Dehydration as a Universal Mechanism for Ion Selectivity in Graphene and Other Atomically Thin Pores

Ion channels play a key role in regulating cell behavior and in electrical signaling. In these settings, polar and charged functional groups -- as well as protein response -- compensate for dehydration in an ion-dependent way, giving rise to the ion selective transport critical to the operation of cells. Dehydration, though, yields ion-dependent free-energy barriers and thus is predicted to give rise to selectivity by itself. However, these barriers are typically so large that they will suppress the ion currents to undetectable levels. Here, we establish that graphene displays a measurable dehydration-only mechanism for selectivity of $\mathrm{K}^+$ over $\mathrm{Cl}^-$. This fundamental mechanism -- one that depends only on the geometry and hydration -- is the starting point for selectivity for all channels and pores. Moreover, while we study selectivity of $\mathrm{K}^+$ over $\mathrm{Cl}^-$, we find that dehydration-based selectivity functions for all ions, i.e., cation over cation selectivity (e.g., $\mathrm{K}^+$ over $\mathrm{Na}^+$). Its likely detection in graphene pores resolves conflicting experimental results, as well as presents a new paradigm for characterizing the operation of ion channels and engineering molecular/ionic selectivity in filtration and other applications.Comment: 27 page

Ionic partition and transport in multi-ionic channels: A Molecular Dynamics Simulation study of the OmpF bacterial porin

We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new interesting experimental findings concerning their selectivity and conductance behaviour at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild type OmpF channel (which contains on one side a cluster with three positive residues and on the other side two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing excess of cations and regions containing excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions in the two mutants, as in the OmpF wild type channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild type OmpF and the mutants, following an electroneutral balance

Phonon-mediated and weakly size-dependent electron and hole cooling in CsPbBr3 nanocrystals revealed by atomistic simulations and ultrafast spectroscopy

We combine state-of-the-art ultrafast photoluminescence and absorption spectroscopy and nonadiabatic molecular dynamics simulations to investigate charge-carrier cooling in CsPbBr3 nanocrystals over a very broad size regime, from 0.8 to 12 nm. Contrary to the prevailing notion that polaron formation slows down charge-carrier cooling in lead-halide perovskites, no suppression of carrier cooling is observed in CsPbBr3 nanocrystals except for a slow cooling (over similar to 10 ps) of "warm" electrons in the vicinity (within similar to 0.1 eV) of the conduction band edge. At higher excess energies, electrons and holes cool with similar rates, on the order of 1 eV ps(-1) carrier(-1), increasing weakly with size. Our ab initio simulations suggest that cooling proceeds via fast phonon-mediated intraband transitions driven by strong and size-dependent electron-phonon coupling. The presented experimental and computational methods yield the spectrum of involved phonons and may guide the development of devices utilizing hot charge carriers

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.Comment: 25 pages, 1 table, 7 figures; preprint submitted to Biophysical Journa

Biodamage via shock waves initiated by irradiation with ions

Radiation damage following the ionising radiation of tissue has different scenarios and mechanisms depending on the projectiles or radiation modality. We investigate the radiation damage effects due to shock waves produced by ions. We analyse the strength of the shock wave capable of directly producing DNA strand breaks and, depending on the ion's linear energy transfer, estimate the radius from the ion's path, within which DNA damage by the shock wave mechanism is dominant. At much smaller values of linear energy transfer, the shock waves turn out to be instrumental in propagating reactive species formed close to the ion's path to large distances, successfully competing with diffusion

Fluctuating hydrodynamic modelling of fluids at the nanoscale

A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the hydrodynamics of nanoscale molecular assemblies are lacking, at least in part because of the stochastic character of the underlying fluctuating hydrodynamic equations. Here we derive a finite volume discretization of the compressible isothermal fluctuating hydrodynamic equations over a regular grid in the Eulerian reference system. We apply it to fluids such as argon at arbitrary densities and water under ambient conditions. To that end, molecular dynamics simulations are used to derive the required fluid properties. The equilibrium state of the model is shown to be thermodynamically consistent and correctly reproduces linear hydrodynamics including relaxation of sound and shear modes. We also consider non-equilibrium states involving diffusion and convection in cavities with no-slip boundary conditions

Molecular modeling to study dendrimers for biomedical applications

© 2014 by the authors; licensee MDPI; Basel; Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). Date of Acceptance: 17/11/2014Molecular modeling techniques provide a powerful tool to study the properties of molecules and their interactions at the molecular level. The use of computational techniques to predict interaction patterns and molecular properties can inform the design of drug delivery systems and therapeutic agents. Dendrimers are hyperbranched macromolecular structures that comprise repetitive building blocks and have defined architecture and functionality. Their unique structural features can be exploited to design novel carriers for both therapeutic and diagnostic agents. Many studies have been performed to iteratively optimise the properties of dendrimers in solution as well as their interaction with drugs, nucleic acids, proteins and lipid membranes. Key features including dendrimer size and surface have been revealed that can be modified to increase their performance as drug carriers. Computational studies have supported experimental work by providing valuable insights about dendrimer structure and possible molecular interactions at the molecular level. The progress in computational simulation techniques and models provides a basis to improve our ability to better predict and understand the biological activities and interactions of dendrimers. This review will focus on the use of molecular modeling tools for the study and design of dendrimers, with particular emphasis on the efforts that have been made to improve the efficacy of this class of molecules in biomedical applications.Peer reviewedFinal Published versio

Manipulating graphene kinks through positive and negative radiation pressure effects

We introduce an idea of experimental verification of the counterintuitive negative radiation pressure effect in some classical field theories by means of buckled graphene. In this effect, a monochromatic plane wave interacting with topological solutions pulls these solutions towards the source of radiation. Using extensive molecular dynamics simulations, we investigate the traveling wave-induced motion of kinks in buckled graphene nanoribbons. It is shown that depending on the driving source frequency, amplitude and direction, the kink behavior varies from attraction to repulsion (the negative and positive radiation pressure effects, respectively). Some preliminary explanations are proposed based on the analogy to certain field theory models. Our findings open the way to a new approach to motion control on the nanoscale