Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices

Donor−acceptor binding of the π-electron-poor cyclophane cyclobis(paraquat-p-phenylene) (CBPQT^(4+)) with the π-electron-rich tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) stations provides the basis for electrochemically switchable, bistable [2]rotaxanes, which have been incorporated and operated within solid-state devices to form ultradense memory circuits (ChemPhysChem 2002, 3, 519−525; Nature 2007, 445, 414−417) and nanoelectromechanical systems. The rate of CBPQT^(4+) shuttling at each oxidation state of the [2]rotaxane dictates critical write-and-retention time parameters within the devices, which can be tuned through chemical synthesis. To validate how well computational chemistry methods can estimate these rates for use in designing new devices, we used molecular dynamics simulations to calculate the free energy barrier for the shuttling of the CBPQT^4+ ring between the TTF and the DNP. The approach used here was to calculate the potential of mean force along the switching pathway, from which we calculated free energy barriers. These calculations find a turn-on time after the rotaxane is doubly oxidized of ~10^9−7) s (suggesting that the much longer experimental turn-on time is determined by the time scale of oxidization). The return barrier from the DNP to the TTF leads to a predicted lifetime of 2.1 s, which is compatible with experiments

Spontaneous patterning of quantum dots at the air-water interface

Nanoparticles deposited at the air-water interface are observed to form circular domains at low density and stripes at higher density. We interpret these patterns as equilibrium phenomena produced by a competition between an attraction and a longer-ranged repulsion. Computer simulations of a generic pair potential with attractive and repulsive parts of this kind, reproduce both the circular and stripe patterns. Such patterns have a potential use in nanoelectronic applications

Kinetic and Thermodynamic Approaches for the Efficient Formation of Mechanical Bonds

Among the growing collection of molecular systems under consideration for nanoscale device applications, mechanically interlocked compounds derived from electrochemically switchable bistable [2]rotaxanes and [2]catenanes show great promise. These systems demonstrate dynamic, relative movements between their components, such as shuttling and circumrotation, enabling them to serve as stimuli-responsive switches operated via reversible, electrochemical oxidation−reduction rather than through the addition of chemical reagents. Investigations into these systems have been intense for a number of years, yet limitations associated with their synthesis have hindered incorporation of their mechanical bonds into more complex architectures and functional materials. We have recently addressed this challenge by developing new template-directed synthetic protocols, operating under both kinetic and thermodynamic control, for the preparation of bistable rotaxanes and catenanes. These methodologies are compatible with the molecular recognition between the π-electron-accepting cyclobis(paraquat-p-phenylene) (CBPQT4+) host and complementary π-electron-donating guests. The procedures that operate under kinetic control rely on mild chemical transformations to attach bulky stoppering groups or perform macrocyclizations without disrupting the host−guest binding of the rotaxane or catenane precursors. Alternatively, the protocols that operate under thermodynamic control utilize a reversible ring-opening reaction of the CBPQT4+ ring, providing a pathway for two cyclic starting materials to thread one another to form more thermodynamically stable catenaned products. These complementary pathways generate bistable rotaxanes and catenanes in high yields, simplify mechanical bond formation in these systems, and eliminate the requirement that the mechanical bonds be introduced into the molecular structure in the final step of the synthesis. These new methods have already been put into practice to prepare previously unavailable rotaxane architectures and novel complex materials. Furthermore, the potential for utilizing mechanically interlocked architectures as device components capable of information storage, the delivery of therapeutic agents, or other desirable functions has increased significantly as a result of the development of these improved synthetic protocols

Juvenile gadoids habitat association and ontogenetic shift observations using stereo-video baited cameras

Understanding habitat variables affecting species distribution and survival is essential to their protection. This is especially important in areas where anthropogenic pressures can have a significant direct impact on not only the survival of the species but also damage their habitat. The Firth of Clyde, southwestern Scotland, was an important commercial fishing area for a variety demersal fish species up until 1973. However, stocks have since declined to near-zero despite fisheries measures put in place to aid recovery. Here we report on Stereo Baited Remote Underwater Video (SBRUV) surveys in the Firth of Clyde between June and September in 2013 and 2014 to determine the habitat of juvenile Atlantic cod Gadus morhua, haddock Melanogrammus aeglefinus, and whiting Merlangius merlangus. Habitat predictor variables explored included substratum type, depth, wave fetch, and bentho-demersal species diversity. G. morhua were most abundant in shallow, sheltered areas composed of gravel-pebble containing maerl. Ontogenetic shifts and density dependence were also observed. M. aeglefinus, and M. merlangus predominated over deeper sand and mud. Relative abundances of all three species were positively related to bentho-demersal diversity. This work demonstrates the potential of SBRUV as a non-destructive survey tool under northern-temperate conditions. Our results indicate that spatial conservation measures to benefit demersal fish should be advised by patterns of bentho-demersal diversity as well as physical substratum types

On the average value of divisor sums in arithmetic progressions

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in International Mathematics Research Notices. The definitive publisher-authenticated version William D. Banks, Roger Heath-Brown and Igor E. Shparlinski, On the average value of divisor sums in arithmetic progressions, Int Math Res Notices 2005 (1): 1-25, is available online at: http://imrn.oxfordjournals.org/content/2005/1/1.abstract. doi: 10.1155/IMRN.2005.1. © 2005 Hindawi Publishing Corporation.We consider very short sums of the divisor function in arithmetic progressions prime to a fixed modulus and show that "on average" these sums are close to the expected value. We also give applications of our result to sums of the divisor function twisted with characters (both additive and multiplicative) taken on the values of various functions, such as rational and exponential functions; in particular, we obtain upper bounds for such twisted sums

Class I–restricted Cross-Presentation of Exogenous Self-Antigens Leads to Deletion of Autoreactive CD8+ T Cells

In this report, we show that cross-presentation of self-antigens can lead to the peripheral deletion of autoreactive CD8+ T cells. We had previously shown that transfer of ovalbumin (OVA)-specific CD8+ T cells (OT-I cells) into rat insulin promoter–membrane-bound form of OVA transgenic mice, which express the model autoantigen OVA in the proximal tubular cells of the kidneys, the β cells of the pancreas, the thymus, and the testis of male mice, led to the activation of OT-I cells in the draining lymph nodes. This was due to class I–restricted cross-presentation of exogenous OVA on a bone marrow–derived antigen presenting cell (APC) population. Here, we show that adoptively transferred or thymically derived OT-I cells activated by cross-presentation are deleted from the peripheral pool of recirculating lymphocytes. Such deletion only required antigen recognition on a bone marrow–derived population, suggesting that cells of the professional APC class may be tolerogenic under these circumstances. Our results provide a mechanism by which the immune system can induce CD8+ T cell tolerance to autoantigens that are expressed outside the recirculation pathway of naive T cells

Crystallization of opals from polydisperse nanoparticles

We report the reversible formation of crystals of nanoparticles (opals) from solutions of polydisperse gold nanocrystals. The structures are identified by transmission electron microscopy, and are characterized by hexagonal domains of large particles at the center, surrounded radially by successively smaller particles. Simulated annealing Monte Carlo calculations are used to demonstrate that these configurations correspond to minimization of the mesoscopic van der Waals energy of polydisperse particles, and the driving force for ordering is the size dependence of dispersional attractions

Major Histocompatibility Complex Class I–restricted Cross-presentation Is Biased towards High Dose Antigens and Those Released during Cellular Destruction

Naive T cells recirculate mainly within the secondary lymphoid compartment, but once activated they can enter peripheral tissues and perform effector functions. To activate naive T cells, foreign antigens must traffic from the site of infection to the draining lymph nodes, where they can be presented by professional antigen presenting cells. For major histocompatibility complex class I–restricted presentation to CD8+ T cells, this can occur via the cross-presentation pathway. Here, we investigated the conditions allowing antigen access to this pathway. We show that the level of antigen expressed by peripheral tissues must be relatively high to facilitate cross-presentation to naive CD8+ T cells. Below this level, peripheral antigens did not stimulate by cross-presentation and were ignored by naive CD8+ T cells, although they could sensitize tissue cells for destruction by activated cytotoxic T lymphocytes (CTLs). Interestingly, CTL-mediated tissue destruction facilitated cross-presentation of low dose antigens for activation of naive CD8+ T cells. This represents the first in vivo evidence that cellular destruction can enhance access of exogenous antigens to the cross-presentation pathway. These data indicate that the cross-presentation pathway focuses on high dose antigens and those released during tissue destruction

B Cells Directly Tolerize CD8+ T Cells

This report investigates the response of CD8+ T cells to antigens presented by B cells. When C57BL/6 mice were injected with syngeneic B cells coated with the Kb-restricted ovalbumin (OVA) determinant OVA257–264, OVA-specific cytotoxic T lymphocyte (CTL) tolerance was observed. To investigate the mechanism of tolerance induction, in vitro–activated CD8+ T cells from the Kb-restricted, OVA-specific T cell receptor transgenic line OT-I (OT-I cells) were cultured for 15 h with antigen-bearing B cells, and their survival was determined. Antigen recognition led to the killing of the B cells and, surprisingly, to the death of a large proportion of the OT-I CTLs. T cell death involved Fas (CD95), since OT-I cells deficient in CD95 molecules showed preferential survival after recognition of antigen on B cells. To investigate the tolerance mechanism in vivo, naive OT-I T cells were adoptively transferred into normal mice, and these mice were coinjected with antigen-bearing B cells. In this case, OT-I cells proliferated transiently and were then lost from the secondary lymphoid compartment. These data provide the first demonstration that B cells can directly tolerize CD8+ T cells, and suggest that this occurs via CD95-mediated, activation-induced deletion