by Keyword: STM

Lagunas, Anna, Belloir, Christine, Briand, Loïc, Gorostiza, Pau, Samitier, Josep, (2022). Determination of the nanoscale electrical properties of olfactory receptor hOR1A1 and their dependence on ligand binding: Towards the development of capacitance-operated odorant biosensors Biosensors & Bioelectronics 218, 114755

Tantai, Xinxing, Liu, Yi, Yeo, Yee Hui, Praktiknjo, Michael, Mauro, Ezequiel, Hamaguchi, Yuhei, Engelmann, Cornelius, Zhang, Peng, Jeong, Jae Yoon, van Vugt, Jeroen Laurens Ad, Xiao, Huijuan, Deng, Huan, Gao, Xu, Ye, Qing, Zhang, Jiayuan, Yang, Longbao, Cai, Yaqin, Liu, Yixin, Liu, Na, Li, Zongfang, Han, Tao, Kaido, Toshimi, Sohn, Joo Hyun, Strassburg, Christian, Berg, Thomas, Trebicka, Jonel, Hsu, Yao-Chun, IJzermans, Jan Nicolaas Maria, Wang, Jinhai, Su, Grace L., Ji, Fanpu, Nguyen, Mindie H., (2022). Effect of sarcopenia on survival of patients with cirrhosis: A meta-analysis Journal Of Hepatology 76, 588-599

The association between sarcopenia and prognosis in patients with cirrhosis remains to be determined. In this study, we aimed to quantify the association between sarcopenia and the risk of mortality in patients with cirrhosis, by sex, underlying liver disease etiology, and severity of hepatic dysfunction.PubMed, Web of Science, EMBASE, and major scientific conference sessions were searched without language restriction through 13 January 2021 with additional manual search of bibliographies of relevant articles. Cohort studies of ?100 patients with cirrhosis and ?12 months of follow-up that evaluated the association between sarcopenia, muscle mass and the risk of mortality were included.22 studies with 6965 patients with cirrhosis were included. The pooled prevalence of sarcopenia in patients with cirrhosis was 37.5% overall (95% CI 32.4%-42.8%), higher in male patients, patients with alcohol associated liver disease (ALD), patients with CTP grade C, and when sarcopenia was defined in patients by lumbar 3- skeletal muscle index (L3-SMI). Sarcopenia was associated with the increased risk of mortality in patients with cirrhosis (adjusted-hazard ratio [aHR] 2.30, 95% CI 2.01-2.63), with similar findings in sensitivity analysis of cirrhosis patients without HCC (aHR 2.35, 95% CI 1.95-2.83) and in subgroup analysis by sex, liver disease etiology, and severity of hepatic dysfunction. The association between quantitative muscle mass index and mortality further supports the poor prognosis for patients with sarcopenia (aHR 0.95, 95% CI 0.93-0.98). There was no significant heterogeneity in all analyses.Sarcopenia was highly and independently associated with higher risk of mortality in patients with cirrhosis.The prevalence of sarcopenia and its association with death in patients with cirrhosis remain unclear. This meta-analysis indicated that sarcopenia affected about one-third of patients with cirrhosis and up to 50% in patients with ALD or Child's class C cirrhosis. Sarcopenia was independently associated with about 2-fold higher risk of mortality in patients with cirrhosis. The mortality rate increased with greater severity or longer period of having sarcopenia. Increasing awareness about the importance of sarcopenia in patients with cirrhosis among stakeholders must be prioritized.Copyright © 2021. Published by Elsevier B.V.

JTD Keywords: alcohol associated liver disease, alcohol-associated liver disease, cirrhosis, failure, frailty, impact, list, mass, model, mortality, prognosis, prognostic value, sarcopenia, severe muscle depletion, skeletal muscle index, Alcohol-associated liver disease, Cirrhosis, Liver-transplant candidates, Prognosis, Sarcopenia, Skeletal muscle index

López Ortiz, Manuel, Zamora, Ricardo A., Giannotti, Marina Inés, Hu, Chen, Croce, Roberta, Gorostiza, Pau, (2022). Distance and Potential Dependence of Charge Transport Through the Reaction Center of Individual Photosynthetic Complexes Small 18, 2104366

Charge separation and transport through the reaction center of photosystem I (PSI) is an essential part of the photosynthetic electron transport chain. A strategy is developed to immobilize and orient PSI complexes on gold electrodes allowing to probe the complex's electron acceptor side, the chlorophyll special pair P700. Electrochemical scanning tunneling microscopy (ECSTM) imaging and current-distance spectroscopy of single protein complex shows lateral size in agreement with its known dimensions, and a PSI apparent height that depends on the probe potential revealing a gating effect in protein conductance. In current-distance spectroscopy, it is observed that the distance-decay constant of the current between PSI and the ECSTM probe depends on the sample and probe electrode potentials. The longest charge exchange distance (lowest distance-decay constant ?) is observed at sample potential 0 mV/SSC (SSC: reference electrode silver/silver chloride) and probe potential 400 mV/SSC. These potentials correspond to hole injection into an electronic state that is available in the absence of illumination. It is proposed that a pair of tryptophan residues located at the interface between P700 and the solution and known to support the hydrophobic recognition of the PSI redox partner plastocyanin, may have an additional role as hole exchange mediator in charge transport through PSI.© 2021 Wiley-VCH GmbH.

JTD Keywords: azurin, current distance decay spectroscopy, cytochrome c(6), electrochemical scanning tunneling microscopy (ecstm), electrochemistry, photosystem i, photosystem-i, plastocyanin, protein electron transfer, recognition, single metalloprotein, single molecules, structural basis, tunneling spectroscopy, 'current, Amino acids, Charge transfer, Chlorine compounds, Current distance decay spectroscopy, Decay spectroscopies, Distance decay, Electrochemical scanning tunneling microscopy, Electrochemical scanning tunneling microscopy (ecstm), Electrodes, Electron transfer, Electron transport properties, Gold compounds, Photosystem i, Photosystems, Protein electron transfer, Protein electron-transfer, Proteins, Scanning tunneling microscopy, Silver halides, Single molecule, Single molecules

Lopez-Martinez, Montserrat, López-Ortiz, Manuel, Antinori, Maria Elena, Wientjes, Emilie, Nin-Hill, Alba, Rovira, Carme, Croce, Roberta, Díez-Pérez, Ismael, Gorostiza, Pau, (2019). Electrochemically gated long distance charge transport in photosystem I Angewandte Chemie International Edition 58, (38), 13280-13284

The transport of electrons along photosynthetic and respiratory chains involves a series of enzymatic reactions that are coupled through redox mediators, including proteins and small molecules. The use of native and synthetic redox probes is key to understand charge transport mechanisms, and to design bioelectronic sensors and solar energy conversion devices. However, redox probes have limited tunability to exchange charge at the desired electrochemical potentials (energy levels) and at different protein sites. Here, we take advantage of electrochemical scanning tunneling microscopy (ECSTM) to control the Fermi level and nanometric position of the ECSTM probe in order to study electron transport in individual photosystem I (PSI) complexes. Current-distance measurements at different potentiostatic conditions indicate that PSI supports long-distance transport that is electrochemically gated near the redox potential of P700, with current extending farther under hole injection conditions.

JTD Keywords: Current decay, ECSTM, Electrochemical gate, Electron transfer, Photosynthesis

Marban, A., Srinivasan, V., Samek, W., Fernández, J., Casals, A., (2019). A recurrent convolutional neural network approach for sensorless force estimation in robotic surgery Biomedical Signal Processing and Control 50, 134-150

Providing force feedback as relevant information in current Robot-Assisted Minimally Invasive Surgery systems constitutes a technological challenge due to the constraints imposed by the surgical environment. In this context, force estimation techniques represent a potential solution, enabling to sense the interaction forces between the surgical instruments and soft-tissues. Specifically, if visual feedback is available for observing soft-tissues’ deformation, this feedback can be used to estimate the forces applied to these tissues. To this end, a force estimation model, based on Convolutional Neural Networks and Long-Short Term Memory networks, is proposed in this work. This model is designed to process both, the spatiotemporal information present in video sequences and the temporal structure of tool data (the surgical tool-tip trajectory and its grasping status). A series of analyses are carried out to reveal the advantages of the proposal and the challenges that remain for real applications. This research work focuses on two surgical task scenarios, referred to as pushing and pulling tissue. For these two scenarios, different input data modalities and their effect on the force estimation quality are investigated. These input data modalities are tool data, video sequences and a combination of both. The results suggest that the force estimation quality is better when both, the tool data and video sequences, are processed by the neural network model. Moreover, this study reveals the need for a loss function, designed to promote the modeling of smooth and sharp details found in force signals. Finally, the results show that the modeling of forces due to pulling tasks is more challenging than for the simplest pushing actions.

JTD Keywords: Convolutional neural networks, Force estimation, LSTM networks, Robotic surgery

Matamoros-Angles, A., Gayosso, L. M., Richaud-Patin, Y., Di Domenico, A., Vergara, C., Hervera, A., Sousa, A., Fernández-Borges, N., Consiglio, A., Gavín, R., López de Maturana, R., Ferrer, Isidro, López de Munain, A., Raya, A., Castilla, J., Sánchez-Pernaute, R., Del Río, J. A., (2018). iPS cell cultures from a Gerstmann-Sträussler-Scheinker patient with the Y218N PRNP mutation recapitulate tau pathology Molecular Neurobiology 55, (4), 3033-3048

Gerstmann-Sträussler-Scheinker (GSS) syndrome is a fatal autosomal dominant neurodegenerative prionopathy clinically characterized by ataxia, spastic paraparesis, extrapyramidal signs and dementia. In some GSS familiar cases carrying point mutations in the PRNP gene, patients also showed comorbid tauopathy leading to mixed pathologies. In this study we developed an induced pluripotent stem (iPS) cell model derived from fibroblasts of a GSS patient harboring the Y218N PRNP mutation, as well as an age-matched healthy control. This particular PRNP mutation is unique with very few described cases. One of the cases presented neurofibrillary degeneration with relevant Tau hyperphosphorylation. Y218N iPS-derived cultures showed relevant astrogliosis, increased phospho-Tau, altered microtubule-associated transport and cell death. However, they failed to generate proteinase K-resistant prion. In this study we set out to test, for the first time, whether iPS cell-derived neurons could be used to investigate the appearance of disease-related phenotypes (i.e, tauopathy) identified in the GSS patient.

JTD Keywords: Cellular prion protein, Gerstmann-Sträussler-Scheinker, Induced pluripotent stem cells, Tau

López-Martínez, Montserrat, Artés, Juan Manuel, Sarasso, Veronica, Carminati, Marco, Díez-Pérez, Ismael, Sanz, Fausto, Gorostiza, Pau, (2017). Differential electrochemical conductance imaging at the nanoscale Small 13, (36), 1700958

Electron transfer in proteins is essential in crucial biological processes. Although the fundamental aspects of biological electron transfer are well characterized, currently there are no experimental tools to determine the atomic-scale electronic pathways in redox proteins, and thus to fully understand their outstanding efficiency and environmental adaptability. This knowledge is also required to design and optimize biomolecular electronic devices. In order to measure the local conductance of an electrode surface immersed in an electrolyte, this study builds upon the current–potential spectroscopic capacity of electrochemical scanning tunneling microscopy, by adding an alternating current modulation technique. With this setup, spatially resolved, differential electrochemical conductance images under bipotentiostatic control are recorded. Differential electrochemical conductance imaging allows visualizing the reversible oxidation of an iron electrode in borate buffer and individual azurin proteins immobilized on atomically flat gold surfaces. In particular, this method reveals submolecular regions with high conductance within the protein. The direct observation of nanoscale conduction pathways in redox proteins and complexes enables important advances in biochemistry and bionanotechnology.

JTD Keywords: Differential electrochemical conductance, ECSTM, Electron transport pathway, Iron passivation, Redox metalloproteins

Aragonès, A. C., Aravena, D., Cerdá, J. I., Acís-Castillo, Z., Li, H., Real, J. A., Sanz, F., Hihath, J., Ruiz, E., Díez-Pérez, I., (2016). Large conductance switching in a single-molecule device through room temperature spin-dependent transport Nano Letters 16, (1), 218-226

Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover FeII complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature.

JTD Keywords: Density functional calculations, Magnetoresistance, Single-molecule junctions, Spin orbit coupling, Spin-crossover complexes, Spinterface, STM break-junction

Aragonès, Albert C., Darwish, Nadim, Im, JongOne, Lim, Boram, Choi, Jeongae, Koo, Sangho, Díez-Pérez, Ismael, (2015). Fine-tuning of single-molecule conductance by tweaking both electronic structure and conformation of side substituents Chemistry – A European Journal , 21, (21), 7716-7720

Herein, we describe a method to fine-tune the conductivity of single-molecule wires by employing a combination of chemical composition and geometrical modifications of multiple phenyl side groups as conductance modulators embedded along the main axis of the electronic pathway. We have measured the single-molecule conductivity of a novel series of phenyl-substituted carotenoid wires whose conductivity can be tuned with high precision over an order of magnitude range by modulating both the electron-donating character of the phenyl substituent and its dihedral angle. It is demonstrated that the electronic communication between the phenyl side groups and the molecular wire is maximized when the phenyl groups are twisted closer to the plane of the conjugated molecular wire. These findings can be refined to a general technique for precisely tuning the conductivity of molecular wires.

JTD Keywords: Carotenoids, Conductance, Self-assembly, Single-molecule studies, STM break junction

Ponce, I., Aragonès, A. C., Darwish, Nadrim, Pla-Vilanova, P., Oñate, R., Rezende, M. C., Zagal, J. H., Sanz, F., Pavez, J., Díez-Pérez, I., (2015). Building nanoscale molecular wires exploiting electrocatalytic interactions Electrochimica Acta 179, 611-167

Herein, we present a novel method to design nanoscale molecular wires by exploiting well-established electrocatalytic molecular platforms based on metallophthalocyanine blocks. Metallophthalocyanines exhibit high catalytic activity for a wide variety of electrochemical reactions of practical interests. To this aim, metallophthalocyanine molecules can be attached to an electrode surface via a conjugated mercaptopyridine axial ligand that provides (i) stable chemical binding to the metal surface through the thiol-anchoring group, and (ii) a good electrical communication between the metallophthalocyanine ring and the electrode surface. Our previous work demonstrates that long mercaptopyridinium blocks act as excellent linkers in such electrocatalytic platform, resulting in an optimal electrocatalytic activity of the metallophthalocyanine unit. Here we profit from this optimized electrocatalytic molecular platform to design new molecular wires that connect a metal nanoscale junction in a highly efficient and tunable way. To this aim, we use an STM break-junction approach to control the formation of a nanometric gap between two Au electrodes, both functionalized with mercaptopyridinium (bottom) and mercaptopyridine (top). When metallophthalocyanine is introduced into the functionalized metal nanojunction, stable molecular connections between the two electrodes are formed through axial coordination to the top and bottom pyridine moieties. We show that the highest conductance of the resulting nanoscale molecular wire corresponds to an Fe-phthalocyanine as compare to a Cu-phthalocyanine, which follows the electrocatalytic trend for such molecular systems. These results not only demonstrate a new strategy to design new families of highly conductive and tunable nanoscale molecular wires, but it also brings a new nanoscale electrical platform to help understanding some fundamental mechanistic aspects of molecular electrocatalysis.

JTD Keywords: Single-molecule wires, Metallophthalocyanine, Electrocatalytic molecular platform, Molecular Electronics, STM break-junction

Pla-Vilanova, P., Aragonès, A. C., Ciampi, S., Sanz, F., Darwish, N., Diez-Perez, I., (2015). The spontaneous formation of single-molecule junctions via terminal alkynes Nanotechnology 26, 381001

Herein, we report the spontaneous formation of single-molecule junctions via terminal alkyne contact groups. Self-assembled monolayers that form spontaneously from diluted solutions of 1, 4-diethynylbenzene (DEB) were used to build single-molecule contacts and assessed using the scanning tunneling microscopy-break junction technique (STM-BJ). The STM-BJ technique in both its dynamic and static approaches was used to characterize the lifetime (stability) and the conductivity of a single-DEB wire. It is demonstrated that single-molecule junctions form spontaneously with terminal alkynes and require no electrochemical control or chemical deprotonation. The alkyne anchoring group was compared against typical contact groups exploited in single-molecule studies, i.e. amine (benzenediamine) and thiol (benzendithiol) contact groups. The alkyne contact showed a conductance magnitude comparable to that observed with amine and thiol groups. The lifetime of the junctions formed from alkynes were only slightly less than that of thiols and greater than that observed for amines. These findings are important as (a) they extend the repertoire of chemical contacts used in single-molecule measurements to 1-alkynes, which are synthetically accessible and stable and (b) alkynes have a remarkable affinity toward silicon surfaces, hence opening the door for the study of single-molecule transport on a semiconducting electronic platform.

JTD Keywords: Ferrocene, Molecular electronics, Single-molecule electronics, Single-molecule junctions, Singlemolecule contacts, STM-break junction, Terminal alkyne

Darwish, Nadim., Aragonès, A. C., Darwish, T., Ciampi, S., Díez-Pérez, I., (2014). Multi-responsive photo- and chemo-electrical single-molecule switches Nano Letters 14, (12), 7064-7070

Incorporating molecular switches as the active components in nanoscale electrical devices represents a current challenge in molecular electronics. It demands key requirements that need to be simultaneously addressed including fast responses to external stimuli and stable attachment of the molecules to the electrodes while mimicking the operation of conventional electronic components. Here, we report a single-molecule switching device that responds electrically to optical and chemical stimuli. A light pointer or a chemical signal can rapidly and reversibly induce the isomerization of bifunctional spiropyran derivatives in the bulk reservoir and, consequently, switch the electrical conductivity of the single-molecule device between a low and a high level. The spiropyran derivatives employed are chemically functionalized such that they can respond in fast but practical time scales. The unique multistimuli response and the synthetic versatility to control the switching schemes of this single-molecule device suggest spiropyran derivatives as key candidates for molecular circuitry.

JTD Keywords: Molecular Electronics, Multi-Responsive Molecular Switches, Photo- and Chemo-Switches Spiropyran, Single-Molecule Conductance, STM Break-Junction, Electronic equipment, Isomerization, Molecular electronics, Photochromism, Electrical conductivity, Electronic component, Molecular switches, Single-molecule conductances, Single-molecule devices, Spiropyran derivatives, Spiropyrans, STM Break-Junction, Molecules

Artés, Juan M., López-Martínez, Montserrat, Díez-Pérez, Ismael, Sanz, Fausto, Gorostiza, Pau, (2014). Conductance switching in single wired redox proteins Small 10, (13), 2537-2541

Switching events in the current flowing through individual redox proteins, (azurin) spontaneously wired between two electrodes, are studied using an electrochemical scanning tunneling microscope (ECSTM). These switching events in the current–time trace are characterized using conductance histograms, and reflect the intrinsic redox thermodynamic dispersion in the azurin population. This conductance switching may pose limitations to miniaturizing redox protein-based devices.

JTD Keywords: Bioelectronics, Protein transistors, Molecular junctions, Switches, STM

Díez-Pérez, Ismael, Guell, Aleix Garcia, Sanz, Fausto, Gorostiza, Pau, (2006). Conductance maps by electrochemical tunneling spectroscopy to fingerprint the electrode electronic structure Analytical Chemistry , 78, (20), 7325-7329

We describe a methodology to perform reliable tunneling spectroscopy in electrochemical media. Sequential in situ tunneling spectra are recorded while the electrochemical potential of the electrode is scanned. Spectroscopic data are presented as conductance maps or conductograms that show the in situ electronic structure of an electrode surface while it undergoes an electrochemical reaction. The conductance map or conductogram represents the redox fingerprint of an electrode/liquid interface in a specific medium and can serve to predict its electrochemical behavior in a quantitative energy scale. The methodology is validated studying the reversible oxidation and passivity of an iron electrode in borate buffer, and we describe the main quantitative information that can be extracted concerning the semiconducting properties of the Fe passive film. This methodology is useful to study heterogeneous catalysis, electrochemical sensing and bioelectronic systems.

JTD Keywords: Passive film, Oxide-film, Stainless-steel, Iron, Microscope, Surfaces, STM, Probes