arXiv subjects

Alex Smolyanitsky

Publications and source records attributed to Alex Smolyanitsky.

9 recordsLinked to original sources

arXiv2025

Entropic modulation of divalent cation transport

Aqueous cations permeate subnanoscale pores by crossing free energy barriers dominated by competing enthalpic contributions from transiently decreased ion-solvent and increased ion-pore electrostatic interactions. This commonly accepted view is rooted in the studies of monovalent cation transport. Divalent cations, however, have significantly higher desolvation costs, requiring considerably larger pores to enable retention of the first hydration shell and subsequently transport. We show that this scenario gives rise to a strong enthalpy-entropy competition. Specifically, the first hydration shell is shown to undergo rotational ordering inside the pore, resulting in a tight transition state. Our results shed light on the basic mechanisms of transport barrier formation for aqueous divalent cations permeating nanoporous 2D membranes.

cond-mat.mes-hall↗

arXiv2024

Synaptic-Like Plasticity in 2D Nanofluidic Memristor from Competitive Bicationic Transport

Synaptic plasticity, the dynamic tuning of signal transmission strength between neurons, serves as a fundamental basis for memory and learning in biological organisms. This adaptive nature of synapses is considered one of the key features contributing to the superior energy efficiency of the brain. In this study, we utilize molecular dynamics simulations to demonstrate synaptic-like plasticity in a subnanoporous 2D membrane. We show that a train of voltage spikes dynamically modifies the membrane's ionic permeability in a process involving competitive bicationic transport. This process is shown to be repeatable after a given resting period. Due to a combination of sub-nm pore size and the atomic thinness of the membrane, this system exhibits energy dissipation of 0.1--100 aJ per voltage spike, which is several orders of magnitude lower than 0.1--10 fJ per spike in the human synapse. We reveal the underlying physical mechanisms at molecular detail and investigate the local energetics underlying this apparent synaptic-like behavior.

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arXiv2024

Memristive response and capacitive spiking in the aqueous ion transport through 2D nanopore arrays

In living organisms, information is processed in interconnected symphonies of ionic currents spiking through protein ion channels. As a result of dynamically switching their conductive states, ion channels exhibit a variety of current-voltage nonlinearities and memory effects. Fueled by the promise of computing architectures entirely different from von Neumann, recent attempts to identify and harness similar phenomena in artificial nanofluidic environments focused on demonstrating analog circuit elements with memory. Here we explore aqueous ionic transport through two-dimensional (2D) membranes featuring arrays of ion-trapping crown-ether-like pores. We demonstrate that for aqueous salts featuring ions with different ion-pore binding affinities, memristive effects emerge through coupling between the time-delayed state of the system and its transport properties. We also demonstrate a nanopore array that behaves as a capacitor with a strain-tunable built-in barrier, yielding behaviors ranging from current spiking to ohmic response. By focusing on the illustrative underlying mechanisms, we demonstrate that realistically observable memory effects may be achieved in nanofluidic systems featuring crown-porous 2D membranes.

cond-mat.mes-hall↗

arXiv2022

High-throughput nanopore fabrication and classification using FIB irradiation and automated pore edge analysis

Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding membrane-wide permeation properties. In this work, we investigate Xe-ion focused ion beam as a tool for scalable, large-area nanopore fabrication on atomically thin, free-standing molybdenum disulphide. The presented irradiation protocol enables designing ultrathin membranes with tunable porosity and pore dimension, along with spatial uniformity across large-area substrates. Fabricated nanoporous membranes were characterized using scanning transmission electron microscopy imaging and the observed nanopore geometries were analyzed through a pore-edge detection script. We further demonstrated that the obtained structural and statistical data can be readily passed on to computational and analytical tools to predict the permeation properties at both individual pore and membrane-wide scales. As an example, membranes featuring angstrom-scale pores were investigated in terms of their emerging water and ion flow properties through extensive all-atom molecular dynamics simulations. We believe that the combination of experimental and analytical approaches presented here should yield accurate physics-based property estimates and thus potentially enable a true function-by-design approach to fabrication for applications such as osmotic power generation, desalination/filtration, as well as their strain-tunable versions.

cond-mat.mtrl-sci↗

arXiv2021

Nanopores in atomically thin 2D nanosheets limit aqueous ssDNA transport

Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (hBN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction $\textit{via}$ transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer hBN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.

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arXiv2018

Graphene deflectometry for sensing molecular processes at the nanoscale

Single-molecule sensing is at the core of modern biophysics and nanoscale science, from revolutionizing healthcare through rapid, low-cost sequencing to understanding various physical, chemical, and biological processes at their most basic level. However, important processes at the molecular scale are often too fast for the detection bandwidth or otherwise outside the detection sensitivity. Moreover, most envisioned biophysical applications are at room temperature, which further limits detection due to significant thermal noise. Here, we theoretically demonstrate reliable transduction of forces into electronic currents via locally suspended graphene nanoribbons subject to ultra-low flexural deflection. The decay of electronic couplings with distance magnifies the effect of the deflection, giving rise to measurable electronic current changes even in aqueous solution. Due to thermal fluctuations, the characteristic charge carrier transmission peak follows a generalized Voigt profile, behavior which is reflected in the optimized sensor. The intrinsic sensitivity is less than 7 fN/$\sqrt{\mathbf{Hz}}$, allowing for the detection of ultra-weak and fast processes at room temperature. Graphene deflectometry thus presents new opportunities in the sensing and detection of molecular-scale processes, from ion dynamics to DNA sequencing and protein folding, in their native environment.

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arXiv2017

Relaxation-limited electronic currents in extended reservoir simulations

Open-system approaches are gaining traction in the simulation of charge transport in nanoscale and molecular electronic devices. In particular, "extended reservoir" simulations, where explicit reservoir degrees of freedom are present, allow for the computation of both real-time and steady-state properties but require relaxation of the extended reservoirs. The strength of this relaxation, $γ$, influences the conductance, giving rise to a "turnover" behavior analogous to Kramers' turnover in chemical reaction rates. We derive explicit, general expressions for the weak and strong relaxation limits. For weak relaxation, the conductance increases linearly with $γ$ and every electronic state of the total explicit system contributes to the electronic current according to its "reduced" weight in the two extended reservoir regions. Essentially, this represents two conductors in series -- one at each interface with the implicit reservoirs that provide the relaxation. For strong relaxation, a "dual" expression -- one with the same functional form -- results, except now proportional to $1/γ$ and dependent on the system of interest's electronic states, reflecting that the strong relaxation is localizing electrons in the extended reservoirs. Higher order behavior (e.g., $γ^2$ or $1/γ^2$) can occur when there is a gap in the frequency spectrum. Moreover, inhomogeneity in the frequency spacing can give rise to a pseudo-plateau regime. These findings yield a physically motivated approach to diagnosing numerical simulations and understanding the influence of relaxation, and we examine their occurrence in both simple models and a realistic, fluctuating graphene nanoribbon.

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arXiv2015

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions.

cond-mat.mes-hall↗

arXiv2014

Effects of surface compliance and relaxation on the frictional properties of lamellar materials

We describe the results of atomic-level stick-slip friction measurements performed on chemically-modified graphite, using atomic force microscopy (AFM). Through detailed molecular dynamics simulations, coarse-grained simulations, and theoretical arguments, we report on complex indentation profiles during AFM scans involving local reversible exfoliation of the top layer of graphene from the underlying graphite sample and its effect on the measured friction force during retraction of the scanning tip. In particular, we report nearly constant lateral stick-slip magnitudes at decreasing loads, which cannot be explained within the standard framework based on continuum mechanics models for the contact area. We explain this anomalous behavior by introducing the effect of local compliance of the topmost graphene layer, which varies when interaction with the AFM tip is enhanced. Such behavior is not observed for non-lamellar materials. We extend our discussion toward the more general understanding of the effects of the top layer relaxation on the friction force under pushing and pulling loads. Our results may provide a more comprehensive understanding of the effectively negative coefficient of friction recently observed on chemically-modified graphite.

cond-mat.mtrl-sci↗