A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent.

Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.

Half-integer anomalous currents in 2D materials from a QFT viewpoint.

Charge carriers in Dirac/Weyl semi-metals exhibit a relativistic-like behavior. In this work we propose a novel type of intrinsic half-integer Quantum Hall effect in 2D materials, thereby also offering a topological protection mechanism for the current. Its existence is rooted in the 2D parity anomaly, without any need for a perpendicular magnetic field. We conjecture that it may occur in disturbed honeycomb lattices where both spin degeneracy and time reversal symmetry are broken. These configurations harbor two distinct gap-opening mechanisms that, when occurring simultaneously, drive slightly different gaps in each valley, causing a net anomalous conductivity when the chemical potential is tuned to be between the distinct gaps. Some examples of promising material setups that fulfill the prerequisites of our proposal are also listed to motivate looking for the effect at the numerical and experimental level.

Quantitative comparison of Anderson impurity solvers applied to transport in quantum dots.

We study the single impurity Anderson model (SIAM) using the equations of motion method (EOM), the non-crossing approximation (NCA), the one-crossing approximation (OCA), and Wilson's numerical renormalization group (NRG). We calculate the density of states and the linear conductance focusing on their dependence on the chemical potential and on the temperature paying special attention to the Kondo and Coulomb blockade regimes for a large range of model parameters. We report that some standard approximations based on the EOM technique display a rather unexpected poor behavior in the Coulomb blockade regime even at high temperatures. Our study offers a critical comparison between the different methods as well as a detailed compilation of the shortcomings and limitations due the approximations involved in each technique, thus allowing for a cost-benefit analysis of the different solvers that considers both numerical precision and computational performance.

Revealing temozolomide resistance mechanisms via genome-wide CRISPR libraries

Glioblastoma is a severe type of brain tumor with a poor prognosis and few therapy options. Temozolomide (TMZ) is one of these options, however, with limited success, and failure is mainly due to tumor resistance. In this work, genome-wide CRISPR-Cas9 lentiviral screen libraries for gene knockout or activation were transduced in the human glioblastoma cell line, aiming to identify genes that modulate TMZ resistance. The sgRNAs enriched in both libraries in surviving cells after TMZ treatment were identified by next-generation sequencing (NGS). Pathway analyses of gene candidates on knockout screening revealed several enriched pathways, including the mismatch repair and the Sonic Hedgehog pathways. Silencing three genes ranked on the top 10 list (MSH2, PTCH2, and CLCA2) confirm cell protection from TMZ-induced death. In addition, a CRISPR activation library revealed that NRF2 and Wnt pathways are involved in TMZ resistance. Consistently, overexpression of FZD6, CTNNB1, or NRF2 genes significantly increased cell survival upon TMZ treatment. Moreover, NRF2 and related genes detected in this screen presented a robust negative correlation with glioblastoma patient survival rates. Finally, several gene candidates from knockout or activation screening are targetable by inhibitors or small molecules, and some of them have already been used in the clinic.

Bias-dependent local structure of water molecules at a metallic interface.

Understanding the local structure of water at the interfaces of metallic electrodes is a key issue in aqueous-based electrochemistry. Nevertheless a realistic simulation of such a setup is challenging, particularly when the electrodes are maintained at different potentials. To correctly compute the effect of an external bias potential applied to truly semi-infinite surfaces, we combine Density Functional Theory (DFT) and Non-Equilibrium Green's Function (NEGF) methods. This framework allows for the out-of-equilibrium calculation of forces and dynamics, and directly correlates to the chemical potential of the electrodes, which is introduced experimentally. In this work, we apply this methodology to study the electronic properties and atomic forces of a water molecule at the interface of a gold surface. We find that the water molecule tends to align its dipole moment with the electric field, and it is either repelled or attracted to the metal depending on the sign and magnitude of the applied bias, in an asymmetric fashion.

Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach.

The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green's function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.

Molecular model for hydrated biological tissues.

A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding and coupling energies, dipole moments, and vibrational frequencies. The results concerning the stability of the confined water clusters, the water-water, and water-collagen interactions were successfully correlated to some important experimental trends of normal and inflammatory tissues.

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport property calculations, that this assumption cannot be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy level positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrode separation. For the thiol junctions, we show that the conductance decreases as the electrode separation increases, whereas the opposite trend is found for the thiolate junctions. Both behaviors have been observed in experiments, therefore pointing to the possible coexistence of both thiol and thiolate junctions. Moreover, the corrected conductance values, for both thiol and thiolate, are up to two orders of magnitude smaller than those calculated with DFT-LDA. This brings the theoretical results in quantitatively good agreement with experimental data.

The effects of water molecules on the electronic and structural properties of peptide nanotubes.

The self-assembly of short amino acid chains appears to be one of the most promising strategies for the fabrication of nanostructures. Their solubility in water and the possibility of chemical modification by targeting the amino or carboxyl terminus give peptide-based nanostructures several advantages over carbon nanotube nanostructures. However, because these systems are synthesized in aqueous solution, a deeper understanding is needed on the effects of water especially with respect to the electronic, structural and transport properties. In this work, the electronic properties of L-diphenylalanine nanotubes (FF-NTs) have been studied using the Self-Consistent Charge Density-Functional-based Tight-Binding method augmented with dispersion interaction. The presence of water molecules in the central hydrophilic channel and their interaction with the nanostructures are addressed. We demonstrate that the presence of water leads to significant changes in the electronic properties of these systems decreasing the band gap which can lead to an increase in the hopping probability and the conductivity.

Ab initio calculations of structural evolution and conductance of benzene-1,4-dithiol on gold leads.

By performing ab initio density functional theory (DFT) calculations and electronic transport simulations based on the DFT nonequilibrium Green's functions method we investigate how the conformational changes of a benzene-1,4-dithiol molecule bonded to gold affect the molecular transport as the electrodes are separated from each other. In particular we consider the full evolution of the stretching process until the junction breaking point and compare results obtained with a standard semilocal exchange and correlation functional to those computed with a self-interaction corrected method. We conclude that the inclusion of self-interaction corrections is fundamental for describing both the molecule conductance and its stability against conformational fluctuations.