560 research outputs found
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 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 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 ( K) and a
higher critical field ( 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 ( K) and critical field ( 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.
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