967 research outputs found
Modeling saltâmediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome
Consciousness and the Wigner's friend problem
It is generally agreed that decoherence theory is, if not a complete answer,
at least a great step forward towards a solution of the quantum measurement
problem. It is shown here however that in the cases in which a sentient being
is explicitly assumed to take cognizance of the outcome the reasons we have for
judging this way are not totally consistent, so that the question has to be
considered anew. It is pointed out that the way the Broglie-Bohm model solves
the riddle suggests a possible clue, consisting in assuming that even very
simple systems may have some sort of a proto-consciousness, but that their
``internal states of consciousness'' are not predictive. It is, next, easily
shown that if we imagine the systems get larger, in virtue of decoherence their
internal states of consciousness progressively gain in predictive value. So
that, for macro-systems, they may be identified (in practice) with the
predictive states of consciousness on which we ground our observational
predictions. The possibilities of carrying over this idea to standard quantum
mechanics are then investigated. Conditions of conceptual consistency are
considered and found rather strict, and, finally, two solutions emerge,
differing conceptually very much from one another but in both of which the,
possibly non-predictive, generalized internal states of consciousness play a
crucial role
Heat conductivity of DNA double helix
Thermal conductivity of isolated single molecule DNA fragments is of
importance for nanotechnology, but has not yet been measured experimentally.
Theoretical estimates based on simplified (1D) models predict anomalously high
thermal conductivity. To investigate thermal properties of single molecule DNA
we have developed a 3D coarse-grained (CG) model that retains the realism of
the full all-atom description, but is significantly more efficient. Within the
proposed model each nucleotide is represented by 6 particles or grains; the
grains interact via effective potentials inferred from classical molecular
dynamics (MD) trajectories based on a well-established all-atom potential
function. Comparisons of 10 ns long MD trajectories between the CG and the
corresponding all-atom model show similar root-mean-square deviations from the
canonical B-form DNA, and similar structural fluctuations. At the same time,
the CG model is 10 to 100 times faster depending on the length of the DNA
fragment in the simulation. Analysis of dispersion curves derived from the CG
model yields longitudinal sound velocity and torsional stiffness in close
agreement with existing experiments. The computational efficiency of the CG
model makes it possible to calculate thermal conductivity of a single DNA
molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the
estimated conductivity coefficient is 0.3 W/mK which is half the value of
thermal conductivity for water. This result is in stark contrast with estimates
of thermal conductivity for simplified, effectively 1D chains ("beads on a
spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D
character of DNA double-helix retained in the proposed model appears to be
essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure
Local Simulation Algorithms for Coulombic Interactions
We consider dynamically constrained Monte-Carlo dynamics and show that this
leads to the generation of long ranged effective interactions. This allows us
to construct a local algorithm for the simulation of charged systems without
ever having to evaluate pair potentials or solve the Poisson equation. We
discuss a simple implementation of a charged lattice gas as well as more
elaborate off-lattice versions of the algorithm. There are analogies between
our formulation of electrostatics and the bosonic Hubbard model in the phase
approximation. Cluster methods developed for this model further improve the
efficiency of the electrostatics algorithm.Comment: Proceedings Statphys22 10 page
Local Simulation Algorithms for Coulomb Interaction
Long ranged electrostatic interactions are time consuming to calculate in
molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic
framework for simulating charged particles which modifies the dynamics so as to
allow equilibration using a local Hamiltonian. The method introduces an
auxiliary field with constrained dynamics so that the equilibrium distribution
is determined by the Coulomb interaction. We demonstrate the efficiency of the
method by simulating a simple, charged lattice gas.Comment: Last figure changed to improve demonstration of numerical efficienc
Tsunami observations by coastal ocean radar
When tsunami waves propagate across the open ocean, they are steered by the Coriolis effect and refraction due to gentle gradients in the bathymetry on scales longer than the wavelength. When the wave encounters steep gradients at the edges of continental shelves and at the coast, the wave becomes nonlinear and conservation of momentum produces squirts of surface current at the head of submerged canyons and in coastal bays. High frequency (HF) coastal ocean
radar is well conditioned to observe the surface current bursts at the edge of the continental shelf and give a warning of 40 minutes to 2 hours when the shelf is 50
to 200km wide. The period of tsunami waves is invariant over changes in bathymetry and is in the range 2 to 30 minutes. Wavelengths for tsunamis (in 500 to 3000m depth) are in the range 8.5 to over 200 km, and on a shelf where the depth is about 50m (as in the Great Barrier Reef (GBR)) the wavelengths are in the range 2.5 to 30 km. In the use of HF radar technology, there is a trade-off between the precision of surface current speed measurements and time
resolution. It is shown that the phased array HF ocean surface radar being deployed in the GBR and operating in a routine way for mapping surface currents, can resolve surface current squirts from tsunamis in the wave period
range 20 to 30 minutes and in the wavelength range greater than about 6 km. An advantage in signal-to-noise ratio can be obtained from the prior knowledge of the spatial pattern of the squirts at the edge of the continental shelf, and it is estimated that, with this analysis, the time resolution of the GBR radar may be reduced to about 2.5 minutes, which corresponds to a capability to detect tsunamis at the shelf edge in the period range 5 to 30 minutes. It is estimated that the lower limit of squirt velocity detection at the shelf edge would correspond to a tsunami with water elevation of about 2.5 cm in the open ocean. This means
that the GBR HF radar is well conditioned for use as a monitor of small, as well as larger, tsunamis and has the potential to contribute to the understanding of tsunami genesis research
Direct and indirect effect of bt cotton and no bt cotton on the development and reproduction of the predator Podisus nigrispinus (Dallas, 1851) (Hemiptera: Pentatomidae).
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Tumour necrosis factor production and natural killer cell activity in peripheral blood during treatment with recombinant tumour necrosis factor.
Tumour necrosis factor (TNF) has been found to be an important immunomodulator. Among other functions TNF activates natural killer (NK) cells and stimulates monocytes/macrophages in an autocrine fashion. TNF production and NK activity in peripheral blood mononuclear cells were determined in a clinical phase I study in which recombinant human (rh) TNF was administered as a continuous infusion weekly for a period of 8 weeks. Even though TNF production and NK activity were significantly reduced directly after rhTNF infusion the effect proved to be transient and most pronounced at the first rhTNF administration. One day after completion of the rhTNF infusion the peripheral cells released more TNF into the supernatant compared to TNF activity immediately before the rhTNF infusion. This effect was conspicuous in non-stimulated cultures. After repeated rhTNF infusions both stimulated and non-stimulated TNF production of the peripheral blood mononuclear cells was increased. NK cell activity was also enhanced after repeated cycles of rhTNF administration as compared to early rhTNF treatment. Thus, repeated rhTNF infusions lead to a stimulatory effect on TNF production and NK activity of peripheral blood cells
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