QMCPACK: Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion quantum Monte Carlo.

We review recent advances in the capabilities of the open source ab initio Quantum Monte Carlo (QMC) package QMCPACK and the workflow tool Nexus used for greater efficiency and reproducibility. The auxiliary field QMC (AFQMC) implementation has been greatly expanded to include k-point symmetries, tensor-hypercontraction, and accelerated graphical processing unit (GPU) support. These scaling and memory reductions greatly increase the number of orbitals that can practically be included in AFQMC calculations, increasing the accuracy. Advances in real space methods include techniques for accurate computation of bandgaps and for systematically improving the nodal surface of ground state wavefunctions. Results of these calculations can be used to validate application of more approximate electronic structure methods, including GW and density functional based techniques. To provide an improved foundation for these calculations, we utilize a new set of correlation-consistent effective core potentials (pseudopotentials) that are more accurate than previous sets; these can also be applied in quantum-chemical and other many-body applications, not only QMC. These advances increase the efficiency, accuracy, and range of properties that can be studied in both molecules and materials with QMC and QMCPACK.

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions.

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces.

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions, and superconducting ground states. In contrast, few of these phenomena have been observed in low-dimensional molecular structures, including thin films, nanoparticles, and molecular blends, not in the least because most of such structures have been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional ionic molecular structures that can capture potential applications. Here, we present detailed analysis of monolayer-thick structures of the canonical TTF-TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctive property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of a 1:1 ratio in the bulk. We propose the existence of the surface phase diagram that controls the structures of TTF-TCNQ on the surfaces and demonstrate phase transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram, and the corresponding phase transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases.

Interplay of Bias-Driven Charging and the Vibrational Stark Effect in Molecular Junctions.

We observe large, reversible, bias driven changes in the vibrational energies of PCBM based on simultaneous transport and surface-enhanced Raman spectroscopy (SERS) measurements on PCBM-gold junctions. A combination of linear and quadratic shifts in vibrational energies with voltage is analyzed and compared with similar measurements involving C60-gold junctions. A theoretical model based on density functional theory (DFT) calculations suggests that both a vibrational Stark effect and bias-induced charging of the junction contribute to the shifts in vibrational energies. In the PCBM case, a linear vibrational Stark effect is observed due to the permanent electric dipole moment of PCBM. The vibrational Stark shifts shown here for PCBM junctions are comparable to or larger than the charging effects that dominate in C60 junctions.

Voltage tuning of vibrational mode energies in single-molecule junctions.

Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been used to manipulate electronic structure and related functional properties of molecules, electrical control of vibrational mode energies has remained elusive. Here we use simultaneous transport and surface-enhanced Raman spectroscopy measurements to demonstrate large, reversible, voltage-driven shifts of vibrational mode energies of C60 molecules in gold junctions. C60 mode energies are found to vary approximately quadratically with bias, but in a manner inconsistent with a simple vibrational Stark effect. Our theoretical model instead suggests that the mode shifts are a signature of bias-driven addition of electronic charge to the molecule. These results imply that voltage-controlled tuning of vibrational modes is a general phenomenon at metal-molecule interfaces and is a means of achieving significant shifts in vibrational energies relative to a pure Stark effect.

Using Molecular Design to Control the Performance of Hydrogen-Producing Polymer-Brush-Modified Photocathodes.

Attachment of difluoroborylcobaloxime catalysts to a polymer-brush-modified GaP semiconductor allows improved hydrogen production levels and photoelectrochemical performance under aqueous acidic conditions (pH = 4.5) as compared to the performance of electrodes without catalyst treatment. The catalytic assembly used in this work incorporates a boron difluoride (BF2) capping group on the glyoximate ligand of the catalyst, a synthetic modification previously used to enhance the stability of nonsurface-attached complexes toward acid hydrolysis and to shift the cobalt reduction potentials of the complex to less negative, and thus technologically more relevant, values. The pH-dependent photoresponses of the cobaloxime- and difluoroborylcobaloxime- modified semiconductors are shown to be consistent with those from analogous studies using non-surface-attached cobaloxime catalysts as well as catalysts supported on conductive electrodes. Thus, this work illustrates the potential to control and optimize the properties of visible-light-absorbing semiconductors using polymeric overcoating techniques coupled with the principles of synthetic molecular design.

Theory of Covalent Adsorbate Frontier Orbital Energies on Functionalized Light-Absorbing Semiconductor Surfaces.

Functional hybrid interfaces between organic molecules and semiconductors are central to many emerging information and solar energy conversion technologies. Here we demonstrate a general, empirical parameter-free approach for computing and understanding frontier orbital energies - or redox levels - of a broad class of covalently bonded organic-semiconductor surfaces. We develop this framework in the context of specific density functional theory (DFT) and many-body perturbation theory calculations, within the GW approximation, of an exemplar interface, thiophene-functionalized silicon (111). Through detailed calculations taking into account structural and binding energetics of mixed-monolayers consisting of both covalently attached thiophene and hydrogen, chlorine, methyl, and other passivating groups, we quantify the impact of coverage, nonlocal polarization, and interface dipole effects on the alignment of the thiophene frontier orbital energies with the silicon band edges. For thiophene adsorbate frontier orbital energies, we observe significant corrections to standard DFT (∼1 eV), including large nonlocal electrostatic polarization effects (∼1.6 eV). Importantly, both results can be rationalized from knowledge of the electronic structure of the isolated thiophene molecule and silicon substrate systems. Silicon band edge energies are predicted to vary by more than 2.5 eV, while molecular orbital energies stay similar, with the different functional groups studied, suggesting the prospect of tuning energy alignment over a wide range for photoelectrochemistry and other applications.

The nature of transport variations in molecular heterojunction electronics.

Transport fluctuations and variations in a series of metal-molecule-metal junctions were quantified through measurements of their thermopower. Thiol bound aromatic molecules of various lengths and degrees of freedom were chosen to understand the magnitude and origins of the variations. Junction thermopower was determined by measuring the voltage difference across molecules trapped between two gold contacts held at different temperatures. While any given measurement was remarkably stable, the breadth of distributions from repeated measurements implies variations in the offset of the highest occupied molecular orbital (HOMO) relative to the Fermi Energy of the contacts, similar in magnitude to the nominal offset itself. Statistical analysis of data shows that these variations are born at the junction formation, increase with molecular length, and are dominated by variations in contact geometry and orbital hybridization, as well as intermolecular interactions.

Identifying the length dependence of orbital alignment and contact coupling in molecular heterojunctions.

Transport in metal-molecule-metal junctions is defined by the alignment and coupling of molecular orbitals with continuum electronic states in the metal contacts. Length-dependent changes in molecular orbital alignment and coupling with contact states were probed via measurements and comparisons of thermopower (S) of a series of phenylenes and alkanes with varying binding groups. S increases linearly with length for phenylenediames and phenylenedithiols while it decreases linearly in alkanedithiols. Comparison of these data suggests that the molecular backbone determines the length dependence of S, while the binding group determines the zero length or contact S. Transport in phenylenes was dominated by the highest occupied molecular orbital (HOMO), which aligns closer to the Fermi energy of the contacts as approximately L(-1), but becomes more decoupled from them as approximately e(-L). In contrast, the decreasing trend in S for alkanedithiols suggests that transmission is largely affected by gold-sulfur metal induced gap states residing between the HOMO and lowest unoccupied molecular orbital.

Probing the chemistry of molecular heterojunctions using thermoelectricity.

Thermopower measurements offer an alternative transport measurement that can characterize the dominant transport orbital and is independent of the number of molecules in the junction. This method is now used to explore the effect of chemical structure on the electronic structure and charge transport. We interrogate junctions, using a modified scanning tunneling microscope break junction technique, where: (i) the 1,4-benzenedithiol (BDT) molecule has been modified by the addition of electron-withdrawing or -donating groups such as fluorine, chlorine, and methyl on the benzene ring; and (ii) the thiol end groups on BDT have been replaced by the cyanide end groups. Cyanide end groups were found to radically change transport relative to BDT such that transport is dominated by the lowest unoccupied molecular orbital in 1,4-benzenedicyanide, while substituents on BDT generated small and predictable changes in transmission.

Racemic single-walled carbon nanotubes exhibit circular dichroism when wrapped with DNA.

We have found that racemic mixtures of chiral single-walled nanotubes (SWNTs) wrapped with d(GT)20 DNA oligomer exhibit circular dichroism (CD). We attribute the CD signal to induced CD arising from the coupling of transition moments of the SWNTs and the DNA. Although the nanotube mixture appears to contain both enantiomers in equal amounts, DNA-SWNT transition moment interaction is more constructive for one SWNT enantiomer over the other, resulting in an overall CD signal.