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End date: 2024 × DDC: 530 × Type: Article × Subject: DNA ×

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Now showing 1 - 3 of 3
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    Knots, links, anyons and statistical mechanics of entangled polymer rings
    (Amsterdam : North-Holland Publ. Co., 2019) Ferrari, Franco; Paturej, Jarosław; Pia̧tek, Marcin; Zhao, Yani
    The field theory approach to the statistical mechanics of a system of N polymer rings linked together is extended to the case of links whose paths in space are characterized by a fixed number 2s of maxima and minima. Such kind of links are called 2s-plats and appear for instance in the DNA of living organisms or in the wordlines of quasiparticles associated with vortices nucleated in a quasi-two-dimensional superfluid. The path integral theory describing the statistical mechanics of polymers subjected to topological constraints is mapped here into a field theory of quasiparticles (anyons). In the particular case of s=2, it is shown that this field theory admits vortex solutions with special self-dual points in which the interactions between the vortices vanish identically. The topological states of the link are distinguished using two topological invariants, namely the Gauss linking number and the so-called bridge number which is related to s. The Gauss linking number is a topological invariant that is relatively weak in distinguishing the different topological configurations of a general link. The addition of topological constraints based on the bridge number allows to get a glimpse into the non-abelian world of quasiparticles, which is relevant for important applications like topological quantum computing and high-TC superconductivity. At the end an useful connection with the cosh-Gordon equation is shown in the case s=2. © 2019
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    Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy
    (Melville, NY : AIP Publishing LLC, 2015) Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas
    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.
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    Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations
    (Melville, NY : AIP Publishing LLC, 2017) Liu, Yingliang; Guchhait, Biswajit; Siebert, Torsten; Fingerhut, Benjamin P.; Elsaesser, Thomas
    Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.