Molecular Spintronics: Spin-Dependent Electron Transport in Molecular Wires

We present a theoretical study of spin-dependent transport through molecular wires bridging ferromagnetic metal nanocontacts. We extend to magnetic systems a recently proposed model that provides a em quantitative explanation of the conductance measurements of Reed et al. on Au break-junctions bridged by self-assembled molecular monolayers (SAMs) of 1,4-benzene-dithiolate (BDT) molecules. Based on our calculations, we predict that spin-valve behavior should be observable in nickel break-junctions bridged by SAM's formed from BDT. We also consider spin transport in systems consisting of a clean ferromagnetic nickel STM tip and SAMs of benzene-thiol molecules on gold and nickel substrates. We find that spin-valve behavior should be possible for the Ni substrate. For the case where the substrate is gold, we show that it should be possible to inject a highly spin-polarized current into the substrate.Comment: 14 pages, 9 figure

Theoretical Study of Electrical Conduction Through a Molecule Connected to Metallic Nanocontacts

We present a theoretical study of electron transport through a molecule connected to two metallic nanocontacts. The system investigated is 1,4 benzene-dithiolate (BDT) chemically bonded to two Au contacts. The surface chemistry is modeled by representing the tips of the Au contacts as two atomic clusters and treating the molecule-cluster complex as a single entity in an extended Huckel tight binding scheme. We model the tips using several different cluster geometries. An ideal lead is attached to each cluster, and the lead to lead transmission is calculated. The role of the molecule-cluster interaction in transport is analyzed by using single channel leads. We then extend the calculations to multi-channel leads that are a more realistic model of the tip's environment. Using the finite-voltage, finite temperature Landauer formula, we calculate the differential conductance for the different systems studied. The similarities and differences between the predictions of the present class of models and recent experimental work are discussed.Comment: 23 pages, 11 figures, accepted PR

Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins

Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity and we quantify this by analyzing the surface exposure distributions of all amino acids. Lastly we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.Comment: 16 pages, 2 tables, 8 figure

Repatriating childhood: issues in the ethical return of Venda children's musical materials from the archival collection of John Blacking

In ethnomusicological research, children are often conceptualised as the next generation of culture bearers who must be entrusted with valuable cultural materials to be sustained into the future. This conception, whether from cultural insiders, invested outsiders, or those in-between, often positions childhood as a place for re-embedding so called ‘endangered musical traditions’. Understanding children as the next generation of culture bearers informs the ways we approach the research process surrounding the documentation, archiving, and repatriation of musical cultures

Current-Driven Conformational Changes, Charging and Negative Differential Resistance in Molecular Wires

We introduce a theoretical approach based on scattering theory and total energy methods that treats transport non-linearities, conformational changes and charging effects in molecular wires in a unified way. We apply this approach to molecular wires consisting of chain molecules with different electronic and structural properties bonded to metal contacts. We show that non-linear transport in all of these systems can be understood in terms of a single physical mechanism and predict that negative differential resistance at high bias should be a generic property of such molecular wires.Comment: 9 pages, 4 figure

Non-Equilibrium Polar Localization of Proteins in Bacterial Cells

Many proteins are observed to localize to the poles within bacterial cells. Some bacteria show unipolar localization, yet under different conditions bipolar patterns can emerge. One mechanism for spontaneous polar localization has been shown to involve the combination of protein aggregation and nucleoid occlusion. Whether the different observed patterns represent global energy minima for the cellular system remains to be determined. In this paper we show that for a model consisting only of protein aggregation along with an excluded volume effect due to the DNA polymer, that unipolar patterns are the global energy ground state regardless of protein concentration and DNA density. We extend the model to allow for proteins to be added to the cellular volume at a constant rate and show that bipolar (or multi-foci) patterns emerge as the result of the system being kinetically trapped in a local energy minimum. Lastly we also consider the situation of a growing cell that starts with a pre-existing aggregate at one of the poles and determine conditions under which either unipolar or bipolar patterns can exist at the point when it is ready to divide. This work sheds new interpretations on recently published experimental data and suggests experiments to test whether such a mechanism can drive patterning in bacteria

Operational Principles for the Dynamics of the In Vitro ParA-ParB System

In many bacteria the ParA-ParB protein system is responsible for actively segregating DNA during replication. ParB proteins move by interacting with DNA bound ParA-ATP, stimulating their unbinding by catalyzing hydrolysis, that leads to rectified motion due to the creation of a wake of depleted ParA. Recent in vitro experiments have shown that a ParB covered magnetic bead can move with constant speed over a DNA covered substrate that is bound by ParA. It has been suggested that the formation of a gradient in ParA leads to diffusion-ratchet like motion of the ParB bead but how it forms and generates a force is still a matter of exploration. Here we develop a deterministic model for the in vitro ParA-ParB system and show that a ParA gradient can spontaneously form due to any amount of initial spatial noise in bound ParA. The speed of the bead is independent of this noise but depends on the ratio of the range of ParA-ParB force on the bead to that of removal of surface bound ParA by ParB. We find that at a particular ratio the speed attains a maximal value. We also consider ParA rebinding (including cooperativity) and ParA surface diffusion independently as mechanisms for ParA recovery on the surface. Depending on whether the DNA covered surface is undersaturated or saturated with ParA, we find that the bead can accelerate persistently or potentially stall. Our model highlights key requirements of the ParA-ParB driving force that are necessary for directed motion in the in vitro system that may provide insight into the in vivo dynamics of the ParA-ParB system

A Model for Cell Population Size Control Using Asymmetric Division

In multicellular organisms one can find examples where a growing tissue divides up until some final fixed cell number. Asymmetric division plays a prevalent feature in tissue differentiation in these organisms, where the daughters of each asymmetric division inherit unequal amounts of a fate determining molecule and as a result follow different developmental fates. In some tissues the accumulation or decrease of cell cycle regulators acts as an intrinsic timing mechanism governing proliferation. Here we present a minimal model based on asymmetric division and dilution of a cell-cycle regulator that can generate any final population size that might be needed. We show that within the model there are a variety of growth mechanisms from linear to non-linear that can lead to the same final cell count. Interestingly, when we include noise at division we find that there are special final cell population sizes that can be generated with high confidence that are flanked by population sizes that are less robust to division noise. When we include further perturbations in the division process we find that these special populations can remain relatively stable and in some cases even improve in their fidelity