39 research outputs found
Formation of Quantum Phase Slip Pairs in Superconducting Nanowires
Macroscopic quantum tunneling (MQT) is a fundamental phenomenon of quantum
mechanics related to the actively debated topic of quantum-to-classical
transition. The ability to realize MQT affects implementation of qubit-based
quantum computing schemes and their protection against decoherence. Decoherence
in qubits can be reduced by means of topological protection, e.g. by exploiting
various parity effects. In particular, paired phase slips can provide such
protection for superconducting qubits. Here, we report on the direct
observation of quantum paired phase slips in thin-wire superconducting loops.
We show that in addition to conventional single phase slips that change
superconducting order parameter phase by , there are quantum transitions
changing the phase by . Quantum paired phase slips represent a
synchronized occurrence of two macroscopic quantum tunneling events, i.e.
cotunneling. We demonstrate the existence of a remarkable regime in which
paired phase slips are exponentially more probable than single ones
Container solutions for HPC Systems: A Case Study of Using Shifter on Blue Waters
Software container solutions have revolutionized application development
approaches by enabling lightweight platform abstractions within the so-called
"containers." Several solutions are being actively developed in attempts to
bring the benefits of containers to high-performance computing systems with
their stringent security demands on the one hand and fundamental resource
sharing requirements on the other.
In this paper, we discuss the benefits and short-comings of such solutions
when deployed on real HPC systems and applied to production scientific
applications.We highlight use cases that are either enabled by or significantly
benefit from such solutions. We discuss the efforts by HPC system
administrators and support staff to support users of these type of workloads on
HPC systems not initially designed with these workloads in mind focusing on
NCSA's Blue Waters system.Comment: 8 pages, 7 figures, in PEARC '18: Proceedings of Practice and
Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA,
US
The Roman Senate During the Period of the Class Struggle in the 6th-4th Centures B.C. The Рroblems of Evolution
Автор исследует эволюцию сената в VI-ІV вв. до
н.э., что позволяет заново осмыслить многие перипетии сословной борьбы патрициев и плебеев
Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores
The
integration of local heat sources with solid-state nanopores
offers new means for controlling the transmembrane transport of charged
biomacromolecules. In the case of electrophoretic transport of DNA,
recent experimental studies revealed unexpected temperature dependences
of the DNA capture rate, the DNA translocation velocity, and the ionic
current blockades produced by the presence of DNA in the nanopore.
Here, we report the results of all-atom molecular dynamics simulations
that elucidated the effect of temperature on the key microscopic processes
governing electric field-driven transport of DNA through nanopores.
Mimicking the experimental setup, we simulated the capture and subsequent
translocation of short DNA duplexes through a locally heated nanopore
at several temperatures and electrolyte conditions. The temperature
dependence of ion mobility at the DNA surface was found to cause the
dependence of the relative conductance blockades on temperature. To
the first order, the effective force on DNA in the nanopore was found
to be independent of temperature, despite a considerable reduction
of solution viscosity. The temperature dependence of the solution
viscosity was found to make DNA translocations faster for a uniformly
heated system but not in the case of local heating that does not affect
viscosity of solution surrounding the untranslocated part of the molecule.
Increasing solution temperature was also found to reduce the lifetime
of bonds formed between cations and DNA. Using a flow suppression
algorithm, we were able to separate the effects of electro-osmotic
flow and direct ion binding, finding the reduced durations of DNA–ion
bonds to increase, albeit weakly, the effective force experienced
by DNA in an electric field. Unexpectedly, our simulations revealed
a considerable temperature dependence of solvent velocity at the DNA
surfaceslip velocity, an effect that can alter hydrodynamic
coupling between the motion of DNA and the surrounding fluid
Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA
With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.Funding Agencies|National Institutes of Health [R01-HG007406, P41-RR005969]; National Science Foundation [DMR-0955959]; Wenner-Gren Foundations; Netherlands Organisation for Scientific Research; XSEDE Allocation Grant [MCA05S028]</p
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface