Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair

Breakdown of Hydrodynamic Transport Theory in the Ordered Phase of Helimagnets

It is shown that strong fluctuations preclude a hydrodynamic description of transport phenomena in helimagnets, such as MnSi, at T>0. This breakdown of hydrodynamics is analogous to the one in chiral liquid crystals. Mode-mode coupling effects lead to infinite renormalizations of various transport coefficients, and the actual macroscopic description is nonlocal. At T=0 these effects are weakened due to the fluctuation-dissipation theorem, and the renormalizations remain finite. Observable consequences of these results, as manifested in the neutron scattering cross-section, are discussedComment: 4pp., 1 eps figur

Wave spectra of 2D dusty plasma solids and liquids

Brownian dynamics simulations were carried out to study wave spectra of two-dimensional dusty plasma liquids and solids for a wide range of wavelengths. The existence of a longitudinal dust thermal mode was confirmed in simulations, and a cutoff wavenumber in the transverse mode was measured. Dispersion relations, resulting from simulations, were compared with those from analytical theories, such as the random-phase approximation (RPA), quasi-localized charged approximation (QLCA), and harmonic approximation (HA). An overall good agreement between the QLCA and simulations was found for wide ranges of states and wavelengths after taking into account the direct thermal effect in the QLCA, while for the RPA and HA good agreement with simulations were found in the high and low temperature limits, respectively.Comment: 26 pages, 9 figure

Developing Peer-to-Peer (P2P) Energy Trading Model for Malaysia:A Review and Proposed Implementation

A decade ago, Malaysia introduced the Renewable Energy Act 2011. This led to the RE proliferation, especially with the adoption of solar photovoltaics as an alternative energy source for prosumers to generate green energy and reduce their energy costs. Since then, the RE policies have evolved with the introduction of feed-in tariff (FiT) and various version of Net Energy Metering (NEM) schemes. Such initiatives may not be holistic enough to benefit all stakeholders; thus, Malaysia introduced its first pilot P2P energy trading in 2019. However, there was no significant progress to the P2P pilot thereafter, with a Go-to-Market plan. As such, this review proposes a model for P2P energy trading for Malaysia based on several key success factors including the market design, trading mechanism, physical and virtual infrastructure, policy and governance and social. Malaysia's electricity market structure is also compared to South Korea, Germany, Thailand, United Kingdom, and Singapore (ranked in the top 20 Ease of Getting Electricity by World Bank in 2019) to understand the implication of P2P energy trading adoption. Apart from that, this paper also highlights the key technical and non-technical reviews of the P2P energy trading implementation.</p

Bubble kinematics in a sheared foam

We characterize the kinematics of bubbles in a sheared two-dimensional foam using statistical measures. We consider the distributions of both bubble velocities and displacements. The results are discussed in the context of the expected behavior for a thermal system and simulations of the bubble model. There is general agreement between the experiments and the simulation, but notable differences in the velocity distributions point to interesting elements of the sheared foam not captured by prevalent models

Molecular Dynamics Simulation of Compressible Fluid Flow in Two-Dimensional Channels

We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream reservoir is kept at vacuum. The channel is sufficiently long in the direction of the flow that the finite length has little effect on the properties of the fluid in the central region. The simulated system is represented by an efficient data structure, whose internal elements are created and manipulated dynamically in a layered fashion. Consequently the code is highly efficient and manifests completely linear performance in simulations of large systems. We obtain the steady-state velocity, temperature, and density distributions in the system. The velocity distribution across the channel is very nearly a quadratic function of the distance from the center of the channel and reveals velocity slip at the boundaries; the temperature distribution is only approximately a quartic function of this distance from the center to the channel. The density distribution across the channel is non-uniform. We attribute this non-uniformity to the relatively high Mach number, approximately 0.5, in the fluid flow. An equation for the density distribution based on simple compressibility arguments is proposed; its predictions agree well with the simulation results. Validity of the concept of local dynamic temperature and the variation of the temperature along the channel are discussed.Comment: 16 pages (in latex) + 8 figures (in a single ps file). Submitted to the Physical Review

DNA binding shifts the redox potential of the transcription factor SoxR

Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR–DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property

Critical dynamics of an isothermal compressible non-ideal fluid

A pure fluid at its critical point shows a dramatic slow-down in its dynamics, due to a divergence of the order-parameter susceptibility and the coefficient of heat transport. Under isothermal conditions, however, sound waves provide the only possible relaxation mechanism for order-parameter fluctuations. Here we study the critical dynamics of an isothermal, compressible non-ideal fluid via scaling arguments and computer simulations of the corresponding fluctuating hydrodynamics equations. We show that, below a critical dimension of 4, the order-parameter dynamics of an isothermal fluid effectively reduces to "model A," characterized by overdamped sound waves and a divergent bulk viscosity. In contrast, the shear viscosity remains finite above two dimensions. Possible applications of the model are discussed.Comment: 19 pages, 7 figures; v3: minor corrections and clarifications; as published in Phys. Rev.

Numerical Methods for the Stochastic Landau-Lifshitz Navier-Stokes Equations

The Landau-Lifshitz Navier-Stokes (LLNS) equations incorporate thermal fluctuations into macroscopic hydrodynamics by using stochastic fluxes. This paper examines explicit Eulerian discretizations of the full LLNS equations. Several CFD approaches are considered (including MacCormack's two-step Lax-Wendroff scheme and the Piecewise Parabolic Method) and are found to give good results (about 10% error) for the variances of momentum and energy fluctuations. However, neither of these schemes accurately reproduces the density fluctuations. We introduce a conservative centered scheme with a third-order Runge-Kutta temporal integrator that does accurately produce density fluctuations. A variety of numerical tests, including the random walk of a standing shock wave, are considered and results from the stochastic LLNS PDE solver are compared with theory, when available, and with molecular simulations using a Direct Simulation Monte Carlo (DSMC) algorithm