Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible polymer looping in the presence of such tensions by using Brownian dynamics simulation combined with an analytical theory. We show a minute tension dramatically changes the looping time, especially for long chains. Considering a dichotomically flipping noise as a simple example of the nonequilibrium tension, we find the phenomenon of resonant activation, where the looping time can be the minimum at an optimal flipping time. We discuss our results in connection with recent experiments.Comment: 7 pages, 8 figures, accepted in the Journal of Chemical Physic

Non-monotonic temperature dependent transport in graphene grown by Chemical Vapor Deposition

Temperature-dependent resistivity of graphene grown by chemical vapor deposition (CVD) is investigated. We observe in low mobility CVD graphene device a strong insulating behavior at low temperatures and a metallic behavior at high temperatures manifesting a non-monotonic in the temperature dependent resistivity.This feature is strongly affected by carrier density modulation. To understand this anomalous temperature dependence, we introduce thermal activation of charge carriers in electron-hole puddles induced by randomly distributed charged impurities. Observed temperature evolution of resistivity is then understood from the competition among thermal activation of charge carriers, temperature-dependent screening and phonon scattering effects. Our results imply that the transport property of transferred CVD-grown graphene is strongly influenced by the details of the environmentComment: 7 pages, 3 figure

Effect of (O, As) dual implantation on p-type doping of ZnO films

Optical and electrical characteristics of ZnOfilms co-implanted with O and As ions have been investigated by photoluminescence(PL), Hall-effect, and current-voltage (I-V) measurements. 100-nm-thick ZnOfilms grown on n-type Si (100) wafers by RF sputtering have been implanted with various fluences of 30 keV O and 100 keV As ions at room temperature, and subsequently annealed at 800 °C for 20 min in a N2 ambient. The dually-implanted ZnOfilms show stable p-type characteristics for particular implant combinations, consistent with the observation of dominant PL peaks at 3.328 and 3.357 eV that are associated with the acceptor levels. For these dually-implanted p-type ZnO films/n-type Si diodes, the I-V curves show rectifying p-n junction behavior. Other singly (As)- or dually-implanted samples show n-type or indeterminable doping characteristics. These results suggest that O implantation plays a key role in forming p-type ZnOfilms by reducing the oxygen vacancy concentration and facilitating the formation of As-related acceptors in ZnO.This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. 2011-0017373)

Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension

In addition to thermal noise, which is essential to promote conformational transitions in biopolymers, cellular environment is replete with a spectrum of athermal fluctuations that are produced from a plethora of active processes. To understand the effect of athermal noise on biological processes, we studied how a small oscillatory force affects the thermally induced folding and unfolding transition of an RNA hairpin, whose response to constant tension had been investigated extensively in both theory and experiments. Strikingly, our molecular simulations performed under overdamped condition show that even at a high (low) tension that renders the hairpin (un)folding improbable, a weak external oscillatory force at a certain frequency can synchronously enhance the transition dynamics of RNA hairpin and increase the mean transition rate. Furthermore, the RNA dynamics can still discriminate a signal with resonance frequency even when the signal is mixed among other signals with nonresonant frequencies. In fact, our computational demonstration of thermally induced resonance in RNA hairpin dynamics is a direct realization of the phenomena called stochastic resonance (SR) and resonant activation (RA). Our study, amenable to experimental tests using optical tweezers, is of great significance to the folding of biopolymers in vivo that are subject to the broad spectrum of cellular noises.Comment: 22 pages, 7 figure

Singlet fermionic dark matter

We propose a renormalizable model of a fermionic dark matter by introducing a gauge singlet Dirac fermion and a real singlet scalar. The bridges between the singlet sector and the standard model sector are only the singlet scalar interaction terms with the standard model Higgs field. The singlet fermion couples to the standard model particles through the mixing between the standard model Higgs and singlet scalar and is naturally a weakly interacting massive particle (WIMP). The measured relic abundance can be explained by the singlet fermionic dark matter as the WIMP within this model. Collider implication of the singlet fermionic dark matter is also discussed. Predicted is the elastic scattering cross section of the singlet fermion into target nuclei for a direct detection of the dark matter. Search of the direct detection of the dark matter provides severe constraints on the parameters of our model.Comment: 12 pages, 7 figure

Mesoscopic Kondo Effect in an Aharonov-Bohm Ring

An interacting quantum dot inserted in a mesoscopic ring is investigated. A variational ansatz is employed to describe the ground state of the system in the presence of the Aharonov-Bohm flux. It is shown that, for even number of electrons with the energy level spacing smaller than the Kondo temperature, the persistent current has a value similar to that of a perfect ring with the same radius. On the other hand, for a ring with odd number electrons, the persistent current is found to be strongly suppressed compared to that of an ideal ring, which implies the suppression of the Kondo-resonant transmission. Various aspects of the Kondo-assisted persistent current are discussed.Comment: 4 pages Revtex, 4 Postscript figures, final version to appear in Phys. Rev. Lett. 85, No.26 (Dec. 25, 2000

Reappraisal of Plasmapheresis as a Supportive Measure in a Patient with Hepatic Failure after Major Hepatectomy

Major resection of cirrhotic livers can result in hepatic failure, but no supportive treatment has been found to be generally effective. We successfully treated a 63-year-old woman with post-hepatectomy liver failure with plasmapheresis. Following right hepatectomy, the initial postoperative recovery of liver function was favorable, except for ascites. One month later, however, the amount of drained ascites increased up to 2 l/day. In addition, serum cholesterol concentration gradually decreased to around 30 mg/dl, and serum total bilirubin rose to 11.1 mg/dl. Plasmapheresis was performed, and after just 2 sessions, serum cholesterol level was rapidly corrected and prothrombin time was restored. After 3 sessions of plasmapheresis, the usual rebound rise of serum bilirubin disappeared, and the amount of ascites drained also decreased slowly. The patient underwent a total of 5 sessions of plasmapheresis over 2 weeks, after which liver function improved slowly, and she was finally discharged 72 days after liver resection. Mild ascites requiring diuretic therapy persisted over 3 months. She is doing well to date 10 months after liver resection without tumor recurrence or hepatic decompensation. This limited experience suggests that plasmapheresis can be a useful liver support for post-hepatectomy liver failure

Activin Signaling in Microsatellite Stable Colon Cancers Is Disrupted by a Combination of Genetic and Epigenetic Mechanisms

Activin receptor 2 (ACVR2) is commonly mutated in microsatellite unstable (MSI) colon cancers, leading to protein loss, signaling disruption, and larger tumors. Here, we examined activin signaling disruption in microsatellite stable (MSS) colon cancers.Fifty-one population-based MSS colon cancers were assessed for ACVR1, ACVR2 and pSMAD2 protein. Consensus mutation-prone portions of ACVR2 were sequenced in primary cancers and all exons in colon cancer cell lines. Loss of heterozygosity (LOH) was evaluated for ACVR2 and ACVR1, and ACVR2 promoter methylation by methylation-specific PCR and bisulfite sequencing and chromosomal instability (CIN) phenotype via fluorescent LOH analysis of 3 duplicate markers. ACVR2 promoter methylation and ACVR2 expression were assessed in colon cancer cell lines via qPCR and IP-Western blots. Re-expression of ACVR2 after demethylation with 5-aza-2'-deoxycytidine (5-Aza) was determined. An additional 26 MSS colon cancers were assessed for ACVR2 loss and its mechanism, and ACVR2 loss in all tested cancers correlated with clinicopathological criteria.Of 51 MSS colon tumors, 7 (14%) lost ACVR2, 2 (4%) ACVR1, and 5 (10%) pSMAD2 expression. No somatic ACVR2 mutations were detected. Loss of ACVR2 expression was associated with LOH at ACVR2 (p<0.001) and ACVR2 promoter hypermethylation (p<0.05). ACVR2 LOH, but not promoter hypermethylation, correlated with CIN status. In colon cancer cell lines with fully methylated ACVR2 promoter, loss of ACVR2 mRNA and protein expression was restored with 5-Aza treatment. Loss of ACVR2 was associated with an increase in primary colon cancer volume (p<0.05).Only a small percentage of MSS colon cancers lose expression of activin signaling members. ACVR2 loss occurs through LOH and ACVR2 promoter hypermethylation, revealing distinct mechanisms for ACVR2 inactivation in both MSI and MSS subtypes of colon cancer