Towfiq Ahmed

Electronic Fingerprints of DNA Bases on Graphene

We calculate the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T), deposited on graphene. We observe significant base-dependent features in the LDOS in an energy range within a few electronvolts of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases in scanning tunneling spectroscopy (STS) experiments that perform image and site dependent spectroscopy on biomolecules. Thus the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS.

Phonon Mode Transformation Across the Orthohombic–Tetragonal Phase Transition in a Lead Iodide Perovskite CH3NH3PbI3: A Terahertz Time-Domain Spectroscopy Approach

We study the temperature-dependent phonon modes of the organometallic lead iodide perovskite CH3NH3PbI3 thin film across the terahertz (0.5-3 THz) and temperature (20-300 K) ranges. These modes are related to the vibration of the Pb-I bonds. We found that two phonon modes in the tetragonal phase at room temperature split into four modes in the low-temperature orthorhombic phase. By use of the Lorentz model fitting, we analyze the critical behavior of this phase transition. The carrier mobility values calculated from the low-temperature phonon mode frequencies, via two theoretical approaches, are found to agree reasonably with the experimental value (∼2000 cm(2) V(-1) s(-1)) from a previous time-resolved THz spectroscopy work. Thus, we have established a possible link between terahertz phonon modes and the transport properties of perovskite-based solar cells.

Role of scaffold network in controlling strain and functionalities of nanocomposite films

The tuning of functional properties in thick oxide films via nanoscaffolds induced large vertical lattice strain. Strain is a novel approach to manipulating functionalities in correlated complex oxides. However, significant epitaxial strain can only be achieved in ultrathin layers. We show that, under direct lattice matching framework, large and uniform vertical strain up to 2% can be achieved to significantly modify the magnetic anisotropy, magnetism, and magnetotransport properties in heteroepitaxial nanoscaffold films, over a few hundred nanometers in thickness. Comprehensive designing principles of large vertical strain have been proposed. Phase-field simulations not only reveal the strain distribution but also suggest that the ultimate strain is related to the vertical interfacial area and interfacial dislocation density. By changing the nanoscaffold density and dimension, the strain and the magnetic properties can be tuned. The established correlation among the vertical interface—strain—properties in nanoscaffold films can consequently be used to tune other functionalities in a broad range of complex oxide films far beyond critical thickness.

Optical properties of organometallic perovskite: An ab initio study using relativistic GW correction and Bethe-Salpeter equation

In the development of highly efficient photovoltaic cells, solid perovskite systems have demonstrated unprecedented promise, with the figure of merit exceeding nineteen percent of efficiency. In this paper, we investigate the optical and vibrational properties of organometallic cubic perovskite CH3NH3PbI3 using first-principles calculations. For accurate theoretical description, we go beyond conventional density functional theory (DFT), and calculated optical conductivity using relativist quasi-particle (GW) correction. Incorporating these many-body effects, we further solve Bethe-Salpeter equations (BSE) for excitons, and found enhanced optical conductivity near the gap edge. Due to the presence of organic methylammonium cations near the center of the perovskite cell, the system is sensitive to low energy vibrational modes. We estimate the phonon modes of CH3NH3PbI3 using small displacement approach, and further calculate the infrared absorption (IR) spectra. Qualitatively, our calculations of low-energy phonon frequencies are in good agreement with our terahertz measurements. Therefore, for both energy scales (around 2 eV and 0-20 meV), our calculations reveal the importance of many-body effects and their contributions to the desirable optical properties in the cubic organometallic perovskites system.

Next-Generation Epigenetic Detection Technique: Identifying Methylated Cytosine Using Graphene Nanopore.

DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, the location and dynamics of methylation have been very precisely pinned down with the 5-cytosine markers on cytosine-phosphate-guanine (CpG) units. Unusual methylation on CpG islands is identified as one of the prime causes for silencing the tumor suppressant genes. Early detection of methylation changes can diagnose the potentially harmful oncogenic evolution of cells and provide promising guideline for cancer prevention. With this motivation, we propose a cytosine methylation detection technique. Our hypothesis is that electronic signatures of DNA acquired as a molecule translocates through a nanopore would be significantly different for methylated and nonmethylated bases. This difference in electronic fingerprints would allow for reliable real-time differentiation of methylated DNA. We calculate transport currents through a punctured graphene membrane while the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyanocytosine for comparison. Our calculations of transmission, current, and tunneling conductance show distinct signatures in their spectrum for each molecular type. Thus, in this work, we provide a theoretical analysis that points to a viability of our hypothesis.

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered graphene-based nanopore device architecture for the recognition of single DNA bases. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to∗To whom correspondence should be addressed †Theoretical Division, Los Alamos National Laboratory ‡Department of Physics and Astronomy, James Madison University ¶Department of Physics, University of Washington §Department of Physics, University of California, San Diego ‖Nordita Roslagstullsbacken 23, 106 91 Stockholm Sweden ⊥Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 #Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 noise ratio and the accuracy, we implement a new ”multi-point cross-correlation” technique for identification of DNA bases or other molecules on the molecular level. we demonstrate that the crosscorrelations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multi-layered graphene nanopore system to illustrate the advantages of proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

Proximity-induced magnetism in transition-metal substituted graphene

We investigate the interactions between two identical magnetic impurities substituted into a graphene superlattice. Using a first-principles approach, we calculate the electronic and magnetic properties for transition-metal substituted graphene systems with varying spatial separation. These calculations are compared for three different magnetic impurities, manganese, chromium, and vanadium. We determine the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, as well as calculate the exchange parameter between the two magnetic atoms as a function of spatial separation. We find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, where the interactions are highly dependent on the spatial and magnetic characteristic between the magnetic and carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, through an analysis of the calculated exchange energies and partial density of states, it is determined that interactions between the magnetic atoms can be classified as an RKKY interaction.

Synthetic magnetoelectric coupling in a nanocomposite multiferroic

Given the paucity of single phase multiferroic materials (with large ferromagnetic moment), composite systems seem an attractive solution to realize magnetoelectric coupling between ferromagnetic and ferroelectric order parameters. Despite having antiferromagnetic order, BiFeO3 (BFO) has nevertheless been a key material due to excellent ferroelectric properties at room temperature. We studied a superlattice composed of 8 repetitions of 6 unit cells of La0.7Sr0.3MnO3 (LSMO) grown on 5 unit cells of BFO. Significant net uncompensated magnetization in BFO, an insulating superlattice, is demonstrated using polarized neutron reflectometry. Remarkably, the magnetization enables magnetic field to change the dielectric properties of the superlattice, which we cite as an example of synthetic magnetoelectric coupling. Importantly, controlled creation of magnetic moment in BFO is a much needed path toward design and implementation of integrated oxide devices for next generation magnetoelectric data storage platforms.

First-Principles Investigation of Nanopore Sequencing Using Variable Voltage Bias on Graphene-Based Nanoribbons

In this study, we examine the mechanism of nanopore-based DNA sequencing using a voltage bias across a graphene nanoribbon. Using density function theory and a nonequilibrium Greens function approach, we determine the transmission spectra and current profile for adenine, guanine, cytosine, thymine, and uracil as a function of bias voltage in an energy minimized configuration. Utilizing the transmission current, we provide a general methodology for the development of a three nanopore graphene-based device that can be used to distinguish between the various nucleobases for DNA/RNA sequencing. From our analysis, we deduce that it is possible to use different transverse currents across a multinanopore device to differentiate between nucleobases using various voltages of 0.5, 1.3, and 1.6 V. Overall, our goal is to improve nanopore design to further DNA/RNA nucleobase sequencing and biomolecule identification techniques.

Magnetic, electronic, and optical properties of double perovskite Bi2FeMnO6

Double perovskite Bi2FeMnO6 is a potential candidate for the single-phase multiferroic system. In this work, we study the magnetic, electronic, and optical properties in BFMO by performing the density functional theory calculations and experimental measurements of magnetic moment. We also demonstrate the strain dependence of magnetization. More importantly, our calculations of electronic and optical properties reveal that the onsite local correlation on Mn and Fe sites is critical to the gap opening in BFMO, which is a prerequisite condition for the ferroelectric ordering. Finally, we calculate the x-ray magnetic circular dichroism spectra of Fe and Mn ions (L2 and L3 edges) in BFMO.