Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Temperature and orientation dependence of kinetic roughening during homoepitaxy: A quantitative x-ray-scattering study of Ag

URL:http://link.aps.org/doi/10.1103/PhysRevB.54.17938 DOI:10.1103/PhysRevB.54.17938Kinetic roughening during homoepitaxial growth was studied for Ag(111) and Ag(001). For Ag(111), from 150 to 500 K, the rms roughness exhibits a power law, σ∝tβ over nearly three decades in thickness. β≈1/2 at low temperatures, and there is an abrupt transition to smaller values above 300 K. In contrast, Ag(001) exhibits layer-by-layer growth with a significantly smaller β. These results are the first to establish the evolution of surface roughness quantitatively for a broad thickness and temperature range, as well as for the case where growth kinetics are dominated by a step-ledge diffusion barrier.Support is acknowledged from the University of Missouri Research Board, the NSF under Contract Nos. DMR-9202528 and DMR-9623827, and the Midwest Superconductivity Consortium ~MISCON! under DOE Grant No. DE-FG02-90ER45427. The SUNY X3 beamline is supported by the DOE under Contract No. DE-FG02-86ER45231, and the NSLS is supported by the DOE, Div. of Materials Sciences and Div. of Chemical Sciences. One of us ~W.C.E.! acknowledges support from the GAANN program of the U.S. Department of Education. We thank Ian Robinson for the Ag~111! crystal

Path integral Monte Carlo simulations of silicates

We investigate the thermal expansion of crystalline SiO$_2$ in the $\beta$-- cristobalite and the $\beta$-quartz structure with path integral Monte Carlo (PIMC) techniques. This simulation method allows to treat low-temperature quantum effects properly. At temperatures below the Debye temperature, thermal properties obtained with PIMC agree better with experimental results than those obtained with classical Monte Carlo methods.Comment: 27 pages, 10 figures, Phys. Rev. B (in press

Rate- and State-Dependent Friction Law and Statistical Properties of Earthquakes

In order to clarify how the statistical properties of earthquakes depend on the constitutive law characterizing the stick-slip dynamics, we make an extensive numerical simulation of the one-dimensional spring-block model with the rate- and state-dependent friction law. Both the magnitude distribution and the recurrence-time distribution are studied with varying the constitutive parameters characterizing the model. While a continuous spectrum of seismic events from smaller to larger magnitudes is obtained, earthquakes described by this model turn out to possess pronounced ``characteristic'' features.Comment: Minor revisions are made in the text and in the figures. Accepted for publication in Europhys. Letter

Environmental barriers to communication for individuals with dysarthria

Poster Symposium: Disorders TrackpostprintThe 2010 Motor Speech Conference, Savannah, GA., 3-7 March 2010

Mitochondrial peroxiredoxin functions as crucial chaperone reservoir in Leishmania infantum

Cytosolic eukaryotic 2-Cys-peroxiredoxins have been widely reported to act as dual-function proteins, either detoxifying reactive oxygen species or acting as chaperones to prevent protein aggregation. Several stimuli, including peroxide-mediated sulfinic acid formation at the active site cysteine, have been proposed to trigger the chaperone activity. However, the mechanism underlying this activation and the extent to which the chaperone function is crucial under physiological conditions in vivo remained unknown. Here we demonstrate that in the vector-borne protozoan parasite Leishmania infantum, mitochondrial peroxiredoxin (Prx) exerts intrinsic ATP-independent chaperone activity, protecting a wide variety of different proteins against heat stress-mediated unfolding in vitro and in vivo. Activation of the chaperone function appears to be induced by temperature-mediated restructuring of the reduced decamers, promoting binding of unfolding client proteins in the center of Prx's ringlike structure. Client proteins are maintained in a folding-competent conformation until restoration of nonstress conditions, upon which they are released and transferred to ATP-dependent chaperones for refolding. Interference with client binding impairs parasite infectivity, providing compelling evidence for the in vivo importance of Prx's chaperone function. Our results suggest that reduced Prx provides a mitochondrial chaperone reservoir, which allows L. infantum to deal successfully with protein unfolding conditions during the transition from insect to the mammalian hosts and to generate viable parasites capable of perpetuating infection.We thank Frederico Silva for help with size-exclusion chromatography experiments, and Ana G. Gomes-Alves and Ricardo Silva for constructing the pSSU-PHLEO-infantum-MTS.His.THR-mTXNPx plasmid. This work was supported by National Institutes of Health Grant GM065318 (to U.J.) and Project "NORTE-07-0124-FEDER-000002-Host-Pathogen Interactions" cofunded by Programa Operacional Regional do Norte under the Quadro de Referencia Estrategico Nacional, through Fundo Europeu de Desenvolvimento Regional, and by the Portuguese Foundation for Science and Technology (FCT) (A.M.T.). F.T. and H.C. were supported by Portuguese FCT Fellowships SFRH/BD/70438/2010 and SFRH/BPD/80836/2011, respectively

Variational method for learning Quantum Channels via Stinespring Dilation on neutral atom systems

The state $|\psi(t)\rangle$ of a closed quantum system evolves under the Schr\"{o}dinger equation, where the reversible evolution of the state is described by the action of a unitary operator $U(t)$ on the initial state $|\psi_0\rangle$, i.e.\ $|\psi(t)\rangle=U(t)|\psi_0\rangle$. However, realistic quantum systems interact with their environment, resulting in non-reversible evolutions, described by Lindblad equations. The solution of these equations give rise to quantum channels $\Phi_t$ that describe the evolution of density matrices according to $\rho(t)=\Phi_t(\rho_0)$, which often results in decoherence and dephasing of the state. For many quantum experiments, the time until which measurements can be done might be limited, e.g. by experimental instability or technological constraints. However, further evolution of the state may be of interest. For instance, to determine the source of the decoherence and dephasing, or to identify the steady state of the evolution. In this work, we introduce a method to approximate a given target quantum channel by means of variationally approximating equivalent unitaries on an extended system, invoking the Stinespring dilation theorem. We report on an experimentally feasible method to extrapolate the quantum channel on discrete time steps using only data on the first time steps. Our approach heavily relies on the ability to spatially transport entangled qubits, which is unique to the neutral atom quantum computing architecture. Furthermore, the method shows promising predictive power for various non-trivial quantum channels. Lastly, a quantitative analysis is performed between gate-based and pulse-based variational quantum algorithms.Comment: 11 pages, 7 figure

The electronic structure of amorphous silica: A numerical study

We present a computational study of the electronic properties of amorphous SiO2. The ionic configurations used are the ones generated by an earlier molecular dynamics simulations in which the system was cooled with different cooling rates from the liquid state to a glass, thus giving access to glass-like configurations with different degrees of disorder [Phys. Rev. B 54, 15808 (1996)]. The electronic structure is described by a tight-binding Hamiltonian. We study the influence of the degree of disorder on the density of states, the localization properties, the optical absorption, the nature of defects within the mobility gap, and on the fluctuations of the Madelung potential, where the disorder manifests itself most prominently. The experimentally observed mismatch between a photoconductivity threshold of 9 eV and the onset of the optical absorption around 7 eV is interpreted by the picture of eigenstates localized by potential energy fluctuations in a mobility gap of approximately 9 eV and a density of states that exhibits valence and conduction band tails which are, even in the absence of defects, deeply located within the former band gap.Comment: 21 pages of Latex, 5 eps figure

Effect of Holstein phonons on the optical conductivity of gapped graphene

We study the optical conductivity of a doped graphene when a sublattice symmetry breaking is occurred in the presence of the electron-phonon interaction. Our study is based on the Kubo formula that is established upon the retarded self-energy. We report new features of both the real and imaginary parts of the quasiparticle self-energy in the presence of a gap opening. We find an analytical expression for the renormalized Fermi velocity of massive Dirac Fermions over broad ranges of electron densities, gap values and the electron-phonon coupling constants. Finally we conclude that the inclusion of the renormalized Fermi energy and the band gap effects are indeed crucial to get reasonable feature for the optical conductivity.Comment: 12 pages, 4 figures. To appear in Eur. Phys. J.

Tunable Excitons in Biased Bilayer Graphene

Recent measurements have shown that a continuously tunable bandgap of up to 250 meV can be generated in biased bilayer graphene [Y. Zhang et al., Nature 459, 820 (2009)], opening up pathway for possible graphene-based nanoelectronic and nanophotonic devices operating at room temperature. Here, we show that the optical response of this system is dominated by bound excitons. The main feature of the optical absorbance spectrum is determined by a single symmetric peak arising from excitons, a profile that is markedly different from that of an interband transition picture. Under laboratory conditions, the binding energy of the excitons may be tuned with the external bias going from zero to several tens of meV's. These novel strong excitonic behaviors result from a peculiar, effective ``one-dimensional'' joint density of states and a continuously-tunable bandgap in biased bilayer graphene. Moreover, we show that the electronic structure (level degeneracy, optical selection rules, etc.) of the bound excitons in a biased bilayer graphene is markedly different from that of a two-dimensional hydrogen atom because of the pseudospin physics