FeCoCp3 Molecular Magnets as Spin Filters

Metallorganic molecules have been proposed as excellent spin filters in molecular spintronics because of the large spin-polarization of their electronic structure. However, most of the studies involving spin transport, have disregarded fundamental aspects such as the magnetic anisotropy of the molecule and the excitation of spin-flip processes during electron transport. Here, we study a molecule containing a Co and an Fe atoms stacked between three cyclopentadienyl rings that presents a large magnetic anisotropy and a S=1. These figures are superior to other molecules with the same transition metal, and improves the spin-filtering capacities of the molecule. Non-equilibrium Green's functions calculations based on density functional theory predict excellent spin-filtering properties both in tunnel and contact transport regimes. However, exciting the first magnetic state drastically reduces the current's spin polarization. Furthermore, a difference of temperature between electrodes leads to strong thermoelectric effects that also suppress spin polarization. Our study shows that in-principle good molecular candidates for spintronics need to be confronted with inelastic and thermoelectric effects

Sociobiological Control of Plasmid copy number

Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer simulation model.

Model:
Our multilevel selection model assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication regulation can act as a “cheater” or “selfish” plasmid and can enjoy a greater within-host-fitness. However the host of a cheater plasmid has to pay a greater cost. As a result, in host level competition, host cell with low copy number plasmid has a greater fitness. Furthermore, another mutant that has lost the genes required for conjugation was introduced in the model. The non-conjugal mutant was assumed to undergo conjugal transfer in the presence of another conjugal plasmid in the host cell.

Results:
The simulatons showed that if the cost of carrying a plasmid was low, the copy-up mutant could drive the wild type to extinction or very low frequencies. Consequently, another mutant with a higher copy number could invade the first invader. This process could result into an increasing copy number. However above a certain copy number within-host selection was overcompensated by host level selection leading to a rock-paper-scissor (RPS) like situation. The RPS situation allowed the coexistence of high and low copy number plasmids. The non-conjugal “hypercheaters” could further arrest the copy numbers to a substantially lower level.

Conclusions:
These sociobiological interactions might explain the stability of copy numbers better than molecular mechanisms of replication regulation alone

Efficiency of Energy Conversion in Thermoelectric Nanojunctions

Using first-principles approaches, this study investigated the efficiency of energy conversion in nanojunctions, described by the thermoelectric figure of merit $ZT$. We obtained the qualitative and quantitative descriptions for the dependence of $ZT$ on temperatures and lengths. A characteristic temperature: $T_{0}= \sqrt{\beta/\gamma(l)}$ was observed. When $T\ll T_{0}$, $ZT\propto T^{2}$. When $T\gg T_{0}$, $ZT$ tends to a saturation value. The dependence of $ZT$ on the wire length for the metallic atomic chains is opposite to that for the insulating molecules: for aluminum atomic (conducting) wires, the saturation value of $ZT$ increases as the length increases; while for alkanethiol (insulating) chains, the saturation value of $ZT$ decreases as the length increases. $ZT$ can also be enhanced by choosing low-elasticity bridging materials or creating poor thermal contacts in nanojunctions. The results of this study may be of interest to research attempting to increase the efficiency of energy conversion in nano thermoelectric devices.Comment: 2 figure

The number of transmission channels through a single-molecule junction

We calculate transmission eigenvalue distributions for Pt-benzene-Pt and Pt-butadiene-Pt junctions using realistic state-of-the-art many-body techniques. An effective field theory of interacting $\pi$-electrons is used to include screening and van der Waals interactions with the metal electrodes. We find that the number of dominant transmission channels in a molecular junction is equal to the degeneracy of the molecular orbital closest to the metal Fermi level.Comment: 9 pages, 8 figure

Heat dissipation in atomic-scale junctions

Atomic and single-molecule junctions represent the ultimate limit to the miniaturization of electrical circuits. They are also ideal platforms to test quantum transport theories that are required to describe charge and energy transfer in novel functional nanodevices. Recent work has successfully probed electric and thermoelectric phenomena in atomic-scale junctions. However, heat dissipation and transport in atomic-scale devices remain poorly characterized due to experimental challenges. Here, using custom-fabricated scanning probes with integrated nanoscale thermocouples, we show that heat dissipation in the electrodes of molecular junctions, whose transmission characteristics are strongly dependent on energy, is asymmetric, i.e. unequal and dependent on both the bias polarity and the identity of majority charge carriers (electrons vs. holes). In contrast, atomic junctions whose transmission characteristics show weak energy dependence do not exhibit appreciable asymmetry. Our results unambiguously relate the electronic transmission characteristics of atomic-scale junctions to their heat dissipation properties establishing a framework for understanding heat dissipation in a range of mesoscopic systems where transport is elastic. We anticipate that the techniques established here will enable the study of Peltier effects at the atomic scale, a field that has been barely explored experimentally despite interesting theoretical predictions. Furthermore, the experimental advances described here are also expected to enable the study of heat transport in atomic and molecular junctions, which is an important and challenging scientific and technological goal that has remained elusive.Comment: supporting information available in the journal web site or upon reques

Effect of Thermoelectric Cooling in Nanoscale Junctions

We propose a thermoelectric cooling device based on an atomic-sized junction. Using first-principles approaches, we investigate the working conditions and the coefficient of performance (COP) of an atomic-scale electronic refrigerator where the effects of phonon's thermal current and local heating are included. It is observed that the functioning of the thermoelectric nano-refrigerator is restricted to a narrow range of driving voltages. Compared with the bulk thermoelectric system with the overwhelmingly irreversible Joule heating, the 4-Al atomic refrigerator has a higher efficiency than a bulk thermoelectric refrigerator with the same $ZT$ due to suppressed local heating via the quasi-ballistic electron transport and small driving voltages. Quantum nature due to the size minimization offered by atomic-level control of properties facilitates electron cooling beyond the expectation of the conventional thermoelectric device theory.Comment: 8 figure

The Influence of Molecular Adsorption on Elongating Gold Nanowires

Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remains relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains and helical structures possessing mechanical stability in excess of what we observe in vacuum. Conversely, we find that a molecular species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry

Electrical resistance: an atomistic view

This tutorial article presents a "bottom-up" view of electrical resistance starting from something really small, like a molecule, and then discussing the issues that arises as we move to bigger conductors. Remarkably, no serious quantum mechanics is needed to understand electrical conduction through something really small, except for unusual things like the Kondo effect that are seen only for a special range of parameters. This article starts with energy level diagrams (section 2), shows that the broadening that accompanies coupling limits the conductance to a maximum of q^2/h per level (sections 3, 4), describes how a change in the shape of the self-consistent potential profile can turn a symmetric current-voltage characteristic into a rectifying one (sections 5, 6), shows that many interesting effects in molecular electronics can be understood in terms of a simple model (section 7), introduces the non-equilibrium Green function (NEGF) formalism as a sophisticated version of this simple model with ordinary numbers replaced by appropriate matrices (section 8) and ends with a personal view of unsolved problems in the field of nanoscale electron transport (section 9). Appendix A discusses the Coulomb blockade regime of transport, while appendix B presents a formal derivation of the NEGF equations. MATLAB codes for numerical examples are listed in the appendix C

Highly Conducting pi-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ resulting in formation of a direct covalent sigma bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated pi-system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the pi-system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G0 = 2e2/h). Junctions formed with methylene terminated oligophenyls with two to four phenyl units show a hundred-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling as they exhibit an exponential dependence of conductance with oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission with a cross-over to tunneling for the longer oligomers.Comment: Accepted to the Journal of the American Chemical Society as a Communication

Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar.Comment: To appear in ACS Nano, 30 pages, 5 figure