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Alan Bishop

Publications and source records attributed to Alan Bishop.

3 recordsLinked to original sources

Helically Enhanced Chiroptical Response and Symmetry Breaking in Conjugated Polymers

Chiral $\pi$-conjugated polymers are an attractive material platform for spin polarized carrier-transport and spectroscopy, but fundamental considerations for how torsional disorder influences the response properties of the material have not been considered. Here we combine atomistic electronic structure modeling with with experimental spectroscopic measurements to examine symmetry breaking in the prototypical $\pi$-conjugated polymer polyacetylene, (CH)$_x$. Chiral (CH)$_x$ oligomers are generated in distinct conformations which differ in their out-of-plane tonsorial ordering. We find that a \textit{helical }conformation introduces orders of magnitude enhanced chiroptical activity due to a solenoid effect. This effect is visualized by the Transition Chiral Tensor analysis which shows signatures of domain ordering which eliminates destructive interference between electric and magnetic contributions. These findings highlight the capability to develop a hierarchical interpretation relating local, fragment symmetry breaking to global, nonlocal interactions governing chiroptical response in emerging chiral materials.

cond-mat.mtrl-sci

Distributions of Bubble Lifetimes and Bubble Lengths in DNA

We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.

physics.bio-ph

Stretching of vortex lines and generation of vorticity in the three-dimensional complex Ginzburg-Landau Equation

The dynamics of curved vortex filaments is studied analytically and numerically in the framework of a three-dimensional complex Ginzburg-Landau equation (CGLE). It is proved that a straight vortex line is unstable with respect to spontaneous stretching and bending in a certain range of parameters of the CGLE, resulting in formation of persistent entangled vortex configurations. The analysis shows that the standard approach relating the velocity of the filament with the local curvature, is insufficient to describe the instability and self-generation of vorticity.

patt-sol