Author Correction: Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms.

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Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms.

The spread of antimicrobial resistance stimulates discovery strategies that place emphasis on mechanisms circumventing the drawbacks of traditional antibiotics and on agents that hit multiple targets. Host defense peptides (HDPs) are promising candidates in this regard. Here we demonstrate that a given HDP sequence intrinsically encodes for tuneable mechanisms of membrane disruption. Using an archetypal HDP (cecropin B) we show that subtle structural alterations convert antimicrobial mechanisms from native carpet-like scenarios to poration and non-porating membrane exfoliation. Such distinct mechanisms, studied using low- and high-resolution spectroscopy, nanoscale imaging and molecular dynamics simulations, all maintain strong antimicrobial effects, albeit with diminished activity against pathogens resistant to HDPs. The strategy offers an effective search paradigm for the sequence probing of discrete antimicrobial mechanisms within a single HDP.

Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions.

Simulation and data analysis have evolved into powerful methods for discovering and understanding molecular modes of action and designing new compounds to exploit these modes. The combination provides a strong impetus to create and exploit new tools and techniques at the interfaces between physics, biology, and data science as a pathway to new scientific insight and accelerated discovery. In this context, we explore the rational design of novel antimicrobial peptides (short protein sequences exhibiting broad activity against multiple species of bacteria). We show how datasets can be harvested to reveal features which inform new design concepts. We introduce new analysis and visualization tools: a graphical representation of the k-mer spectrum as a fundamental property encoded in antimicrobial peptide databases and a data-driven representation to illustrate membrane binding and permeation of helical peptides.

Structure and hydrogen bonding at the limits of liquid water stability.

Liquid water exhibits unconventional behaviour across its wide range of stability - from its unusually high liquid-vapour critical point down to its melting point and below where it reaches a density maximum and exhibits negative thermal expansion allowing ice to float. Understanding the molecular underpinnings of these anomalies presents a challenge motivating the study of water for well over a century. Here we examine the molecular structure of liquid water across its range of stability, from mild supercooling to the negative pressure and high temperature regimes. We use a recently-developed, electronically-responsive model of water, constructed from gas-phase molecular properties and incorporating many-body, long-range interactions to all orders; as a result the model has been shown to have high transferability from ice to the supercritical regime. We report a link between the anomalous thermal expansion of water and the behaviour of its second coordination shell and an anomaly in hydrogen bonding, which persists throughout liquid water's range of stability - from the high temperature limit of liquid water to its supercooled regime.

Engineering monolayer poration for rapid exfoliation of microbial membranes.

The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics.

First realization of the piezoelectronic stress-based transduction device.

We present the first realization of a monolithically integrated piezoelectronic transistor (PET), a new transduction-based computer switch which could potentially operate conventional computer logic at 1/50 the power requirements of current Si-based transistors (Chen 2014 Proc. IEEE ICICDT pp 1-4; Mamaluy et al 2014 Proc. IWCE pp 1-2). In PET operation, an input gate voltage expands a piezoelectric element (PE), transducing the input into a pressure pulse which compresses a piezoresistive element (PR). The PR resistance goes down, transducing the signal back to voltage and turning the switch 'on'. This transduction physics, in principle, allows fast, low-voltage operation. In this work, we address the processing challenges of integrating chemically incompatible PR and PE materials together within a surrounding cage against which the PR can be compressed. This proof-of-concept demonstration of a fully integrated, stand-alone PET device is a key step in the development path toward a fast, low-power very large scale integration technology.

Signature properties of water: Their molecular electronic origins.

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water's crystalline phases and amorphous states. We show that many-body responses arising from water's electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a "strong coupling" approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water's complexity and its molecular origin, predicting water's signature physical properties from ice, through liquid-vapor coexistence, to the critical point.

Phase diagram of cuprate high-temperature superconductors described by a field theory based on anharmonic oxygen degrees of freedom.

In high temperature superconductors, although some phenomena such as the Mott transition (MT) at low doping are clearly driven by electron correlations, recent experimental data imply that anharmonic oxygen degrees of freedom-characteristic of perovskite materials-are playing a significant role. A key test of the role of anharmonic oxygen is to reproduce the complex cuprate phase diagram from a simple model. Here, we show that a field theory based on nonlinear coupling to anharmonic oxygens, parametrized from ab initio calculations, quantitatively reproduces the cuprate phase diagram for dopings above the MT. Pairing is mediated by renormalized oxygen vibrations transmuted into excitations of the pseudogap. The observed strong dependence of gap to transition temperature ratio on Tc also emerges from this field theory. This work suggests that including vibrational degrees of freedom is key to developing a complete understanding of the cuprates.

Hydrogen bonding and molecular orientation at the liquid-vapour interface of water.

We determine the molecular structure and orientation at the liquid-vapour interface of water using an electronically coarse grained model constructed to include all long-range electronic responses within Gaussian statistics. The model, fit to the properties of the isolated monomer and dimer, is sufficiently responsive to generate the temperature dependence of the surface tension from ambient conditions to the critical point. Acceptor hydrogen bonds are shown to be preferentially truncated at the free surface under ambient conditions and a related asymmetry in hydrogen bonding preference is identified in bulk water. We speculate that this bonding asymmetry in bulk water is the microscopic origin of the observed surface structure.

Anti-antimicrobial peptides: folding-mediated host defense antagonists.

Antimicrobial or host defense peptides are innate immune regulators found in all multicellular organisms. Many of them fold into membrane-bound α-helices and function by causing cell wall disruption in microorganisms. Herein we probe the possibility and functional implications of antimicrobial antagonism mediated by complementary coiled-coil interactions between antimicrobial peptides and de novo designed antagonists: anti-antimicrobial peptides. Using sequences from native helical families such as cathelicidins, cecropins, and magainins we demonstrate that designed antagonists can co-fold with antimicrobial peptides into functionally inert helical oligomers. The properties and function of the resulting assemblies were studied in solution, membrane environments, and in bacterial culture by a combination of chiroptical and solid-state NMR spectroscopies, microscopy, bioassays, and molecular dynamics simulations. The findings offer a molecular rationale for anti-antimicrobial responses with potential implications for antimicrobial resistance.

Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers.

Antimicrobial peptides are postulated to disrupt microbial phospholipid membranes. The prevailing molecular model is based on the formation of stable or transient pores although the direct observation of the fundamental processes is lacking. By combining rational peptide design with topographical (atomic force microscopy) and chemical (nanoscale secondary ion mass spectrometry) imaging on the same samples, we show that pores formed by antimicrobial peptides in supported lipid bilayers are not necessarily limited to a particular diameter, nor they are transient, but can expand laterally at the nano-to-micrometer scale to the point of complete membrane disintegration. The results offer a mechanistic basis for membrane poration as a generic physicochemical process of cooperative and continuous peptide recruitment in the available phospholipid matrix.

Crown Graphene Nanomeshes: Highly Stable Chelation-Doped Semiconducting Materials.

Graphene nanomeshes (GNMs) formed by the creation of pore superlattices in graphene are a possible route to graphene-based electronics due to their semiconducting properties, including the emergence of fractional electronvolt band gaps. The utility of GNMs would be markedly increased if a scheme to stably and controllably dope them was developed. In this work, a chemically motivated approach to GNM doping based on selective pore-perimeter passivation and subsequent ion chelation is proposed. It is shown by first-principles calculations that ion chelation leads to stable doping of the passivated GNMs-both n- and p-doping are achieved within a rigid-band picture. Such chelated or "crown" GNM structures are stable, high mobility semiconducting materials possessing intrinsic doping-concentration control; these can serve as building blocks for edge-free graphene nanoelectronics including GNM-based complementary metal oxide semiconductor (CMOS)-type logic switches.

High response piezoelectric and piezoresistive materials for fast, low voltage switching: simulation and theory of transduction physics at the nanometer-scale.

Field effect transistors are reaching the limits imposed by the scaling of materials and the electrostatic gating physics underlying the device. In this Communication, a new type of switch based on different physics, which combines known piezoelectric and piezoresistive materials, is described and is shown by theory and simulation to achieve gigahertz digital switching at low voltage (0.1 V).

Slowing and controlling the translocation of DNA in a solid-state nanopore.

DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the solution to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using electric signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concentration or temperature. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielectric layers has been proposed as a solution. Molecular dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.

Membrane mediated regulation in free peptides of HIV-1 gp41: minimal modulation of the hemifusion phase.

Membrane-mediated structural modulation in two short fragments of the human HIV-1 envelope protein gp41 is demonstrated. Derived from the C-terminal membrane proximal external (MPE) and N-terminal fusion peptide proximal (FPP) regions, these peptides are widely separated in the primary sequence but form tertiary contacts during the intermediate (hemifusion) phase of HIV infection. The structural perturbations observed at the membrane interface offer evidence of rudimentary regulatory mechanisms operating in the free peptides which may be relevant in the biological system. No such regulatory phenomena were observed for the individual peptides in a membrane environment or between the peptides in aqueous solutions. Structure determination is made using a combination of circular and linear dichroism spectroscopy (supported by calorimetric measurements) and molecular dynamics simulations. Specifically, we show that these peptides interact locally without the conformational support of helical heptad repeat regions in native gp41 and that the modulation is not mutual with the FPP peptide operating as a primary regulator of the MPE-FPP interactions in the hemifusion phase.

Characterizing and controlling the motion of ssDNA in a solid-state nanopore.

Sequencing DNA in a synthetic solid-state nanopore is potentially a low-cost and high-throughput method. Essential to the nanopore-based DNA sequencing method is the ability to control the motion of a single-stranded DNA (ssDNA) molecule at single-base resolution. Experimental studies showed that the average translocation speed of DNA driven by a biasing electric field can be affected by ionic concentration, solvent viscosity, or temperature. Even though it is possible to slow down the average translocation speed, instantaneous motion of DNA is too diffusive to allow each DNA base to stay in front of a sensor site for its measurement. Using extensive all-atom molecular dynamics simulations, we study the diffusion constant, friction coefficient, electrophoretic mobility, and effective charge of ssDNA in a solid-state nanopore. Simulation results show that the spatial fluctuation of ssDNA in 1 ns is comparable to the spacing between neighboring nucleotides in ssDNA, which makes the sensing of a DNA base very difficult. We demonstrate that the recently proposed DNA transistor could potentially solve this problem by electrically trapping ssDNA inside the DNA transistor and ratcheting ssDNA base-by-base in a biasing electric field. When increasing the biasing electric field, we observed that the translocation of ssDNA changes from ratcheting to steady-sliding. The simulated translocation of ssDNA in the DNA transistor was theoretically characterized using Fokker-Planck analysis.

Conductance through multilayer graphene films.

The ballistic conductance through junctions between multilayer graphene films and several different metals is studied using ab initio calculations within the local density approximation. The system consists of films of up to four graphene layers (Bernal stacking) between metallic electrodes, assuming reasonable metal-graphene epitaxial relationships. For some metals, the conductance decays exponentially with increasing number of layers, while for others the conductance saturates with film thickness. This difference in asymptotic behavior stems from the crystal momentum (mis)match between the bulk Fermi-level states in the electrode and those in the film. In contrast, for sufficiently thin films the bonding between the metal and the adjacent graphene layer dominates, giving a metal dependence for graphene similar to that seen experimentally for single-wall carbon nanotubes. Among the metals considered here, we find Pd to be the best for electrodes to films with up to 4 graphene layers.

Electrochemical protection of thin film electrodes in solid state nanopores.

Solid state nanopores are a core element of next-generation single molecule tools in the field of nano-biotechnology. Thin film electrodes integrated into a pore can interact with charges and fields within the pore. In order to keep the nanopore open and thus functional electrochemically induced surface alteration of electrode surfaces and bubble formation inside the pore have to be eliminated. This paper provides electrochemical analyses of nanopores drilled into TiN membranes which in turn were employed as thin film electrodes. We studied physical pore integrity and the occurrence of water decomposition yielding bubble formation inside pores by applying voltages between -4.5 and +4.5 V to membranes in various protection stages continuously for up to 24 h. During potential application pores were exposed to selected electrolyte-solvent systems. We have investigated and successfully eliminated electrochemical pore oxidation and reduction as well as water decomposition inside nanopores of various diameters ranging from 3.5 to 25 nm in 50 nm thick TiN membranes by passivating the nanopores with a plasma-oxidized layer and using a 90% solution of glycerol in water as KCl solvent. Nanopore ionic conductances were measured before and after voltage application in order to test for changes in pore diameter due to electrochemical oxidation or reduction. TEM imaging was used to confirm these observations. While non-passivated pores were electrochemically oxidized, neither electrochemical oxidation nor reduction was observed for passivated pores. Bubble formation through water decomposition could be detected in non-passivated pores in KCl/water solutions but was not observed in 90% glycerol solutions. The use of a protective self-assembled monolayer of hexadecylphosphonic acid (HDPA) was also investigated.

Antibody recognition of a human chorionic gonadotropin epitope (hCGbeta66-80) depends on local structure retained in the free peptide.

Human chorionic gonadotropin (hCG) is an important biomarker in pregnancy and oncology, where it is routinely detected and quantified by specific immunoassays. Intelligent epitope selection is essential to achieving the required assay performance. We present binding affinity measurements demonstrating that a typical ß3-loop-specific monoclonal antibody (8G5) is highly selective in competitive immunoassays and distinguishes between hCGß(66-80) and the closely related luteinizing hormone (LH) fragment LHß(86-100), which differ only by a single amino acid residue. A combination of optical spectroscopic measurements and atomistic computer simulations on these free peptides reveals differences in turn type stabilized by specific hydrogen bonding motifs. We propose that these structural differences are the basis for the observed selectivity in the full protein.

Nonlinear screening in multilayer graphene systems.

Electrostatic screening in multilayer graphene is highly nonlinear due to the vanishing density of states at the Fermi level. Using a discrete model we study the charge screening normal to the layers. Our model shows a strong charge and temperature dependence and has a simple continuum limit at T=0 for undoped systems. Doped systems can exhibit more complex behavior due to minority-carrier screening. Most importantly we find that the screening length can vary more than an order of magnitude depending on the experimental conditions, reconciling the large range of screening lengths reported in previous experiments. This has important consequences for technological applications of multilayer graphene used in electrodes or transistor channels.