3,607 research outputs found
Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect
Rotational friction on proteins and macromolecules is known to derive
contributions from at least two distinct sources -- hydrodynamic (due to
viscosity) and dielectric friction (due to polar interactions). In the existing
theoretical approaches, the effect of the latter is taken into account in an
{\it ad hoc} manner, by increasing the size of the protein with the addition of
a hydration layer. Here we calculate the rotational dielectric friction on a
protein () by using a generalized arbitrary charge distribution
model (where the charges are obtained from quantum chemical calculation) and
the hydrodynamic friction with stick boundary condition,
() by using the sophisticated theoretical technique known
as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp.
Biol. Med. {\bf 12}, 75 (1982)]. The calculation of hydrodynamic friction is
done with only the dry volume of the protein (no hydration layer). We find that
the total friction obtained by summing up and
gives reasonable agreement with the experimental results,
i.e.,
A balanced Memristor-CMOS ternary logic family and its application
The design of balanced ternary digital logic circuits based on memristors and
conventional CMOS devices is proposed. First, balanced ternary minimum gate
TMIN, maximum gate TMAX and ternary inverters are systematically designed and
verified by simulation, and then logic circuits such as ternary encoders,
decoders and multiplexers are designed on this basis. Two different schemes are
then used to realize the design of functional combinational logic circuits such
as a balanced ternary half adder, multiplier, and numerical comparator.
Finally, we report a series of comparisons and analyses of the two design
schemes, which provide a reference for subsequent research and development of
three-valued logic circuits.Comment: 15 pages, 30 figure
Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery
Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc
Epitope Mapping of SERCA2a Identifies an Antigenic Determinant That Induces Mainly Atrial Myocarditis in A/J Mice
Sarcoplasmic/endoplasmic reticulum Ca2+ adenosine triphosphatase (SERCA)2a, a critical regulator of calcium homeostasis, is known to be decreased in heart failure. Patients with myocarditis or dilated cardiomyopathy develop autoantibodies to SERCA2a suggesting that they may have pathogenetic significance. In this report, we describe epitope mapping analysis of SERCA2a in A/J mice that leads us to make five observations: 1) SERCA2a contains multiple T cell epitopes that induce varying degrees of myocarditis. One epitope, SERCA2a 971–990, induces widespread atrial inflammation without affecting noncardiac tissues; the cardiac abnormalities could be noninvasively captured by echocardiography, electrocardiography, and magnetic resonance microscopy imaging. 2) SERCA2a 971–990-induced disease was associated with the induction of CD4 T cell responses and the epitope preferentially binds MHC class II/IAk rather than IEk. By creating IAk/and IEk/SERCA2a 971–990 dextramers, the T cell responses were determined by flow cytometry to be Ag specific. 3) SERCA2a 971–990-sensitized T cells produce both Th1 and Th17 cytokines. 4) Animals immunized with SERCA2a 971–990 showed Ag-specific Abs with enhanced production of IgG2a and IgG2b isotypes, suggesting that SERCA2a 971–990 can potentially act as a common epitope for both T cells and B cells. 5) Finally, SERCA2a 971–990-sensitized T cells were able to transfer disease to naive recipients. Together, these data indicate that SERCA2a is a critical autoantigen in the mediation of atrial inflammation in mice and that our model may be helpful to study the inflammatory events that underlie the development of conditions such as atrial fibrillation in humans
Finding influential users for different time bounds in social networks using multi-objective optimization
Online social networks play an important role in marketing services. Influence maximization is a major challenge, in which the goal is to find the most influential users in a social network. Increasing the number of influenced users at the end of a diffusion process while decreasing the time of diffusion are two main objectives of the influence maximization problem. The goal of this paper is to find multiple sets of influential users such that each of them is the best set to spread influence for a specific time bound. Considering two conflicting objectives, increasing influence and decreasing diffusion time, we employ the NSGA-II algorithm which is a powerful algorithm in multi-objective optimization to find different seed sets with high influence at different diffusion times. Since social networks are large, computing influence and diffusion time of all chromosomes in each iteration will be challenging and computationally expensive. Therefore, we propose two methods which can estimate the expected influence and diffusion time of a seed set in an efficient manner. Providing the set of all potentially optimal solutions helps a decision maker evaluate the trade-offs between the two objectives, i.e., the number of influenced users and diffusion time. In addition, we develop an approach for selecting seed sets, which have optimal influence for specific time bounds, from the resulting Pareto front of the NSGA-II. Finally, we show that applying our algorithm to real social networks outperforms existing algorithms for the influence maximization problem. The results show a good compromise between the two objectives and the final seed sets result in high influence for different time bounds
Heavy Quarks and Heavy Quarkonia as Tests of Thermalization
We present here a brief summary of new results on heavy quarks and heavy
quarkonia from the PHENIX experiment as presented at the "Quark Gluon Plasma
Thermalization" Workshop in Vienna, Austria in August 2005, directly following
the International Quark Matter Conference in Hungary.Comment: 8 pages, 5 figures, Quark Gluon Plasma Thermalization Workshop
(Vienna August 2005) Proceeding
Production of phi mesons at mid-rapidity in sqrt(s_NN) = 200 GeV Au+Au collisions at RHIC
We present the first results of meson production in the K^+K^- decay channel
from Au+Au collisions at sqrt(s_NN) = 200 GeV as measured at mid-rapidity by
the PHENIX detector at RHIC. Precision resonance centroid and width values are
extracted as a function of collision centrality. No significant variation from
the PDG accepted values is observed. The transverse mass spectra are fitted
with a linear exponential function for which the derived inverse slope
parameter is seen to be constant as a function of centrality. These data are
also fitted by a hydrodynamic model with the result that the freeze-out
temperature and the expansion velocity values are consistent with the values
previously derived from fitting single hadron inclusive data. As a function of
transverse momentum the collisions scaled peripheral.to.central yield ratio RCP
for the is comparable to that of pions rather than that of protons. This result
lends support to theoretical models which distinguish between baryons and
mesons instead of particle mass for explaining the anomalous proton yield.Comment: 326 authors, 24 pages text, 23 figures, 6 tables, RevTeX 4. To be
submitted to Physical Review C as a regular article. Plain text data tables
for the points plotted in figures for this and previous PHENIX publications
are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Single Electrons from Heavy Flavor Decays in p+p Collisions at sqrt(s) = 200 GeV
The invariant differential cross section for inclusive electron production in
p+p collisions at sqrt(s) = 200 GeV has been measured by the PHENIX experiment
at the Relativistic Heavy Ion Collider over the transverse momentum range $0.4
<= p_T <= 5.0 GeV/c at midrapidity (eta <= 0.35). The contribution to the
inclusive electron spectrum from semileptonic decays of hadrons carrying heavy
flavor, i.e. charm quarks or, at high p_T, bottom quarks, is determined via
three independent methods. The resulting electron spectrum from heavy flavor
decays is compared to recent leading and next-to-leading order perturbative QCD
calculations. The total cross section of charm quark-antiquark pair production
is determined as sigma_(c c^bar) = 0.92 +/- 0.15 (stat.) +- 0.54 (sys.) mb.Comment: 329 authors, 6 pages text, 3 figures. Submitted to Phys. Rev. Lett.
Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Longitudinal double-spin asymmetry and cross section for inclusive neutral pion production at midrapidity in polarized proton collisions at sqrt(s) = 200 GeV
We report a measurement of the longitudinal double-spin asymmetry A_LL and
the differential cross section for inclusive Pi0 production at midrapidity in
polarized proton collisions at sqrt(s) = 200 GeV. The cross section was
measured over a transverse momentum range of 1 < p_T < 17 GeV/c and found to be
in good agreement with a next-to-leading order perturbative QCD calculation.
The longitudinal double-spin asymmetry was measured in the range of 3.7 < p_T <
11 GeV/c and excludes a maximal positive gluon polarization in the proton. The
mean transverse momentum fraction of Pi0's in their parent jets was found to be
around 0.7 for electromagnetically triggered events.Comment: 6 pages, 3 figures, submitted to Phys. Rev. D (RC
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