1,369 research outputs found
Backbone and Sidechain Ordering in a small Protein
We investigate the relation between backbone and side-chain ordering in a
small protein. For this purpos e we have performed multicanonical simulations
of the villin headpiece subdomain HP-36, an often used to y model in protein
studies. Concepts of circular statistics are introduced to analyze side-chain
fluctuations. In contrast to earlier studies on homopolypeptides (Wei et al.,
J. Phys. Chem. B, 111 (2007) 4244) we do not find collective effects leading to
a separate transition. Rather, side-chain ordering is spread over a wide
temperature range. Our results indicate a thermal hierarchy of ordering events,
with side-chain ordering appearing at temperatures below the helix-coil
transition but above the folding transition. We conjecture that this thermal
hierarchy reflects an underlying temporal order, and that side-chain ordering
facilitates the search for the correct backbone topology.Comment: accepted in J. Chem. Phy
Generalized Ensemble and Tempering Simulations: A Unified View
From the underlying Master equations we derive one-dimensional stochastic
processes that describe generalized ensemble simulations as well as tempering
(simulated and parallel) simulations. The representations obtained are either
in the form of a one-dimensional Fokker-Planck equation or a hopping process on
a one-dimensional chain. In particular, we discuss the conditions under which
these representations are valid approximate Markovian descriptions of the
random walk in order parameter or control parameter space. They allow a unified
discussion of the stationary distribution on, as well as of the stationary flow
across each space. We demonstrate that optimizing the flow is equivalent to
minimizing the first passage time for crossing the space, and discuss the
consequences of our results for optimizing simulations. Finally, we point out
the limitations of these representations under conditions of broken ergodicity.Comment: 11 pages Latex, 2 eps figures, revised version, typos corrected, PRE
in pres
Diffusion in the Continuous-Imaginary-Time Quantum World-Line Monte Carlo Simulations with Extended Ensembles
The dynamics of samples in the continuous-imaginary-time quantum world-line
Monte Carlo simulations with extended ensembles are investigated. In the case
of a conventional flat ensemble on the one-dimensional quantum S=1 bi-quadratic
model, the asymmetric behavior of Monte Carlo samples appears in the diffusion
process in the space of the number of vertices. We prove that a local
diffusivity is asymptotically proportional to the number of vertices, and we
demonstrate the asymmetric behavior in the flat ensemble case. On the basis of
the asymptotic form, we propose the weight of an optimal ensemble as
, where denotes the number of vertices in a sample. It is shown
that the asymmetric behavior completely vanishes in the case of the proposed
ensemble on the one-dimensional quantum S=1 bi-quadratic model.Comment: 4 pages, 2 figures, update a referenc
Random Walks on a Fluctuating Lattice: A Renormalization Group Approach Applied in One Dimension
We study the problem of a random walk on a lattice in which bonds connecting
nearest neighbor sites open and close randomly in time, a situation often
encountered in fluctuating media. We present a simple renormalization group
technique to solve for the effective diffusive behavior at long times. For
one-dimensional lattices we obtain better quantitative agreement with
simulation data than earlier effective medium results. Our technique works in
principle in any dimension, although the amount of computation required rises
with dimensionality of the lattice.Comment: PostScript file including 2 figures, total 15 pages, 8 other figures
obtainable by mail from D.L. Stei
Simulations of grafted polymers in a good solvent
We present improved simulations of three-dimensional self avoiding walks with
one end attached to an impenetrable surface on the simple cubic lattice. This
surface can either be a-thermal, having thus only an entropic effect, or
attractive. In the latter case we concentrate on the adsorption transition, We
find clear evidence for the cross-over exponent to be smaller than 1/2, in
contrast to all previous simulations but in agreement with a re-summed field
theoretic -expansion. Since we use the pruned-enriched Rosenbluth
method (PERM) which allows very precise estimates of the partition sum itself,
we also obtain improved estimates for all entropic critical exponents.Comment: 5 pages with 9 figures included; minor change
STAT4 deficiency reduces the development of atherosclerosis in mice
Atherosclerosis is a chronic inflammatory process that leads to plaque formation in large and medium sized vessels. T helper 1 (Th1) cells constitute the majority of plaque infiltrating pro-atherogenic T cells and are induced via IFNγ-dependent activation of T-box (Tbet) and/or IL-12-dependent activation of signal transducer and activator of transcription 4 (STAT4). We thus aimed to define a role for STAT4 in atherosclerosis. STAT4-deficiency resulted in a ∼71% reduction (p < 0.001) in plaque burden in Stat4(-/-)Apoe(-/-) vs Apoe(-/-) mice fed chow diet and significantly attenuated atherosclerosis (∼31%, p < 0.01) in western diet fed Stat4(-/-)Apoe(-/-) mice. Surprisingly, reduced atherogenesis in Stat4(-/-)Apoe(-/-) mice was not due to attenuated IFNγ production in vivo by Th1 cells, suggesting an at least partially IFNγ-independent pro-atherogenic role of STAT4. STAT4 is expressed in T cells, but also detected in macrophages (MΦs). Stat4(-/-)Apoe(-/-)in vitro differentiated M1 or M2 MΦs had reduced cytokine production compare to Apoe(-/-) M1 and M2 MΦs that was accompanied by reduced induction of CD69, I-A(b), and CD86 in response to LPS stimulation. Stat4(-/-)Apoe(-/-) MΦs expressed attenuated levels of CCR2 and demonstrated reduced migration toward CCL2 in a transwell assay. Importantly, the percentage of aortic CD11b(+)F4/80(+)Ly6C(hi) MΦs was reduced in Stat4(-/-)Apoe(-/-) vs Apoe(-/-) mice. Thus, this study identifies for the first time a pro-atherogenic role of STAT4 that is at least partially independent of Th1 cell-derived IFNγ, and primarily involving the modulation of MΦ responses
A New Monte Carlo Algorithm for Protein Folding
We demonstrate that the recently proposed pruned-enriched Rosenbluth method
(P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient
algorithms for the folding of simple model proteins. We test them on several
models for lattice heteropolymers, and compare to published Monte Carlo
studies. In all cases our algorithms are faster than all previous ones, and in
several cases we find new minimal energy states. In addition to ground states,
our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett.,
revised version with changes in the tex
Photoswitchable diacylglycerols enable optical control of protein kinase C.
Increased levels of the second messenger lipid diacylglycerol (DAG) induce downstream signaling events including the translocation of C1-domain-containing proteins toward the plasma membrane. Here, we introduce three light-sensitive DAGs, termed PhoDAGs, which feature a photoswitchable acyl chain. The PhoDAGs are inactive in the dark and promote the translocation of proteins that feature C1 domains toward the plasma membrane upon a flash of UV-A light. This effect is quickly reversed after the termination of photostimulation or by irradiation with blue light, permitting the generation of oscillation patterns. Both protein kinase C and Munc13 can thus be put under optical control. PhoDAGs control vesicle release in excitable cells, such as mouse pancreatic islets and hippocampal neurons, and modulate synaptic transmission in Caenorhabditis elegans. As such, the PhoDAGs afford an unprecedented degree of spatiotemporal control and are broadly applicable tools to study DAG signaling
Heterosexual interactions of pairs of laboratory-housed stumptail macaques (Macaca arctoides) under continuous observation with closed-circuit video recording
Female-male interaction of heterosexual pairs of stumptail macaques, housed together continuously, was studied 24 hr per day using closed-circuit video recording. Two pairs were studied for approximately 2 months each. Although no generalizations can be made from such a small sample, no aspect of behavioral interaction varied significantly with the stage of the menstrual cycle of the female partner. Copulation occurred regularly but only during the daylight hours. Both pairs showed several peak ejaculation days (5-21 ejaculations/day), which were distributed throughout the entire menstrual cycle. In general, the highest number of ejaculations was observed to occur when the animals were put together either for the first time or following a separation of a few days. In one pair the female became pregnant, and from the fifth week of pregnancy onward there was a gradual increase in male aggression, coinciding with a decrease in male sexual and grooming behavior. In a second study eight different pairs were observed during the first day together and male copulatory behavior was studied. Two patterns of copulatory behavior could be discerned: pairs displaying a high number of ejaculations (19-38) and pairs displaying a low number of ejaculations (4-8). With regard to the interejaculatory interval (IEI), the male stumptail appeared to be unique. In contrast to what has been reported for other mammals, i.e., a steady increase in IEI with subsequent ejaculations, the stumptail showed increasing IEIs only during the first three to four, as well as between the last, ejaculations; in between, the IEI remained relatively constant. The maximum number of consecutive ejaculations observed was 38, displayed during a 10-hr time period (mean (± SEM)IEI, 12.9 ± 3.5 min)
The Shadows of the Past
We examined associations between two orientations based on historical group trauma, a form of enduring group victimhood (Perpetual Ingroup Victimhood Orientation [PIVO]) and the belief that one’s group might itself become a victimizer (Fear of Victimizing [FOV]), and attitudes, cognitions, and emotions related to intergroup conflicts. PIVO was positively and FOV was negatively related to aggressive attitudes and emotions toward the outgroup (Studies 1a-1c, Israeli–Palestinian conflict), and to the attribution of responsibility for a series of hostilities to the outgroup (Study 3, Israeli–Palestinian conflict). PIVO was negatively and FOV positively related to support for forgiveness and reconciliation (Study 2, Northern Ireland conflict). In Experimental Study 4, FOV predicted greater accuracy in remembering harm, regardless of victims’ group identity, whereas PIVO was associated with reduced accuracy only when victims were Palestinians (outgroup members). Taken together, these findings indicate that both orientations have a significant impact on intergroup conflicts and their resolution
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