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Living cells are neither perfectly elastic nor liquid and return a viscoelastic response to external stimuli. Nanoindentation provides force distance curves allowing the investigation of cell mechanical properties, and yet, these curves can differ from point to point on cell surface revealing its inhomogeneous character. In the present work, we propose a mathematical method to estimate both viscoelastic and noise properties of cells, as these are depicted on the values of the scaling exponents of relaxation function and power spectral density respectively. The method uses as input the time derivative of the response force in a nanoindentation experiment. Generalized moments method and/or rescaled range analysis are used to study the resulting time series depending on their non-stationary or stationary nature. We conducted experiments in living Ulocladium Chartarum spores. We found that spores, in the approaching phase present a viscoelastic behavior with the corresponding scaling exponent in the range 0.25-0.52, and in the retracting phase present a liquid-like behavior with exponents in the range 0.67-0.85. This substantial difference of the scaling exponents in the two phases suggests the formation of biomemory as response of the spores to the indenting AFM mechanical stimulus. The retracting phase may be described as a process driven by bluish noises, while the approaching one is driven by persistent noise.
Evangelos Bakalis; Vassilios Gavriil; Alkiviadis-Constantinos Cefalas; Zoe Kollia; Francesco Zerbetto; Evangelia Sarantopoulou. Viscoelasticity and Noise Properties Reveal the Formation of Biomemory in Cells. 2021, 1 .
AMA StyleEvangelos Bakalis, Vassilios Gavriil, Alkiviadis-Constantinos Cefalas, Zoe Kollia, Francesco Zerbetto, Evangelia Sarantopoulou. Viscoelasticity and Noise Properties Reveal the Formation of Biomemory in Cells. . 2021; ():1.
Chicago/Turabian StyleEvangelos Bakalis; Vassilios Gavriil; Alkiviadis-Constantinos Cefalas; Zoe Kollia; Francesco Zerbetto; Evangelia Sarantopoulou. 2021. "Viscoelasticity and Noise Properties Reveal the Formation of Biomemory in Cells." , no. : 1.
Almost three-quarters of known volcanic activity on Earth occurs in underwater locations. The presence of active hydrothermal vent fields in such environments is a potential natural hazard for the environment, society, and economy. Despite its importance for risk assessment and risk mitigation, the monitoring of volcanic activity is impeded by the remoteness and the extreme conditions of many underwater volcanoes. The morphology and the activity of the submarine caldera, Avyssos, at the northern part of Nisyros volcano in the South Aegean Sea (Greece), were studied using a remotely operated underwater vehicle. The recorded time series of temperature and conductivity over the submarine volcano have been analyzed in terms of the Generalized Moments Method. This type of analysis can be used as an indicator for the state of activity of a submarine volcano. Here, we expand the work conducted for the first time in 2018. We present the findings of the geological exploration and the mathematical analysis, obtained from the data collected in October 2010. The temperature and conductivity time series show minor fluctuations in a rather stable environment. Based on these results, the impact of developing appropriate mechanisms and policies to avoid the associated natural hazard is expected to be important.
Ana Dura; Theo Mertzimekis; Paraskevi Nomikou; Andreas Gondikas; Martín Gómez Míguez; Evangelos Bakalis; Francesco Zerbetto. The Hydrothermal Vent Field at the Eastern Edge of the Hellenic Volcanic Arc: The Avyssos Caldera (Nisyros). Geosciences 2021, 11, 290 .
AMA StyleAna Dura, Theo Mertzimekis, Paraskevi Nomikou, Andreas Gondikas, Martín Gómez Míguez, Evangelos Bakalis, Francesco Zerbetto. The Hydrothermal Vent Field at the Eastern Edge of the Hellenic Volcanic Arc: The Avyssos Caldera (Nisyros). Geosciences. 2021; 11 (7):290.
Chicago/Turabian StyleAna Dura; Theo Mertzimekis; Paraskevi Nomikou; Andreas Gondikas; Martín Gómez Míguez; Evangelos Bakalis; Francesco Zerbetto. 2021. "The Hydrothermal Vent Field at the Eastern Edge of the Hellenic Volcanic Arc: The Avyssos Caldera (Nisyros)." Geosciences 11, no. 7: 290.
Summary Because of proteins' many degrees of conformational freedom, programming protein folding dynamics, overall elasticity, and motor functions remains an elusive objective. Instead, smaller and simpler objects, such as synthetic foldamers, may be amenable to design. However, little is known about their mechanical performance. Here, we show that reducing molecular size may not compromise mechanical properties. We report that helical aromatic oligoamides as small as 1 nm possess outstanding elasticity and outperform most natural helices. Using single-molecule force spectroscopy, we characterize their folding trajectories and intermediate states. We show that they cooperatively and reversibly unwind at high forces. They extend up to 3.8 times their original length and rewind against considerable forces on a timescale of 10 μs. Pulling and relaxing cycles follow the same trace up to a very high loading rate, indicating that the mechanical energy accumulated during the stretching does not dissipate and is immediately reusable.
Floriane Devaux; Xuesong Li; Damien Sluysmans; Victor Maurizot; Evangelos Bakalis; Francesco Zerbetto; Ivan Huc; Anne-Sophie Duwez. Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding. Chem 2021, 7, 1333 -1346.
AMA StyleFloriane Devaux, Xuesong Li, Damien Sluysmans, Victor Maurizot, Evangelos Bakalis, Francesco Zerbetto, Ivan Huc, Anne-Sophie Duwez. Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding. Chem. 2021; 7 (5):1333-1346.
Chicago/Turabian StyleFloriane Devaux; Xuesong Li; Damien Sluysmans; Victor Maurizot; Evangelos Bakalis; Francesco Zerbetto; Ivan Huc; Anne-Sophie Duwez. 2021. "Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding." Chem 7, no. 5: 1333-1346.
Liquid-cell transmission electron microscopy (LCTEM) is a powerful in situ videography technique that has the potential to allow us to observe solution-phase dynamic processes at the nanoscale, including imaging the diffusion and interaction of nanoparticles. Artefactual effects imposed by the irradiated and confined liquid-cell vessel alter the system from normal “bulk-like” behavior in multiple ways. These artefactual LCTEM effects will leave their fingerprints in the motion behavior of the diffusing objects, which can be revealed through careful analysis of the object-motion trajectories. Improper treatment of the motion data can lead to erroneous descriptions of the LCTEM system’s conditions. Here, we advance our anomalous diffusion object-motion analysis (ADOMA) method to extract a detailed description of the liquid-cell system conditions during any LCTEM experiment by applying a multistep analysis of the data and treating the x/y vectors of motion independently and in correlation with each other and with the object’s orientation/angle.
Evangelos Bakalis; Lucas R. Parent; Maria Vratsanos; Chiwoo Park; Nathan C. Gianneschi; Francesco Zerbetto. Complex Nanoparticle Diffusional Motion in Liquid-Cell Transmission Electron Microscopy. The Journal of Physical Chemistry C 2020, 124, 14881 -14890.
AMA StyleEvangelos Bakalis, Lucas R. Parent, Maria Vratsanos, Chiwoo Park, Nathan C. Gianneschi, Francesco Zerbetto. Complex Nanoparticle Diffusional Motion in Liquid-Cell Transmission Electron Microscopy. The Journal of Physical Chemistry C. 2020; 124 (27):14881-14890.
Chicago/Turabian StyleEvangelos Bakalis; Lucas R. Parent; Maria Vratsanos; Chiwoo Park; Nathan C. Gianneschi; Francesco Zerbetto. 2020. "Complex Nanoparticle Diffusional Motion in Liquid-Cell Transmission Electron Microscopy." The Journal of Physical Chemistry C 124, no. 27: 14881-14890.
Molecules near surfaces are regularly trapped in small cavitations. Molecular confinement, especially water confinement, shows intriguing and unexpected behavior including surface entropy adjustment; nevertheless, observations of entropic variation during molecular confinement are scarce. An experimental assessment of the correlation between surface strain and entropy during molecular confinement in tiny crevices is difficult because strain variances fall in the nanometer scale. In this work, entropic variations during water confinement in 2D nano/micro cavitations were observed. Experimental results and random walk simulations of water molecules inside different size nanocavitations show that the mean escaping time of molecular water from nanocavities largely deviates from the mean collision time of water molecules near surfaces, crafted by 157 nm vacuum ultraviolet laser light on polyacrylamide matrixes. The mean escape time distribution of a few molecules indicates a non-thermal equilibrium state inside the cavity. The time differentiation inside and outside nanocavities reveals an additional state of ordered arrangements between nanocavities and molecular water ensembles of fixed molecular length near the surface. The configured number of microstates correctly counts for the experimental surface entropy deviation during molecular water confinement. The methodology has the potential to identify confined water molecules in nanocavities with life science importance.
Vassilios Gavriil; Margarita Chatzichristidi; Dimitrios Christofilos; Gerasimos A. Kourouklis; Zoe Kollia; Evangelos Bakalis; Alkiviadis-Constantinos Cefalas; Evangelia Sarantopoulou. Entropy and Random Walk Trails Water Confinement and Non-Thermal Equilibrium in Photon-Induced Nanocavities. Nanomaterials 2020, 10, 1101 .
AMA StyleVassilios Gavriil, Margarita Chatzichristidi, Dimitrios Christofilos, Gerasimos A. Kourouklis, Zoe Kollia, Evangelos Bakalis, Alkiviadis-Constantinos Cefalas, Evangelia Sarantopoulou. Entropy and Random Walk Trails Water Confinement and Non-Thermal Equilibrium in Photon-Induced Nanocavities. Nanomaterials. 2020; 10 (6):1101.
Chicago/Turabian StyleVassilios Gavriil; Margarita Chatzichristidi; Dimitrios Christofilos; Gerasimos A. Kourouklis; Zoe Kollia; Evangelos Bakalis; Alkiviadis-Constantinos Cefalas; Evangelia Sarantopoulou. 2020. "Entropy and Random Walk Trails Water Confinement and Non-Thermal Equilibrium in Photon-Induced Nanocavities." Nanomaterials 10, no. 6: 1101.
Almost three quarters of known volcanic activity on Earth occurs in underwater locations. The presence of active hydrothermal vent fields in such environments is a potential natural hazard for the environment, the society, and the economy. Despite its importance for risk assessment and risk mitigation, monitoring of the activity is impeded by the remoteness and the extreme conditions of underwater volcanoes. The large difference of population present on Santorini between the winter and summer seasons, all within a partially enclosed system, make the Santorini-Kolumbo volcanic field, an ideal place for detailed exploration. In 2017, GEOMAR in collaboration with the National and Kapodistrian University of Athens (mission: POS-510 ANYDROS), used an Autonomous Underwater Vehicle (AUV) to map the NE–trending Santorini–Kolumbo line, where it also collected CTD data. Here we present the preliminary results from the 15-hour survey held on the 25th March 2017, during the POS-510 expedition targeting the vent field which is located in the North Basin of Santorini Caldera. Detailed CTD 3D profiles have been reconstructed from the raw data of Santorini’s vent field. An anomaly emerges at the depth of 350 m in the Conductivity and Salinity depth profiles, as the CTD sensor is placed directly above the vent sources. Anomalies were evident in the 3D maps reconstructed, showing for the first time a rather weak, but underlying hydrothermal vent activity at various locations. As the present results are the first ones produced from this expedition, further investigation is required incorporating the full dataset. Based on those results, the impact of developing appropriate mechanisms and policies to avoid the associated natural hazard is expected to be immense.
Ana Dura; Theo J. Mertzimekis; Evangelos Bakalis; Paraskevi Nomikou; Andreas Gondikas; Mark D. Hannington; Sven Petersen. CTD data profiling to assess the natural hazard of active submarine vent fields: the case of Santorini Island. Bulletin of the Geological Society of Greece 2020, 56, 70 -83.
AMA StyleAna Dura, Theo J. Mertzimekis, Evangelos Bakalis, Paraskevi Nomikou, Andreas Gondikas, Mark D. Hannington, Sven Petersen. CTD data profiling to assess the natural hazard of active submarine vent fields: the case of Santorini Island. Bulletin of the Geological Society of Greece. 2020; 56 (1):70-83.
Chicago/Turabian StyleAna Dura; Theo J. Mertzimekis; Evangelos Bakalis; Paraskevi Nomikou; Andreas Gondikas; Mark D. Hannington; Sven Petersen. 2020. "CTD data profiling to assess the natural hazard of active submarine vent fields: the case of Santorini Island." Bulletin of the Geological Society of Greece 56, no. 1: 70-83.
Evangelos Bakalis; Hiroyuki Fujie; Francesco Zerbetto; Yasuto Tanaka. Multifractal structure of microscopic eye–head coordination. Physica A: Statistical Mechanics and its Applications 2018, 512, 945 -953.
AMA StyleEvangelos Bakalis, Hiroyuki Fujie, Francesco Zerbetto, Yasuto Tanaka. Multifractal structure of microscopic eye–head coordination. Physica A: Statistical Mechanics and its Applications. 2018; 512 ():945-953.
Chicago/Turabian StyleEvangelos Bakalis; Hiroyuki Fujie; Francesco Zerbetto; Yasuto Tanaka. 2018. "Multifractal structure of microscopic eye–head coordination." Physica A: Statistical Mechanics and its Applications 512, no. : 945-953.
High levels of blood cholesterol are conventionally linked to an increased risk of developing cardiovascular disease (Grundy, 1986). Here we examine the molecular mode of action of natural products with known cholesterol-lowering activity, such as for example the green tea ingredient epigallocatechin gallate and a short pentapeptide, Ile-Ile-Ala-Glu-Lys. Molecular Dynamics simulations are used to gain insight into the formation process of mixed micelles and, correspondingly, how active agents epigallocatechin gallate and Ile-Ile-Ala-Glu-Lys could possibly interfere with it. Self-assembly of physiological micelles occurs on the order of 35–50 ns; most of the structural properties of mixed micelles are unaffected by epigallocatechin gallate or Ile-Ile-Ala-Glu-Lys which integrate into the micellar surface; the diffusive motion of constituting lipids palmitoyl-oleoyl-phosphatidylcholine and cholesterol is significantly down-regulated by both epigallocatechin gallate and Ile-Ile-Ala-Glu-Lys; The molecular mode of action of natural compounds epigallocatechin gallate and Ile-Ile-Ala-Glu-Lys is a significant down-regulation of the diffusive motion of micellar lipids. Natural compounds like the green tea ingredient epigallocatechin gallate and a short pentapeptide, Ile-Ile-Ala-Glu-Lys, lead to a significant down-regulation of the diffusive motion of micellar lipids thereby modulating cholesterol absorption into physiological micelles.
Francesco Giangreco; Siegfried Höfinger; Evangelos Bakalis; Francesco Zerbetto. Impact of the green tea ingredient epigallocatechin gallate and a short pentapeptide (Ile-Ile-Ala-Glu-Lys) on the structural organization of mixed micelles and the related uptake of cholesterol. Biochimica et Biophysica Acta (BBA) - General Subjects 2018, 1862, 1956 -1963.
AMA StyleFrancesco Giangreco, Siegfried Höfinger, Evangelos Bakalis, Francesco Zerbetto. Impact of the green tea ingredient epigallocatechin gallate and a short pentapeptide (Ile-Ile-Ala-Glu-Lys) on the structural organization of mixed micelles and the related uptake of cholesterol. Biochimica et Biophysica Acta (BBA) - General Subjects. 2018; 1862 (9):1956-1963.
Chicago/Turabian StyleFrancesco Giangreco; Siegfried Höfinger; Evangelos Bakalis; Francesco Zerbetto. 2018. "Impact of the green tea ingredient epigallocatechin gallate and a short pentapeptide (Ile-Ile-Ala-Glu-Lys) on the structural organization of mixed micelles and the related uptake of cholesterol." Biochimica et Biophysica Acta (BBA) - General Subjects 1862, no. 9: 1956-1963.
The morphology and the activity of a submarine caldera, Avyssos, at the northern part of Nisyros volcano in the South Aegean Sea (Greece), has been studied by means of remotely-operated underwater vehicle dives. The recorded time series of temperature and conductivity over the submarine volcano have been analyzed in terms of the generalized moments method. The findings of the mathematical analysis shed light on the volcanic activity, but also on the morphology (shape) of the submarine volcano. The conductivity time series indicates that the volcano is at rest, in agreement with other types of observations. On the other hand, temperature fluctuations, which in general describe a multifractal process, show that the submarine caldera operates as an open system that interacts with its surroundings. This type of analysis can be used as an indicator for the state of activity and the morphological structure (closed or open system) of a submarine volcano.
Evangelos Bakalis; Theo J. Mertzimekis; Paraskevi Nomikou; Francesco Zerbetto. Temperature and Conductivity as Indicators of the Morphology and Activity of a Submarine Volcano: Avyssos (Nisyros) in the South Aegean Sea, Greece. Geosciences 2018, 8, 193 .
AMA StyleEvangelos Bakalis, Theo J. Mertzimekis, Paraskevi Nomikou, Francesco Zerbetto. Temperature and Conductivity as Indicators of the Morphology and Activity of a Submarine Volcano: Avyssos (Nisyros) in the South Aegean Sea, Greece. Geosciences. 2018; 8 (6):193.
Chicago/Turabian StyleEvangelos Bakalis; Theo J. Mertzimekis; Paraskevi Nomikou; Francesco Zerbetto. 2018. "Temperature and Conductivity as Indicators of the Morphology and Activity of a Submarine Volcano: Avyssos (Nisyros) in the South Aegean Sea, Greece." Geosciences 8, no. 6: 193.
Revolutions in science and engineering frequently result from the development, and wide adoption, of a new, powerful characterization or imaging technique. Beginning with the first glass lenses and telescopes in astronomy, to the development of visual-light microscopy, staining techniques, confocal microscopy, and fluorescence super-resolution microscopy in biology, and most recently aberration-corrected, cryogenic, and ultrafast (4D) electron microscopy, X-ray microscopy, and scanning probe microscopy in nanoscience. Through these developments, our perception and understanding of the physical nature of matter at length-scales beyond ordinary perception have been fundamentally transformed. Despite this progression in microscopy, techniques for observing nanoscale chemical processes and solvated/hydrated systems are limited, as the necessary spatial and temporal resolution presents significant technical challenges. However, the standard reliance on indirect or bulk phase characterization of nanoscale samples in liquids is undergoing a shift in recent times with the realization (Williamson et al. Nat. Mater.2003, 2, 532−536) of liquid-cell (scanning) transmission electron microscopy, LC(S)TEM, where picoliters of solution are hermetically sealed between electron-transparent “windows,” which can be directly imaged or videoed at the nanoscale using conventional transmission electron microscopes. This Account seeks to open a discussion on the topic of standardizing strategies for conducting imaging experiments with a view to characterizing dynamics and motion of nanoscale materials. This is a challenge that could be described by critics and proponents alike, as analogous to doing chemistry in a lightning storm; where the nature of the solution, the nanomaterial, and the dynamic behaviors are all potentially subject to artifactual influence by the very act of our observation.
Lucas R. Parent; Evangelos Bakalis; Maria Proetto; Yiwen Li; Chiwoo Park; Francesco Zerbetto; Nathan C. Gianneschi. Tackling the Challenges of Dynamic Experiments Using Liquid-Cell Transmission Electron Microscopy. Accounts of Chemical Research 2017, 51, 3 -11.
AMA StyleLucas R. Parent, Evangelos Bakalis, Maria Proetto, Yiwen Li, Chiwoo Park, Francesco Zerbetto, Nathan C. Gianneschi. Tackling the Challenges of Dynamic Experiments Using Liquid-Cell Transmission Electron Microscopy. Accounts of Chemical Research. 2017; 51 (1):3-11.
Chicago/Turabian StyleLucas R. Parent; Evangelos Bakalis; Maria Proetto; Yiwen Li; Chiwoo Park; Francesco Zerbetto; Nathan C. Gianneschi. 2017. "Tackling the Challenges of Dynamic Experiments Using Liquid-Cell Transmission Electron Microscopy." Accounts of Chemical Research 51, no. 1: 3-11.
Amphiphilic small molecules and polymers form commonplace nanoscale macromolecular compartments and bilayers, and as such are truly essential components in all cells and in many cellular processes. The nature of these architectures, including their formation, phase changes, and stimuli-response behaviors, is necessary for the most basic functions of life, and over the past half-century, these natural micellar structures have inspired a vast diversity of industrial products, from biomedicines to detergents, lubricants, and coatings. The importance of these materials and their ubiquity have made them the subject of intense investigation regarding their nanoscale dynamics with increasing interest in obtaining sufficient temporal and spatial resolution to directly observe nanoscale processes. However, the vast majority of experimental methods involve either bulk-averaging techniques including light, neutron, and X-ray scattering, or are static in nature including even the most advanced cryogenic transmission electron microscopy techniques. Here, we employ in situ liquid-cell transmission electron microscopy (LCTEM) to directly observe the evolution of individual amphiphilic block copolymer micellar nanoparticles in solution, in real time with nanometer spatial resolution. These observations, made on a proof-of-concept bioconjugate polymer amphiphile, revealed growth and evolution occurring by unimer addition processes and by particle–particle collision-and-fusion events. The experimental approach, combining direct LCTEM observation, quantitative analysis of LCTEM data, and correlated in silico simulations, provides a unique view of solvated soft matter nanoassemblies as they morph and evolve in time and space, enabling us to capture these phenomena in solution.
Lucas R. Parent; Evangelos Bakalis; Abelardo Ramírez-Hernández; Jacquelin K. Kammeyer; Chiwoo Park; Juan De Pablo; Francesco Zerbetto; Joseph Patterson; Nathan C. Gianneschi. Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy. Journal of the American Chemical Society 2017, 139, 17140 -17151.
AMA StyleLucas R. Parent, Evangelos Bakalis, Abelardo Ramírez-Hernández, Jacquelin K. Kammeyer, Chiwoo Park, Juan De Pablo, Francesco Zerbetto, Joseph Patterson, Nathan C. Gianneschi. Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy. Journal of the American Chemical Society. 2017; 139 (47):17140-17151.
Chicago/Turabian StyleLucas R. Parent; Evangelos Bakalis; Abelardo Ramírez-Hernández; Jacquelin K. Kammeyer; Chiwoo Park; Juan De Pablo; Francesco Zerbetto; Joseph Patterson; Nathan C. Gianneschi. 2017. "Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy." Journal of the American Chemical Society 139, no. 47: 17140-17151.
Submarine volcanoes, such as Kolumbo (Santorini, Greece) are natural laboratories for fostering multidisciplinary studies. Their investigation requires the most innovative marine technology together with advanced data analysis. Conductivity and temperature of seawater were recorded directly above Kolumbo’s hydrothermal vent system. The respective time series have been analyzed in terms of non–equilibrium techniques. The energy dissipation of the volcanic activity is monitored by the temperature variations of seawater. The venting dynamics of chemical products is monitored by water conductivity. The analysis of the time series in terms of stochastic processes delivers scaling exponents with turning points between consecutive regimes for both conductivity and temperature. Changes of conductivity are shown to behave as a universal multifractal and their variance is subdiffusive as the scaling exponents indicate. Temperature is constant over volcanic rest periods and a universal multifractal behavior describes its changes in line with a subdiffusive character otherwise. The universal multifractal description illustrates the presence of non–conservative conductivity and temperature fields showing that the system never retains a real equilibrium state. The existence of a repeated pattern of the combined effect of both seawater and volcanic activity is predicted. The findings can shed light on the dynamics of chemical products emitted from the vents and point to the presence of underlying mechanisms that govern potentially hazardous, underwater volcanic environments.
Evangelos Bakalis; Theo J. Mertzimekis; Paraskevi Nomikou; Francesco Zerbetto. Breathing modes of Kolumbo submarine volcano (Santorini, Greece). Scientific Reports 2017, 7, 46515 .
AMA StyleEvangelos Bakalis, Theo J. Mertzimekis, Paraskevi Nomikou, Francesco Zerbetto. Breathing modes of Kolumbo submarine volcano (Santorini, Greece). Scientific Reports. 2017; 7 (1):46515.
Chicago/Turabian StyleEvangelos Bakalis; Theo J. Mertzimekis; Paraskevi Nomikou; Francesco Zerbetto. 2017. "Breathing modes of Kolumbo submarine volcano (Santorini, Greece)." Scientific Reports 7, no. 1: 46515.
The anomalous diffusion of a particle that moves in complex environments is analytically studied by means of the time fractional diffusion equation. The influence on the dynamics of a random moving particle caused by a uniform external field is taken into account. We extract analytical solutions in terms either of the Mittag-Leffler functions or of the M- Wright function for the probability distribution, for the velocity autocorrelation function as well as for the mean and the mean square displacement. Discussion of the applicability of the model to real systems is made in order to provide new insight of the medium from the analysis of the motion of a particle embedded in it.
Evangelos Bakalis; Francesco Zerbetto. Time Fractional Diffusion Equations and Analytical Solvable Models. Journal of Physics: Conference Series 2016, 738, 12106 .
AMA StyleEvangelos Bakalis, Francesco Zerbetto. Time Fractional Diffusion Equations and Analytical Solvable Models. Journal of Physics: Conference Series. 2016; 738 ():12106.
Chicago/Turabian StyleEvangelos Bakalis; Francesco Zerbetto. 2016. "Time Fractional Diffusion Equations and Analytical Solvable Models." Journal of Physics: Conference Series 738, no. : 12106.
Enzymatic reactions in complex environments often take place with concentrations of enzyme comparable to that of substrate molecules. Two such cases occur when an enzyme is used to detect low concentrations of substrate/analyte or inside a living cell. Such concentrations do not agree with standard in vitro conditions, aimed at satisfying one of the founding hypotheses of the Michaelis-Menten reaction scheme, MM. It would be desirable to generalize the classical approach and show its applicability to complex systems. A permeable micrometrically structured hydrogel matrix was fabricated by protein cross-linking. Glucose oxidase enzyme (GOx) was embedded in the matrix and used as a prototypical system. The concentration of H2O2 was monitored in time and fitted by an accurate solution of the enzymatic kinetic scheme, which is expressed in terms of simple functions. The approach can also find applications in digital microfluidics and in systems biology where the kinetics response in the linear regimes often employed must be replaced.
Evangelos O. Bakalis; Alice Solda'; Marios K. Kosmas; Stefania Rapino; Francesco Zerbetto. Complex Media and Enzymatic Kinetics. Analytical Chemistry 2016, 88, 5790 -5796.
AMA StyleEvangelos O. Bakalis, Alice Solda', Marios K. Kosmas, Stefania Rapino, Francesco Zerbetto. Complex Media and Enzymatic Kinetics. Analytical Chemistry. 2016; 88 (11):5790-5796.
Chicago/Turabian StyleEvangelos O. Bakalis; Alice Solda'; Marios K. Kosmas; Stefania Rapino; Francesco Zerbetto. 2016. "Complex Media and Enzymatic Kinetics." Analytical Chemistry 88, no. 11: 5790-5796.
Nadja Sändig; Evangelos Bakalis; Francesco Zerbetto. Stochastic analysis of movements on surfaces: The case of C60 on Au(111). Chemical Physics Letters 2015, 633, 163 -168.
AMA StyleNadja Sändig, Evangelos Bakalis, Francesco Zerbetto. Stochastic analysis of movements on surfaces: The case of C60 on Au(111). Chemical Physics Letters. 2015; 633 ():163-168.
Chicago/Turabian StyleNadja Sändig; Evangelos Bakalis; Francesco Zerbetto. 2015. "Stochastic analysis of movements on surfaces: The case of C60 on Au(111)." Chemical Physics Letters 633, no. : 163-168.
Molecular dynamics simulations of a bi-layer membrane made by the same number of 1-palmitoyl-2-oleoyl-glycero-3-phospho-ethanolamine and palmitoyl-oleoyl phosphatidylserine lipids reveal sub-diffusional motion, which presents a crossover between two different power laws. Fractional Brownian motion is the stochastic mechanism that governs the motion in both regimes. The location of the crossover point is justified with simple geometrical arguments and is due to the activation of the mechanism of circumrotation of lipids about each other.
Evangelos Bakalis; Siegfried Höfinger; Alessandro Venturini; Francesco Zerbetto. Crossover of two power laws in the anomalous diffusion of a two lipid membrane. The Journal of Chemical Physics 2015, 142, 215102 .
AMA StyleEvangelos Bakalis, Siegfried Höfinger, Alessandro Venturini, Francesco Zerbetto. Crossover of two power laws in the anomalous diffusion of a two lipid membrane. The Journal of Chemical Physics. 2015; 142 (21):215102.
Chicago/Turabian StyleEvangelos Bakalis; Siegfried Höfinger; Alessandro Venturini; Francesco Zerbetto. 2015. "Crossover of two power laws in the anomalous diffusion of a two lipid membrane." The Journal of Chemical Physics 142, no. 21: 215102.
Silvana Fiorito; Emmanuel Flahaut; Stefania Rapino; Francesco Paolucci; Federica Andreola; Noemi Moroni; Eugenia Pittaluga; Manuela Zonfrillo; Giovanni Valenti; Arianna Mastrofrancesco; Flavia Groppi; Enrico Sabbioni; Evangelos Bakalis; Francesco Zerbetto; Annalucia Serafino. Redox active Double Wall Carbon Nanotubes show intrinsic anti-proliferative effects and modulate autophagy in cancer cells. Carbon 2014, 78, 589 -600.
AMA StyleSilvana Fiorito, Emmanuel Flahaut, Stefania Rapino, Francesco Paolucci, Federica Andreola, Noemi Moroni, Eugenia Pittaluga, Manuela Zonfrillo, Giovanni Valenti, Arianna Mastrofrancesco, Flavia Groppi, Enrico Sabbioni, Evangelos Bakalis, Francesco Zerbetto, Annalucia Serafino. Redox active Double Wall Carbon Nanotubes show intrinsic anti-proliferative effects and modulate autophagy in cancer cells. Carbon. 2014; 78 ():589-600.
Chicago/Turabian StyleSilvana Fiorito; Emmanuel Flahaut; Stefania Rapino; Francesco Paolucci; Federica Andreola; Noemi Moroni; Eugenia Pittaluga; Manuela Zonfrillo; Giovanni Valenti; Arianna Mastrofrancesco; Flavia Groppi; Enrico Sabbioni; Evangelos Bakalis; Francesco Zerbetto; Annalucia Serafino. 2014. "Redox active Double Wall Carbon Nanotubes show intrinsic anti-proliferative effects and modulate autophagy in cancer cells." Carbon 78, no. : 589-600.
The short answer to the title question is no. Despite their tremendous complexity, many nanomachines are simply one‐dimensional systems undergoing a biased, that is, unidirectional, walk on a two‐minima potential energy curve. The initially prepared state, or station, is higher in energy than the final equilibrium state that is reached after overcoming an energy barrier. All chemical reactions comply with this scheme, which does not necessarily imply that a generic chemical reaction is a potential molecular motor. If the barrier is low, the system may walk back and the motion will have a large purely Brownian component. Alternatively, a large distance from the barrier of either of the two stations may introduce a Brownian component. Starting from a general inequality that leverages on the idea that the amount of heat dissipated along the potential energy curve is a good indication of the effectiveness of the biased walk, we provide guidelines for the selection of the features of artificial molecular motors.
Evangelos Bakalis; Francesco Zerbetto. Are Two-Station Biased Random Walkers Always Potential Molecular Motors? ChemPhysChem 2014, 16, 104 -107.
AMA StyleEvangelos Bakalis, Francesco Zerbetto. Are Two-Station Biased Random Walkers Always Potential Molecular Motors? ChemPhysChem. 2014; 16 (1):104-107.
Chicago/Turabian StyleEvangelos Bakalis; Francesco Zerbetto. 2014. "Are Two-Station Biased Random Walkers Always Potential Molecular Motors?" ChemPhysChem 16, no. 1: 104-107.
A general framework is provided that makes possible the estimation of time-dependent properties of a stochastic system moving far from equilibrium. The process is investigated and discussed in general terms of nonequilibrium thermodynamics. The approach is simple and can be exploited to gain insight into the dynamics of any molecular-level machine. As a case study, the dynamics of an artificial molecular rotary motor, similar to the inversion of a helix, which drives the motor from a metastable state to equilibrium, are examined. The energy path that the motor walks was obtained from the results of atomistic calculations. The motor undergoes unidirectional rotation and its entropy, internal energy, free energy, and net exerted force are given as a function of time, starting from the solution of Smoluchowski's equation. The rather low value of the organization index, that is, the ratio of the work done by the particle against friction during the unidirectional motion per available free energy, reveals that the motion is mainly subject to randomness, and the amount of energy converted to heat due to the directional motion is very small.
Lorenzo Moro; Matteo Di Giosia; Matteo Calvaresi; Evangelos Bakalis; Francesco Zerbetto. Operations and Thermodynamics of an Artificial Rotary Molecular Motor in Solution. ChemPhysChem 2014, 15, 1834 -1840.
AMA StyleLorenzo Moro, Matteo Di Giosia, Matteo Calvaresi, Evangelos Bakalis, Francesco Zerbetto. Operations and Thermodynamics of an Artificial Rotary Molecular Motor in Solution. ChemPhysChem. 2014; 15 (9):1834-1840.
Chicago/Turabian StyleLorenzo Moro; Matteo Di Giosia; Matteo Calvaresi; Evangelos Bakalis; Francesco Zerbetto. 2014. "Operations and Thermodynamics of an Artificial Rotary Molecular Motor in Solution." ChemPhysChem 15, no. 9: 1834-1840.
The Henry–Michaelis–Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k 2 of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k 2 small compared to k −1, we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E o and S o , which can be comparable or much different.
Evangelos Bakalis; Marios Kosmas; Emmanouel M. Papamichael. Perturbation Theory in the Catalytic Rate Constant of the Henri–Michaelis–Menten Enzymatic Reaction. Bulletin of Mathematical Biology 2012, 74, 1 .
AMA StyleEvangelos Bakalis, Marios Kosmas, Emmanouel M. Papamichael. Perturbation Theory in the Catalytic Rate Constant of the Henri–Michaelis–Menten Enzymatic Reaction. Bulletin of Mathematical Biology. 2012; 74 (11):1.
Chicago/Turabian StyleEvangelos Bakalis; Marios Kosmas; Emmanouel M. Papamichael. 2012. "Perturbation Theory in the Catalytic Rate Constant of the Henri–Michaelis–Menten Enzymatic Reaction." Bulletin of Mathematical Biology 74, no. 11: 1.