a cell membrane-double labelling method, using cholera toxin, specific for the ganglioside GM1, and sticholysin II. The results obtained show that there is no cross-reactivity between the two toxins, confirming that sticholysin II is able to discriminate among membrane domains with sphingomyelin with

  11. Probing carrier dynamics in wide-bandgap semiconductor-metal nanoparticle hybrids (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Ratchford, Daniel; Dunkelberger, Adam D.; Owrutsky, Jeff C.; Pehrsson, Pehr E.

    2016-09-01

    Transient absorption spectra were measured to demonstrate carrier injection in multi-layered stacks of Au nanoparticles sandwiched in between TiO2 atomic layer deposited (ALD) thin films. Similar structures were fabricated with ALD Al2O3 for control samples. Sub-percolation thin films of Au resulted in <20 nm particles with plasmon resonances at 650 nm ( 590 nm) in the TiO2 (Al2O3) samples. Two separate pump-probe experiments were preformed to monitor transient heating of the metal and carrier injection in the TiO2. In the first experiment, the metal nanoparticles were excited at 400 nm, and the metal electron dynamics were probed at wavelengths around the plasmon resonance. We measured a decay time of 1.7 ps in the TiO2-Au layered samples compared to 2.2 ps in the Al2O3-Au layered samples. The decay times are attributed to electron-phonon coupling. The faster decay in TiO2 may be the result of charge injection into the TiO2. In the second experiment, carriers were excited in the Au nanoparticles by pumping on the plasmon resonance, and the system was probed in the mid-IR to measure free carrier absorption in the TiO2. The TiO2-Au layered sample exhibited transient signals similar to the free carrier absorption signals following excitation of TiO2 films, however, no signal was observed on the Al2O3-Au layered sample. This provides clear evidence that the signal measured in the TiO2-Au layered sample was not from the Au nanoparticles alone but instead originated from charge injection from the Au into the TiO2.

  12. Black-hole horizons as probes of black-hole dynamics. II. Geometrical insights

    NASA Astrophysics Data System (ADS)

    Jaramillo, José Luis; Macedo, Rodrigo P.; Moesta, Philipp; Rezzolla, Luciano

    2012-04-01

    In a companion paper [J. L. Jaramillo, R. P. Macedo, P. Moesta, and L. Rezzolla, preceding Article, Phys. Rev. DPRVDAQ1550-7998 85, 084030 (2012).], we have presented a cross-correlation approach to near-horizon physics in which bulk dynamics is probed through the correlation of quantities defined at inner and outer spacetime hypersurfaces acting as test screens. More specifically, dynamical horizons provide appropriate inner screens in a 3+1 setting and, in this context, we have shown that an effective-curvature vector measured at the common horizon produced in a head-on collision merger can be correlated with the flux of linear Bondi momentum at null infinity. In this paper we provide a more sound geometric basis to this picture. First, we show that a rigidity property of dynamical horizons, namely, foliation uniqueness, leads to a preferred class of null tetrads and Weyl scalars on these hypersurfaces. Second, we identify a heuristic horizon newslike function, depending only on the geometry of spatial sections of the horizon. Fluxes constructed from this function offer refined geometric quantities to be correlated with Bondi fluxes at infinity, as well as a contact with the discussion of quasilocal 4-momentum on dynamical horizons. Third, we highlight the importance of tracking the internal horizon dual to the apparent horizon in spatial 3-slices when integrating fluxes along the horizon. Finally, we discuss the link between the dissipation of the nonstationary part of the horizon’s geometry with the viscous-fluid analogy for black holes, introducing a geometric prescription for a “slowness parameter” in black-hole recoil dynamics.

  13. Experimental probing of conical intersection dynamics in the photodissociation of thioanisole.

    PubMed

    Lim, Jeong Sik; Kim, Sang Kyu

    2010-08-01

    Chemical reactions that occur in the ground electronic state are described well by invoking the Born-Oppenheimer approximation, which allows their development to be rationalized by nuclear rearrangements that smoothly traverse an adiabatic potential energy surface. The situation is different, however, for reactions in electronically excited states, where non-adiabatic transitions occur between adiabatic surfaces. The conical intersection, in which two adiabatic surfaces touch, is accepted widely as the dynamic funnel for efficient non-adiabatic transitions, but its direct experimental probing is rare. Here, we investigate the photodissociation of thioanisole and observe a striking dependence of the relative yields of two reaction channels on the photoexcitation energy as indicated by a dynamic resonance in the product branching ratio. This results from the interference of two different adiabatic states that are in close proximity in the region of a conical intersection. The location of the observed resonance on the multidimensional potential energy surface thus reveals the nuclear configuration of the conical intersection and its dynamic role in the non-adiabatic transition.

  14. Spatiotemporal effects of a controlled-release anti-inflammatory drug on the cellular dynamics of host response

    PubMed Central

    Dang, Tram T.; Bratlie, Kaitlin M.; Bogatyrev, Said R.; Chen, Xiao Y.; Langer, Robert; Anderson, Daniel G.

    2017-01-01

    In general, biomaterials induce a non-specific host response when implanted in the body. This reaction has the potential to interfere with the function of the implanted materials. One method for controlling the host response is through local, controlled release of anti-inflammatory agents. Herein, we investigate the spatial and temporal effects of an anti-inflammatory drug on the cellular dynamics of the innate immune response to subcutaneously implanted poly(lactic-co-glycolic) microparticles. Noninvasive fluorescence imaging was used to investigate the influence of dexamethasone drug loading and release kinetics on the local and systemic inhibition of inflammatory cellular activities. Temporal monitoring of host response showed that inhibition of inflammatory proteases in the early phase was correlated with decreased cellular infiltration in the later phase of the foreign body response. We believe that using controlled-release anti-inflammatory platforms to modulate early cellular dynamics will be useful in reducing the foreign body response to implanted biomaterials and medical devices. PMID:21429573

  15. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study.

    PubMed

    do Canto, António M T M; Robalo, João R; Santos, Patrícia D; Carvalho, Alfredo J Palace; Ramalho, J P Prates; Loura, Luís M S

    2016-11-01

    Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.

  16. 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.

  17. Electronic dynamics in helium nanodroplets studied via femtosecond XUV pump / UV probe photoelectron imaging

    NASA Astrophysics Data System (ADS)

    Ziemkiewicz, Michael; Bacellar, Camila; Leone, Stephen; Neumark, Daniel; Gessner, Oliver

    2014-05-01

    Superfluid helium nanodroplets consisting of ~ 2 × 106 atoms are examined using femtosecond time-resolved photoelectron imaging. The droplets are excited by a 23.6(2) eV extreme ultraviolet (XUV) pulse in resonance with an electronically excited band associated largely with the 1s3p Rydberg level of free He atoms. Relaxation dynamics are monitored by ionizing transient states with a 3.2 eV probe pulse and measuring the time-dependent photoelectron kinetic energy distributions using velocity map imaging (VMI). A broad, intense signal associated with the initially excited 1s3p band (Ekin ~ 2.5 eV) appears within the experimental time resolution and decays within 190(70) fs. Concomitantly, a second photoelectron feature with kinetic energies ranging from 0 to 0.5 eV appears on a time scale of ~ 200 fs. The new feature is identified as originating from the 1s2p droplet Rydberg band, indicating the direct observation of a previously suggested interband relaxation within the droplet. This feature also decays within ~ 200 fs, likely due to intraband relaxation within the 1s2p/1s2s manifold to states which are too deeply bound to be ionized by the 3.2 eV probe pulse.

  18. Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments.

    PubMed

    Chelli, Riccardo; Volkov, Victor V; Righini, Roberto

    2008-07-15

    We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.

  19. 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

  20. Metals on the move: zinc ions in cellular regulation and in the coordination dynamics of zinc proteins.

    PubMed

    Maret, Wolfgang

    2011-06-01

    Homeostatic control maintains essential transition metal ions at characteristic cellular concentrations to support their physiological functions and to avoid adverse effects. Zinc is especially widely used as a catalytic or structural cofactor in about 3000 human zinc proteins. In addition, the homeostatic control of zinc in eukaryotic cells permits functions of zinc(II) ions in regulation and in paracrine and intracrine signaling. Zinc ions are released from proteins through ligand-centered reactions in zinc/thiolate coordination environments, and from stores in cellular organelles, where zinc transporters participate in zinc loading and release. Muffling reactions allow zinc ions to serve as signaling ions (second messengers) in the cytosol that is buffered to picomolar zinc ion concentrations at steady-state. Muffling includes zinc ion binding to metallothioneins, cellular translocations of metallothioneins, delivery of zinc ions to transporter proteins, and zinc ion fluxes through cellular membranes with the result of removing the additional zinc ions from the cytosol and restoring the steady-state. Targets of regulatory zinc ions are proteins with sites for transient zinc binding, such as membrane receptors, enzymes, protein-protein interactions, and sensor proteins that control gene expression. The generation, transmission, targets, and termination of zinc ion signals involve proteins that use coordination dynamics in the inner and outer ligand spheres to control metal ion association and dissociation. These new findings establish critically important functions of zinc ions and zinc metalloproteins in cellular control.

  1. 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.

  2. Dynamical probe of thermodynamical properties in three-dimensional hairy AdS black holes

    NASA Astrophysics Data System (ADS)

    Zou, De-Cheng; Liu, Yunqi; Zhang, Cheng-Yong; Wang, Bin

    2016-11-01

    We study separatively the quasinormal modes (QNM) of electromagnetic perturbations around three-dimensional anti-de Sitter (AdS) black holes in Jordan and Einstein frames, which are related by the conformal transformations and a redefinition of a scalar field. We find that, in the Jordan frame, the imaginary parts of QNM frequencies can reflect the thermodynamical stabilities of hairy black holes, including the possible phase transition between the hairy black hole and BTZ black hole, disclosed by examining the corresponding free energies. Similar results are also uncovered in the Einstein frame. The obtained results further support that the QNM can be a dynamic probe of the thermodynamic properties in black holes.

  3. Dissipative dynamics of a system passing through a conical intersection: Ultrafast pump-probe observables

    NASA Astrophysics Data System (ADS)

    Gelman, David; Katz, Gil; Kosloff, Ronnie; Ratner, Mark A.

    2005-10-01

    The dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment, is studied with the purpose of identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semigroup formalism and the surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reflecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.

  4. Probing spin-orbit-interaction-induced electron dynamics in the carbon atom by multiphoton ionization

    NASA Astrophysics Data System (ADS)

    Rey, H. F.; van der Hart, H. W.

    2014-09-01

    We use R-matrix theory with time dependence (RMT) to investigate multiphoton ionization of ground-state atomic carbon with initial orbital magnetic quantum number ML=0 and ML=1 at a laser wavelength of 390 nm and peak intensity of 1014W/cm2. Significant differences in ionization yield and ejected-electron momentum distribution are observed between the two values for ML. We use our theoretical results to model how the spin-orbit interaction affects electron emission along the laser polarization axis. Under the assumption that an initial C atom is prepared at zero time delay with ML=0, the dynamics with respect to time delay of an ionizing probe pulse modeled by using RMT theory is found to be in good agreement with available experimental data.

  5. 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

    2014-04-09

    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).

  6. 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.

  7. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

    SciTech Connect

    Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou; Chourey, Karuna; Hettich, Robert L.; Pan, Chongle; Orphan, V.

    2016-04-29

    Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteins were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin

  8. Bases for time-resolved probing of transient carrier dynamics by optical pump-probe scanning tunneling microscopy.

    PubMed

    Yokota, Munenori; Yoshida, Shoji; Mera, Yutaka; Takeuchi, Osamu; Oigawa, Haruhiro; Shigekawa, Hidemi

    2013-10-07

    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.

  9. 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.

  10. 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

  11. 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.

  12. Probing structure-nanoaggregation relations of polyaromatic surfactants: a molecular dynamics simulation and dynamic light scattering study.

    PubMed

    Teklebrhan, Robel B; Ge, Lingling; Bhattacharjee, Subir; Xu, Zhenghe; Sjöblom, Johan

    2012-05-24

    Four synthetic perylene bisimide-based polyaromatic (PA) surfactants with a structural or functional group difference in their attached hydrophilic/hydrophobic substituent side chains were used to probe structure-nanoaggregation relations in organic media by molecular dynamics simulations and dynamic light scattering. The results from the simulated radial distribution functions and light scattering experiments indicate that variation in the structure of side chains and polarity of functional groups leads to significant variations in molecular association, dynamics of molecular nanoaggregation and structure of nanoaggregates. The aggregates of PA surfactant molecules grow to much larger sizes in heptane than in toluene. The aromatic solvent is shown to hinder molecular association by weakening π-π stacking, demonstrating the control of molecular aggregation by tuning solvent properties. In aliphatic solvent, the aggregates formed from PA surfactants of aliphatic alkyl groups and phenylalanine derivatives as a side chain usually have a higher solvent accessible surface area to accessible volume ratio (SASA:AV) than that of tryptophan derivatives in their side chains. PA surfactants with an aliphatic functional group in both side chains does not form polyaromatic π-π stacking (T-stacking) due to its strong steric hindrance in both solvents. Depending on the nature of the side chains attached, various stacking distributions, aggregation sizes, and SASA:AV ratios were obtained. In PA surfactant nanoaggregates, all of the solvent molecules were found to be excluded from the interstices of the stacked polyaromatic cores, regardless of whether the solvent molecules are aliphatic or aromatic. Although the change in the structure of side chain substituent in polyaromatic surfactants has a negligible impact on their self-diffusivity, it can strongly influence their intermolecular interactions, leading to different aggregate diffusion coefficients.

  13. Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations

    PubMed Central

    2015-01-01

    Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C–H- and N–H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C–H and N–H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution. PMID:24803857

  14. Shock Induced Chemistry: Application and Development of Ultrafast Nonlinear Probes of the Energy Dynamics of Molecules in Solids

    DTIC Science & Technology

    1988-01-01

    the distribution of time scales. 9 Dephasing experiments have traditionally been treated with optical bsorption formalisms. That is, the lineshape is...7 - w Fiur: 16 D. 3as Phase Dynamics and Spectroscopy Probed with Picosecond Transient Grating Experiments Picosecond transient grating...experiments (24] have been applied recently to the study of gas phase dynamics and spectroscopy for the first time in this laboratory [25,26,27]. The approach

  15. 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.

  16. Understanding Earth's radiation belt electron dynamics: Van Allen Probes observations and simulations

    NASA Astrophysics Data System (ADS)

    Li, Wen; Ma, Qianli; Thorne, Richard; Bortnik, Jacob; Zhang, Xiaojia

    2016-10-01

    Various physical processes are known to cause acceleration, loss, and transport of energetic electrons in the Earth's radiation belts, but their quantitative roles in different time and space need further investigation. In the present paper, we evaluate the relative roles of various physical processes during geomagnetic storms using a 3D diffusion simulation. By quantitatively comparing the electron evolution observed by Van Allen Probes and simulation, we found that whistler-mode chorus waves play a critical role in accelerating electrons up to several MeV through efficient energy diffusion. By only including radial diffusion driven by ultra-low-frequency waves, the simulation underestimates the observed electron acceleration, while radial diffusion plays an important role in redistributing electrons. Although an additional loss process is required to fully explain the overestimated electron fluxes at multi-MeV, the combined physical processes of radial diffusion and scattering by whistler-mode waves reproduce the observed electron dynamics remarkably well, suggesting that quasi-linear diffusion theory is reasonable to evaluate radiation belt electron dynamics, and the importance of nonlinear wave-particle interaction may still remain as an open question. We would like to acknowledge AFOSR Award FA9550-15-1-0158, NASA Grants NNX15AI96G, NNX15AF61G, and the NSF Grant AGS 1564510 for supporting this research.

  17. 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.

  18. Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots

    PubMed Central

    Katrukha, Eugene A.; Mikhaylova, Marina; van Brakel, Hugo X.; van Bergen en Henegouwen, Paul M.; Akhmanova, Anna; Hoogenraad, Casper C.; Kapitein, Lukas C.

    2017-01-01

    The cytoplasm is a highly complex and heterogeneous medium that is structured by the cytoskeleton. How local transport depends on the heterogeneous organization and dynamics of F-actin and microtubules is poorly understood. Here we use a novel delivery and functionalization strategy to utilize quantum dots (QDs) as probes for active and passive intracellular transport. Rapid imaging of non-functionalized QDs reveals two populations with a 100-fold difference in diffusion constant, with the faster fraction increasing upon actin depolymerization. When nanobody-functionalized QDs are targeted to different kinesin motor proteins, their trajectories do not display strong actin-induced transverse displacements, as suggested previously. Only kinesin-1 displays subtle directional fluctuations, because the subset of microtubules used by this motor undergoes prominent undulations. Using actin-targeting agents reveals that F-actin suppresses most microtubule shape remodelling, rather than promoting it. These results demonstrate how the spatial heterogeneity of the cytoskeleton imposes large variations in non-equilibrium intracellular dynamics. PMID:28322225

  19. 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.

  20. 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.

  1. 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

  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. Systematic computation of nonlinear cellular and molecular dynamics with low-power CytoMimetic circuits: a simulation study.

    PubMed

    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.

  4. Probing dynamics and pinning of single vortices in superconductors at nanometer scales.

    PubMed

    Embon, L; Anahory, Y; Suhov, A; Halbertal, D; Cuppens, J; Yakovenko, A; Uri, A; Myasoedov, Y; Rappaport, M L; Huber, M E; Gurevich, A; Zeldov, E

    2015-01-07

    The dynamics of quantized magnetic vortices and their pinning by materials defects determine electromagnetic properties of superconductors, particularly their ability to carry non-dissipative currents. Despite recent advances in the understanding of the complex physics of vortex matter, the behavior of vortices driven by current through a multi-scale potential of the actual materials defects is still not well understood, mostly due to the scarcity of appropriate experimental tools capable of tracing vortex trajectories on nanometer scales. Using a novel scanning superconducting quantum interference microscope we report here an investigation of controlled dynamics of vortices in lead films with sub-Angstrom spatial resolution and unprecedented sensitivity. We measured, for the first time, the fundamental dependence of the elementary pinning force of multiple defects on the vortex displacement, revealing a far more complex behavior than has previously been recognized, including striking spring softening and broken-spring depinning, as well as spontaneous hysteretic switching between cellular vortex trajectories. Our results indicate the importance of thermal fluctuations even at 4.2 K and of the vital role of ripples in the pinning potential, giving new insights into the mechanisms of magnetic relaxation and electromagnetic response of superconductors.

  5. 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.

  6. 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.

  7. Beyond structure: ultrafast X-ray absorption spectroscopy as a probe of non-adiabatic wavepacket dynamics.

    PubMed

    Neville, Simon P; Averbukh, Vitali; Patchkovskii, Serguei; Ruberti, Marco; Yun, Renjie; Chergui, Majed; Stolow, Albert; Schuurman, Michael S

    2016-12-16

    The excited state non-adiabatic dynamics of polyatomic molecules, leading to the coupling of structural and electronic dynamics, is a fundamentally important yet challenging problem for both experiment and theory. Ongoing developments in ultrafast extreme vacuum ultraviolet (XUV) and soft X-ray sources present new probes of coupled electronic-structural dynamics because of their novel and desirable characteristics. As one example, inner-shell spectroscopy offers localized, atom-specific probes of evolving electronic structure and bonding (via chemical shifts). In this work, we present the first on-the-fly ultrafast X-ray time-resolved absorption spectrum simulations of excited state wavepacket dynamics: photo-excited ethylene. This was achieved by coupling the ab initio multiple spawning (AIMS) method, employing on-the-fly dynamics simulations, with high-level algebraic diagrammatic construction (ADC) X-ray absorption cross-section calculations. Using the excited state dynamics of ethylene as a test case, we assessed the ability of X-ray absorption spectroscopy to project out the electronic character of complex wavepacket dynamics, and evaluated the sensitivity of the calculated spectra to large amplitude nuclear motion. In particular, we demonstrate the pronounced sensitivity of the pre-edge region of the X-ray absorption spectrum to the electronic and structural evolution of the excited-state wavepacket. We conclude that ultrafast time-resolved X-ray absorption spectroscopy may become a powerful tool in the interrogation of excited state non-adiabatic molecular dynamics.

  8. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

    DOE PAGES

    Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou; ...

    2016-04-29

    Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to

  9. Dynamics of glass-forming liquids. VIII. Dielectric signature of probe rotation and bulk dynamics in branched alkanes.

    PubMed

    Shahriari, Shervin; Mandanici, Andrea; Wang, Li-Min; Richert, Ranko

    2004-11-08

    We have measured the dielectric relaxation of several glass forming branched alkanes with very low dielectric loss in the frequency range 50 Hz-20 kHz. The molecular liquids of this study are 3-methylpentane, 3-methylheptane, 4-methylheptane, 2,3-dimethylpentane, and 2,4,6-trimethylheptane. All liquids display asymmetric loss peaks typical of supercooled liquids and slow beta relaxations of similar amplitudes. As an unusual feature, deliberate doping with 2-ethyl-1-hexanol, 5-methyl-2-hexanol, 2-methyl-1-butanol, 1-propanol, or 2-methyltetrahydrofuran at the 1 wt % level generates additional relaxation peaks at frequencies below those of the alpha relaxation. The relaxation times of these sub-alpha-peaks increase systematically with the size of the dopant molecules. Because these features are spectrally separate from the bulk dynamics, the rotational behavior and effective dipole moments of the probes can be studied in detail. For the alcohol guest molecules, the large relative rotational time scales and small effective dipole moments are indicative of hydrogen bonded clusters instead of individual molecules.

  10. 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.

  11. Structural dynamics of N-propionyl-D-glucosamine probed by infrared spectroscopies and ab initio computations.

    PubMed

    Han, Chen; Zhao, Juan; Yang, Fan; Wang, Jianping

    2013-07-25

    N-Acylglucosamine is an important component in many oligosaccharides in eukaryotes, where it plays a very important biological role. Located between a glucose ring and an alkyl group of such species is an amide unit (-CONH-), which exhibits an infrared absorption band, mainly due to the C═O stretching, in the region of 1600-1700 cm(-1), similar to the amide-I band found in polypeptides. In this work, vibrational properties of such an "amide-I mode" in N-propionyl-d-glucosamine (GlcNPr) are examined in three typical solvents (water, methanol, and dimethylsulfoxide) by using steady-state infrared and femtosecond infrared dispersed pump-probe spectroscopies. As a result of solute-solvent interactions, multiple structured GlcNPr-solvent clusters are formed in water and methanol but are unlikely in dimethylsulfoxide. The vibrational relaxation rate of the amide-I mode is slightly frequency-dependent, supporting the presence of multiple solvated structures. Further, the amide-I lifetime is significantly shorter in GlcNPr than that in a well-known monopeptide, N-methylacetamide, which can be attributed to the presence of additional downstream vibrational modes caused by the sugar unit. Ab initio molecular dynamics simulations are used to reveal microscopic details of the first solvation shell of GlcNPr. Our results demonstrate that the amide-I mode in glucosamine exhibits both structural and solvent sensitivities that can be used to characterize the three-dimensional arrangement of sugar residues and their structural dynamics in glycopeptides.

  12. 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.

  13. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    SciTech Connect

    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, or 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 dynamic

  14. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    DOE PAGES

    Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen; ...

    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

  15. Electronic dynamics by ultrafast pump photoelectron detachment probed by ionization: a dynamical simulation of negative-neutral-positive in LiH(-).

    PubMed

    Mignolet, B; Levine, R D; Remacle, F

    2014-08-21

    The control of electronic dynamics in the neutral electronic states of LiH before the onset of significant nuclei motion is investigated using a negative-neutral-positive (NeNePo) ultrafast IR pump-attoescond pulse train (APT) probe scheme. Starting from the ground state of the anion (LiH(-)), multiphoton ultrafast electron detachment and subsequent excitation of the neutral by a few femtosecond intense IR pulse produces a non-equilibrium electronic density in neutral LiH. The coherent electronic wave packet is then probed by angularly resolved photoionization to the cation by an APT generated from a replica of the pump IR pulse at several time delays. Realistic parameters for the pump and the APT are used. Several NeNePo schemes are simulated using different IR carrier frequencies, showing that the delay between the successive attosecond pulses in the train can be used as a filter to probe the different pairs of states present in the coherent electronic wave packet produced by the pump pulse. The dynamical simulations include the pump and the probe pulses to all orders by solving the time-dependent Schrödinger equation using a coupled equation scheme for the manifolds of the anion, neutral, and cation subspaces. We show that an incomplete molecular orientation of the molecule in the laboratory frame does not prevent probing the electronic density localization by angularly resolved photoelectron maps.

  16. Ultrafast Hydration Dynamics Probed by Tryptophan at Protein Surface and Protein-DNA Interface

    NASA Astrophysics Data System (ADS)

    Qin, Yangzhong

    As we all live in a special water planet Earth, the significance of water to life has been universally recognized. The reason why water is so important to life has intrigued many researchers. This dissertation will focus on the ultrafast dynamics of protein surface water and protein-DNA interfacial water which have direct importance to the protein structure and function. Using tryptophan as an intrinsic fluorescence probe, combined with site-directed mutagenesis and ultrafast fluorescence up-conversion spectroscopy, we can achieve single residue spatial resolution and femtosecond temporal resolution. We can also precisely determine the local hydration water dynamics by monitoring the Stokes shift of tryptophan one at a time. Previously, the protein surface hydration has been extensively studied by our group. In this thesis, we will provide more details on the methods we are using to extract the hydration dynamics, and also validate our methods from both experimental and theoretical perspectives. To further interrogate the interfacial water hydration dynamics relative to the protein surface hydration, we studied two DNA polymerases: DNA Polymerase IV (Dpo4) and DNA Polymerase Beta (Pol beta). Both proteins show typical surface hydration pattern with three distinct time components including: (i) the ultrafast sub-picosecond component reflects the bulk type water motion; (ii) a few picoseconds component shows the inner water relaxation mainly corresponding to the local libration and reorientation; (iii) the tens to hundred picoseconds component represents the water-protein coupled motion involving the whole water network reorganization. Dpo4, a loosely DNA binding protein, exhibits very flexible interfacial water which resembles its surface water yet with a significantly reduced ultrafast component. Such dynamic interfacial water not only maintains interfacial flexibility, but also contributes to the low fidelity of the protein. In contrast to the Dpo4, pol beta

  17. 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

    2016-08-12

    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.

  18. Order and dynamics inside H-PDLC nanodroplets: an ESR spin probe study.

    PubMed

    Bacchiocchi, Corrado; Miglioli, Isabella; Arcioni, Alberto; Vecchi, Ilaria; Rai, Kashma; Fontecchio, Adam; Zannoni, Claudio

    2009-04-23

    We have performed a detailed study of the order and dynamics of the commercially available BL038 liquid crystal (LC) inside nanosized (50-300 nm) droplets of a reflection-mode holographic-polymer dispersed liquid crystal (H-PDLC) device where LC nanodroplet layers and polymer layers are alternately arranged, forming a diffraction grating. We have determined the configuration of the LC local director and derived a model of the nanodroplet organization inside the layers. To achieve this, we have taken advantage of the high sensitivity of the ESR spin probe technique to study a series of temperatures ranging from the nematic to the isotropic phase of the LC. Using also additional information on the nanodroplet size and shape distribution provided by SEM images of the H-PDLC cross section, the observed director configuration has been modeled as a bidimensional distribution of elongated nanodroplets whose long axis is, on the average, parallel to the layers and whose internal director configuration is a uniaxial quasi-monodomain aligned along the nanodroplet long axis. Interestingly, at room temperature the molecules tend to keep their average orientation even when the layers are perpendicular to the magnetic field, suggesting that the molecular organization is dictated mainly by the confinement. This result might explain, at least in part, (i) the need for switching voltages significantly higher and (ii) the observed faster turn-off times in H-PDLCs compared to standard PDLC devices.

  19. 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.

  20. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    NASA Astrophysics Data System (ADS)

    Collins, Liam; Belianinov, Alex; Somnath, Suhas; Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen

    2016-08-01

    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.

  1. 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.

  2. Ultrafast Pump-Probe Study of Halide Dependence in Primary Reaction Dynamics of Halorhodopsin

    NASA Astrophysics Data System (ADS)

    Nakamura, Takumi; Takeuchi, Satoshi; Shibata, Mikihiro; Kandori, Hideki; Tahara, Tahei

    2007-03-01

    Halorhodopsin is a retinal protein in Haloarchaeal cell membrane. The light-induced all-trans to 13-cis isomerization of the retinal chromophore triggers unidirectional chloride-ion pump in millisecond timescale. Here, we present pump-probe study of the primary ultrafast dynamics of Natronobacterium pharaonis halorhodopsin that contains Cl^-, Br^- or I^-. All the temporal behaviors of the S1 absorption, ground-state bleaching, and stimulated emission consisted of three components, and their time constants showed halide-ion dependency. The ˜50-fs component corresponds to the spectral shift of the S1 absorption and stimulated emission bands, which is due to the wavepacket motion from the Franck-Condon region, forming the reactive and nonreactive S1 states. Referring to previous reports, the ˜2-ps component is assignable to the isomerization process from the reactive S1 state to the ground-state 13-cis form via the conical intersection, while the ˜5-ps component to the internal conversion of the nonreactive S1 state. Quantitative analysis indicated that the isomerization quantum yield increased in order of Cl^-, Br^- and I^-. On the basis of the halide-ion dependence observed, we discuss the relation between the initial halide-ion pump process and the isomerization mechanism.

  3. 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

  4. 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

  5. Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dai, L.; Sorkin, V.; Zhang, Y. W.

    2017-04-01

    We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

  6. Stability limits and defect dynamics in Ag nanoparticles probed by Bragg coherent diffractive imaging

    DOE PAGES

    Liu, Y.; Lopes, P. P.; Cha, W.; ...

    2017-02-10

    Dissolution is critical to nanomaterial stability, especially for partially dealloyed nanoparticle catalysts. Unfortunately, highly active catalysts are often not stable in their reactive environments, preventing widespread application. Thus, focusing on the structure–stability relationship at the nanoscale is crucial and will likely play an important role in meeting grand challenges. Recent advances in imaging capability have come from electron, X-ray, and other techniques but tend to be limited to specific sample environments and/or two-dimensional images. Here, we report investigations into the defect-stability relationship of silver nanoparticles to voltage-induced electrochemical dissolution imaged in situ in three dimensional detail by Bragg coherent diffractivemore » imaging. We first determine the average dissolution kinetics by stationary probe rotating disk electrode in combination with inductively coupled plasma mass spectrometry, which allows in situ measurement of Ag+ ion formation. We then observe the dissolution and redeposition processes in single nanocrystals, providing unique insight about the role of surface strain, defects, and their coupling to the dissolution chemistry. Finally, the methods developed and the knowledge gained go well beyond a “simple” silver electrochemistry and are applicable to all electrocatalytic reactions where functional links between activity and stability are controlled by structure and defect dynamics.« less

  7. 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.

  8. Probing the interaction of nanoparticles with mucin for drug delivery applications using dynamic light scattering.

    PubMed

    Griffiths, Peter Charles; Cattoz, Beatrice; Ibrahim, Mervat Shafik; Anuonye, Josephine Chibuzor

    2015-11-01

    Drug delivery via the eye, nose, gastrointestinal tract and lung is of great interest as they represent patient-compliant and facile methods to administer drugs. However, for a drug to reach the systemic circulation it must penetrate the "mucus barrier". An understanding of the characteristics of the mucus barrier is therefore important in the design of mucus penetrating drug delivery vehicles e.g. nanoparticles. Here, a range of nanoparticles - silica, aluminium coated silica, poly (lactic-co-glycolic acid) (PLGA) and PEGylated PLGA - each with known but different physicochemical characteristics were examined in the presence of mucin to identify those characteristics that engender nanoparticle/mucin interactions and thus, to define "design rules" for mucus penetrating (nano)particles (MPP), at least in terms of the surface characteristics of charge and hydrophilicity. Dynamic light scattering (DLS) and rheology have been used to assess the interaction between such nanoparticles and mucin. It was found that negatively charged and hydrophilic nanoparticles do not exhibit an interaction with mucin whereas positively charged and hydrophobic nanoparticles show a strong interaction. Surface grafted poly (ethylene glycol) (PEG) chains significantly reduced this interaction. This study clearly demonstrates that the established colloid science techniques of DLS and rheology are very powerful screening tools to probe nanoparticle/mucin interactions.

  9. 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.

  10. Almost Periodic Dynamics for Memristor-Based Shunting Inhibitory Cellular Neural Networks with Leakage Delays

    PubMed Central

    Lu, Lin

    2016-01-01

    We investigate a class of memristor-based shunting inhibitory cellular neural networks with leakage delays. By applying a new Lyapunov function method, we prove that the neural network which has a unique almost periodic solution is globally exponentially stable. Moreover, the theoretical findings of this paper on the almost periodic solution are applied to prove the existence and stability of periodic solution for memristor-based shunting inhibitory cellular neural networks with leakage delays and periodic coefficients. An example is given to illustrate the effectiveness of the theoretical results. The results obtained in this paper are completely new and complement the previously known studies of Wu (2011) and Chen and Cao (2002). PMID:27840634

  11. A Stochastic Cellular Automata Approach to Population Dynamics of Cells in a HIV Immune Response Model

    NASA Astrophysics Data System (ADS)

    Pandey, Ras B.

    1998-03-01

    A stochastic cellular automata (SCA) approach is introduced to study the growth and decay of cellular population in an immune response model relevant to HIV. Four cell types are considered: macrophages (M), helper cells (H), cytotoxic cells (C), and viral infected cells (V). Mobility of the cells is introduced and viral mutation is considered probabilistically. In absence of mutation, the population of the host cells, helper (N_H) and cytotxic (N_C) cells in particular, dominates over the viral population (N_V), i.e., N_H, NC > N_V, the immune system wins over the viral infection. Variation of cellular population with time exhibits oscillations. The amplitude of oscillations in variation of N_H, NC and NV with time decreases at high mobility even at low viral mutation; the rate of viral growth is nonmonotonic with NV > N_H, NC in the long time regime. The viral population is much higher than that of the host cells at higher mutation rate, a possible cause of AIDS.

  12. 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.

  13. 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.

  14. FAST TRACK COMMUNICATION: Femtosecond isomerization dynamics in the ethylene cation measured in an EUV-pump NIR-probe configuration

    NASA Astrophysics Data System (ADS)

    Tilborg, J. van; Allison, T. K.; Wright, T. W.; Hertlein, M. P.; Falcone, R. W.; Liu, Y.; Merdji, H.; Belkacem, A.

    2009-04-01

    Dynamics in the excited ethylene cation C2H+4 lead to isomerization to the ethylidene configuration (HC-CH3)+, which is predicted to be a transient configuration for electronic relaxation. With an intense femtosecond extreme ultraviolet pump pulse to populate the excited state, and a near infrared probe pulse to produce the fragments CH+ and CH+3 (which provides a direct signature of ethylidene), we measure optimum fragment yields at a probe delay of 80 fs. Also, an H2-stretch transient configuration, yielding H+2 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.

  15. 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

  16. Ligand-binding dynamics rewire cellular signaling via Estrogen Receptor-α

    PubMed Central

    Srinivasan, Sathish; Nwachukwu, Jerome C.; Parent, Alex A.; Cavett, Valerie; Nowak, Jason; Hughes, Travis S.; Kojetin, Douglas J.; Katzenellenbogen, John A.; Nettles, Kendall W.

    2013-01-01

    Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands). Proliferation of breast cancer cells directed by constrained ligands is associated with DNA binding, coactivator recruitment and activation of the estrogen-induced gene GREB1, reflecting a highly interconnected signaling network. In contrast, proliferation driven by dynamic ligands is associated with induction of ERα-mediated transcription in a DNA-binding domain (DBD)-dependent manner. Further, dynamic ligands displayed enhanced anti-inflammatory activity. The DBD-dependent profile was predictive of these signaling patterns in a larger diverse set of natural and synthetic ligands. Thus, ligand dynamics directs unique signaling pathways, and reveals a novel role of the DBD in allosteric control of ERα-mediated signaling. PMID:23524984

  17. a Study of Dynamic Recrystallization in TA15 Titanium Alloy during Hot Deformation by Cellular Automata Model

    NASA Astrophysics Data System (ADS)

    He, Dong; Zhu, Jing Chuan; Wang, Yang; Liu, Yong

    The dynamic recrystallization (DRX) of TA15 (Ti-6Al-2Zr-1Mo-1V) titanium alloy during the hot deformation process was studied by the Cellular Automata (CA) model which is base on the dislocation density theory. To build the CA model, the dislocation density model, dynamic recovery model, nucleation model and grain growth model were introduced and developed. The influences of strain rate on the microstructure evolution and flow stress character were investigated which shows that high strain rate leads to later DRX appearance, high flow stress peak value, small mean size of recrystallizing grains(R-grains) and low DRX percentage, but they have the similar Avrami curve. The characteristic of DRX process in a modeling non-uniform temperature filed (NTF) has been studied. All the simulation results show good agreement with the pioneer's work and experimental results.

  18. Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli

    PubMed Central

    Ghosh, Anirban; Passaris, Ioannis; Tesfazgi Mebrhatu, Mehari; Rocha, Susana; Vanoirbeek, Kristof; Hofkens, Johan; Aertsen, Abram

    2014-01-01

    In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction endonuclease of Escherichia coli K12, in response to different conditions. In absence of stimuli triggering its activity, Mrr was found to be strongly associated with the nucleoid as a number of discrete foci, suggesting the presence of Mrr hotspots on the chromosome. Previously established elicitors of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or expression of the HhaII methyltransferase, both caused nucleoid condensation and an unexpected coalescence of Mrr foci. However, although the resulting Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr typically led to cellular blebbing, suggesting a link between chromosome and cellular integrity. Interestingly, Mrr variants could be isolated that were specifically compromised in either HhaII- or HP-dependent activation, underscoring a mechanistic difference in the way both triggers activate Mrr. In general, our results reveal that Mrr can take part in complex spatial distributions on the nucleoid and can be engaged in distinct modes of activity. PMID:24423871

  19. 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.

  20. Energy transfer as a probe of protein dynamics in the proteins transferrin and calmodulin.

    PubMed Central

    O'Hara, P B; Gorski, K M; Rosen, M A

    1988-01-01

    We have initiated an investigation into the usefulness of fluorescence energy transfer in probing protein dynamics. Our analysis involves measuring the energy transfer efficiency while perturbing the protein conformational equilibrium with heat. As the temperature increases, the amplitudes of vibrations increase, and fluorescence energy transfer should also increase if the donor and acceptor are in a flexible region of the protein. A theoretical analysis developed by Somogyi and co-workers for the temperature dependence of dipole-dipole energy transfer (Somogyi, B., J. Matko, S. Papp, J. Hevessey, G. R. Welch, and S. Damjanovich. 1984. Biochemistry. 23:3403-3411) was tested by the authors in one protein system. Energy transfer from tryptophan to a pyridoxamine derivatized side group in RNase increased 40% over 25 degrees C. Here we report further testing of this model in two additional protein systems: calmodulin, a calcium activated regulatory protein, and transferrin, a blood serum iron shuttle. Our studies show a slight differential sensitivity of the transfer efficiency to heat for the two systems. Normalized energy transfer over 6.5 A in calmodulin from a tyrosine donor to a Tb(III) acceptor increases 40% from 295 to 320 K. Normalized energy transfer over 42 A in transferrin from a Tb(III) donor to an Fe(III) acceptor increases 35% over the same temperature range. Whereas these results demonstrate that thermally induced fluctuations do increase energy transfer as predicted by Somogyi, they also appear rather insensitive to the nature of the protein host environment. In contrast to the Förster processes examined above, energy transfer over very short distances has shown an anomalously high temperature dependence. PMID:3395656

  1. ReAsH as a Quantitative Probe of In-Cell Protein Dynamics.

    PubMed

    Gelman, Hannah; Wirth, Anna Jean; Gruebele, Martin

    2016-04-05

    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.

  2. Dynamic high pressure measurements using a Fiber Bragg Grating probe and an arrayed waveguide grating spectrometer

    NASA Astrophysics Data System (ADS)

    Barbarin, Y.; Lefrançois, A.; Magne, S.; Woirin, K.; Sinatti, F.; Osmont, A.; Luc, J.

    2016-08-01

    High pressure shock profiles are monitored using a long Fiber Bragg Grating (FBG). Such thin probe, with a diameter of typically 150 μm, can be inserted directly into targets for shock plate experiments. The shocked FBG's portion is stressed under compression, which increases its optical group index and shortens its grating period. Placed along the 2D symmetrical axis of the cylindrical target, the second effect is stronger and the reflected spectrum shifts towards the shorter wavelengths. The dynamic evolution of FBG spectra is recorded with a customized Arrayed Waveguide Grating (AWG) spectrometer covering the C+L band. The AWG provides 40 channels of 200-GHz spacing with a special flattop design. The output channels are fiber-connected to photoreceivers (bandwidth: DC - 400 MHz or 10 kHz - 2 GHz). The experimental setup was a symmetric impact, completed in a 110-mm diameter single-stage gas gun with Aluminum (6061T6) impactors and targets. The FBG's central wavelength was 1605 nm to cover the pressure range of 0 - 8 GPa. The FBG was 50-mm long as well as the target's thickness. The 20-mm thick impactor maintains a shock within the target over a distance of 30 mm. For the impact at 522 m/s, the sustained pressure of 3.6 GPa, which resulted in a Bragg shift of (26.2 +/- 1.5) nm, is measured and retrieved with respectively thin-film gauges and the hydrodynamic code Ouranos. The shock sensitivity of the FBG is about 7 nm/GPa, but it decreases with the pressure level. The overall spectra evolution is in good agreement with the numerical simulations.

  3. ECM-modulated cellular dynamics as a driving force for tissue morphogenesis.

    PubMed

    Daley, William P; Yamada, Kenneth M

    2013-08-01

    The extracellular matrix (ECM) plays diverse regulatory roles throughout development. Coordinate interactions between cells within a tissue and the ECM result in the dynamic remodeling of ECM structure. Both chemical signals and physical forces that result from such microenvironmental remodeling regulate cell behavior that sculpts tissue structure. Here, we review recent discoveries illustrating different ways in which ECM remodeling promotes dynamic cell behavior during tissue morphogenesis. We focus first on new insights that identify localized ECM signaling as a regulator of cell migration, shape, and adhesion during branching morphogenesis. We also review mechanisms by which the ECM and basement membrane can both sculpt and stabilize epithelial tissue structure, using as examples Drosophila egg chamber development and cleft formation in epithelial organs. Finally, we end with an overview of the dynamic mechanisms by which the ECM can regulate stem cell differentiation to contribute to proper tissue morphogenesis.

  4. ECM Signaling Regulates Collective Cellular Dynamics to Control Pancreas Branching Morphogenesis.

    PubMed

    Shih, Hung Ping; Panlasigui, Devin; Cirulli, Vincenzo; Sander, Maike

    2016-01-12

    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; additionally, 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.

  5. Spike integration and cellular memory in a rhythmic network from Na+/K+ pump current dynamics

    PubMed Central

    Pulver, Stefan R.

    2009-01-01

    The output of a neural circuit results from an interaction between the intrinsic properties of neurons within the circuit and the features of the synaptic connections between them. The plasticity of intrinsic properties has been primarily attributed to modification of ion channel function and/or number. In this study, we demonstrate a mechanism for intrinsic plasticity in rhythmically active Drosophila neurons that is not conductance-based. Larval motor neurons show a long lasting sodium-dependent afterhyperpolarization (AHP) following bursts of action potentials that is mediated by the electrogenic activity of Na+/K+ ATPase. This AHP persists for multiple seconds following volleys of action potentials and is able to function as a pattern-insensitive integrator of spike number that is independent of external calcium. This current also interacts with endogenous Shal K+ conductances to modulate spike timing for multiple seconds following rhythmic activity, providing a cellular memory of network activity on a behaviorally relevant time scale. PMID:19966842

  6. 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

  7. 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.

  8. Interface dynamics of immiscible two-phase lattice-gas cellular automata: a model with random dynamic scatterers and quenched disorder in two dimensions.

    PubMed

    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.

  9. 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.

  10. Collective dynamics of a photosynthetic protein probed by neutron spin-echo spectroscopy and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Dellerue, S.; Petrescu, A.; Smith, J. C.; Longeville, S.; Bellissent-Funel, M.-C.

    2000-03-01

    We have studied the collective dynamics of an hydrated soluble protein, the C-phycocyanin by using neutron spin-echo spectroscopy. Molecular dynamics simulations, performed with the same system, showed that the main dynamic contribution comes from backbone and side-chain motions. Both the experimental and spectra exhibit a dynamic relaxation with a characteristic time of about 10 ps.

  11. A dynamic view of cellular processes by in vivo fluorescence auto- and cross-correlation spectroscopy.

    PubMed

    Bacia, Kirsten; Schwille, Petra

    2003-01-01

    Fluorescence correlation spectroscopy (FCS) is becoming increasingly popular as a technique that aims at complementing live cell images with biophysical information. This article provides both a short overview over recent intracellular FCS applications and a practical guide for investigators, who are seeking to integrate FCS into live cell imaging to obtain information on particle mobility, local concentrations, and molecular interactions. A brief introduction to the principles of FCS is provided, particularly emphasizing practical aspects such as the choice of appropriate dyes and positioning of the measurement volume in the sample. Possibilities and limitations in extracting parameters from autocorrelation curves are discussed, and attention is drawn to potential artifacts, such as photobleaching and probe aggregation. The principle of dual-color cross-correlation is reviewed along with considerations for proper setup and adjustment. Practical implications of nonideal conditions including incomplete focus overlap and spectral cross-talk are considered. Recent examples of both auto- and cross-correlation applications demonstrate the potential of FCS for cell biology.

  12. Dynamic Relation between Expansion and Cellular Turgor in Growing Grape (Vitis vinifera L.) Leaves 1

    PubMed Central

    Shackel, Kenneth A.; Matthews, Mark A.; Morrison, Janice C.

    1987-01-01

    Measurements of the growth and water relations of expanding grape (Vitis vinifera L.) leaves have been used to determine the relationship between leaf expansion rate and leaf cell turgor. Direct measurement of turgor on the small (approximately 15 micrometer diameter) epidermal cells over the midvein of expanding grape leaves was made possible by improvements in the pressure probe technique. Leaf expansion rate and leaf water status were perturbed by environmentally induced changes in plant transpiration. After establishing a steady state growth rate, a step decrease in plant transpiration resulted in a rapid and large increase in leaf cell turgor (0.25 megapascal in 5 minutes), and leaf expansion rate. Subsequently, leaf expansion rate returned to the original steady state rate with no change in cell turgor. These results indicate that the expansion rate of leaves may not be strongly related to the turgor of the leaf cells, and that substantial control of leaf expansion rate, despite changes in turgor, may be part of normal plant function. It is suggested that a strictly physical interpretation of the parameters most commonly used to describe the relationship between turgor and growth in plant cells (cell wall extensibility and yield threshold) may be inappropriate when considering the process of plant cell expansion. PMID:16665579

  13. 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

  14. Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Balke, Nina; Jesse, Stephen; Carmichael, Ben; Baris Okatan, M.; Kravchenko, Ivan I.; Kalinin, Sergei V.; Tselev, Alexander

    2017-02-01

    Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm-1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

  15. Quantification of In-Contact Probe-Sample Electrostatic Forces with Dynamic Atomic Force Microscopy.

    PubMed

    Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M; Kravchenko, Ivan; Kalinin, Sergei; Tselev, Alexander

    2016-12-13

    Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V/nm at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

  16. Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy.

    PubMed

    Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M Baris; Kravchenko, Ivan I; Kalinin, Sergei V; Tselev, Alexander

    2017-01-04

    Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm(-1) at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

  17. Dynamic cellular and molecular modulations of diabetes mediated head and neck carcinogenesis.

    PubMed

    Liu, Chung-Ji; Chang, Wan-Jung; Chen, Chang-Yi; Sun, Fang-Ju; Cheng, Hui-Wen; Chen, Tsai-Ying; Lin, Shu-Chun; Li, Wan-Chun

    2015-10-06

    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.

  18. Mapping and controlling ultrafast dynamics of highly excited H2 molecules by VUV-IR pump-probe schemes

    NASA Astrophysics Data System (ADS)

    Sturm, F. P.; Tong, X. M.; Palacios, A.; Wright, T. W.; Zalyubovskaya, I.; Ray, D.; Shivaram, N.; Martín, F.; Belkacem, A.; Ranitovic, P.; Weber, Th.

    2017-01-01

    We used ultrashort femtosecond vacuum ultraviolet (VUV) and infrared (IR) pulses in a pump-probe scheme to map the dynamics and nonequilibrium dissociation channels of excited neutral H2 molecules. A nuclear wave packet is created in the B Σ+1u state of the neutral H2 molecule by absorption of the ninth harmonic of the driving infrared laser field. Due to the large stretching amplitude of the molecule excited in the B Σ+1u electronic state, the effective H2+ ionization potential changes significantly as the nuclear wave packet vibrates in the bound, highly electronically and vibrationally excited B potential-energy curve. We probed such dynamics by ionizing the excited neutral molecule using time-delayed VUV-or-IR radiation. We identified the nonequilibrium dissociation channels by utilizing three-dimensional momentum imaging of the ion fragments. We found that different dissociation channels can be controlled, to some extent, by changing the IR laser intensity and by choosing the wavelength of the probe laser light. Furthermore, we concluded that even in a benchmark molecular system such as H2*, the interpretation of the nonequilibrium multiphoton and multicolor ionization processes is still a challenging task, requiring intricate theoretical analysis.

  19. Wide-field multiphoton imaging of cellular dynamics in thick tissue by temporal focusing and patterned illumination

    PubMed Central

    Therrien, O. D.; Aubé, B.; Pagès, S.; Koninck, P. De; Côté, D.

    2011-01-01

    Wide-field temporal focusing is a novel technique that provides optical sectioning for imaging without the need for beam scanning. However, illuminating over large areas greatly reduces the photon density which limits the technique applicability to small regions, precluding functional imaging of cellular networks. Here we present a strategy that combines beam shaping and temporal focusing of amplified pulses (>1 µJ/pulse) for fast imaging of cells from the central nervous system in acute slices. Multiphoton video-rate imaging over total areas as wide as 4800 µm2 with an optical sectioning under 10 µm at 800 nm is achieved with our setup, leading to imaging of calcium dynamics of multiple cells simultaneously in thick tissue. PMID:21412473

  20. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

    NASA Astrophysics Data System (ADS)

    Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

    2017-01-01

    Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

  1. 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.

  2. 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.

  3. Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in Neurospora crassa.

    PubMed

    Araujo-Palomares, Cynthia L; Richthammer, Corinna; Seiler, Stephan; Castro-Longoria, Ernestina

    2011-01-01

    Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.

  4. In vitro assessment of blood compatibility: residual and dynamic markers of cellular activation.

    PubMed

    Johnson, Greg; Curry, Benjamin; Cahalan, Linda; Prater, Roni; Beeler, Michael; Gartner, Mark; Biggerstaff, John; Cahalan, Patrick

    2013-05-01

    The blood compatibility of materials and surfaces used for medical device fabrication is a crucial factor in their function and effectiveness. Expansion of device use into more sensitive and longer term applications warrants increasingly detailed evaluations of blood compatibility that reach beyond the customary measures mandated by regulatory requirements. A panel of tests that assess both deposition on the surface and activation of circulating blood in contact with the surface has been developed. Specifically, the ability of a surface to modulate the biological response of blood is assessed by measuring: (1) dynamic thrombin generation; (2) surface-bound thrombin activity after exposure to blood; (3) activation of monocytes, polymorphonuclear leukocytes, lymphocytes, and platelets; (4) activation of complement; and (5) adherent monocytes, polymorphonuclear leukocytes, lymphocytes, and platelets on blood-contacting surfaces. The tests were used to evaluate surfaces modified with immobilized heparin (Ension's proprietary bioactive surface) and demonstrated that the modified surfaces reduced platelet activation, leukocyte activation, and complement activation in flowing human blood. Perfusion of the surfaces with human platelet-rich plasma showed that the immobilized heparin surfaces also reduce both dynamic thrombin levels in the circulating plasma and residual thrombin generated at the material surface.

  5. 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.

  6. Mapping global sensitivity of cellular network dynamics: sensitivity heat maps and a global summation law.

    PubMed

    Rand, D A

    2008-08-06

    The dynamical systems arising from gene regulatory, signalling and metabolic networks are strongly nonlinear, have high-dimensional state spaces and depend on large numbers of parameters. Understanding the relation between the structure and the function for such systems is a considerable challenge. We need tools to identify key points of regulation, illuminate such issues as robustness and control and aid in the design of experiments. Here, I tackle this by developing new techniques for sensitivity analysis. In particular, I show how to globally analyse the sensitivity of a complex system by means of two new graphical objects: the sensitivity heat map and the parameter sensitivity spectrum. The approach to sensitivity analysis is global in the sense that it studies the variation in the whole of the model's solution rather than focusing on output variables one at a time, as in classical sensitivity analysis. This viewpoint relies on the discovery of local geometric rigidity for such systems, the mathematical insight that makes a practicable approach to such problems feasible for highly complex systems. In addition, we demonstrate a new summation theorem that substantially generalizes previous results for oscillatory and other dynamical phenomena. This theorem can be interpreted as a mathematical law stating the need for a balance between fragility and robustness in such systems.

  7. Imaging the Impact of Chemically Inducible Proteins on Cellular Dynamics In Vivo

    PubMed Central

    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

  8. 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.

  9. Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy

    PubMed Central

    Fingerhut, Benjamin P.; Dorfman, Konstantin E.; Mukamel, Shaul

    2013-01-01

    Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale. PMID:23914288

  10. Theoretical Investigation of Dynamic Properties of Magnetic Molecule Systems as Probed by NMR and Pulsed Fields Experiments

    SciTech Connect

    Rousochatzakis, Ioannis

    2005-12-17

    The field of molecular magnetism[l-6] has become a subject of intense theoretical and experimental interest and has rapidly evolved during the last years. This inter-disciplinary field concerns magnetic systems at the molecular or "nanoscopic" level, whose realization has become feasible due to recent advances in the field of chemical synthesis. The present theoretical work provides a first step towards exploiting the possibilities that are offered by probing magnetic molecules using external magnetic fields with high sweep rates. These probes, apart for providing information specific to magnetic molecules, offer the possibility of conducting a detailed study of the relaxational behavior of interacting spin systems as a result of their coupling with a "heat bath" and in particular the excitations of the host lattice. Development of a broad theoretical framework for dealing with relaxational phenomena induced by dynamical magnetic fields is indeed a worthy goal.

  11. Biodynsensing: Sensing Through Dynamics of Hybrid Affinity/Cellular Platforms; Towards Appraisal of Environmental and Biological Risks of Nanobiotechnology

    NASA Astrophysics Data System (ADS)

    Gheorghiu, E.; Gheorghiu, M.; David, S.; Polonschii, C.

    Chemical cues and nano-topographies present on the surface or in the extracellular medium strongly influence the fate and adhesion of biological cells. Careful tuning of cell—matrix interaction via engineered surfaces, either attractive or repulsive, require non-invasive, long time monitoring capabilities and lay the foundation of sensing platforms for risk assessment. Aiming to assess changes underwent by biointerfaces due to cell—environment interaction (in particular nanotechnology products), we have developed hybrid cellular platforms allowing for time based dual assays, i.e., impedance/dielectric spectroscopy (IS) and Surface Plasmon Resonance (SPR). Such platforms comprising Flow Injection Analysis (FIA) have been advanced to assess the interaction between selected (normal and malignant) cells and nano-patterned and/or chemically modified surfaces, as well as the impact of engineered nanoparticles, revealed by the related changes exhibited by cell membrane, morphology, adhesion and monolayer integrity. Besides experimental aspects dealing with measurement set-up, we will emphasize theoretical aspects related to: dielectric modeling. Aiming for a quantitative approach, microscopic models on dielectric behavior of ensembles of interconnected cells have been developed and their capabilities will be outlined within the presentation. Assessment of affinity reactions as revealed by dielectric/impedance assays of biointerfaces. Modeling the dynamics of the impedance in relation to the “quality” of cell layer and sensor's active surface, this study presents further developments of our approach described in Analytical Chemistry, 2002. Data analysis. This issue is related to the following basic question: Are there “simple” Biosensing Platforms? When coping with cellular platforms, either in suspension or immobilized (on filters, adhered on surfaces or entrapped, e.g., on using set-ups) there is an intrinsic nonlinear behavior of biological systems related

  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

    2015-01-29

    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. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.

    PubMed

    Ju, Young Seok; Martincorena, Inigo; Gerstung, Moritz; Petljak, Mia; Alexandrov, Ludmil B; Rahbari, Raheleh; Wedge, David C; Davies, Helen R; Ramakrishna, Manasa; Fullam, Anthony; Martin, Sancha; Alder, Christopher; Patel, Nikita; Gamble, Steve; O'Meara, Sarah; Giri, Dilip D; Sauer, Torril; Pinder, Sarah E; Purdie, Colin A; Borg, Åke; Stunnenberg, Henk; van de Vijver, Marc; Tan, Benita K T; Caldas, Carlos; Tutt, Andrew; Ueno, Naoto T; van 't Veer, Laura J; Martens, John W M; Sotiriou, Christos; Knappskog, Stian; Span, Paul N; Lakhani, Sunil R; Eyfjörd, Jórunn Erla; Børresen-Dale, Anne-Lise; Richardson, Andrea; Thompson, Alastair M; Viari, Alain; Hurles, Matthew E; Nik-Zainal, Serena; Campbell, Peter J; Stratton, Michael R

    2017-03-30

    Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. Here we use whole-genome sequences of normal blood from 241 adults to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.

  20. 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

  1. DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii.

    PubMed

    Lestini, Roxane; Delpech, Floriane; Myllykallio, Hannu

    2015-11-01

    Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea.

  2. 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.

  3. 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…

  4. 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

  5. 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...

  6. 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.

  7. I. Dynamics at the Galileo probe site on Jupiter and II. Orbital and thermal evolution of Ganymede

    NASA Astrophysics Data System (ADS)

    Showman, Adam Peter

    1999-11-01

    The low abundances of water and H2S measured by the Galileo probe at Jupiter suggest that the probe entered a downdraft where dry air from above cloud top advects to 10 bars or deeper. I use basic physical constraints to extract dynamical information from three aspects of Galileo probe data. First, I suggest that to remain dry, the downdraft must be underlain by a stable layer which inhibits mixing of volatiles from below; this requires the downdraft to be mechanically forced. Second, on rapidly rotating planets, the Coriolis and centripetal forces caused by winds usually balance the horizontal pressure-gradient force (which gives information about horizontal density differences). Therefore, I use the known winds versus depth at the probe site to infer horizontal density differences between the probe site and its surroundings. Under reasonable assumptions, these densities are consistent with a downdraft at the probe site. Third, I use ideas of horizontal mixing and column stretching to explain how the observed vertical profiles of ammonia, H2S, and water vapor can be produced in a downdraft. Finally, I discuss some apparent inconsistencies between these simple models. I also describe preliminary efforts to explore the origin, stability, and evolution of the downdrafts using the shallow water equations. The differences between Ganymede and Callisto have led to speculation that Ganymede's history was shaped by tidal heating from an orbital resonance. Using the numerical model developed by Malhotra (1991, Icarus 94, 399), I demonstrate that Io, Europa, and Ganymede could have passed through either of two (previously unexplored) Laplace-like resonances en route to the current Laplace resonance. Under reasonable conditions, these resonances produce great enough tidal heating in Ganymede to be geophysically significant. I also coupled the orbital evolution to an internal model of Ganymede to explore the effect of the resonance on Ganymede's interior. If Ganymede's tidal

  8. Extended pump-probe Faraday rotation spectroscopy of the submicrosecond electron spin dynamics in n -type GaAs

    NASA Astrophysics Data System (ADS)

    Belykh, V. V.; Evers, E.; Yakovlev, D. R.; Fobbe, F.; Greilich, A.; Bayer, M.

    2016-12-01

    We develop an extended pump-probe Faraday rotation technique to study submicrosecond electron spin dynamics with picosecond time resolution in a wide range of magnetic fields. The electron spin dephasing time T2* and the longitudinal spin relaxation time T1, both approaching 250 ns in weak fields, are measured thereby in n -type bulk GaAs. By tailoring the pump pulse train through increasing the contained number of pulses, the buildup of resonant spin amplification is demonstrated for the electron spin polarization. The spin precession amplitude in high magnetic fields applied in the Voigt geometry shows a nonmonotonic dynamics deviating strongly from a monoexponential decay and revealing slow beatings. The beatings indicate a two spin component behavior with a g -factor difference of Δ g ˜4 ×10-4 , much smaller than the Δ g expected for free and donor-bound electrons. This g -factor variation indicates efficient, but incomplete spin exchange averaging.

  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. On the mutual relationships between spin probe mobility, free volume and relaxation dynamics in organic glass-formers: Glycerol

    NASA Astrophysics Data System (ADS)

    Bartoš, J.; Švajdlenková, H.

    2017-02-01

    The rotation dynamics of the spin probe TEMPO in glycerol from ESR is compared with the ortho-positronium (o-Ps) annihilation from PALS and interpreted using the relaxation dynamics from BDS. Rotation time scale within the slow motion regime exhibits two Arrhenius regions with the characteristic ESR temperature, TX1τ, close to the characteristic PALS temperature, Tb1L, which is related to the secondary β process above Tg. Next, a slow to fast motion regime transition at the characteristic ESR temperature, Tcτ, close to the characteristic PALS temperature, Tb2L, followed by non-Arrhenius fast motion regime region is fully coupled with the primary α process.

  11. Probing ultrafast spin dynamics through a magnon resonance in the antiferromagnetic multiferroic HoMnO3

    DOE PAGES

    Bowlan, P.; Trugman, S. A.; Bowlan, J.; ...

    2016-09-26

    Here, we demonstrate an approach for directly tracking antiferromagnetic (AFM) spin dynamics by measuring ultrafast changes in a magnon resonance. We also test this idea on the multiferroic HoMnO 3 by optically photoexciting electrons, after which changes in the spin order are probed with a THz pulse tuned to a magnon resonance. This reveals a photoinduced change in the magnon line shape that builds up over 5–12 picoseconds, which we show to be the spin-lattice thermalization time, indicating that electrons heat the spins via phonons. We compare our results to previous studies of spin-lattice thermalization in ferromagnetic manganites, giving insightmore » into fundamental differences between the two systems. Finally, our work sheds light on the microscopic mechanism governing spin-phonon interactions in AFMs and demonstrates a powerful approach for directly monitoring ultrafast spin dynamics.« less

  12. Probing the dynamic structure factor of a neutral Fermi superfluid along the BCS-BEC crossover using atomic impurity qubits

    NASA Astrophysics Data System (ADS)

    Mitchison, Mark T.; Johnson, Tomi H.; Jaksch, Dieter

    2016-12-01

    We study an impurity atom trapped by an anharmonic potential, immersed within a cold atomic Fermi gas with attractive interactions that realizes the crossover from a Bardeen-Cooper-Schrieffer superfluid to a Bose-Einstein condensate. Considering the qubit comprising the lowest two vibrational energy eigenstates of the impurity, we demonstrate that its dynamics probes the equilibrium density fluctuations encoded in the dynamic structure factor of the superfluid. Observing the impurity's evolution is thus shown to facilitate nondestructive measurements of the superfluid order parameter and the contact between collective and single-particle excitation spectra. Our setup constitutes a model of an open quantum system interacting with a thermal reservoir, the latter supporting both bosonic and fermionic excitations that are also coupled to each other.

  13. Stealth CD44-targeted hyaluronic acid supramolecular nanoassemblies for doxorubicin delivery: probing the effect of uncovalent pegylation degree on cellular uptake and blood long circulation.

    PubMed

    Han, Xiaopeng; Li, Zhenbao; Sun, Jin; Luo, Cong; Li, Lin; Liu, Yuhai; Du, Yuqian; Qiu, Shuhong; Ai, Xiaoyu; Wu, Chunnuan; Lian, He; He, Zhonggui

    2015-01-10

    Stealth active targeting nanoparticles (NPs) usually include two types of ligand sites: ligand anchored on distal ends of the polyethylene glycol (PEG) and ligand buried under pegylated layer. The latter typical case is hyaluronic acid (HA)-based NPs; however, there is little information available for the latter NPs about effect of the optimal density of surface PEG coating on the blood circulation time, cellular uptake and in vivo anticancer activity. Thus, in this study, in order to optimize the anticancer effects of HA-based NPs, we focus on how uncovalent pegylation degree modulates blood circulation time and cellular uptake of HA-based NPs. We firstly designed a new double-hydrophilic copolymer by conjugating HP-β-cyclodextrin with HA, and this carrier was further pegylated with adamantyl-peg (ADA-PEG) to form inclusion complex HA-HPCD/ADA-PEG, termed as HCPs. The supramolecular nanoassemblies were fabricated by host-guest and polar interactions between HCPs and doxorubicin (Dox), with vitamin E succinate (VES) being a nanobridge. Despite the active recognition between HA and CD44 receptor, the cellular uptake and targeting efficiency of HA-NPs decreased with the increasing peg density, demonstrating HA was partly buried by high density peg coating. However, the high density of peg coating was beneficial to long circulation time, tumor biodistribution and anticancer activity in vivo. NPs with 5% peg coating had the optimal cellular targeting efficiency in vitro and anticancer effects in vivo. The findings suggest that balancing long circulation property and cellular uptake is important to achieve the optimal antitumor efficacy for pegylated HA-based NPs, and that PEG coating densities cannot be extended beyond a certain density for shielding effect without compromising the efficacy of hyaluronic acid targeted delivery.

  14. 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.

  15. On the spatial dynamics and oscillatory behavior of a predator-prey model based on cellular automata and local particle swarm optimization.

    PubMed

    Molina, Mario Martínez; Moreno-Armendáriz, Marco A; Carlos Seck Tuoh Mora, Juan

    2013-11-07

    A two-dimensional lattice model based on Cellular Automata theory and swarm intelligence is used to study the spatial and population dynamics of a theoretical ecosystem. It is found that the social interactions among predators provoke the formation of clusters, and that by increasing the mobility of predators the model enters into an oscillatory behavior.

  16. Wave packet theory of dynamic stimulated Raman spectra in femtosecond pump-probe spectroscopy.

    PubMed

    Sun, Zhigang; Jin, Zhongqi; Lu, J; Zhang, Dong H; Lee, Soo-Y

    2007-05-07

    The quantum theory for stimulated Raman spectroscopy from a moving wave packet using the third-order density matrix and polarization is derived. The theory applies, in particular, to the new technique of femtosecond broadband stimulated Raman spectroscopy (FSRS). In the general case, a femtosecond actinic pump pulse first prepares a moving wave packet on an excited state surface which is then interrogated with a coupled pair of picosecond Raman pump pulse and a femtosecond Raman probe pulse and the Raman gain in the direction of the probe pulse is measured. It is shown that the third-order polarization in the time domain, whose Fourier transform governs the Raman gain, is given simply by the overlap of a first-order wave packet created by the Raman pump on the upper electronic state with a second-order wave packet on the initial electronic state that is created by the coupling of the Raman pump and probe fields acting on the molecule. Calculations are performed on model potentials to illustrate and interpret the FSRS spectra.

  17. A quantitative analysis of L-glutamate-regulated Na+ dynamics in mouse cortical astrocytes: implications for cellular bioenergetics.

    PubMed

    Chatton, J Y; Marquet, P; Magistretti, P J

    2000-11-01

    The mode of Na+ entry and the dynamics of intracellular Na+ concentration ([Na+]i) changes consecutive to the application of the neurotransmitter glutamate were investigated in mouse cortical astrocytes in primary culture by video fluorescence microscopy. An elevation of [Na+]i was evoked by glutamate, whose amplitude and initial rate were concentration dependent. The glutamate-evoked Na+ increase was primarily due to Na+-glutamate cotransport, as inhibition of non-NMDA ionotropic receptors by 6-cyano-7-nitroquinoxiline-2,3-dione (CNQX) only weakly diminished the response and D-aspartate, a substrate of the glutamate transporter, produced [Na+]i elevations similar to those evoked by glutamate. Non-NMDA receptor activation could nevertheless be demonstrated by preventing receptor desensitization using cyclothiazide. Thus, in normal conditions non-NMDA receptors do not contribute significantly to the glutamate-evoked Na+ response. The rate of Na+ influx decreased during glutamate application, with kinetics that correlate well with the increase in [Na+]i and which depend on the extracellular concentration of glutamate. A tight coupling between Na+ entry and Na+/K+ ATPase activity was revealed by the massive [Na+]i increase evoked by glutamate when pump activity was inhibited by ouabain. During prolonged glutamate application, [Na+]i remains elevated at a new steady-state where Na+ influx through the transporter matches Na+ extrusion through the Na+/K+ ATPase. A mathematical model of the dynamics of [Na+]i homeostasis is presented which precisely defines the critical role of Na+ influx kinetics in the establishment of the elevated steady state and its consequences on the cellular bioenergetics. Indeed, extracellular glutamate concentrations of 10 microM already markedly increase the energetic demands of the astrocytes.

  18. 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.

  19. Real-time in vivo imaging of butterfly wing development: revealing the cellular dynamics of the pupal wing tissue.

    PubMed

    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

  20. 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

  1. Fabrication of quantum dot microarrays using electron beam lithography for applications in analyte sensing and cellular dynamics.

    PubMed

    Palankar, Raghavendra; Medvedev, Nikolay; Rong, Alena; Delcea, Mihaela

    2013-05-28

    Quantum dot (QD) based micro-/nanopatterned arrays are of broad interest in applications ranging from electronics, photonics, to sensor devices for biomedical purposes. Here, we report on a rapid, physico-chemically mild approach to generate high fidelity micropattern arrays of prefunctionalized water-soluble quantum dots using electron beam lithography. We show that such patterns retain their fluorescence and bioaffinity upon electron beam lithography and, based on the streptavidin-biotin interaction, allow for detection of proteins, colloidal gold nanoparticles and magnetic microparticles. Furthermore, we demonstrate the applicability of QD based microarray patterns differing in their shape (circles, squares, grid-like), size (from 1 to 10 μm) and pitch distance to study the adhesion, spreading and migration of human blood derived neutrophils. Using live cell confocal fluorescence microscopy, we show that pattern geometry and pitch distance influence the adhesion, spreading and migratory behavior of neutrophils. Research reported in this work paves the way for producing QD microarrays with multiplexed functionalities relevant for applications in analyte sensing and cellular dynamics.

  2. Fine structure of the spectra of the Kondo lattice model: Two-site cellular dynamical mean-field theory study

    NASA Astrophysics Data System (ADS)

    Osolin, Žiga; Žitko, Rok

    2017-01-01

    We study the antiferromagnetic and paramagnetic Kondo insulator phases of the Kondo lattice model on the cubic lattice at half filling using the cellular dynamical mean-field theory (CDMFT) with the numerical renormalization group (NRG) as the impurity solver, focusing on the fine details of the spectral function and self-energy. We find that the nonlocal correlations increase the gap in both the antiferromagnetic and Kondo insulator phases and shrink the extent of the antiferromagnetic phase in the phase diagram but do not alter any properties qualitatively. The agreement between the numerical CDMFT results and those within a simple hybridization picture, which adequately describes the overall band structure of the system but neglects all effects on the inelastic-scattering processes, is similar to that of the single-site DMFT results; there are deviations that are responsible for the additional fine structure, in particular for the asymmetric spectral resonances or dips that become more pronounced in the strong-coupling regime close to the antiferromagnet-paramagnetic quantum phase transition. These features appear broader in the CDMFT mostly due to numerical artifacts linked to more aggressive state truncation required in the NRG.

  3. Probing the equilibrium dynamics of colloidal hard spheres above the mode-coupling glass transition.

    PubMed

    Brambilla, G; El Masri, D; Pierno, M; Berthier, L; Cipelletti, L; Petekidis, G; Schofield, A B

    2009-02-27

    We use dynamic light scattering and computer simulations to study equilibrium dynamics and dynamic heterogeneity in concentrated suspensions of colloidal hard spheres. Our study covers an unprecedented density range and spans seven decades in structural relaxation time, tau(alpha0, including equilibrium measurements above phi(c), the location of the glass transition deduced from fitting our data to mode-coupling theory. Instead of falling out of equilibrium, the system remains ergodic above phi(c) and enters a new dynamical regime where tau(alpha) increases with a functional form that was not anticipated by previous experiments, while the amplitude of dynamic heterogeneity grows slower than a power law with tau(alpha), as found in molecular glass formers close to the glass transition.

  4. Development of a Clickable Probe for Profiling of Protein Glutathionylation in the Central Cellular Metabolism of E. coli and Drosophila.

    PubMed

    Feng, Shan; Chen, Yuling; Yang, Fan; Zhang, Lei; Gong, Yiyi; Adilijiang, Gulishana; Gao, Yan; Deng, Haiteng

    2015-11-19

    Protein glutathionylation is an important post-translational modification that regulates many cellular processes, including energy metabolism, signal transduction, and protein homeostasis. Global profiling of glutathionylated proteins (denoted as glutathionylome) is crucial for understanding redox-regulated signal transduction. Here, we developed a novel method based on click reaction and proteomics to enrich and identify the glutathionylated peptides in Escherichia coli and Drosophila lysates, in which 937 and 1,930 potential glutathionylated peptides were identified, respectively. Bioinformatics analysis showed that the cysteine residue next to negatively charged amino acid residues has a higher frequency of glutathionylation. Importantly, we found that most proteins associated with metabolic pathways were glutathionylated and that the glutathionylation sites of metabolic enzymes were highly conserved among different species. Our results indicate that the glutathione analog is a useful tool to characterize protein glutathionylation, and glutathionylation of metabolic enzymes, which play important roles in regulating cellular metabolism, is conserved.

  5. Ionic liquid containing microemulsions: probe by conductance, dynamic light scattering, diffusion-ordered spectroscopy NMR measurements, and study of solvent relaxation dynamics.

    PubMed

    Pramanik, Rajib; Sarkar, Souravi; Ghatak, Chiranjib; Rao, Vishal Govind; Sarkar, Nilmoni

    2011-03-17

    Room-temperature ionic liquid (RTIL), N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([P(13)][Tf(2)N]), was substituted for polar water and formed nonaqueous microemulsions with benzene by the aid of nonionic surfactant TX-100. The phase behavior of the ternary system was investigated, and microregions of [P(13)][Tf(2)N]-in-benzene (IL/O), bicontinuous, and benzene-in-[P(13)][Tf(2)N] (O/IL) were identified by traditional electrical conductivity measurements. Dynamic light scattering (DLS) revealed the formation of these IL microemulsions because with gradual increase of RTIL contents the droplet sizes of the microemulsions are also gradually increasing. Pulsed-field gradient spin-echo NMR have been studied to measure the diffusion coefficients of neat [P(13)][Tf(2)N] and [P(13)][Tf(2)N] in microemulsions which indicate ionic liquid containing microemulsions is formed. Moreover, the dynamics of solvent relaxation have been investigated in [P(13)][Tf(2)N]/TX100/benzene microemulsions using steady-state and time-resolved fluorescence spectroscopy using coumarin 153 (C-153) and coumarin 480 (C-480) fluorescence probe with variation of RTIL contents in microemulsions. For both of the probes with increasing amount of ionic liquids in microemulsions the relative contribution of the fast components increases and the slow components contribution decreases; therefore the average solvation time decreases.

  6. 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.

  7. Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study.

    PubMed

    Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil

    2012-10-01

    The nature of binding of specially designed charge transfer (CT) fluorophore at the hydrophobic protein interior of human serum albumin (HSA) has been explored by massive blue-shift (82 nm) of the polarity sensitive probe emission accompanying increase in emission intensity, fluorescence anisotropy, red edge excitation shift, and average fluorescence lifetimes. Thermal unfolding of the intramolecular CT probe bound HSA produces almost opposite spectral changes. The spectral responses of the molecule reveal that it can be used as an extrinsic fluorescent reporter for similar biological systems. Circular dichrosim spectra, molecular docking, and molecular dynamics simulation studies scrutinize this binding process and stability of the protein probe complex more closely.

  8. Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

    PubMed Central

    Benítez, Mariana; Espinosa-Soto, Carlos; Padilla-Longoria, Pablo; Alvarez-Buylla, Elena R

    2008-01-01

    Background Dynamical models are instrumental for exploring the way information required to generate robust developmental patterns arises from complex interactions among genetic and non-genetic factors. We address this fundamental issue of developmental biology studying the leaf and root epidermis of Arabidopsis. We propose an experimentally-grounded model of gene regulatory networks (GRNs) that are coupled by protein diffusion and comprise a meta-GRN implemented on cellularised domains. Results Steady states of the meta-GRN model correspond to gene expression profiles typical of hair and non-hair epidermal cells. The simulations also render spatial patterns that match the cellular arrangements observed in root and leaf epidermis. As in actual plants, such patterns are robust in the face of diverse perturbations. We validated the model by checking that it also reproduced the patterns of reported mutants. The meta-GRN model shows that interlinked sub-networks contribute redundantly to the formation of robust hair patterns and permits to advance novel and testable predictions regarding the effect of cell shape, signalling pathways and additional gene interactions affecting spatial cell-patterning. Conclusion The spatial meta-GRN model integrates available experimental data and contributes to further understanding of the Arabidopsis epidermal system. It also provides a systems biology framework to explore the interplay among sub-networks of a GRN, cell-to-cell communication, cell shape and domain traits, which could help understanding of general aspects of patterning processes. For instance, our model suggests that the information needed for cell fate determination emerges from dynamic processes that depend upon molecular components inside and outside differentiating cells, suggesting that the classical distinction of lineage versus positional cell differentiation may be instrumental but rather artificial. It also suggests that interlinkage of nonlinear and redundant

  9. 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

  10. Probing heterogeneous dynamics from spatial density correlation in glass-forming liquids

    NASA Astrophysics Data System (ADS)

    Li, Yan-Wei; Zhu, You-Liang; Sun, Zhao-Yan

    2016-12-01

    We numerically investigate the connection between spatial density correlation and dynamical heterogeneity in glass-forming liquids. We demonstrate that the cluster size defined by the spatial aggregation of densely packed particles (DPPs) can better capture the difference between the dynamics of the Lennard-Jones glass model and the Weeks-Chandler-Andersen truncation model than the commonly used pair correlation functions. More interestingly, we compare the mobility of DPPs and loosely packed particles, and we find that high local density correlates well with slow dynamics in systems with relatively hard repulsive interactions but links to mobile ones in the system with soft repulsive interactions at one relaxation time scale. Our results show clear evidence that the above model dependence behavior stems from the hopping motion of DPPs at the end of the caging stage due to the compressive nature of soft repulsive spheres, which activates the dynamics of DPPs in the α relaxation stage.

  11. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes.

    PubMed

    Sergé, Arnauld; Bertaux, Nicolas; Rigneault, Hervé; Marguet, Didier

    2008-08-01

    Although the highly dynamic and mosaic organization of the plasma membrane is well-recognized, depicting a resolved, global view of this organization remains challenging. We present an analytical single-particle tracking (SPT) method and tool, multiple-target tracing (MTT), that takes advantage of the high spatial resolution provided by single-fluorophore sensitivity. MTT can be used to generate dynamic maps at high densities of tracked particles, thereby providing global representation of molecular dynamics in cell membranes. Deflation by subtracting detected peaks allows detection of lower-intensity peaks. We exhaustively detected particles using MTT, with performance reaching theoretical limits, and then reconnected trajectories integrating the statistical information from past trajectories. We demonstrate the potential of this method by applying it to the epidermal growth factor receptor (EGFR) labeled with quantum dots (Qdots), in the plasma membrane of live cells. We anticipate the use of MTT to explore molecular dynamics and interactions at the cell membrane.

  12. Dynamics of Phenanthrenequinone on Carbon Nano-Onion Surfaces Probed by Quasielastic Neutron Scattering

    SciTech Connect

    Anjos, Daniela M; Mamontov, Eugene; Brown, Gilbert M; Overbury, Steven {Steve} H; Mavila Chathoth, Suresh

    2012-01-01

    We used quasielastic neutron scattering (QENS) to study the dynamics of phenanthrenequinone (PQ) on the surface of onion-like carbon (OLC), or so called carbon onions, as a function of surface coverage and temperature. For both the high- and low-coverage samples, we observed two diffusion processes; a faster process and nearly an order of magnitude slower process. On the high-coverage surface, the slow diffusion process is of long-range translational character, whereas the fast diffusion process is spatially localized on the length scale of ~ 4.7 . On the low-coverage surface, both diffusion processes are spatially localized; on the same length scale of ~ 4.7 for the fast diffusion and a somewhat larger length scale for the slow diffusion. Arrhenius temperature dependence is observed except for the long-range diffusion on the high-coverage surface. We attribute the fast diffusion process to the generic localized in-cage dynamics of PQ molecules, and the slow diffusion process to the long-range translational dynamics of PQ molecules, which, depending on the coverage, may be either spatially restricted, or long-range. On the low-coverage surface, uniform surface coverage is not attained, and the PQ molecules experience the effect of spatial constraints on their long-range translational dynamics. Unexpectedly, the dynamics of PQ molecules on OLC as a function of temperature and surface coverage bears qualitative resemblance to the dynamics of water molecules on oxide surfaces, including practically temperature-independent residence times for the low-coverage surface. The dynamics features that we observed may be universal across different classes of surface adsorbates.

  13. Polhode dynamics and gyroscope asymmetry analysis of Gravity Probe B using gyroscope position data

    NASA Astrophysics Data System (ADS)

    Dolphin, Michael D. M.

    2007-12-01

    Gravity Probe B is a joint NASA/Stanford University satellite-based experiment designed to measure two predictions of Einstein's General Theory of Relativity: the geodetic and frame-dragging effects. The two effects are predicted to cause spin axis drift of a gyroscope with respect to the fixed stars at a rate of 3.203 x10-5 and 1.89x10-7 radians (6606 and 39 milli-arcseconds) per year, respectively. The frame-dragging effect has not previously been observed experimentally. The sensors for this experiment are four round gyroscopes of radius 19 mm, spherical to within 20 nm for largest peak to valley distance on their surface. For the success of the mission, it is essential that the measurement of the spin axis orientation be both precise and accurate to within 5 nrad. Polhode motion is a well understood motion of a body rotating in a torque-free environment. It was believed that the polhode motion would remain constant over the course of the mission. Early in the data analysis it was revealed that the polhode motion changed its behavior over time. To obtain the accuracy desired for the mission, a detailed understanding of the polhode behavior for each of the four gyroscopes is required. The main focus of this research is to understand and fully characterize the polhode motion. Analysis of the equations reveals that one parameter characterizes the shape of the polhode path, designated as Q. The exact timing of the polhode behavior is captured in the analysis of the polhode phase. To obtain an estimate of Q and the polhode phase, the gyroscope suspension system data is analyzed to reveal variations of measured gyroscope position at spin frequency. A model of the gyroscopes' surface shape is created and used to find the most likely value of Q by means of a multi parameter search. The value for Q is obtained to an accuracy of 0.05 for two of the gyroscopes. The parameters defining the gyroscopes' surface shape are obtained to within sub nanometer levels for all four

  14. Probing the out-of-equilibrium dynamics of two interacting atoms

    NASA Astrophysics Data System (ADS)

    Keller, Tim; Fogarty, Thomás

    2016-12-01

    We study the out-of-equilibrium dynamics of two interacting atoms in a one-dimensional harmonic trap after a quench by a tightly pinned impurity atom. We make use of an approximate variational calculation called the Lagrange-mesh method to solve the Schrödinger equation as a function of interparticle interaction and impurity quench strength. We investigate the out-of-equilibrium dynamics by calculating the Loschmidt echo which quantifies the irreversibility of the system following the quench, while its probability distribution after long times can be used to identify distinct dynamical regimes. These quantities are related to the spectral function which describes the full dynamical spectrum, and we show through a thorough examination of the parameter space the existence of distinct scattering states and collective oscillations. This work demonstrates how these dynamics are strongly dependent on the interaction strength between the atoms and may be tuned to observe the establishment of the orthogonality catastrophe in few-body systems.

  15. Ultrafast dynamics of nonequilibrium resonance energy transfer and probing globular protein flexibility of myoglobin.

    PubMed

    Stevens, Jeffrey A; Link, Justin J; Zang, Chen; Wang, Lijuan; Zhong, Dongping

    2012-03-22

    Protein structural plasticity is critical to many biological activities and accurate determination of its temporal and spatial fluctuations is challenging and difficult. Here, we report our extensive characterization of global flexibility of a globular heme protein of myoglobin using resonance energy transfer as a molecular ruler. With site-directed mutagenesis, we use a tryptophan scan to examine local structural fluctuations from B to H helices utilizing 10 tryptophan-heme energy transfer pairs with femtosecond resolution. We observed ultrafast resonance energy transfer dynamics by following a nearly single exponential behavior in 10-100 ps, strongly indicating that the globular structure of myoglobin is relatively rigid, with no observable static or slow dynamic conformational heterogeneity. The observation is against our molecular dynamics simulations, which show large local fluctuations and give multiple exponential energy transfer behaviors, suggesting too flexible of the global structure and thus raising a serious issue of the force fields used in simulations. Finally, these ultrafast energy transfer dynamics all occur on the similar time scales of local environmental relaxations (solvation), leading to nonexponential processes caused by energy relaxations, not structural fluctuations. Our analyses of such processes reveal an intrinsic compressed- and/or stretched-exponential behaviors and elucidate the nature of inherent nonequilibrium of ultrafast resonance energy transfer in proteins. This new concept of compressed nonequilibrium transfer dynamics should be applied to all protein studies by time-resolved Förster resonance energy transfer (FRET).

  16. Encapsulated guest-host dynamics: guest rotational barriers and tumbling as a probe of host interior cavity space.

    PubMed

    Mugridge, Jeffrey S; Szigethy, Géza; Bergman, Robert G; Raymond, Kenneth N

    2010-11-17

    The supramolecular host assembly [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) encapsulates cationic guest molecules within its hydrophobic cavity and catalyzes a variety of chemical transformations within its confined interior space. Despite the well-defined structure, the host ligand framework and interior cavity are very flexible and 1 can accommodate a wide range of guest shapes and sizes. These observations raise questions about the steric effects of confinement within 1 and how encapsulation fundamentally changes the motions of guest molecules. Here we examine the motional dynamics (guest bond rotation and tumbling) of encapsulated guest molecules to probe the steric consequences of encapsulation within host 1. Encapsulation is found to increase the Ph-CH(2) bond rotational barrier for ortho-substituted benzyl phosphonium guest molecules by 3 to 6 kcal/mol, and the barrier is found to depend on both guest size and shape. The tumbling dynamics of guests encapsulated in 1 were also investigated, and here it was found that longer, more prolate-shaped guest molecules tumble more slowly in the host cavity than larger but more spherical guest molecules. The prolate guests reduce the host symmetry from T to C(1) in solution at low temperatures, and the distortion of the host framework that is in part responsible for this symmetry reduction is observed directly in the solid state. Analysis of guest motional dynamics is a powerful method for interrogating host structure and fundamental host-guest interactions.

  17. A Dual-Colour Architecture for Pump-Probe Spectroscopy of Ultrafast Magnetization Dynamics in the Sub-10-femtosecond Range

    PubMed Central

    Gonçalves, C. S.; Silva, A. S.; Navas, D.; Miranda, M.; Silva, F.; Crespo, H.; Schmool, D. S.

    2016-01-01

    Current time-resolution-limited dynamic measurements clearly show the need for improved techniques to access processes on the sub-10-femtosecond timescale. To access this regime, we have designed and constructed a state-of-the-art time-resolved magneto-optic Kerr effect apparatus, based on a new dual-color scheme, for the measurement of ultrafast demagnetization and precessional dynamics in magnetic materials. This system can operate well below the current temporal ranges reported in the literature, which typically lie in the region of around 50 fs and above. We have used a dual-colour scheme, based on ultra broadband hollow-core fibre and chirped mirror pulse compression techniques, to obtain unprecedented sub-8-fs pump and probe pulse durations at the sample plane. To demonstrate the capabilities of this system for ultrafast demagnetization and precessional dynamics studies, we have performed measurements in a ferrimagnetic GdFeCo thin film. Our study has shown that the magnetization shows a sudden drop within the first picosecond after the pump pulse, a fast recovery (remagnetization) within a few picoseconds, followed by a clear oscillation or precession during a slower magnetization recovery. Moreover, we have experimentally confirmed for the first time that a sub-10-fs pulse is able to efficiently excite a magnetic system such as GdFeCo. PMID:26976721

  18. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling.

    PubMed

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future.

  19. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling

    PubMed Central

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    2016-01-01

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future. PMID:27669518

  20. Rocky Mountain evolution: Tying Continental Dynamics of the Rocky Mountains and Deep Probe seismic experiments with receiver functions

    USGS Publications Warehouse

    Rumpfhuber, E.-M.; Keller, Gordon R.; Sandvol, E.; Velasco, A.A.; Wilson, D.C.

    2009-01-01

    In this study, we have determined the crustal structure using three different receiver function methods using data collected from the northern transect of the Continental Dynamics of the Rocky Mountains (CD-ROM) experiment. The resulting migrated image and crustal thickness determinations confirm and refine prior crustal thickness measurements based on the CD-ROM and Deep Probe experiment data sets. The new results show a very distinct and thick lower crustal layer beneath the Archean Wyoming province. In addition, we are able to show its termination at 42??N latitude, which provides a seismic tie between the CD-ROM and Deep Probe seismic experiments and thus completes a continuous north-south transect extending from New Mexico into Alberta, Canada. This new tie is particularly important because it occurs close to a major tectonic boundary, the Cheyenne belt, between an Archean craton and a Proterozoic terrane. We used two different stacking techniques, based on a similar concept but using two different ways to estimate uncertainties. Furthermore, we used receiver function migration and common conversion point (CCP) stacking techniques. The combined interpretation of all our results shows (1) crustal thinning in southern Wyoming, (2) strong northward crustal thickening beginning in central Wyoming, (3) the presence of an unusually thick and high-velocity lower crust beneath the Wyoming province, and (4) the abrupt termination of this lower crustal layer north of the Cheyenne belt at 42??N latitude. Copyright 2009 by the American Geophysical Union.