Biogeochemistry of oxygen minimum zone (OMZ) sediments, which are characterized by high input of labile organic matter, have crucial bearings on the benthic biota, gas and metal fluxes across the sediment-water interface, and carbon-sulfur cycling. Here we couple pore-fluid chemistry and comprehensive microbial diversity data to reveal the sedimentary carbon-sulfur cycle across a water-depth transect covering the entire thickness of eastern Arabian Sea OMZ, off the west coast of India. Geochemical data show remarkable increase in average total organic carbon content and aerial sulfate reduction rate (JSO42−) in the sediments of the OMZ center coupled with shallowing of sulfate methane transition zone and hydrogen sulfide and ammonium build–up. Total bacterial diversity, including those of complex organic matter degraders, fermentative and exoelectrogenic bacteria, and sulfate-reducers (that utilize only simple carbon compounds) were also found to be highest in the same region. The above findings indicate that higher organic carbon sequestration from the water-columns (apparently due to lower benthic consumption, biodegradation and biotransformation) and greater bioavailability of simple organic carbon compounds (apparently produced by fermetative microflora of the sediments) are instrumental in intensifying the carbon-sulfur cycle in the sediments of the OMZ center.
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy is demonstrated.
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged basepair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.
We have presented a simple approach to quantum theory of Brownian motion and barrier crossing dynamics. Based on an initial coherent state representation of bath oscillators and an equilibrium canonical distribution of quantum-mechanical mean values of their co-ordinates and momenta we have derived a c number generalized quantum Langevin equation. The approach allows us to implement the method of classical non-Markovian Brownian motion to realize an exact generalized non-Markovian quantum Kramers' equation. The equation is valid for arbitrary temperature and friction. We have solved this equation in the spatial diffusion-limited regime to derive quantum Kramers' rate of barrier crossing and analyze its variation as a function of the temperature and friction. While almost all the earlier theories rest on quasiprobability distribution functions (e.g., Wigner function) and path integral methods, the present work is based on true probability distribution functions and is independent of path integral techniques. The theory is a natural extension of the classical theory to quantum domain and provides a unified description of thermally activated processes and tunneling.
We consider a system-reservoir model where the reservoir is modulated by an external noise. Both the internal noise of the reservoir and the external noise are stationary, Gaussian and are characterized by arbitrary decaying correlation functions. Based on a relation between the dissipation of the system and the response function of the reservoir driven by external noise we numerically examine the model using a full bistable potential to show that one can recover the turn-over features of the usual Kramers' dynamics when the external noise modulates the reservoir rather than the system directly.We derive the generalized Kramers' rate for this nonequilibrium open system.
Based on a coherent state representation of noise operator and an ensemble averaging procedure using Wigner canonical thermal distribution for harmonic oscillators, a generalized quantum Langevin equation has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, 051106 (2002)] to derive the equations of motion for probability distribution functions in c-number phase-space. We extend the treatment to explore several systematic approximation schemes for the solutions of the Langevin equation for nonlinear potentials for a wide range of noise correlation, strength and temperature down to the vacuum limit. The method is exemplified by an analytic application to harmonic oscillator for arbitrary memory kernel and with the help of a numerical calculation of barrier crossing, in a cubic potential to demonstrate the quantum Kramers' turnover and the quantum Arrhenius plot.
Abstract. -We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.Introduction. -Under a large range of salt conditions and temperatures, the double-helix is the thermodynamically stable configuration of DNA [1,2]. This stability is effected by the Watson-Crick H-bonding of base-pairs (bps), and the stronger base-stacking of neighbouring, planar aromatic bps, that by hydrophobic interactions stabilize the helical structure [3,4]. At the same time, double-stranded DNA (dsDNA) is distinguished by the ease with which locally the molecule can open up (and later rejoin), to produce flexible bubbles of single-stranded DNA (ssDNA), see figure 1a [1,2]. The formation of DNA-bubbles, despite the rather large enthalpy necessary to break the base-stacking, is made possible by the entropy gain, due to which the free energy for breaking additional bps is of the order of k B T , after overcoming a bubble initiation barrier σ 0 ≃ 10 −5 . . . 10 −3 [5]. At room or physiological temperature, bubbles of 20 to 30 broken bps are created [2]. DNA-bubbles preferentially form in regions rich in the weaker AT bps [5], and they are related to physiological processes such as transcription initiation [6].Traditionally measured in bulk by UV-absorption at elevated temperatures [7], it is now possible to probe the time series of the size fluctuations of a single DNA-bubble (DNAbreathing) by fluorescence correlation techniques in short, designed DNA-stretches [8]. These DNA-constructs contain a well-defined (AT) M breathing domain, that is labelled by a fluorophore-quencher pair. Such a model system allows for a precise quantitative analysis, from which the parameters of the underlying theoretical model (usually the Poland-Scheraga model) can be determined. This fluorescence technique is being developed further to measure longer bubble domains, also at higher temperatures. It is therefore of interest to provide a theoretical model to understand DNA-breathing in a homopolymer domain quantitatively. One
Based on a Fokker-Planck description of external Ornstein-Uhlenbeck noise and cross-correlated noise processes driving a dynamical system we examine the interplay of the properties of noise processes and the dissipative characteristic of the dynamical system in the steady state entropy production and flux. Our analysis is illustrated with appropriate examples.
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