1,477 research outputs found
Electron-beam-induced shift in the apparent position of a pinned vortex in a thin superconducting film
When an electron beam strikes a superconducting thin film near a pinned
vortex, it locally increases the temperature-dependent London penetration depth
and perturbs the circulating supercurrent, thereby distorting the vortex's
magnetic field toward the heated spot. This phenomenon has been used to
visualize vortices pinned in SQUIDs using low-temperature scanning electron
microscopy. In this paper I develop a quantitative theory to calculate the
displacement of the vortex-generated magnetic-flux distribution as a function
of the distance of the beam spot from the vortex core. The results are
calculated using four different models for the spatial distribution of the
thermal power deposited by the electron beam.Comment: 9 pages, 6 figures, resubmitted to PRB with referee-suggested
revisions, includes new paragraph on numerical evaluatio
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
Volume-energy correlations in the slow degrees of freedom of computer-simulated phospholipid membranes
Constant-pressure molecular-dynamics simulations of phospholipid membranes in
the fluid phase reveal strong correlations between equilibrium fluctuations of
volume and energy on the nanosecond time-scale. The existence of strong
volume-energy correlations was previously deduced indirectly by Heimburg from
experiments focusing on the phase transition between the fluid and the ordered
gel phases. The correlations, which are reported here for three different
membranes (DMPC, DMPS-Na, and DMPSH), have volume-energy correlation
coefficients ranging from 0.81 to 0.89. The DMPC membrane was studied at two
temperatures showing that the correlation coefficient increases as the phase
transition is approached
Dynamics of ions in the selectivity filter of the KcsA channel
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications
Quantitative nanoscale vortex-imaging using a cryogenic quantum magnetometer
Microscopic studies of superconductors and their vortices play a pivotal role
in our understanding of the mechanisms underlying superconductivity. Local
measurements of penetration depths or magnetic stray-fields enable access to
fundamental aspects of superconductors such as nanoscale variations of
superfluid densities or the symmetry of their order parameter. However,
experimental tools, which offer quantitative, nanoscale magnetometry and
operate over the large range of temperature and magnetic fields relevant to
address many outstanding questions in superconductivity, are still missing.
Here, we demonstrate quantitative, nanoscale magnetic imaging of Pearl vortices
in the cuprate superconductor YBCO, using a scanning quantum sensor in form of
a single Nitrogen-Vacancy (NV) electronic spin in diamond. The sensor-to-sample
distance of ~10nm we achieve allows us to observe striking deviations from the
prevalent monopole approximation in our vortex stray-field images, while we
find excellent quantitative agreement with Pearl's analytic model. Our
experiments yield a non-invasive and unambiguous determination of the system's
local London penetration depth, and are readily extended to higher temperatures
and magnetic fields. These results demonstrate the potential of quantitative
quantum sensors in benchmarking microscopic models of complex electronic
systems and open the door for further exploration of strongly correlated
electron physics using scanning NV magnetometry.Comment: Main text (5 pages, 4 figures) plus supplementary material (5 pages,
6 figures). Comments welcome. Further information under
http://www.quantum-sensing.c
Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation
In this paper, we investigate the conformational dynamics of alanine
dipeptide under an external electric field by nonequilibrium molecular dynamics
simulation. We consider the case of a constant and of an oscillatory field. In
this context we propose a procedure to implement the temperature control, which
removes the irrelevant thermal effects of the field. For the constant field
different time-scales are identified in the conformational, dipole moment, and
orientational dynamics. Moreover, we prove that the solvent structure only
marginally changes when the external field is switched on. In the case of
oscillatory field, the conformational changes are shown to be as strong as in
the previous case, and non-trivial nonequilibrium circular paths in the
conformation space are revealed by calculating the integrated net probability
fluxes.Comment: 23 pages, 12 figure
Maximum Flux Transition Paths of Conformational Change
Given two metastable states A and B of a biomolecular system, the problem is
to calculate the likely paths of the transition from A to B. Such a calculation
is more informative and more manageable if done for a reduced set of collective
variables chosen so that paths cluster in collective variable space. The
computational task becomes that of computing the "center" of such a cluster. A
good way to define the center employs the concept of a committor, whose value
at a point in collective variable space is the probability that a trajectory at
that point will reach B before A. The committor "foliates" the transition
region into a set of isocommittors. The maximum flux transition path is defined
as a path that crosses each isocommittor at a point which (locally) has the
highest crossing rate of distinct reactive trajectories. (This path is
different from that of the MaxFlux method of Huo and Straub.) It is argued that
such a path is nearer to an ideal path than others that have been proposed with
the possible exception of the finite-temperature string method path. To make
the calculation tractable, three approximations are introduced, yielding a path
that is the solution of a nonsingular two-point boundary-value problem. For
such a problem, one can construct a simple and robust algorithm. One such
algorithm and its performance is discussed.Comment: 7 figure
Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study
Hemoglobin exhibits allosteric structural changes upon ligand binding due to
the dynamic interactions between the ligand binding sites, the amino acids
residues and some other solutes present under physiological conditions. In the
present study, the dynamical and quaternary structural changes occurring in two
unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures
of adult human hemoglobin were investigated with molecular dynamics. It is
shown that, in the sub-microsecond time scale, there is no marked difference in
the global dynamics of the amino acids residues in both the oxy- and the deoxy-
forms of the individual structures. In addition, the R, R2 are relatively
stable and do not present quaternary conformational changes within the time
scale of our simulations while the T structure is dynamically more flexible and
exhibited the T\rightarrow R quaternary conformational transition, which is
propagated by the relative rotation of the residues at the {\alpha}1{\beta}2
and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B
DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ
Ground State Vortex Lattice Structures in d-wave Superconductors
We show in a realistic symmetry gap model for a cuprate
superconductor that the clean vortex lattice has discontinuous structural
transitions (at and near T=0), as a function of the magnetic field along
the c-axis. The transitions arise from the singular nonlocal and anisotropic
susceptibility of the superconductor to the perturbation
caused by supercurrents associated with vortices. The susceptibility, due to
virtual Dirac quasiparticle-hole excitation, is calculated carefully, and leads
to a ground state transition for the triangular lattice from an orientation
along one of the crystal axis to one at 45 to them, i.e, along the gap zero
direction. The field scale is seen to be 5 Tesla , where is the gap maximum, is the
nearest neighbour hopping, is the lattice constant, and is the
flux quantum. At much higher fields () there is a discontinuous
transition to a centred square structure. The source of the differences from
existing calculations, and experimental observability are discussed, the latter
especially in view of the very small (a few degrees per vortex) differences
in the ground state energy.Comment: To be published in Phys. Rev.
A two-domain elevator mechanism for sodium/proton antiport
Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis1. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets2. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli1, 3, for which both electron microscopy and crystal structures are available4, 5, 6. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein1, 4. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur7. The only reported NhaA crystal structure so far is of the low pH inactivated form4. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 Å resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding1, 8, 9 directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20° against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second3, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general
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