9,917 research outputs found
WRN participates in translesion synthesis pathway through interaction with NBS1.
Werner syndrome (WS), caused by mutation of the WRN gene, is an autosomal recessive disorder associated with premature aging and predisposition to cancer. WRN belongs to the RecQ DNA helicase family, members of which play a role in maintaining genomic stability. Here, we demonstrate that WRN rapidly forms discrete nuclear foci in an NBS1-dependent manner following DNA damage. NBS1 physically interacts with WRN through its FHA domain, which interaction is important for the phosphorylation of WRN. WRN subsequently forms DNA damage-dependent foci during the S phase, but not in the G1 phase. WS cells exhibit an increase in spontaneous focus formation of poleta and Rad18, which are important for translesion synthesis (TLS). WRN also interacts with PCNA in the absence of DNA damage, but DNA damage induces the dissociation of PCNA from WRN, leading to the ubiquitination of PCNA, which is essential for TLS. This dissociation correlates with ATM/NBS1-dependent degradation of WRN. Moreover, WS cells show constitutive ubiquitination of PCNA and interaction between PCNA and Rad18 E3 ligase in the absence of DNA damage. Taken together, these results indicate that WRN participates in the TLS pathway to prevent genomic instability in an ATM/NBS1-dependent manner
New Insights into Traffic Dynamics: A Weighted Probabilistic Cellular Automaton Model
From the macroscopic viewpoint for describing the acceleration behavior of
drivers, this letter presents a weighted probabilistic cellular automaton model
(the WP model, for short) by introducing a kind of random acceleration
probabilistic distribution function. The fundamental diagrams, the
spatio-temporal pattern are analyzed in detail. It is shown that the presented
model leads to the results consistent with the empirical data rather well,
nonlinear velocity-density relationship exists in lower density region, and a
new kind of traffic phenomenon called neo-synchronized flow is resulted.
Furthermore, we give the criterion for distinguishing the high-speed and
low-speed neo-synchronized flows and clarify the mechanism of this kind of
traffic phenomena. In addition, the result that the time evolution of
distribution of headways is displayed as a normal distribution further
validates the reasonability of the neo-synchronized flow. These findings
suggest that the diversity and randomicity of drivers and vehicles has indeed
remarkable effect on traffic dynamics.Comment: 12 pages, 5 figures, submitted to Europhysics Letter
Data production models for the CDF experiment
The data production for the CDF experiment is conducted on a large Linux PC
farm designed to meet the needs of data collection at a maximum rate of 40
MByte/sec. We present two data production models that exploits advances in
computing and communication technology. The first production farm is a
centralized system that has achieved a stable data processing rate of
approximately 2 TByte per day. The recently upgraded farm is migrated to the
SAM (Sequential Access to data via Metadata) data handling system. The software
and hardware of the CDF production farms has been successful in providing large
computing and data throughput capacity to the experiment.Comment: 8 pages, 9 figures; presented at HPC Asia2005, Beijing, China, Nov 30
- Dec 3, 200
Data processing model for the CDF experiment
The data processing model for the CDF experiment is described. Data
processing reconstructs events from parallel data streams taken with different
combinations of physics event triggers and further splits the events into
datasets of specialized physics datasets. The design of the processing control
system faces strict requirements on bookkeeping records, which trace the status
of data files and event contents during processing and storage. The computing
architecture was updated to meet the mass data flow of the Run II data
collection, recently upgraded to a maximum rate of 40 MByte/sec. The data
processing facility consists of a large cluster of Linux computers with data
movement managed by the CDF data handling system to a multi-petaByte Enstore
tape library. The latest processing cycle has achieved a stable speed of 35
MByte/sec (3 TByte/day). It can be readily scaled by increasing CPU and
data-handling capacity as required.Comment: 12 pages, 10 figures, submitted to IEEE-TN
Scarred Patterns in Surface Waves
Surface wave patterns are investigated experimentally in a system geometry
that has become a paradigm of quantum chaos: the stadium billiard. Linear waves
in bounded geometries for which classical ray trajectories are chaotic are
known to give rise to scarred patterns. Here, we utilize parametrically forced
surface waves (Faraday waves), which become progressively nonlinear beyond the
wave instability threshold, to investigate the subtle interplay between
boundaries and nonlinearity. Only a subset (three main types) of the computed
linear modes of the stadium are observed in a systematic scan. These correspond
to modes in which the wave amplitudes are strongly enhanced along paths
corresponding to certain periodic ray orbits. Many other modes are found to be
suppressed, in general agreement with a prediction by Agam and Altshuler based
on boundary dissipation and the Lyapunov exponent of the associated orbit.
Spatially asymmetric or disordered (but time-independent) patterns are also
found even near onset. As the driving acceleration is increased, the
time-independent scarred patterns persist, but in some cases transitions
between modes are noted. The onset of spatiotemporal chaos at higher forcing
amplitude often involves a nonperiodic oscillation between spatially ordered
and disordered states. We characterize this phenomenon using the concept of
pattern entropy. The rate of change of the patterns is found to be reduced as
the state passes temporarily near the ordered configurations of lower entropy.
We also report complex but highly symmetric (time-independent) patterns far
above onset in the regime that is normally chaotic.Comment: 9 pages, 10 figures (low resolution gif files). Updated and added
references and text. For high resolution images:
http://physics.clarku.edu/~akudrolli/stadium.htm
Fluctuation Theorems for Entropy Production and Heat Dissipation in Periodically Driven Markov Chains
Asymptotic fluctuation theorems are statements of a Gallavotti-Cohen symmetry
in the rate function of either the time-averaged entropy production or heat
dissipation of a process. Such theorems have been proved for various general
classes of continuous-time deterministic and stochastic processes, but always
under the assumption that the forces driving the system are time independent,
and often relying on the existence of a limiting ergodic distribution. In this
paper we extend the asymptotic fluctuation theorem for the first time to
inhomogeneous continuous-time processes without a stationary distribution,
considering specifically a finite state Markov chain driven by periodic
transition rates. We find that for both entropy production and heat
dissipation, the usual Gallavotti-Cohen symmetry of the rate function is
generalized to an analogous relation between the rate functions of the original
process and its corresponding backward process, in which the trajectory and the
driving protocol have been time-reversed. The effect is that spontaneous
positive fluctuations in the long time average of each quantity in the forward
process are exponentially more likely than spontaneous negative fluctuations in
the backward process, and vice-versa, revealing that the distributions of
fluctuations in universes in which time moves forward and backward are related.
As an additional result, the asymptotic time-averaged entropy production is
obtained as the integral of a periodic entropy production rate that generalizes
the constant rate pertaining to homogeneous dynamics
Direct measurements of the effects of salt and surfactant on interaction forces between colloidal particles at water-oil interfaces
The forces between colloidal particles at a decane-water interface, in the
presence of low concentrations of a monovalent salt (NaCl) and of the
surfactant sodium dodecylsulfate (SDS) in the aqueous subphase, have been
studied using laser tweezers. In the absence of electrolyte and surfactant,
particle interactions exhibit a long-range repulsion, yet the variation of the
interaction for different particle pairs is found to be considerable. Averaging
over several particle pairs was hence found to be necessary to obtain reliable
assessment of the effects of salt and surfactant. It has previously been
suggested that the repulsion is consistent with electrostatic interactions
between a small number of dissociated charges in the oil phase, leading to a
decay with distance to the power -4 and an absence of any effect of electrolyte
concentration. However, the present work demonstrates that increasing the
electrolyte concentration does yield, on average, a reduction of the magnitude
of the interaction force with electrolyte concentration. This implies that
charges on the water side also contribute significantly to the electrostatic
interactions. An increase in the concentration of SDS leads to a similar
decrease of the interaction force. Moreover the repulsion at fixed SDS
concentrations decreases over longer times. Finally, measurements of three-body
interactions provide insight into the anisotropic nature of the interactions.
The unique time-dependent and anisotropic interactions between particles at the
oil-water interface allow tailoring of the aggregation kinetics and structure
of the suspension structure.Comment: Submitted to Langmui
Second harmonic generation in SiC polytypes
LMTO calculations are presented for the frequency dependent second harmonic
generation (SHG) in the polytypes 2H, 4H, 6H, 15R and 3C of SiC. All
independent tensor components are calculated. The spectral features and the
ratios of the 333 to 311 tensorial components are studied as a function of the
degree of hexagonality. The relationship to the linear optical response and the
underlying band structure are investigated. SHG is suggested to be a sensitive
tool for investigating the near band edge interband excitations.Comment: 12 pages, 10 figure
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