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  1. Article ; Online: In vivo Assessment of Lysosomal Stress in the

    Martelli, Felipe

    Bio-protocol

    2023  Volume 13, Issue 2, Page(s) e4599

    Abstract: Lysosomes play a central role in signaling, nutrient sensing, response to stress, and the degradation and recycling of cellular content. Defects in lysosomal digestive enzymes or structural components can impair lysosomal function with dire consequences ... ...

    Abstract Lysosomes play a central role in signaling, nutrient sensing, response to stress, and the degradation and recycling of cellular content. Defects in lysosomal digestive enzymes or structural components can impair lysosomal function with dire consequences to the cell, such as neurodegeneration. A number of methods exist to assess lysosomal stress in the model
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4599
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Electrolyte Permeability in Plastic Ice VII.

    Martelli, Fausto

    The journal of physical chemistry. B

    2023  Volume 127, Issue 30, Page(s) 6734–6742

    Abstract: Deep brines in water-rich planets form when electrolytes diffuse from the rocky interior through layers of thick dense ice such as ice VII and the hypothesized plastic ice VII. We perform classical molecular dynamics simulations of ... ...

    Abstract Deep brines in water-rich planets form when electrolytes diffuse from the rocky interior through layers of thick dense ice such as ice VII and the hypothesized plastic ice VII. We perform classical molecular dynamics simulations of Li
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c01576
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  3. Article ; Online: Steady-like topology of the dynamical hydrogen bond network in supercooled water.

    Martelli, Fausto

    PNAS nexus

    2022  Volume 1, Issue 3, Page(s) pgac090

    Abstract: We investigate the link between topology of the hydrogen bond network (HBN) and large-scale density fluctuations in water from ambient conditions to the glassy state. We observe a transition from a temperature-dependent topology at high temperatures, to ... ...

    Abstract We investigate the link between topology of the hydrogen bond network (HBN) and large-scale density fluctuations in water from ambient conditions to the glassy state. We observe a transition from a temperature-dependent topology at high temperatures, to a steady-like topology below the Widom temperature
    Language English
    Publishing date 2022-06-17
    Publishing country England
    Document type Journal Article
    ISSN 2752-6542
    ISSN (online) 2752-6542
    DOI 10.1093/pnasnexus/pgac090
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  4. Article ; Online: Evaluation of Mitochondrial Turnover Using Fluorescence Microscopy in

    Martelli, Felipe

    Bio-protocol

    2022  Volume 12, Issue 17

    Abstract: Mitochondrial dysfunction is associated with perturbations in the cellular oxidative status, changes in energy production and metabolic rate, and the onset of pathological processes. Classic methods of assessing mitochondrial dysfunction rely on indirect ...

    Abstract Mitochondrial dysfunction is associated with perturbations in the cellular oxidative status, changes in energy production and metabolic rate, and the onset of pathological processes. Classic methods of assessing mitochondrial dysfunction rely on indirect measures, such as evaluating mitochondrial DNA copy numbers, or direct but more costly and skilled techniques, such as electron microscopy. The protocol presented here was recently implemented to evaluate mitochondrial dysfunction in response to insecticide exposure in
    Language English
    Publishing date 2022-09-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4498
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Electrofreezing of liquid water at ambient conditions.

    Cassone, Giuseppe / Martelli, Fausto

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1856

    Abstract: Water is routinely exposed to external electric fields. Whether, for example, at physiological conditions, in contact with biological systems, or at the interface of polar surfaces in countless technological settings, water responds to fields on the ... ...

    Abstract Water is routinely exposed to external electric fields. Whether, for example, at physiological conditions, in contact with biological systems, or at the interface of polar surfaces in countless technological settings, water responds to fields on the order of a few V Å
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46131-z
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  6. Article ; Online: Molecular rotations trigger a glass-to-plastic fcc heterogeneous crystallization in high-pressure water.

    Zimoń, Małgorzata J / Martelli, Fausto

    The Journal of chemical physics

    2023  Volume 158, Issue 11, Page(s) 114501

    Abstract: We report a molecular dynamics study of the heterogeneous crystallization of high-pressure glassy water using (plastic) ice VII as a substrate. We focus on the thermodynamic conditions P ∈ [6-8] GPa and T ∈ [100-500] K, at which (plastic) ice VII and ... ...

    Abstract We report a molecular dynamics study of the heterogeneous crystallization of high-pressure glassy water using (plastic) ice VII as a substrate. We focus on the thermodynamic conditions P ∈ [6-8] GPa and T ∈ [100-500] K, at which (plastic) ice VII and glassy water are supposed to coexist in several (exo)planets and icy moons. We find that (plastic) ice VII undergoes a martensitic phase transition to a (plastic) fcc crystal. Depending on the molecular rotational lifetime τ, we identify three rotational regimes: for τ > 20 ps, crystallization does not occur; for τ ∼ 15 ps, we observe a very sluggish crystallization and the formation of a considerable amount of icosahedral environments trapped in a highly defective crystal or in the residual glassy matrix; and for τ < 10 ps, crystallization takes place smoothly, resulting in an almost defect-free plastic fcc solid. The presence of icosahedral environments at intermediate τ is of particular interest as it shows that such a geometry, otherwise ephemeral at lower pressures, is, indeed, present in water. We justify the presence of icosahedral structures based on geometrical arguments. Our results represent the first study of heterogeneous crystallization occurring at thermodynamic conditions of relevance for planetary science and unveil the role of molecular rotations in achieving it. Our findings (i) show that the stability of plastic ice VII, widely reported in the literature, should be reconsidered in favor of plastic fcc, (ii) provide a rationale for the role of molecular rotations in achieving heterogeneous crystallization, and (iii) represent the first evidence of long-living icosahedral structures in water. Therefore, our work pushes forward our understanding of the properties of water.
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0138368
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  7. Article ; Online: High-dimensional order parameters and neural network classifiers applied to amorphous ices.

    Faure Beaulieu, Zoé / Deringer, Volker L / Martelli, Fausto

    The Journal of chemical physics

    2024  Volume 160, Issue 8

    Abstract: Amorphous ice phases are key constituents of water's complex structural landscape. This study investigates the polyamorphic nature of water, focusing on the complexities within low-density amorphous ice (LDA), high-density amorphous ice, and the recently ...

    Abstract Amorphous ice phases are key constituents of water's complex structural landscape. This study investigates the polyamorphic nature of water, focusing on the complexities within low-density amorphous ice (LDA), high-density amorphous ice, and the recently discovered medium-density amorphous ice (MDA). We use rotationally invariant, high-dimensional order parameters to capture a wide spectrum of local symmetries for the characterization of local oxygen environments. We train a neural network to classify these local environments and investigate the distinctiveness of MDA within the structural landscape of amorphous ice. Our results highlight the difficulty in accurately differentiating MDA from LDA due to structural similarities. Beyond water, our methodology can be applied to investigate the structural properties and phases of disordered materials.
    Language English
    Publishing date 2024-02-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0193340
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  8. Article ; Online: Unravelling the contribution of local structures to the anomalies of water: The synergistic action of several factors.

    Martelli, Fausto

    The Journal of chemical physics

    2019  Volume 150, Issue 9, Page(s) 94506

    Abstract: We investigate the microscopic origin of water's anomalies by inspecting the hydrogen bond network (HBN) and the spatial organization of low-density-liquid (LDL) like and high-density-liquid (HDL) like environments. Specifically, we simulate-via ... ...

    Abstract We investigate the microscopic origin of water's anomalies by inspecting the hydrogen bond network (HBN) and the spatial organization of low-density-liquid (LDL) like and high-density-liquid (HDL) like environments. Specifically, we simulate-via classical molecular dynamics simulations-the isobaric cooling of a sample composed of 512 water molecules from ambient to deeply undercooled conditions at three pressures, namely, 1 bar, 400 bars, and 1000 bars. In correspondence with the Widom line (WL), (i) the HDL-like dominating cluster undergoes fragmentation caused by the percolation of LDL-like aggregates following a spinodal-like kinetics; (ii) such fragmentation always occurs at a "critical" concentration of ∼20%-30% in LDL; (iii) the HBN within LDL-like environments is characterized by an equal number of pentagonal and hexagonal rings that create a state of maximal frustration between a configuration that promotes crystallization (hexagonal ring) and a configuration that hinders it (pentagonal ring); (iv) the spatial organization of HDL-like environments shows a marked variation. Moreover, the inspection of the global symmetry shows that the intermediate-range order decreases in correspondence with the WL and such a decrease becomes more pronounced upon increasing the pressure, hence supporting the hypothesis of a liquid-liquid critical point. Our results reveal and rationalize the complex microscopic origin of water's anomalies as the cooperative effect of several factors acting synergistically. Beyond implications for water, our findings may be extended to other materials displaying anomalous behaviours.
    Language English
    Publishing date 2019-02-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.5087471
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  9. Article: Editorial: Nucleic acid-based therapies for cardiovascular diseases.

    Martelli, Fabio / Mishra, Paras Kumar / Caporali, Andrea

    Frontiers in cardiovascular medicine

    2024  Volume 11, Page(s) 1392073

    Language English
    Publishing date 2024-03-22
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2024.1392073
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  10. Article ; Online: Signatures of sluggish dynamics and local structural ordering during ice nucleation.

    Martelli, Fausto / Palmer, Jeremy C

    The Journal of chemical physics

    2022  Volume 156, Issue 11, Page(s) 114502

    Abstract: We investigate the microscopic pathway of spontaneous crystallization in the ST2 model of water under deeply supercooled conditions via unbiased classical molecular dynamics simulations. After quenching below the liquid-liquid critical point, the ST2 ... ...

    Abstract We investigate the microscopic pathway of spontaneous crystallization in the ST2 model of water under deeply supercooled conditions via unbiased classical molecular dynamics simulations. After quenching below the liquid-liquid critical point, the ST2 model spontaneously separates into low-density liquid (LDL) and high-density liquid phases, respectively. The LDL phase, which is characterized by lower molecular mobility and enhanced structural order, fosters the formation of a sub-critical ice nucleus that, after a stabilization time, develops into the critical nucleus and grows. Polymorphic selection coincides with the development of the sub-critical nucleus and favors the formation of cubic (Ic) over hexagonal (Ih) ice. We rationalize polymorphic selection in terms of geometric arguments based on differences in the symmetry of second neighbor shells of ice Ic and Ih, which are posited to favor formation of the former. The rapidly growing critical nucleus absorbs both Ic and Ih crystallites dispersed in the liquid phase, a crystal with stacking faults. Our results are consistent with, and expand upon, recent observations of non-classical nucleation pathways in several systems.
    Language English
    Publishing date 2022-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0083638
    Database MEDical Literature Analysis and Retrieval System OnLINE

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