Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)(n) repeats or (TG)(n) repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)(n) sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)(n) sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.National Research Foundation NRF-2012 R1A1A3013044 NRF-2014R1A1A2055681NRF-2012R1A1A2021736IBS-R023-D1NRF-2015R1A2A2A01005916Chemistr

Helices at Interfaces

Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar squeezed conformations often resembling looped waves, spirals or circles. Using theory and Monte-Carlo simulations we illuminate here the mechanics and the unusual statistical mechanics of confined helices and show that their fluctuations can be understood in terms of moving and interacting discrete particle-like entities - the "twist-kinks". We show that confined filaments can thermally switch between discrete topological twist quantized states, with some of the states exhibiting dramatically enhanced circularization probability while others displaying surprising hyperflexibility

Superconducting fluctuations in organic molecular metals enhanced by Mott criticality

Unconventional superconductivity typically occurs in materials in which a small change of a parameter such as bandwidth or doping leads to antiferromagnetic or Mott insulating phases. As such competing phases are approached, the properties of the superconductor often become increasingly exotic. For example, in organic superconductors and underdoped high-$T_\mathrm{c}$ cuprate superconductors a fluctuating superconducting state persists to temperatures significantly above $T_\mathrm{c}$. By studying alloys of quasi-two-dimensional organic molecular metals in the $\kappa$-(BEDT-TTF)$_2$X family, we reveal how the Nernst effect, a sensitive probe of superconducting phase fluctuations, evolves in the regime of extreme Mott criticality. We find strong evidence that, as the phase diagram is traversed through superconductivity towards the Mott state, the temperature scale for superconducting fluctuations increases dramatically, eventually approaching the temperature at which quasiparticles become identifiable at all.Comment: 19 pages, 4 figures, 1 tabl

The voltage-gated potassium channel Shaker promotes sleep via thermosensitive GABA transmission

Genes and neural circuits coordinately regulate animal sleep. However, it remains elusive how these endogenous factors shape sleep upon environmental changes. Here, we demonstrate that Shaker (Sh)-expressing GABAergic neurons projecting onto dorsal fan-shaped body (dFSB) regulate temperature-adaptive sleep behaviors in Drosophila. Loss of Sh function suppressed sleep at low temperature whereas light and high temperature cooperatively gated Sh effects on sleep. Sh depletion in GABAergic neurons partially phenocopied Sh mutants. Furthermore, the ionotropic GABA receptor, Resistant to dieldrin (Rdl), in dFSB neurons acted downstream of Sh and antagonized its sleep-promoting effects. In fact, Rdl inhibited the intracellular cAMP signaling of constitutively active dopaminergic synapses onto dFSB at low temperature. High temperature silenced GABAergic synapses onto dFSB, thereby potentiating the wake-promoting dopamine transmission. We propose that temperature-dependent switching between these two synaptic transmission modalities may adaptively tune the neural property of dFSB neurons to temperature shifts and reorganize sleep architecture for animal fitness. Ji-hyung Kim and Yoonhee Ki et al. show that low temperatures suppress sleep in Drosophila by increasing GABA transmission in Shaker-expressing GABAergic neurons projecting onto the dorsal fan-shaped body, while high temperatures potentiate dopamine-induced arousal by reducing GABA transmission. This study highlights a role for Shaker in sleep modulation via a temperature-dependent switch in GABA signaling

Social Exclusion Online: A Literature Review and suggestions for Future Research

Because the belonging need is fundamental, an exclusion experience thwarts this need and causes cognitive, behavioral, and affective consequences for human functioning. This paper aims to integrate the enumerated effects of social exclusion in a real-world setting. Also, as the boundary between the real world and cyberspace is blurred, it became crucial to understand the dynamics of social relationships in an online environment. Thus, this paper also intends to review the influences of social exclusion in the online environment. Based on a review of previous findings, this study provides several suggestions for future research. There are interesting research opportunities to investigate how ostracized people react to being excluded, especially in cyberspace