Microsecond simulations of DNA and ion transport in nanopores with novel ion–ion and ion–nucleotides effective potentials

We developed a novel scheme based on the grand‐canonical Monte Carlo/Brownian dynamics simulations and have extended it to studies of ion currents across three nanopores with the potential for single‐stranded DNA (ssDNA) sequencing: solid‐state nanopore Si₃N₄, α‐hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide‐specific ion dynamics compatible with ssDNA coarse‐grained model, we used the inverse Monte Carlo protocol, which maps the relevant ion–nucleotide distribution functions from all‐atom molecular dynamics (MD) simulations. Combined with the previously developed simulation platform for Brownian dynamics simulations of ion transport, it allows for microsecond‐ and millisecond‐long simulations of ssDNA dynamics in the nanopore with a conductance computation accuracy that equals or exceeds that of all‐atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all‐atom MD simulations. © 2014 Wiley Periodicals, Inc.     

Electric field-controlled water permeation coupled to ion transport through a nanopore

We report molecular dynamics simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na(+) concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium conditions, but the strong electric field caused by the ionic concentration gradient drives water molecules in. The density and structure of water in the pore are highly field dependent. In a typical simulation run, we observe a succession of cation passages through the pore, characterized by approximately bulk mobility. These ion passages reduce the electric field, until the pore empties of water and closes to further ion transport, thus providing a possible mechanism for biological ion channel gating.     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

The effect of the interaction between nanopore and chain monomer on the translocation of a single polymer chain confined in a finite size square through an interacting nanopore to a large space has been studied by two-dimensional bond fluctuation model with Monte Carlo simulation. Results indicate that the free energy barrier before the successful translocation of the chain depends linearly on the chain length as well as the nanopore length for different pore-polymer interaction, and the attractive interaction reduces the free energy barrier, leading to the reduction of the average trapping time.     

Enabling grand‐canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy ). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte‐Carlo/molecular dynamics (MD) simulations in the grand‐canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand‐canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand‐canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand‐canonical scheme is only minimal. © 2012 Wiley Periodicals, Inc.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. This review focuses on the analysis of ions and small molecules with nanopores including nanopipettes, polymer film nanopores, Si₃N₄ nanopores, graphene nanopores, MoS₂ nanopores and MOFs.     

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. The research field of solid-state nanopore starts from mimicking the biological nanopore in living cells. Understanding the transport mechanism of biological nanopore in vivo is a big challenge because of the experimental difficulty, so it is essential to establish the basic research of artificial nanopores in vitro especially for the analysis of ions and small molecules. The performance of solid-state nanopores could be evaluated by monitoring currents when ions and molecules passed through. The comparison of the two types of nanopores based on current-derived information can reveal the principle of biological nanopores, while the solid-state nanopores are applied into practical bioanalysis. In this review, we focus on the researches of the solid-state nanopores in the fabrication process and in the analysis of ions and small molecules. Fabrication methods of nanopores, ion transport mechanism, small molecule analysis and theoretical studies are discussed in detail.     

Modeling electrokinetics in ionic liquids

Using direct numerical simulations, we provide a thorough study regarding the electrokinetics of ionic liquids. In particular, modified Poisson–Nernst–Planck equations are solved to capture the crowding and overscreening effects characteristic of an ionic liquid. For modeling electrokinetic flows in an ionic liquid, the modified Poisson‐Nernst‐Planck equations are coupled with Navier–Stokes equations to study the coupling of ion transport, hydrodynamics, and electrostatic forces. Specifically, we consider the ion transport between two parallel charged surfaces, charging dynamics in a nanopore, capacitance of electric double‐layer capacitors, electroosmotic flow in a nanochannel, electroconvective instability on a plane ion‐selective surface, and electroconvective flow on a curved ion‐selective surface. We also discuss how crowding and overscreening and their interplay affect the electrokinetic behaviors of ionic liquids in these application problems.     

Nanopore‐Based Sequencing and Detection of Nucleic Acids

Nanopore‐based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single‐molecule detection. The technology allows the real‐time, selective, high‐throughput analysis of nucleic acids through both biological and solid‐state nanopores. In this Minireview, the background and latest progress in nanopore‐based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore‐based detection.     

Comparative study between continuum and atomistic approaches of liquid flow through a finite length cylindrical nanopore

Steady state pressure driven flow of liquid argon through a finite length cylindrical nanopore was investigated numerically by classical Navier-Stokes (NS) hydrodynamic models and nonequilibrium molecular dynamics (MD) simulations. In both approaches, the nanopore was nominally 2.2 nm in diameter and 6 nm long. For the MD simulations, the intermolecular properties of the walls were specified independently from the liquid. Comparisons between the approaches were made in terms of the gross feature of total flow rate through the nanopore, as well as the more refined considerations of the spatial distributions of pressure, density, and velocity. The results showed that for the NS equations to predict the same trends in total flow rate with increasing pressure difference as the MD simulation, submodels for variations in density and viscosity with pressure are needed to be included. The classical NS boundary conditions quantitatively agreed with the flow rate predictions from MD simulations only under the condition of having a neutral-like solid-liquid interaction. Under these conditions, the NS and MD models also agreed well in streamwise distributions of pressure, density, and velocity, but not in the radial direction.     

Coulomb replica‐exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

We propose a new type of the Hamiltonian replica‐exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free‐energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica‐exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local‐minimum free‐energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid‐β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β‐helix, α‐helix, 3₁₀‐helix, β‐hairpin, and β‐sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free‐energy landscape. © 2012 Wiley Periodicals, Inc.     

BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores

A theoretical framework is presented to model ion and DNA translocation across a nanopore confinement under an applied electric field. A combined Grand Canonical Monte Carlo Brownian Dynamics (GCMC/BD) algorithm offers a general approach to study ion permeation through wide molecular pores with a direct account of ion-ion and ion-DNA correlations. This work extends previously developed theory by incorporating the recently developed coarse-grain polymer model of DNA by de Pablo and colleagues [Knotts, T. A.; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. J. Chem. Phys. 2007, 126] with explicit ions for simulations of polymer dynamics. Atomistic MD simulations were used to guide model developments. The power of the developed scheme is illustrated with studies of single-stranded DNA (ss-DNA) oligomer translocation in two model cases: a cylindrical pore with a varying radius and a well-studied experimental system, the staphylococcal α-hemolysin channel. The developed model shows good agreement with experimental data for model studies of two homopolymers: ss-poly(dA)(n) and ss-poly(dC)(n). The developed protocol allows for direct evaluation of different factors (charge distribution and pore shape and size) controlling DNA translocation in a variety of nanopores.     

DNA‐Based Nanopore Sensing

Nanopore sensing is an attractive, label‐free approach that can measure single molecules. Although initially proposed for rapid and low‐cost DNA sequencing, nanopore sensors have been successfully employed in the detection of a wide variety of substrates. Early successes were mostly achieved based on two main strategies by 1) creating sensing elements inside the nanopore through protein mutation and chemical modification or 2) using molecular adapters to enhance analyte recognition. Over the past five years, DNA molecules started to be used as probes for sensing rather than substrates for sequencing. In this Minireview, we highlight the recent research efforts of nanopore sensing based on DNA‐mediated characteristic current events. As nanopore sensing is becoming increasingly important in biochemical and biophysical studies, DNA‐based sensing may find wider applications in investigating DNA‐involving biological processes.     

Simulation Study on Translocation of Confined Chain Through Interacting Nanopore

The translocation of a confined polymer chain through an interacting nanopore has been studied using two-dimensional bond fluctuation model with Monte Carlo dynamics. For different pore-polymer interaction, the average escaping time〈Τesc〉of the polymer chain through the nanopore, increases roughly linearly with the chain length and the nanopore length, respectively. However, the large repulsive and attractive pore-polymer interaction adds the difficulty of the monomers of the chain entering and leaving the nanopore, respec-tively, leading to the nonmonotonical dependence of〈Τesc〉on the pore-polymer interaction. The detailed translocation dynamics of the chain through the interacting nanopore is inves-tigated too.     

Molecular simulation of the adsorption and structure of benzene confined in mesoporous silicas

Grand Canonical Monte Carlo simulations are used to study the adsorption of benzene at 298 K in an atomistic cylindrical silica nanopore of a diameter 3.6 nm. The adsorption involves a transition from a partially filled pore (a two layers thick film at the pore surface) to a completely filled pore configuration. Strong layering of the benzene molecules at the pore surface is observed. It is found that the layering decays as the distance to the pore surface increases. The position of the peaks for the density of the C, H atoms and the center of mass of the molecules shows that benzene molecules prefer an orientation in which their ring is perpendicular to the pore surface. This result is corroborated by calculating orientational order parameters and examining the distribution of the distances between the H and C atoms of the benzene molecules and the H and O atoms of the silica substrate.     

Multiparticle moves in acceptance rate optimized monte carlo

Molecular Dynamics (MD) and Monte Carlo (MC) based simulation methods are widely used to investigate molecular and nanoscale structures and processes. While the investigation of systems in MD simulations is limited by very small time steps, MC methods are often stifled by low acceptance rates for moves that significantly perturb the system. In many Metropolis MC methods with hard potentials, the acceptance rate drops exponentially with the number of uncorrelated, simultaneously proposed moves. In this work, we discuss a multiparticle Acceptance Rate Optimized Monte Carlo approach (AROMoCa) to construct collective moves with near unit acceptance probability, while preserving detailed balance even for large step sizes. After an illustration of the protocol, we demonstrate that AROMoCa significantly accelerates MC simulations in four model systems in comparison to standard MC methods. AROMoCa can be applied to all MC simulations where a gradient of the potential is available and can help to significantly speed up molecular simulations. © 2015 Wiley Periodicals, Inc.     

Water-silica force field for simulating nanodevices

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.     

Biomimetic smart nanopores and nanochannels

Nature provides a huge range of biological materials, just as ion channels, with various smart functions over millions of years of evolution, and which serve as a big source of bio-inspiration for biomimetic materials. In this critical review, a strategy for the design and synthesis of biomimetic smart nanopores and nanochannels is presented and put into context with recent progress in this rapidly growing field from biological, inorganic, organic to composite nanopore and nanochannel materials, which can respond to single/multiple external stimuli, e.g., pH, temperature, light, and so on. This review is intended to utilize a specific responsive behavior for regulating ionic transport properties inside the single nanopore or nanochannel as an example to demonstrate the feasibility of the design strategy, and provide an overview of this fascinating research field (109 references).     

Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.     

MOCASSIN: Metropolis and kinetic Monte Carlo for solid electrolytes

The combination of density functional theory and Monte Carlo simulations is a powerful approach for the atomistic modeling of defect transport in solid electrolytes. The present contribution introduces the MOCASSIN software (Monte Carlo for Solid State Ionics) for kinetic and Metropolis Monte Carlo simulations of crystalline materials. MOCASSIN combines model building, visualization, and simulation, aiming to provide accessible MC for end users. Developed for the investigation of solid electrolytes, MOCASSIN is ideal for screening common variation parameters, such as temperature and doping fraction. The input effort is minimized using space groups for processing symmetry. The graphical interface for model building allows complex model input, including multiple mobile species, multiple migration paths, small polaron hopping, vehicle movements, multiple complex migration mechanisms, and custom interaction clusters. The software is provided free of charge for noncommercial usage.