Andrew J. Spakowitz

Selective dispersion of high purity semiconducting single-walled carbon nanotubes with regioregular poly(3-alkylthiophene)s

Conjugated polymers, such as polyfluorene and poly(phenylene vinylene), have been used to selectively disperse semiconducting single-walled carbon nanotubes (sc-SWNTs), but these polymers have limited applications in transistors and solar cells. Regioregular poly(3-alkylthiophene)s (rr-P3ATs) are the most widely used materials for organic electronics and have been observed to wrap around SWNTs. However, no sorting of sc-SWNTs has been achieved before. Here we report the application of rr-P3ATs to sort sc-SWNTs. Through rational selection of polymers, solvent and temperature, we achieved highly selective dispersion of sc-SWNTs. Our approach enables direct film preparation after a simple centrifugation step. Using the sorted sc-SWNTs, we fabricate high-performance SWNT network transistors with observed charge-carrier mobility as high as 12 cm(2) V(-1) s(-1) and on/off ratio of >10(6). Our method offers a facile and a scalable route for separating sc-SWNTs and fabrication of electronic devices.

Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci

Chromosomal loci jiggle in place between segregation events in prokaryotic cells and during interphase in eukaryotic nuclei. This motion seems random and is often attributed to Brownian motion. However, we show here that locus dynamics in live bacteria and yeast are sensitive to metabolic activity. When ATP synthesis is inhibited, the apparent diffusion coefficient decreases, whereas the subdiffusive scaling exponent remains constant. Furthermore, the magnitude of locus motion increases more steeply with temperature in untreated cells than in ATP-depleted cells. This “superthermal” response suggests that untreated cells have an additional source of molecular agitation, beyond thermal motion, that increases sharply with temperature. Such ATP-dependent fluctuations are likely mechanical, because the heat dissipated from metabolic processes is insufficient to account for the difference in locus motion between untreated and ATP-depleted cells. Our data indicate that ATP-dependent enzymatic activity, in addition to thermal fluctuations, contributes to the molecular agitation driving random (sub)diffusive motion in the living cell.

Effect of force on mononucleosomal dynamics

Using single-molecule optical-trapping techniques, we examined the force-induced dynamic behavior of a single nucleosome core particle. Our experiments using the DNA construct containing the 601 nucleosome-positioning sequence revealed that the nucleosome unravels in at least two major stages. The first stage, which we attributed to the unraveling of the first DNA wrap around the histone octamer, could be mechanically induced in a reversible manner, and when kept at constant force within a critical force range, exhibited two-state hopping behavior. From the hopping data, we determined the force-dependent equilibrium constant and rates for opening/closing of the outer wrap. Our investigation of the second unraveling event at various loading rates, which we attributed to the inner DNA wrap, revealed that this unraveling event cannot be described as a simple two-state process. We also looked at the behavior of the mononucleosome in a high-salt buffer, which revealed that the outer DNA wrap is more sensitive to changes in the ionic environment than the inner DNA wrap. These findings are needed to understand the energetics of nucleosome remodeling.

An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier

The ciliary permeability barrier is mechanistically distinct from other cellular diffusion barriers and allows soluble proteins under ∼100 kD in size to enter cilia in the absence of active transport.

Topological constraints in nucleic acid hybridization kinetics

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.

Single molecule imaging reveals a major role for diffusion in the exploration of ciliary space by signaling receptors

The dynamic organization of signaling cascades inside primary cilia is key to signal propagation. Yet little is known about the dynamics of ciliary membrane proteins besides a possible role for motor-driven Intraflagellar Transport (IFT). To characterize these dynamics, we imaged single molecules of Somatostatin Receptor 3 (SSTR3, a GPCR) and Smoothened (Smo, a Hedgehog signal transducer) in the ciliary membrane. While IFT trains moved processively from one end of the cilium to the other, single SSTR3 and Smo underwent mostly diffusive behavior interspersed with short periods of directional movements. Statistical subtraction of instant velocities revealed that SSTR3 and Smo spent less than a third of their time undergoing active transport. Finally, SSTR3 and IFT movements could be uncoupled by perturbing either membrane protein diffusion or active transport. Thus ciliary membrane proteins move predominantly by diffusion, and attachment to IFT trains is transient and stochastic rather than processive or spatially determined. DOI: http://dx.doi.org/10.7554/eLife.00654.001

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers

Significance Semiconducting polymers have promising applications in transistors, light-emitting diodes, and solar cells. These materials have microstructures that exhibit heterogeneity over multiple length scales, which obscures the relationship between properties, processing conditions, and device performance. Our work provides a theoretical framework to address the role of polymer conformations in electronic transport through disordered semiconducting polymers. We present a simple model that reconciles observations at the local scale with device-scale measurements of charge mobility (charges move quickly at short distances and slowly at long distances). The main features are the use of well-known models to describe the conformations of individual polymer chains and the inclusion of the kinetics of electronic transport between sites on a single polymer and between adjacent chains. Existing models for the electronic properties of conjugated polymers do not capture the spatial arrangement of the disordered macromolecular chains over which charge transport occurs. Here, we present an analytical and computational description in which the morphology of individual polymer chains is dictated by well-known statistical models and the electronic coupling between units is determined using Marcus theory. The multiscale transport of charges in these materials (high mobility at short length scales, low mobility at long length scales) is naturally described with our framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational variability and spatial correlation. Our model offers a predictive approach to connecting processing conditions with transport behavior.

Analytical Tools To Distinguish the Effects of Localization Error, Confinement, and Medium Elasticity on the Velocity Autocorrelation Function

Single particle tracking is a powerful technique for investigating the dynamic behavior of biological molecules. However, many of the analytical tools are prone to generate results that can lead to mistaken interpretations of the underlying transport process. Here, we explore the effects of localization error and confinement on the velocity autocorrelation function, Cυ. We show that calculation of Cυ across a range of discretizations can distinguish the effects of localization error, confinement, and medium elasticity. Thus, under certain regimes, Cυ can be used as a diagnostic tool to identify the underlying mechanism of anomalous diffusion. Finally, we apply our analysis to experimental data sets of chromosomal loci and RNA-protein particles in Escherichia coli.

Dynamic strategies for target-site search by DNA-binding proteins.

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion alone. It has been proposed that nonspecific binding aids the search by allowing proteins to slide and hop along DNA. We develop a reaction-diffusion theory of protein translocation that accounts for transport both on and off the strand and incorporates the physical conformation of DNA. For linear DNA modeled as a wormlike chain, the distribution of hops available to a protein exhibits long, power-law tails that make the long-time displacement along the strand superdiffusive. Our analysis predicts effective superdiffusion coefficients for given nonspecific binding and unbinding rate parameters. Translocation rate exhibits a maximum at intermediate values of the binding rate constant, while search efficiency is optimized at larger binding rate constant values. Thus, our theory predicts a region of values of the nonspecific binding and unbinding rate parameters that balance the protein translocation rate and the efficiency of the search. Published data for several proteins falls within this predicted region of parameter values.

Semiflexible polymer solutions. I. Phase behavior and single-chain statistics

We study the thermodynamics and single-chain statistics of wormlike polymer solutions with Maier–Saupe-type interactions using self-consistent-field (SCF) theory. The SCF equations are derived using a systematic field-theoretical approach which yields the SCF equations as the lowest order approximation, but permits fluctuation corrections to be incorporated. We solve the SCF equations using the spheroidal functions, which provides a nonperturbative description of the thermodynamics and single-chain statistics in the nematic state for arbitrary degrees of nematic order. Several types of phase diagrams are predicted, with an emphasis on the limit of metastability (spinodal) associated with each phase. The shape and location of these spinodals suggest interesting scenarios for the phase transition kinetics. A large but finite persistence length is shown to significantly decrease the isotropic–nematic transition temperature relative to that for rigid rods. In the nematic state, the mean-square end-to-end distance in the parallel and perpendicular directions are governed by two separate correlation lengths. An exact relationship between these correlation lengths and the eigenvalues of the spheroidal functions is provided, which reproduces the analytical expressions predicted from earlier studies in the limit of large nematic strength. The dominant contribution to the single-chain thermodynamics is shown to arise from small amplitude undulations in the directions perpendicular to the nematic direction; the presence of hairpins, though crucial for determining the dimensions of the polymer, has insignificant consequences on the single-chain thermodynamics.