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1.
Chemphyschem ; : e202400395, 2024 Aug 19.
Artículo en Inglés | MEDLINE | ID: mdl-39161129

RESUMEN

The salinity gradient power extracted from the mixing of electrolyte solutions at dierent concentrations through selective nanoporous membranes is a promising route to renewable energy. However, several challenges need to be addressed to make this technology protable, one of the most relevant being the increase of the extractable power per membrane area. Here, the performance of asymmetric conical and bullet-shaped nanopores in a 50 nm thick membrane are studied via electrohydrodynamic simulations, varying the pore radius, curvature, and surface charge. The output power reaches ∼ 60 pW per pore for positively charged membranes (surface charge σw =160 mC/m2 ) and ∼ 30 pW for negatively charges ones, σw =-160 mC/m2 and it is robust to minor variations of nanopore shape and radius. A theoretical argument that takes into account the interaction among neighbour pores allows to extrapolate the single-pore performance to multi-pore membranes showing that power densities from tens to hundreds of W/m2 can be reached by proper tuning of the nanopore number density and the boundary layer thickness. Our model for scaling single-pore performance to multi-pore membrane can be applied also to experimental data providing a simple tool to effectively compare different nanopore membranes in blue energy applications.

2.
J Chem Phys ; 161(8)2024 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-39189655

RESUMEN

The Martini model, a coarse-grained forcefield for biomolecular simulations, has experienced a vast increase in popularity in the past decade. Its building-block approach balances computational efficiency with high chemical specificity, enabling the simulation of organic and inorganic molecules. The modeling of coarse-grained beads as Lennard-Jones particles poses challenges for the accurate reproduction of liquid-vapor interfacial properties, which are crucial in various applications, especially in the case of water. The latest version of the forcefield introduces refined interaction parameters for water beads, tackling the well-known artifact of Martini water freezing at room temperature. In addition, multiple sizes of water beads are available for simulating the solvation of small cavities, including the smallest pockets of proteins. This work focuses on studying the interfacial properties of Martini water, including surface tension and surface thickness. Employing the test-area method, we systematically compute the liquid-vapor surface tension across various combinations of water bead sizes and for temperatures from 300 to 350 K. These findings are of interest to the Martini community as they allow users to account for the low interfacial tension of Martini water by properly adjusting observables computed via coarse-grained simulations to allow for accurate matching against all-atom or experimental results. Surface tension data are also interpreted in terms of local enrichment of the various mixture components at the liquid-vapor interface by means of Gibbs' adsorption formalism. Finally, the critical scaling of the Martini surface tension with temperature is reported to be consistent with the critical exponent of the 3D Ising universality class.

3.
Nano Lett ; 24(33): 10098-10105, 2024 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-39121066

RESUMEN

Solid-state nanopores are a key platform for single-molecule detection and analysis that allow engineering of their properties by controlling size, shape, and chemical functionalization. However, approaches relying on polymers have limits for what concerns hardness, robustness, durability, and refractive index. Nanopores made of oxides with high dielectric constant would overcome such limits and have the potential to extend the suitability of solid-state nanopores toward optoelectronic technologies. Here, we present a versatile method to fabricate three-dimensional nanopores made of different dielectric oxides with convex, straight, and concave shapes and demonstrate their functionality in a series of technologies and applications such as ionic nanochannels, ionic current rectification, memristors, and DNA sensing. Our experimental data are supported by numerical simulations that showcase the effect of different shapes and oxide materials. This approach toward robust and tunable solid-state nanopores can be extended to other 3D shapes and a variety of dielectrics.

4.
J Phys Chem C Nanomater Interfaces ; 128(29): 12036-12045, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39081555

RESUMEN

Forced wetting (intrusion) and spontaneous dewetting (extrusion) of hydrophobic/lyophobic nanoporous materials by water/nonwetting liquid are of great importance for a broad span of technological and natural systems such as shock-absorbers, molecular springs, separation, chromatography, ion channels, nanofluidics, and many more. In most of these cases, the process of intrusion-extrusion is not complete due to the stochastic nature of external stimuli under realistic operational conditions. However, understanding of these partial processes is limited, as most of the works are focused on an idealized complete intrusion-extrusion cycle. In this work, we show an experimental system operating under partial intrusion/extrusion conditions and present a simple model that captures its main features. We rationalize these operational conditions in terms of the pore entrance and cavity size distributions of the material, which control the range of intrusion/extrusion pressures.

5.
Nat Commun ; 15(1): 5076, 2024 Jun 13.
Artículo en Inglés | MEDLINE | ID: mdl-38871721

RESUMEN

Although coveted in applications, few materials expand when subject to compression or contract under decompression, i.e., exhibit negative compressibility. A key step to achieve such counterintuitive behaviour is the destabilisations of (meta)stable equilibria of the constituents. Here, we propose a simple strategy to obtain negative compressibility exploiting capillary forces both to precompress the elastic material and to release such precompression by a threshold phenomenon - the reversible formation of a bubble in a hydrophobic flexible cavity. We demonstrate that the solid part of such metastable elastocapillary systems displays negative compressibility across different scales: hydrophobic microporous materials, proteins, and millimetre-sized laminae. This concept is applicable to fields such as porous materials, biomolecules, sensors and may be easily extended to create unexpected material susceptibilities.

6.
ArXiv ; 2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38764592

RESUMEN

The large-conductance, calcium-activated potassium (BK) channel lacks the typical intracellular bundle-crossing gate present in most ion channels of the 6TM family. This observation, initially inferred from Ca$^{2+}$-free-pore accessibility experiments and recently corroborated by a CryoEM structure of the non-conductive state, raises a puzzling question: how can gating occur in absence of steric hindrance? To answer this question, we carried out molecular simulations and accurate free energy calculations to obtain a microscopic picture of the sequence of events that, starting from a Ca$^{2+}$-free state leads to ion conduction upon Ca$^{2+}$ binding. Our results highlight an unexpected role for annular lipids, which turn out to be an integral part of the gating machinery. Due to the presence of fenestrations, the "closed" Ca$^{2+}$-free pore can be occupied by the methyl groups from the lipid alkyl chains. This dynamic occupancy triggers and stabilizes the nucleation of a vapor bubble into the inner pore cavity, thus hindering ion conduction. By contrast, Ca$^{2+}$ binding results into a displacement of these lipids outside the inner cavity, lowering the hydrophobicity of this region and thus allowing for pore hydration and conduction. This lipid-mediated hydrophobic gating rationalizes several seemingly problematic experimental observations, including the state-dependent pore accessibility of blockers.

7.
Nat Commun ; 14(1): 8390, 2023 Dec 18.
Artículo en Inglés | MEDLINE | ID: mdl-38110352

RESUMEN

Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.


Asunto(s)
Nanoporos , Fenómenos Electrofisiológicos , Semiconductores , Electricidad , Encéfalo
9.
ACS Nano ; 17(21): 21287-21296, 2023 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-37856254

RESUMEN

A general method to obtain a representation of the structural landscape of nanoparticles in terms of a limited number of variables is proposed. The method is applied to a large data set of parallel tempering molecular dynamics simulations of gold clusters of 90 and 147 atoms, silver clusters of 147 atoms, and copper clusters of 147 atoms, covering a plethora of structures and temperatures. The method leverages convolutional neural networks to learn the radial distribution functions of the nanoclusters and distills a low-dimensional chart of the structural landscape. This strategy is found to give rise to a physically meaningful and differentiable mapping of the atom positions to a low-dimensional manifold in which the main structural motifs are clearly discriminated and meaningfully ordered. Furthermore, unsupervised clustering on the low-dimensional data proved effective at further splitting the motifs into structural subfamilies characterized by very fine and physically relevant differences such as the presence of specific punctual or planar defects or of atoms with particular coordination features. Owing to these peculiarities, the chart also enabled tracking of the complex structural evolution in a reactive trajectory. In addition to visualization and analysis of complex structural landscapes, the presented approach offers a general, low-dimensional set of differentiable variables that has the potential to be used for exploration and enhanced sampling purposes.

10.
J Chem Phys ; 159(11)2023 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-37724724

RESUMEN

The liquid-to-vapor transition can occur under unexpected conditions in nanopores, opening the door to fundamental questions and new technologies. The physics of boiling in confinement is progressively introduced, starting from classical nucleation theory, passing through nanoscale effects, and terminating with the material and external parameters that affect the boiling conditions. The relevance of boiling in specific nanoconfined systems is discussed, focusing on heterogeneous lyophobic systems, chromatographic columns, and ion channels. The current level of control of boiling in nanopores enabled by microporous materials such as metal organic frameworks and biological nanopores paves the way to thrilling theoretical challenges and to new technological opportunities in the fields of energy, neuromorphic computing, and sensing.

11.
J Chem Phys ; 159(9)2023 Sep 07.
Artículo en Inglés | MEDLINE | ID: mdl-37668252

RESUMEN

Finite-temperature structures of Cu, Ag, and Au metal nanoclusters are calculated in the entire temperature range from 0 K to melting using a computational methodology that we proposed recently [M. Settem et al., Nanoscale 14, 939 (2022)]. In this method, Harmonic Superposition Approximation (HSA) and Parallel Tempering Molecular Dynamics (PTMD) are combined in a complementary manner. HSA is accurate at low temperatures and fails at higher temperatures. PTMD, on the other hand, effectively samples the high temperature region and melts. This method is used to study the size- and system-dependent competition between various structural motifs of Cu, Ag, and Au nanoclusters in the size range 1-2 nm. Results show that there are mainly three types of structural changes in metal nanoclusters, depending on whether a solid-solid transformation occurs. In the first type, the global minimum is the dominant motif in the entire temperature range. In contrast, when a solid-solid transformation occurs, the global minimum transforms either completely to a different motif or partially, resulting in the co-existence of multiple motifs. Finally, nanocluster structures are analyzed to highlight the system-specific differences across the three metals.

12.
J Chem Inf Model ; 63(15): 4888-4899, 2023 08 14.
Artículo en Inglés | MEDLINE | ID: mdl-37504578

RESUMEN

hERG is a voltage-gated potassium channel involved in the heart contraction whose defections are associated with the cardiac arrhythmia Long QT Syndrome type 2. The activator RPR260243 (RPR) represents a possible candidate to pharmacologically treat LQTS2 because it enhances the opening of the channel. However, the molecular detail of its action mechanism remains quite elusive. Here, we address the problem using a combination of docking, molecular dynamics simulations, and network analysis. We show that the drug preferably binds at the interface between the voltage sensor and the pore, enhancing the canonical activation path and determining a whole-structure rearrangement of the channel that slightly impairs inactivation.


Asunto(s)
Canales de Potasio Éter-A-Go-Go , Corazón , Humanos , Canales de Potasio Éter-A-Go-Go/metabolismo , Piperidinas , Arritmias Cardíacas/tratamiento farmacológico , Canal de Potasio ERG1
13.
Nano Lett ; 23(12): 5430-5436, 2023 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-37294683

RESUMEN

Zeolitic Imidazolate Frameworks (ZIF) find application in storage and dissipation of mechanical energy. Their distinctive properties linked to their (sub)nanometer size and hydrophobicity allow for water intrusion only under high hydrostatic pressure. Here we focus on the popular ZIF-8 material investigating the intrusion mechanism in its nanoscale cages, which is the key to its rational exploitation in target applications. In this work, we used a joint experimental/theoretical approach combining in operando synchrotron experiments during high-pressure intrusion experiments, molecular dynamics simulations, and stochastic models to reveal that water intrusion into ZIF-8 occurs by a cascade filling of connected cages rather than a condensation process as previously assumed. The reported results allowed us to establish structure/function relations in this prototypical microporous material, representing an important step to devise design rules to synthesize porous media.

14.
J Chem Phys ; 158(20)2023 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-37222298

RESUMEN

Understanding intrusion and extrusion in nanoporous materials is a challenging multiscale problem of utmost importance for applications ranging from energy storage and dissipation to water desalination and hydrophobic gating in ion channels. Including atomistic details in simulations is required to predict the overall behavior of such systems because the statics and dynamics of these processes depend sensitively on microscopic features of the pore, such as the surface hydrophobicity, geometry, and charge distribution, and on the composition of the liquid. On the other hand, the transitions between the filled (intruded) and empty (extruded) states are rare events that often require long simulation times, which are difficult to achieve with standard atomistic simulations. In this work, we explored the intrusion and extrusion processes using a multiscale approach in which the atomistic details of the system, extracted from molecular dynamics simulations, informed a simple Langevin model of water intrusion/extrusion in the pore. We then used the Langevin simulations to compute the transition times at different pressures, validating our coarse-grained model by comparing it with nonequilibrium molecular dynamics simulations. The proposed approach reproduces experimentally relevant features such as the time and temperature dependence of the intrusion/extrusion cycles, as well as specific details about the shape of the cycle. This approach also drastically increases the timescales that can be simulated, reducing the gap between simulations and experiments and showing promise for more complex systems.

15.
J Colloid Interface Sci ; 645: 775-783, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37172487

RESUMEN

HYPOTHESIS: The behavior of Heterogeneous Lyophobic Systems (HLSs) comprised of a lyophobic porous material and a corresponding non-wetting liquid is affected by a variety of different structural parameters of the porous material. Dependence on exogenic properties such as crystallite size is desirable for system tuning as they are much more facilely modified. We explore the dependence of intrusion pressure and intruded volume on crystallite size, testing the hypothesis that the connection between internal cavities and bulk water facilitates intrusion via hydrogen bonding, a phenomenon that is magnified in smaller crystallites with a larger surface/volume ratio. EXPERIMENTS: Water intrusion/extrusion pressures and intrusion volume were experimentally measured for ZIF-8 samples of various crystallite sizes and compared to previously reported values. Alongside the practical research, molecular dynamics simulations and stochastic modeling were performed to illustrate the effect of crystallite size on the properties of the HLSs and uncover the important role of hydrogen bonding within this phenomenon. FINDINGS: A reduction in crystallite size led to a significant decrease of intrusion and extrusion pressures below 100 nm. Simulations indicate that this behavior is due to a greater number of cages being in proximity to bulk water for smaller crystallites, allowing cross-cage hydrogen bonds to stabilize the intruded state and lower the threshold pressure of intrusion and extrusion. This is accompanied by a reduction in the overall intruded volume. Simulations demonstrate that this phenomenon is linked to ZIF-8 surface half-cages exposed to water being occupied by water due to non-trivial termination of the crystallites, even at atmospheric pressure.

16.
J Chem Phys ; 158(13): 134708, 2023 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-37031130

RESUMEN

In this work, an extended classical nucleation theory (CNT), including line tension, is used to disentangle classical and non-classical effects in the nucleation of vapor from a liquid confined between two hydrophobic plates at a nanometer distance. The proposed approach allowed us to gauge, from the available simulation work, the importance of elusive nanoscale effects, such as line tension and non-classical modifications of the nucleation mechanism. Surprisingly, the purely macroscopic theory is found to be in quantitative accord with the microscopic data, even for plate distances as small as 2 nm, whereas in extreme confinement (<1.5 nm), the CNT approximations proved to be unsatisfactory. These results suggest how classical nucleation theory still offers a computationally inexpensive and predictive tool useful in all domains where nanoconfined evaporation occurs-including nanotechnology, surface science, and biology.

17.
Nanoscale ; 15(14): 6865, 2023 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-36942669

RESUMEN

Correction for 'Tempering of Au nanoclusters: capturing the temperature-dependent competition among structural motifs' by Manoj Settem et al., Nanoscale, 2022, 14, 939-952, https://doi.org/10.1039/D1NR05078H.

18.
Nat Commun ; 14(1): 1110, 2023 02 27.
Artículo en Inglés | MEDLINE | ID: mdl-36849440

RESUMEN

Voltage-gated potassium channels are involved in many physiological processes such as nerve impulse transmission, the heartbeat, and muscle contraction. However, for many of them the molecular determinants of the gating mechanism remain elusive. Here, using a combination of theoretical and experimental approaches, we address this problem focusing on the cardiac hERG potassium channel. Network analysis of molecular dynamics trajectories reveals the presence of a kinematic chain of residues that couples the voltage sensor domain to the pore domain and involves the S4/S1 and S1/S5 subunit interfaces. Mutagenesis experiments confirm the role of these residues and interfaces in the activation and inactivation mechanisms. Our findings demonstrate the presence of an electromechanical transduction path crucial for the non-domain-swapped hERG channel gating that resembles the noncanonical path identified in domain-swapped K+ channels.


Asunto(s)
Contracción Muscular , Canales de Potasio con Entrada de Voltaje , Frecuencia Cardíaca , Mutagénesis , Transmisión Sináptica
19.
ACS Nano ; 17(1): 587-596, 2023 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-36537367

RESUMEN

The solidification of AgCo, AgNi, and AgCu nanodroplets is studied by molecular dynamics simulations in the size range of 2-8 nm. All these systems tend to phase separate in the bulk solid with surface segregation of Ag. Despite these similarities, the simulations reveal clear differences in the solidification pathways. AgCo and AgNi already separate in the liquid phase, and they solidify in configurations close to equilibrium. They can show a two-step solidification process in which Co-/Ni-rich parts solidify at higher temperatures than the Ag-rich part. AgCu does not separate in the liquid and solidifies in one step, thereby remaining in a kinetically trapped state down to room temperature. The solidification mechanisms and the size dependence of the solidification temperatures are analyzed, finding qualitatively different behaviors in AgCo/AgNi compared to AgCu. These differences are rationalized by an analytical model.

20.
Commun Biol ; 5(1): 165, 2022 02 24.
Artículo en Inglés | MEDLINE | ID: mdl-35210539

RESUMEN

The elusive activation/deactivation mechanism of hERG is investigated, a voltage-gated potassium channel involved in severe inherited and drug-induced cardiac channelopathies, including the Long QT Syndrome. Firstly, the available structural data are integrated by providing a homology model for the closed state of the channel. Secondly, molecular dynamics combined with a network analysis revealed two distinct pathways coupling the voltage sensor domain with the pore domain. Interestingly, some LQTS-related mutations known to impair the activation/deactivation mechanism are distributed along the identified pathways, which thus suggests a microscopic interpretation of their role. Split channels simulations clarify a surprising feature of this channel, which is still able to gate when a cut is introduced between the voltage sensor domain and the neighboring helix S5. In summary, the presented results suggest possible activation/deactivation mechanisms of non-domain-swapped potassium channels that may aid in biomedical applications.


Asunto(s)
Canales de Potasio Éter-A-Go-Go , Simulación de Dinámica Molecular , Canal de Potasio ERG1/química , Canal de Potasio ERG1/genética , Canal de Potasio ERG1/metabolismo , Canales de Potasio Éter-A-Go-Go/química , Canales de Potasio Éter-A-Go-Go/genética , Canales de Potasio Éter-A-Go-Go/metabolismo , Activación del Canal Iónico , Mutación
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