Topological interactions between ring polymers: Implications for chromatin loops

Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e. loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the non-catenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.Comment: 12 pages, 11 figures. The article has been accepted by The Journal Of Chemical Physics. After it is published, it will be found at http://jcp.aip.or

Effect of flow on the acoustic reflection coefficient at a duct inlet

The effect of duct Mach number upon the acoustic reflection coefficient at the inlet of a duct with mean flow is investigated. An analysis, which models the duct inlet as a very short, one-dimensional nozzle over which the mean flow is accelerated from rest, gives good agreement with some recent experimental results. Discrepancies between the analysis and the experimental results are discussed in terms of radiation losses at the inlet and real fluid-flow effects within the duct

Dynamics of ultracold molecules in confined geometry and electric field

We present a time-independent quantum formalism to describe the dynamics of molecules with permanent electric dipole moments in a two-dimensional confined geometry such as a one-dimensional optical lattice, in the presence of an electric field. Bose/Fermi statistics and selection rules play a crucial role in the dynamics. As examples, we compare the dynamics of confined fermionic and bosonic polar KRb molecules under different confinements and electric fields. We show how chemical reactions can be suppressed, either by a "statistical suppression" which applies for fermions at small electric fields and confinements, or by a "potential energy suppression", which applies for both fermions and bosons at high electric fields and confinements. We also explore collisions that transfer molecules from one state of the confining potential to another. Although these collisions can be significant, we show that they do not play a role in the loss of the total number of molecules in the gas.Comment: 13 pages, 6 figure

Critical superfluid velocity in a trapped dipolar gas

We investigate the superfluid properties of a dipolar Bose-Einstein condensate (BEC) in a fully three-dimensional trap. Specifically, we calculate a superfluid critical velocity for this system by applying the Landau criterion to its discrete quasiparticle spectrum. We test this critical velocity by direct numerical simulation of condensate depletion as a blue-detuned laser moves through the condensate. In both cases, the presence of the roton in the spectrum serves to lower the critical velocity beyond a critical particle number. Since the shape of the dispersion, and hence the roton minimum, is tunable as a function of particle number, we thereby propose an experiment that can simultaneously measure the Landau critical velocity of a dipolar BEC and demonstrate the presence of the roton in this system.Comment: 5 pages, 4 figures, version accepted to PR

Predicting Bullying Among High School Students Using Individual and School Factors: Analysis of a National Survey

Being bullied has been recognized as a problem within the U.S. school systems. Individuals who have been bullied physically, verbally, relationally, or electronically typically suffer from mental health problems as a result. As it has been shown that males are more at risk for being bullied, it is important to understand what variables can predict males being bullied in order to design appropriate preventions and interventions to curb bullying in the schools. Four forms of school bullying behaviors among U.S. adolescent males and their association with type of bullying, school environment, and school performance and engagement variables were examined. Data were examined from the National Crime Victimization Survey School Crime Supplement. A sample of 1,636 males ages 14 to 18 was used from the survey. A series of logistic regression analyses were performed for each type of bullying (physical, verbal, relational, and cyber) and school environment (presence of gangs, guns, graffiti, drugs, and number of school safety measures in place) and school performance and engagement predictors (grades, extracurricular activity engagement, truancy, and number of fights). Linear regression analyses were also used to look at all the predictor variables and the frequency of each type of bullying. Results: The R2 values for the logistic regression analyses were quite small. However, trends could be observed from the odds ratios showing that fighting, drug availability, and graffiti were predictive of all four forms of bullying. The linear regression analyses also produced small R2 values. Effect plots were created to identify which significant variables had a greater effect on the frequency of being bullied. Conclusion: Schools should focus on removing graffiti and drugs from the schools. Prevention work should be used to help students find alternative ways to deal with problems other than resorting to fighting. Problems with reliability and validity of the survey are also discussed

Transformation of biomass carbohydrates by transition metal catalysts

By selectively removing functional groups from biomass derived carbohydrates, valuable platform chemicals can be generated from renewable sources. Through dehydration chemistry glucose can be upgraded into 5-(Hydroxymethyl)-2-furfuraldehyde (HMF) and levulinic acid. Iron (III) chloride hexahydrate has shown moderate activity to transform glucose into HMF and has also shown high yields and selectivity for the production of levulinic acid. Typically synthesized from acidic solutions made with mineral acids, levulinic acid has now been produced in high yields with a metal salt. The difference between maximizing production for HMF or levulinic acid from the same catalyst relies on the control of the reaction conditions. By using microwave irradiation, improved collisions and stabilized transition states allow for selective production of desired products while eliminating undesired reaction pathways. ^ Understanding the improvement of biomass carbohydrates also requires understanding how they are incorporated into the plant structures. By utilizing fluorescent tagging strategies a two part marking system was used to follow the incorporation of fucose into the plant cell wall. Fucose is limited in its use by plants only becoming incorporated into branched xylan chains that help to link cellulose and hemicellulose together. The synthesis of xylan in the plant Golgi also utilizes extracellular sugar. By feeding plant cells a specially designed azido tagged sugar it should become incorporated into the cell wall. On its own, the azido tagged sugar has very little fluorescent properties; however the attached azide group becomes important for click reactions. Click reactions involve two small functional groups that selectively combine. In this case the azide is clicked to an alkyne group to form a triazole. The alkyne group is part of a naphthalimide compound that has strong fluorescent properties due to its aromatic structure. By adding a triazole to the fluorescent naphthalimide complex, a much stronger fluorescent signal can be generated. By reproducing this strategy with plant cells it was hoped that the strong fluorescent signals could be imaged after their incorporation into plants. However issues with reproducibility of fluorescent emission spectrum and only two-fold intensity differences rather than the desired order of magnitude difference proved to be experimentally challenging