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Berlin Brandenburg

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  • 1
    Language: English
    In: The journal of physical chemistry. B, 07 June 2012, Vol.116(22), pp.6233-49
    Description: We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.
    Keywords: Molecular Dynamics Simulation
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 2
    Language: English
    In: The journal of physical chemistry. B, 23 October 2008, Vol.112(42), pp.13359-66
    Description: Two different methods are proposed to estimate the persistence length ( P) of DNA from the measured torsion elastic constant (alpha) and the twist energy parameter ( E T ) that governs the supercoiling free energy. The first method involves Monte Carlo simulations and reversible-work calculations of E T for model DNAs that possess the measured alpha and selected trial values of P. Comparison of the computed E T values with the experimental value allows estimation of P (or equivalently the bending elastic constant (kappa beta)) by interpolation. A far simpler, though less accurate, alternative is to solve a previously conjectured analytical relation connecting E T , alpha, kappa beta (or P), and an unknown "constant" ( B). The present simulations are used to ascertain the optimum value of B and to assess the validity and accuracy of that relation. Within the simulation errors, P values obtained from the measured alpha and E T via this analytical expression agree with those determined from the simulations and E T values reckoned from the input alpha and kappa beta by this analytical expression agree with the corresponding simulated values. Although B is found to be insensitive to variation in alpha, it appears to decline slightly with increasing kappa beta. The original analytical expression is modified to take this apparent variation of B with kappa beta into account. By using this modified analytical relation to estimate P (from the measured alpha and E T ) or E T (from the input alpha and kappa beta), much closer agreement is obtained respectively with the values of P or E T obtained from the simulations. As specific examples, these methods are applied to determine P in 0 and 20 w/v % ethylene glycol, which has been shown to induce a structural transition in duplex DNA.
    Keywords: Torsion, Mechanical ; DNA, Superhelical -- Chemistry ; Elasticity -- Drug Effects ; Ethylene Glycol -- Pharmacology
    ISSN: 1520-6106
    E-ISSN: 15205207
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  • 3
    Language: English
    In: Soil Science Society of America Journal, Jan, 2013, Vol.77(1), p.54(6)
    Description: Until recently, the custom manufacture of equipment for laboratory or field experiments in soil science required appreciable know-how, and was extremely time-consuming. Technological advances in rapid prototyping and o3-D printingo in the last decade afford significant, and as yet untapped, opportunities to manufacture equipment in a very different way. In the present note, we demonstrate with two concrete examples that 3-D printing is not only a very effective and versatile technique to produce laboratory or field equipment. It also alleviates some of the restrictive technical constraints imposed by lathes and molding processes used traditionally, and it permits a much more efficient sharing of information among researchers. Given the tremendous advances in 3-D printing unfolding at the moment, it is anticipated that this technology will revolutionize the way we design, and especially replicate, experiments in soil science.
    Keywords: Rapid Prototyping -- Technology Application ; 3d Printing -- Technology Application ; Technological Innovations -- Usage
    ISSN: 0361-5995
    E-ISSN: 14350661
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  • 4
    Language: English
    In: The journal of physical chemistry. B, 31 July 2008, Vol.112(30), pp.9219-36
    Description: The weakly bending rod (WBR) model of double-stranded DNA (dsDNA) is adapted to analyze the internal dynamics of dsDNA as observed in electron paramagnetic resonance (EPR) measurements of the spin-lattice relaxation rate, R(1e), for spin probes rigidly attached to nucleic acid-bases. The WBR theory developed in this work models dsDNA base-pairs as diffusing rigid cylindrical discs connected by bending and twisting springs whose elastic force constants are kappa and alpha, respectively. Angular correlation functions for both rotational displacement and velocity are developed in detail so as to compute values for R(1e) due to four relaxation mechanisms: the chemical shift anisotropy (CSA), the electron-nuclear dipolar (END), the spin rotation (SR), and the generalized spin diffusion (GSD) relaxation processes. Measured spin-lattice relaxation rates in dsDNA under 50 bp in length are much faster than those calculated for the same DNAs modeled as rigid rods. The simplest way to account for this difference is by allowing for internal flexibility in models of DNA. Because of this discrepancy, we derive expressions for the spectral densities due to CSA, END, and SR mechanisms directly from a weakly bending rod model for DNA. Special emphasis in this development is given to the SR mechanism because of the lack of such detail in previous treatments. The theory developed in this paper provides a framework for computing relaxation rates from the WBR model to compare with magnetic resonance relaxation data and to ascertain the twisting and bending force constants that characterize DNA.
    Keywords: Movement ; Spin Labels ; DNA -- Chemistry
    ISSN: 1520-6106
    E-ISSN: 15205207
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  • 5
    Language: English
    In: Biophysical Journal, 2005, Vol.89(4), pp.2258-2276
    Description: A simple and complete derivation of the relation between concentration-based preferential interaction coefficients and integrals over the relevant pair correlation functions is presented for the first time. Certain omissions from the original treatment of pair correlation functions in multicomponent thermodynamics are also addressed. Connections between these concentration-based quantities and the more common molality-based preferential interaction coefficients are also derived. The pair correlation functions and preferential interaction coefficients of both solvent (water) and cosolvent (osmolyte) in the neighborhood of a macromolecule contain contributions from short-range repulsions and generic long-range attractions originating from the macromolecule, as well as from osmolyte-solvent exchange reactions beyond the macromolecular surface. These contributions are evaluated via a heuristic analysis that leads to simple insightful expressions for the preferential interaction coefficients in terms of the volumes excluded to the centers of the water and osmolyte molecules and a sum over the contributions of exchanging sites in the surrounding solution. The preferential interaction coefficients are predicted to exhibit the experimentally observed dependence on osmolyte concentration. Molality-based preferential interaction coefficients that were reported for seven different osmolytes interacting with bovine serum albumin are analyzed using the this formulation together with geometrical parameters reckoned from the crystal structure of human serum albumin. In all cases, the excluded volume contribution, which is the volume excluded to osmolyte centers minus that excluded to water centers in units of exceeds in magnitude the contribution of the exchange reactions. Under the assumption that the exchange contribution is dominated by sites in the first surface-contiguous layer, the ratio of the average exchange constant to its neutral random value is determined for each osmolyte. These ratios all lie in the range 1.0 ± 0.15, which indicates rather slight deviations from random occupation near the macromolecular surface. Finally, a mechanism is proposed whereby the chemical identity of an osmolyte might be concealed from partially ordered multilayers of water in clefts, grooves, and pits, and its consequences are noted.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 6
    Language: English
    In: Biophysical Journal, 15 May 2008, Vol.94(10), pp.3798-3809
    Description: A simulated continuous wave electron paramagnetic resonance spectrum of a nitroxide spin label can be obtained from the Fourier transform of a free induction decay. It has been previously shown that the free induction decay can be calculated by solving the time-dependent stochastic Liouville equation for a set of Brownian trajectories defining the rotational dynamics of the label. In this work, a quaternion-based Monte Carlo algorithm has been developed to generate Brownian trajectories describing the global rotational diffusion of a spin-labeled protein. Also, molecular dynamics simulations of two spin-labeled mutants of T4 lysozyme, T4L F153R1, and T4L K65R1 have been used to generate trajectories describing the internal dynamics of the protein and the local dynamics of the spin-label side chain. Trajectories from the molecular dynamics simulations combined with trajectories describing the global rotational diffusion of the protein are used to account for all of the dynamics of a spin-labeled protein. Spectra calculated from these combined trajectories correspond well to the experimental spectra for the buried site T4L F153R1 and the helix surface site T4L K65R1. This work provides a framework to further explore the modeling of the dynamics of the spin-label side chain in the wide variety of labeling environments encountered in site-directed spin labeling studies.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 7
    Language: English
    In: Biophysical Journal, 2004, Vol.86(5), pp.3079-3096
    Description: Mesoscopic models of unmelted and locally melted supercoiled DNAs in 20 mM ionic strength are simulated over a range of linking difference from Δ = 0 to −26 turns, or superhelix density from = 0 to −0.062. A domain containing = 0, 28, or 56 melted basepairs (out of 4349 total) is modeled simply by a region of suitable length with substantially reduced torsion and bending elastic constants. Average structural properties are calculated from the saved configurations, and a reversible work protocol is used to calculate the supercoiling free energy, The cross-writhe between duplex and melted regions (defined herein) is found to be negligibly small. The total writhe, radius of gyration, and ordered elements of the diagonalized inertial tensor are found to be nearly universal functions of the residual linking difference ( ) associated with the duplex region, independent of . However, deformability of the tertiary structure, as manifested by the variance of those same properties, is not a universal function of but depends upon . varies with more strongly than due to the low ionic strength. The twist energy parameter, obtained from the simulated and net twisting strain of the melted region, is found to be independent of , hence also of the torsion and bending elastic constants of the melted region. However, increases linearly with which leads to 1), a small overestimation of for any given when is determined from the observed and by the protocol of Bauer and Benham; and 2), a significant enhancement of the apparent slope, obtained via the protocol of Bauer and Benham, relative to the actual slope fixed After taking these two effects into account, the theoretical and experimental values and values agree rather well. For the larger the melted regions are found preferentially in the linker domains between interwound arms, rather than in the apical regions at the ends of interwound arms.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 8
    Language: English
    In: Biopolymers, November 2004, Vol.75(4), pp.291-313
    Description: Both theory and experiments are employed to investigate the effects of small neutral osmolytes on the average intrinsic twist (), the torsion and bending elastic constants, and the twist energy parameter () that governs the supercoiling free energy. The experimental data for ethylene glycol and acetamide at 37°C suggest, and are interpreted in terms of, a model wherein the DNA exhibits an equilibrium between two distinct conformational states that possess different numbers of bound water molecules and exhibit different intrinsic twists and torsion and bending elastic constants. Expressions are derived to relate the effective and to the equilibrium constant, water activity (), and number () of bound water molecules released per cooperative domain undergoing the two‐state transition. The variations of and with −ln() are similar for acetamide and ethylene glycol at 37°C. Fitting the theory to those data yields the range = 103–125 for ethylene glycol and = 71–113 for acetamide, depending on the assumed value of for the dehydrated state. The cooperative domain size of the two‐state transition is estimated to exceed about 25–30 base pairs (bp). Between 0 and 19.4 w/v % ethylene glycol, the torsion elastic constant, measured by time‐resolved fluorescence polarization anisotropy (FPA), by 1.37‐fold, whereas the measured by 1.15‐fold over that same range. The implied in bending rigidity over that range is by a factor of about 0.7. The variations of and with increasing −ln() due to added ethylene glycol at 37°C are far smaller than the corresponding variations observed previously at 14 and 15°C. However, at 21°C, upon adding either ethylene glycol or acetamide, and initially decline steeply with increasing −ln(), with slopes possibly comparable to those seen at 14 and 15°C, but then flatten out and follow curves similar to those at 37°C. Possible origins of such mixed behavior are discussed. The effects of betaine at both 37 and 21°C differ qualitatively and quantitatively in various respects from those of ethylene glycol and acetamide. Upon adding sucrose, initially jumps to plateaus at both 37 and 21°C, but its effects on cannot be reliably assessed, due to the limited range of −ln(). © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
    Keywords: Dna ; Supercoiling Free Energy ; Small Neutral Osmolytes ; Average Intrinsic Twist ; Torsion And Bending Elastic Constants ; Twist Energy Parameter ; Ethylene Glycol ; Acetamide
    ISSN: 0006-3525
    E-ISSN: 1097-0282
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  • 9
    Language: English
    In: Biopolymers, 15 February 2007, Vol.85(3), pp.222-232
    Description: Upon increasing the concentration of ethylene glycol (EG) at 37°C, the twist energy parameter, , which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant () of linear p30δ DNA and on the hydrodynamic radius () of a synthetic 24 bp duplex DNA were examined at both 40 and 20°C. The time‐resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) ; (2) ; (3) the lifetimes of intercalated and non‐intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40°C, addition of 20 w/v % EG caused a substantial (1.27‐ to 1.35‐fold) increase in , a significant change in the CD spectrum, and a very small, marginally significant increase in , but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of , these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40°C. At 20°C, addition of 20 w/v % EG caused a marginally significant decrease in and very little change in any other measured properties. Also at 20°C, addition of 30 w/v % betaine caused a marginally significant increase in and significant but modest change in the CD spectrum, but very little change in any other properties. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 222–232, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
    Keywords: Dna ; Fluorescence Polarization Anisotropy ; Torsion Elastic Constant ; Hyrdrodynamic Radius ; Circular Dichroism Spectroscopy ; Fluorimetry ; Ethylene Glycol ; Betaine Glycine ; Secondary Structure
    ISSN: 0006-3525
    E-ISSN: 1097-0282
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  • 10
    Language: English
    In: Social Issues in Living Color : Challenges and Solutions from the Perspective of Ethnic Minority Psychology: Promoting Health and Well-Being
    ISBN: 978-1-4408-3337-3
    Source: Gale Virtual Reference Library (GVRL)
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