Coherent Signal Amplification in Bistable Nanomechanical Oscillators by Stochastic Resonance

Stochastic resonance is a counter-intuitive concept[1,2], ; the addition of noise to a noisy system induces coherent amplification of its response. First suggested as a mechanism for the cyclic recurrence of ice ages, stochastic resonance has been seen in a wide variety of macroscopic physical systems: bistable ring lasers[3], SQUIDs[4,5], magnetoelastic ribbons[6], and neurophysiological systems such as the receptors in crickets[7] and crayfish[8]. Although it is fundamentally important as a mechanism of coherent signal amplification, stochastic resonance is yet to be observed in nanoscale systems. Here we report the observation of stochastic resonance in bistable nanomechanical silicon oscillators, which can play an important role in the realization of controllable high-speed nanomechanical memory cells. Our nanomechanical systems were excited into a dynamic bistable state and modulated in order to induce controllable switching; the addition of white noise showed a marked amplification of the signal strength. Stochastic resonance in nanomechanical systems paves the way for exploring macroscopic quantum coherence and tunneling, and controlling nanoscale quantum systems for their eventual use as robust quantum logic devices.Comment: 18 pages, 4 figure

Production and Characterization of Antifungal Compounds Produced by Lactobacillus plantarum IMAU10014

Lactobacillus plantarum IMAU10014 was isolated from koumiss that produces a broad spectrum of antifungal compounds, all of which were active against plant pathogenic fungi in an agar plate assay. Two major antifungal compounds were extracted from the cell-free supernatant broth of L. plantarum IMAU10014. 3-phenyllactic acid and Benzeneacetic acid, 2-propenyl ester were carried out by HPLC, LC-MS, GC-MS, NMR analysis. It is the first report that lactic acid bacteria produce antifungal Benzeneacetic acid, 2-propenyl ester. Of these, the antifungal products also have a broad spectrum of antifungal activity, namely against Botrytis cinerea, Glomerella cingulate, Phytophthora drechsleri Tucker, Penicillium citrinum, Penicillium digitatum and Fusarium oxysporum, which was identified by the overlay and well-diffusion assay. F. oxysporum, P. citrinum and P. drechsleri Tucker were the most sensitive among molds

Ethics, politics and embodied imagination in crafting scientific knowledge

This article explores ‘research-as-craft’ as a sensitizing concept for disclosing the presence of ethics and politics, as well as embodiment and imagination, in the doing and representation of scientific activity. Routinely unnoticed, marginalized or suppressed in methodology sections of articles and methodology textbooks, research-as-craft gestures towards messy, tacit, uncertain, yet rarely thematized, practices that are central to getting science done. To acknowledge and address the significance of research-as-craft in knowledge production, we show how it relates to three forms of reflexivity – constitutive, epistemic and disruptive. Through this we demonstrate the craftiness that is required when struggling with the indeterminacy that is endemic to the production and communication of scientific knowledge. By showing how empirical situations require imaginative interpretation by embodied researchers, we argue that our conception of research-as-craft facilitates appreciation of scientific inquiry as an indexical activity that involves the crafted object and the researcher in an ethico-political process of co-constituting knowledge

Electrocatalytic performance of SiO2-SWCNT nanocomposites prepared by electroassisted deposition

“The final publication is available at Springer via http://dx.doi.org/10.1007/s12678-013-0144-3”Composite materials made of porous SiO2 matrices filled with single-walled carbon nanotubes (SWCNTs) were deposited on electrodes by an electroassisted deposition method. The synthesized materials were characterized by several techniques, showing that porous silica prevents the aggregation of SWCNT on the electrodes, as could be observed by transmission electron microscopy and Raman spectroscopy. Different redox probes were employed to test their electrochemical sensing properties. The silica layer allows the permeation of the redox probes to the electrode surface and improves the electrochemical reversibility indicating an electrocatalytic effect by the incorporation of dispersed SWCNT into the silica films.This work was financed by the following research projects: MAT2010-15273 of the Spanish Ministerio de Economia y Competitividad and FEDER, PROMETEO/2013/038 of the GV, and CIVP16A1821 of the Fundacion Ramon Areces. Alonso Gamero-Quijano and David Salinas-Torres acknowledge Generalitat Valenciana (Santiago Grisolia Program) and Ministerio de Economia y Competitividad, respectively, for the funding of their research fellowships.Gamero-Quijano, A.; Huerta, F.; Salinas-Torres, D.; Morallón, E.; Montilla, F. (2013). Electrocatalytic performance of SiO2-SWCNT nanocomposites prepared by electroassisted deposition. Electrocatalysis. 4(4):259-266. https://doi.org/10.1007/s12678-013-0144-3S25926644P. Alivisatos, Nat. Biotechnol. 22, 47 (2004)S. Stankovich, D.A. Dikin, G.H. Dommett, K.M. Kohlhaas, E.J. Zimney, E.A. Stach, R.D. Piner, S.T. Nguyen, R.S. Ruoff, Nature 442, 282 (2006)D.W. Schaefer, R.S. Justice, Macromolecules 40, 8501 (2007)M. Endo, M.S. Strano, P.M. Ajayan, Carbon Nanotubes 111, 13 (2008)C.E. Banks, R.G. Compton, Analyst 131, 15 (2006)R.H. Baughman, A.A. Zakhidov, W.A. de Heer, Science 297, 787 (2002)Y.H. Lin, F. Lu, Y. Tu, Z.F. Ren, Nano Letters 4, 191 (2004)B.R. Azamian, J.J. Davis, K.S. Coleman, C.B. Bagshaw, M.L.H. Green, J. Am. Chem. Soc. 124, 12664 (2002)W. Yang, K. Ratinac, S. Ringer, P. Thordarson, J.G. Gooding, F. Braet, Angew. Chem. Int. Ed. 49, 2114 (2010)C.E. Banks, R.G. Compton, Analyst 130, 1232 (2005)L. Mazurenko, M. Etienne, O. Tananaiko, V. Zaitsev, A. Walcarius, Electrochim. Acta 83, 359 (2012)J.M.P. Paloma Yáñez-Sedeño, J. Riu, F.X. Rius, TrAC Trends in Analytical Chemistry 29, 939 (2010)Z.J. Wang, M. Etienne, S. Poller, W. Schuhmann, G.W. Kohring, V. Mamane, A. Walcarius, Electroanalysis 24, 376 (2012)R. Bandyopadhyaya, E. Nativ-Roth, O. Regev, R. Yerushalmi-Rozen, Nano Letters 2, 25 (2002)C. Park, Z. Ounaies, K.A. Watson, R.E. Crooks, J. Smith, S.E. Lowther, J.W. Connell, E.J. Siochi, J.S. Harrison, T.L.S. Clair, Chem. Phys. Lett. 364, 303 (2002)O. Matarredona, H. Rhoads, Z.R. Li, J.H. Harwell, L. Balzano, D.E. Resasco, Journal of Physical Chemistry B 107, 13357 (2003)L. Vaisman, H. Wagner, G. Marom, Advances in Colloid and Interface Science 128, 37 (2006)Y.C. Xing, Journal of Physical Chemistry B 108, 19255 (2004)J.J. Liang, Y. Huang, L. Zhang, Y. Wang, Y.F. Ma, T.Y. Guo, Y.S. Chen, Adv. Funct. Mater. 19, 2297 (2009)D. Salinas-Torres, F. Huerta, F. Montilla, E. Morallón, Electrochim. Acta 56, 2464 (2011)Z.F. Ren, Z.P. Huang, J.W. Xu, J.H. Wang, P. Bush, M.P. Siegal, P.N. Provencio, Science 282, 1105 (1998)W.Z. Li, S.S. Xie, L.X. Qian, B.H. Chang, B.S. Zou, W.Y. Zhou, R.A. Zhao, G. Wang, Science 274, 1701 (1996)M. Terrones, N. Grobert, J. Olivares, J.P. Zhang, H. Terrones, K. Kordatos, W.K. Hsu, J.P. Hare, P.D. Townsend, K. Prassides, A.K. Cheetham, H.W. Kroto, D.R.M. Walton, Nature 388, 52 (1997)R. Toledano, D. Mandler, Chem. Mater. 22, 3943 (2010)J.H. Rouse, Langmuir 21, 1055 (2005)X.B. Yan, B.K. Tay, Y. Yang, Journal of Physical Chemistry B 110, 25844 (2006)J. Lim, P. Malati, F. Bonet, B. Dunn, J. Electrochem. Soc. 154, A140 (2007)L.D. Zhu, C.Y. Tian, J.L. Zhai, R.L. Yang, Sensors and Actuators B-Chemical 125, 254 (2007)F. Montilla, M.A. Cotarelo, E. Morallón, J. Mater. Chem. 19, 305 (2009)D. Salinas-Torres, F. Montilla, F. Huerta, E. Morallón, Electrochim. Acta 56, 3620 (2011)T. Dobbins, R. Chevious, Y. Lvov, Polymers 3, 942 (2011)R. Esquembre, J.A. Poveda, C.R. Mateo, Journal of Physical Chemistry B 113, 7534 (2009)M.L. Ferrer, R. Esquembre, I. Ortega, C.R. Mateo, F. del Monte, Chem. Mater. 18, 554 (2006)M.J. O'Connell, S. Sivaram, S.K. Doorn, Physical Review B 69, 235415 (2004)C. Domingo, G. Santoro, Opt. Pura Apl 40, 175 (2007)M.S. Dresselhaus, G. Dresselhaus, R. Saito, A. Jorio, Physics Reports 409, 47 (2005)R.L. McCreery, Chem. Rev. 108, 2646 (2008)C.G. Zoski, in Handbook of Electrochemistry, 1st ed (Elsevier, Amsterdam, 2007

Pathogenesis and Host Response in Syrian Hamsters following Intranasal Infection with Andes Virus

Hantavirus pulmonary syndrome (HPS), also referred to as hantavirus cardiopulmonary syndrome (HCPS), is a rare but frequently fatal disease caused by New World hantaviruses. In humans HPS is associated with severe pulmonary edema and cardiogenic shock; however, the pathogenesis of this disease remains unclear largely due to a lack of suitable animal models for the study of disease progression. In this study we monitored clinical, virological, pathophysiological parameters and host immunological responses to decipher pathological factors and events in the lethal Syrian hamster model of HPS following intranasal inoculation of Andes virus. Transcriptional profiling of the host gene responses demonstrated a suppression of innate immune responses in most organs analyzed during the early stage of infection, except for in the lung which had low level activation of several pro-inflammatory genes. During this phase Andes virus established a systemic infection in hamsters, with viral antigen readily detectable in the endothelium of the majority of tissues analyzed by 7–8 days post-inoculation. Despite wide-spread infection, histological analysis confirmed pathological abnormalities were almost exclusively found in the lungs. Immediately preceding clinical signs of disease, intense activation of pro-inflammatory and Th1/Th2 responses were observed in the lungs as well as the heart, but not in peripheral organs, suggesting that localized immune-modulations by infection is paramount to pathogenesis. Throughout the course of infection a strong suppression of regulatory T-cell responses was noted and is hypothesized to be the basis of the aberrant immune activations. The unique and comprehensive monitoring of host immune responses to hantavirus infection increases our understanding of the immuno-pathogenesis of HPS and will facilitate the development of treatment strategies targeting deleterious host immunological responses

The Role of Phe82 and Phe351 in Auxin-Induced Substrate Perception by TIR1 Ubiquitin Ligase: A Novel Insight from Molecular Dynamics Simulations

It is well known that Auxin plays a key role in controlling many aspects of plant growth and development. Crystal structures of Transport inhibitor response 1 (TIR1), a true receptor of auxin, were very recently determined for TIR1 alone and in complexes with auxin and different synthetic analogues and an Auxin/Indole-3-Acetic Acid (Aux/IAA) substrate peptide. However, the dynamic conformational changes of the key residues of TIR1 that take place during the auxin and substrate perception by TIR1 and the detailed mechanism of these changes are still unclear. In the present study, various computational techniques were integrated to uncover the detailed molecular mechanism of the auxin and Aux/IAA perception process; these simulations included molecular dynamics (MD) simulations on complexes and the free enzyme, the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) calculations, normal mode analysis, and hydrogen bond energy (HBE) calculations. The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy. In addition, a more detailed model for auxin and Aux/IAA perception was also proposed, indicating that Phe82 and Phe351 played a pivotal role in Aux/IAA perception. Upon auxin binding, Phe82 underwent conformational changes to accommodate the subsequent binding of Aux/IAA. As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a “molecular glue”. Besides, Phe351 acts as a “fastener” to further improve the substrate binding. The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues

Deciphering the functional role of spatial and temporal muscle synergies in whole-body movements

International audienceVoluntary movement is hypothesized to rely on a limited number of muscle synergies, the recruitment of which translates task goals into effective muscle activity. In this study, we investigated how to analytically characterize the functional role of different types of muscle synergies in task performance. To this end, we recorded a comprehensive dataset of muscle activity during a variety of whole-body pointing movements. We decomposed the electromyographic (EMG) signals using a space-by-time modularity model which encompasses the main types of synergies. We then used a task decoding and information theoretic analysis to probe the role of each synergy by mapping it to specific task features. We found that the temporal and spatial aspects of the movements were encoded by different temporal and spatial muscle synergies, respectively, consistent with the intuition that there should a correspondence between major attributes of movement and major features of synergies. This approach led to the development of a novel computational method for comparing muscle synergies from different participants according to their functional role. This functional similarity analysis yielded a small set of temporal and spatial synergies that describes the main features of whole-body reaching movements

Explaining oscillations and variability in the p53-Mdm2 system

<p>Abstract</p> <p>Background</p> <p>In individual living cells p53 has been found to be expressed in a series of discrete pulses after DNA damage. Its negative regulator Mdm2 also demonstrates oscillatory behaviour. Attempts have been made recently to explain this behaviour by mathematical models but these have not addressed explicit molecular mechanisms. We describe two stochastic mechanistic models of the p53/Mdm2 circuit and show that sustained oscillations result directly from the key biological features, without assuming complicated mathematical functions or requiring more than one feedback loop. Each model examines a different mechanism for providing a negative feedback loop which results in p53 activation after DNA damage. The first model (ARF model) looks at the mechanism of p14^ARFwhich sequesters Mdm2 and leads to stabilisation of p53. The second model (ATM model) examines the mechanism of ATM activation which leads to phosphorylation of both p53 and Mdm2 and increased degradation of Mdm2, which again results in p53 stabilisation. The models can readily be modified as further information becomes available, and linked to other models of cellular ageing.</p> <p>Results</p> <p>The ARF model is robust to changes in its parameters and predicts undamped oscillations after DNA damage so long as the signal persists. It also predicts that if there is a gradual accumulation of DNA damage, such as may occur in ageing, oscillations break out once a threshold level of damage is acquired. The ATM model requires an additional step for p53 synthesis for sustained oscillations to develop. The ATM model shows much more variability in the oscillatory behaviour and this variability is observed over a wide range of parameter values. This may account for the large variability seen in the experimental data which so far has examined ARF negative cells.</p> <p>Conclusion</p> <p>The models predict more regular oscillations if ARF is present and suggest the need for further experiments in ARF positive cells to test these predictions. Our work illustrates the importance of systems biology approaches to understanding the complex role of p53 in both ageing and cancer.</p