RNA secondary structure design

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called designable. We implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer whether such a sequence exists. The bound required by the branch-and-bound algorithm are calculated by a dynamic programming algorithm. We consider different alphabet sizes and an ensemble of random structures, which we want to design. We find that for two letters almost none of these structures are designable. The designability improves for the three-letter case, but still a significant fraction of structures is undesignable. This changes when we look at the natural four-letter case with two pairs of complementary bases: undesignable structures are the exception, although they still exist. Finally, we also study the relation between designability and the algorithmic complexity of the branch-and-bound algorithm. Within the ensemble of structures, a high average degree of undesignability is correlated to a long time to prove that a given structure is (un-)designable. In the four-letter case, where the designability is high everywhere, the algorithmic complexity is highest in the region of naturally occurring RNA.Comment: 11 pages, 10 figure

A fabrication guide for planar silicon quantum dot heterostructures

We describe important considerations to create top-down fabricated planar quantum dots in silicon, often not discussed in detail in literature. The subtle interplay between intrinsic material properties, interfaces and fabrication processes plays a crucial role in the formation of electrostatically defined quantum dots. Processes such as oxidation, physical vapor deposition and atomic-layer deposition must be tailored in order to prevent unwanted side effects such as defects, disorder and dewetting. In two directly related manuscripts written in parallel we use techniques described in this work to create depletion-mode quantum dots in intrinsic silicon, and low-disorder silicon quantum dots defined with palladium gates. While we discuss three different planar gate structures, the general principles also apply to 0D and 1D systems, such as self-assembled islands and nanowires.Comment: Accepted for publication in Nanotechnology. 31 pages, 12 figure

Hard superconducting gap and diffusion-induced superconductors in Ge-Si nanowires

We show a hard induced superconducting gap in a Ge-Si nanowire Josephson transistor up to in-plane magnetic fields of $250$ mT, an important step towards creating and detecting Majorana zero modes in this system. A hard induced gap requires a highly homogeneous tunneling heterointerface between the superconducting contacts and the semiconducting nanowire. This is realized by annealing devices at $180$ $^\circ$C during which aluminium inter-diffuses and replaces the germanium in a section of the nanowire. Next to Al, we find a superconductor with lower critical temperature ($T_\mathrm{C}=0.9$ K) and a higher critical field ($B_\mathrm{C}=0.9-1.2$ T). We can therefore selectively switch either superconductor to the normal state by tuning the temperature and the magnetic field and observe that the additional superconductor induces a proximity supercurrent in the semiconducting part of the nanowire even when the Al is in the normal state. In another device where the diffusion of Al rendered the nanowire completely metallic, a superconductor with a much higher critical temperature ($T_\mathrm{C}=2.9$ K) and critical field ($B_\mathrm{C}=3.4$ T) is found. The small size of diffusion-induced superconductors inside nanowires may be of special interest for applications requiring high magnetic fields in arbitrary direction

Literature review – assessing groundwater recharge estimates under conventional tillage and conservation agriculture

The purpose of this review is to identify studies from across the world that evaluated the impact of conservation agriculture (CA) on potential groundwater recharge in comparison to conventional tillage (CT), taking into consideration the techniques that have been used in measuring the soil or groundwater fluxes. In this review, we quantify case studies in which direct and indirect methods have been used to calculate a direct or proxy value of groundwater recharge under the different agricultural treatments of CA and CT. This review revealed that CA systems have the potential to improve infiltration or deep drainage and therefore potential recharge to the groundwater as evidenced by 54% of the case studies, including all studies (n=5) in the SADC region, however significant proportion of studies, mainly from the Americas and Europe, also reported either reduced potential recharge or no significant difference under different treatments. A majority of these studies used infiltration rates as a proxy. This review demonstrates that consideration on the methods used in estimating infiltration rates is important when evaluating the impact of agricultural systems on groundwater recharge in different climate zones. Issues such as the infiltration measurement technique used, timing of the measurements within the season, rainfall intensity, and soil type, are some of the parameters that must be carefully stated in studies to allow the infiltration rates within and across treatments to be comparable. The review revealed a gap in the literature for studies that used direct methods of recharge estimation to evaluate the impact of CA vs CT treatments. Unsaturated zone techniques provide only estimates of potential recharge based on drainage rates below the root zone and in some cases, drainage is diverted laterally and does not reach the water table. Use of direct methods that allow collection of data from the saturated zone such as groundwater level fluctuations in monitoring boreholes and environmental tracers such as Cl and stable isotopes of water, would be greatly beneficial to further our understanding of groundwater recharge processes beneath CA and CT systems. However, direct observations are more challenging to acquire and do have limitations

Estimation of groundwater recharge due to conservation agriculture practice

A review of groundwater recharge studies in Sub-Saharan Africa demonstrates a strong relationship between rainfall and recharge, but with considerable uncertainty due to significant impact of land cover and in particular land clearing and agriculture. This research project focuses on impacts of conservation agriculture (CA) practice on groundwater recharge. Conservation agriculture is being encouraged by governments over conventional methods in the understanding that CA practices such as minimum tillage, retention of crop residue and crop diversity improves crop resilience under dry conditions. However, there has been little consideration of the direct impact of such practices on groundwater. In this study, we setup three experimental sites in Zambia, Zimbabwe and Malawi to quantify recharge patterns under CA in comparison to conventional farming practice. Each site will be instrumented with soil moisture monitoring probes, a weather station, monitoring boreholes and electrical-resistivity tomography (ERT) equipment. Environmental isotopes and tracers (such as CFCs and SF6) and water chemistry will also be analysed. The monitoring will help to elucidate processes in the unsaturated zone around the plant root zone through to groundwater. Ultimately, this will help understand groundwater dynamics and fractioning below surface of CA field

Confirmation of Anomalous Dynamical Arrest in attractive colloids: a molecular dynamics study

Previous theoretical, along with early simulation and experimental, studies have indicated that particles with a short-ranged attraction exhibit a range of new dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singularity in the density correlation functions, and the existence of `attractive' and `repulsive' glasses. Here we carry out extensive molecular dynamics calculations on dense systems interacting via a square-well potential. This is one of the simplest systems with the required properties, and may be regarded as canonical for interpreting the phase diagram, and now also the dynamical arrest. We confirm the theoretical predictions for re-entrance, logarithmic singularity, and give the first direct evidence of the coexistence, independent of theory, of the two coexisting glasses. We now regard the previous predictions of these phenomena as having been established.Comment: 15 pages,15 figures; submitted to Phys. Rev.