Mobile linkers on DNA-coated colloids: valency without patches.

Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal "molecules." However, in order to design DNACC-based molecules, we must be able to control the valency of the colloids, i.e., the number of partners to which a given DNACC can bind. One obvious, but not very simple approach is to decorate the colloidal surface with patches of single-stranded DNA that selectively bind those on other colloids. Here we propose a design principle that exploits many-body effects to control the valency of otherwise isotropic colloids. Using a combination of theory and simulation, we show that we can tune the valency of colloids coated with mobile ssDNA, simply by tuning the nonspecific repulsion between the particles. Our simulations show that the resulting effective interactions lead to low-valency colloids self-assembling in peculiar open structures, very different from those observed in DNACCs with immobile DNA linkers.This is the author's accepted manuscript. The final version is published by APS in Physical Review Letters (http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.128303)

Theory and simulation of DNA-coated colloids: a guide for rational design.

By exploiting the exquisite selectivity of DNA hybridization, DNA-coated colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptor are used to control interactions.This is the final version of the article. It first appeared from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C5CP06981

Communication: Free energy of ligand-receptor systems forming multimeric complexes.

Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson and Tkachenko [J. Chem. Phys. 144, 094903 (2016)], both featuring functionalized Brownian particles interacting via three-linker complexes.LDM and LP acknowledge support from the EPSRC Programme Grant CAPITALS number EP/J017566/1. LDM acknowledges support from the Oppenheimer Fund and Emmanuel College Cambridge. SB and BMM are supported by the Universit´e Libre de Bruxelles (ULB)

A general theory of DNA-mediated and other valence-limited interactions

We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and combinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations. With suitable approximations and in particular geometries, our theory reduces to previous successful treatments, which are now united in a common and extensible framework. We expect our tools to be useful to other researchers investigating ligand-mediated interactions. A complete and well-documented Python implementation is freely available at http://github.com/patvarilly/DNACC .Comment: 18 pages, 10 figure

Designing stimulus-sensitive colloidal walkers.

Colloidal particles with DNA "legs" that can bind reversibly to receptors on a surface can be made to 'walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how controllable parameters, e.g. coating density and binding strength, affect the dynamics of such colloids. We find that competition between thermodynamic and kinetic trends imply that there is an optimal value for both the binding strength and the number of "legs" for which transport is the fastest. Using available thermodynamic data on DNA binding, we indicate how directionally reversible, temperature-controlled transport of colloidal walkers can be achieved. In particular, the present results should make it possible to design a chromatographic technique that can be used to separate colloids with different DNA functionalizations

A new configurational bias scheme for sampling supramolecular structures.

This is the author accepted manuscript. The final version is available from the American Institute of Physics via http://dx.doi.org/10.1063/1.4904727We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand-receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking

Captura massal da mosca-das-frutas sul-americana Anastrepha fraterculus (Diptera: Tephritidae) como estratégia para a supressão populacional em cultivo protegido de uva fina de mesa.

O Sul do Brasil é a principal região produtora de frutas de clima temperado (FACHINELLO et al., 2011; IBGE, 2017). No Rio Grande do Sul, merece destaque o cultivo de uvas para processamento, principalmente na região da Serra Gaúcha, RS (MELLO, 2016; IBGE, 2017).bitstream/item/163950/1/CircTec136.pd

Maize-Urochloa grass intercropping: an option for improving sustainable agriculture in the Brazilian Savannah.

Intercropping annual cash crops with grasses is a strategy that promotes both diversification and intensification of production in the same area, contributing to sustainable food systems. This study evaluated the impact of intercropping maize with different Urochloa species on maize and subsequent soybean yields over three years in the Brazilian Savannah. The treatments included: (1) maize monoculture; (2) maize intercropped with Urochloa ruziziensis; (3) maize intercropped with U. brizantha cv. Marandu; and (4) maize intercropped with U. brizantha cv. BRS Paiaguás. The evaluations included maize grain yield, land equivalent ratio (LER), forage biomass and soybean yield in succession. The results confirmed that maize intercropped with U. brizantha cv. Marandu and U. brizantha cv. BRS Paiaguás achieved grain yields comparable to monoculture. Demonstrating that these forage species do not significantly compete with maize in 2018 and 2019 in Montividiu and 2018 and 2020 in Rio Verde. In Montividiu, intercropping with U. brizantha cv. BRS Paiaguás resulted in an average LER of 1.13 over three years, highlighting its advantage in optimising land use. In addition, the intercropping system was particularly beneficial in sandy soils, where faster biomass decomposition accelerated improvements in soil structure, moisture retention, and nutrient availability, leading to earlier benefits in soybeans grain yield compared to clay soils. These findings emphasise the potential of maize-forage intercropping to enhance land-use efficiency and soil health while maintaining crop yields in tropical agroecosystems. However, site-specific management is essential to maximise benefits and minimise trade-offs. Future research should focus on long-term soil health dynamics and refining intercropping strategies to improve sustainability in different environmental conditions