31 research outputs found
DNA Translocation through Graphene Nanopores
Nanopores -- nanosized holes that can transport ions and molecules -- are
very promising devices for genomic screening, in particular DNA sequencing.
Both solid-state and biological pores suffer from the drawback, however, that
the channel constituting the pore is long, viz. 10-100 times the distance
between two bases in a DNA molecule (0.5 nm for single-stranded DNA). Here, we
demonstrate that it is possible to realize and use ultrathin nanopores
fabricated in graphene monolayers for single-molecule DNA translocation. The
pores are obtained by placing a graphene flake over a microsize hole in a
silicon nitride membrane and drilling a nanosize hole in the graphene using an
electron beam. As individual DNA molecules translocate through the pore,
characteristic temporary conductance changes are observed in the ionic current
through the nanopore, setting the stage for future genomic screening
Quadrupole collectivity in Ca 42 from low-energy Coulomb excitation with AGATA
A Coulomb-excitation experiment to study electromagnetic properties of Ca42 was performed using a 170-MeV calcium beam from the TANDEM XPU facility at INFN Laboratori Nazionali di Legnaro. γ rays from excited states in Ca42 were measured with the AGATA spectrometer. The magnitudes and relative signs of ten E2 matrix elements coupling six low-lying states in Ca42, including the diagonal E2 matrix elements of 21+ and 22+ states, were determined using the least-squares code gosia. The obtained set of reduced E2 matrix elements was analyzed using the quadrupole sum rule method and yielded overall quadrupole deformation for 01,2+ and 21,2+ states, as well as triaxiality for 01,2+ states, establishing the coexistence of a weakly deformed ground-state band and highly deformed slightly triaxial sideband in Ca42. The experimental results were compared with the state-of-the-art large-scale shell-model and beyond-mean-field calculations, which reproduce well the general picture of shape coexistence in Ca42
Superdeformed and Triaxial States in Ca 42
Shape parameters of a weakly deformed ground-state band and highly deformed slightly triaxial sideband in ^{42}Ca were determined from E2 matrix elements measured in the first low-energy Coulomb excitation experiment performed with AGATA. The picture of two coexisting structures is well reproduced by new state-of-the-art large-scale shell model and beyond-mean-field calculations. Experimental evidence for superdeformation of the band built on 0_{2}^{+} has been obtained and the role of triaxiality in the A∼40 mass region is discussed. Furthermore, the potential of Coulomb excitation as a tool to study superdeformation has been demonstrated for the first time
Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design
The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2
Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age 6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score 652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701
Measurement of the Docking Time of a DNA Molecule onto a Solid-State Nanopore
We present measurements of the change in ionic conductance
due
to double-stranded (ds) DNA
translocation through small (6 nm diameter) nanopores at low salt
(100 mM KCl). At both low (<200 mV) and high (>600 mV) voltages
we observe a current enhancement during DNA translocation, similar
to earlier reports. Intriguingly, however, in the intermediate voltage
range, we observe a new type of composite events, where within each
single event the current first decreases and then increases. From
the voltage dependence of the magnitude and timing of these current
changes, we conclude that the current decrease is caused by the docking
of the DNA random coil onto the nanopore. Unexpectedly, we find that
the docking time is exponentially dependent on voltage (<i>t</i> ∝ e<sup>–<i>V</i>/<i>V</i><sub>0</sub></sup>). We discuss a physical picture where the docking time
is set by the time that a DNA end needs to move from a random location
within the DNA coil to the nanopore. Upon entrance of the pore, the
current subsequently increases due to enhanced flow of counterions
along the DNA. Interestingly, these composite events thus allow to
independently measure the actual translocation time as well as the
docking time before translocation
Slowing down DNA Translocation through a Nanopore in Lithium Chloride
The charge of a DNA molecule is a crucial parameter in
many DNA
detection and manipulation schemes such as gel electrophoresis and
lab-on-a-chip applications. Here, we study the partial reduction of
the DNA charge due to counterion binding by means of nanopore translocation
experiments and all-atom molecular dynamics (MD) simulations. Surprisingly,
we find that the translocation time of a DNA molecule through a solid-state
nanopore strongly increases as the counterions decrease in size from
K<sup>+</sup> to Na<sup>+</sup> to Li<sup>+</sup>, both for double-stranded
DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate
the microscopic origin of this effect: Li<sup>+</sup> and Na<sup>+</sup> bind DNA stronger than K<sup>+</sup>. These fundamental insights
into the counterion binding to DNA also provide a practical method
for achieving at least 10-fold enhanced resolution in nanopore applications
Fast Translocation of Proteins through Solid State Nanopores
Measurements on protein translocation through solid-state
nanopores
reveal anomalous (non-Smoluchowski) transport behavior, as evidenced
by extremely low detected event rates; that is, the capture rates
are orders of magnitude smaller than what is theoretically expected.
Systematic experimental measurements of the event rate dependence
on the diffusion constant are performed by translocating proteins
ranging in size from 6 to 660 kDa. The discrepancy is observed to
be significantly larger for smaller proteins, which move faster and
have a lower signal-to-noise ratio. This is further confirmed by measuring
the event rate dependence on the pore size and concentration for a
large 540 kDa protein and a small 37 kDa protein, where only the large
protein follows the expected behavior. We dismiss various possible
causes for this phenomenon and conclude that it is due to a combination
of the limited temporal resolution and low signal-to-noise ratio.
A one-dimensional first-passage time-distribution model supports this
and suggests that the bulk of the proteins translocate on time scales
faster than can be detected. We discuss the implications for protein
characterization using solid-state nanopores and highlight several
possible routes to address this problem