The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation

Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field

Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy

Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, light-harvesting complex stress-related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work, we propose a structural model of LHCSR1 from the moss P. patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses

Towards accurate solvation free energies of large biological systems

Continuum solvation models like PCM or COSMO are the standard tool to calculate solvation free energies in a quantum level, but have been typically limited to small biological molecules due to its large computational cost. Recently, a new implementation of COSMO based on a domain decomposition strategy (ddCOSMO) [1] has been presented, which speeds up calculations by several orders of magnitude, thus paving the way for its application to very large systems. Here, we report the parameterization of ddCOSMO to the prediction of hydration free energies based on the MST solvation model developed in Barcelona, [2][3]. The parameterization is based on the PM6 semi-empirical Hamiltonian, on a set of over 200 experimental hydration free energies. The new model opens the way to the accurate prediction of hydration free energies of very large biomolecules, thus going beyond the usual classical MM-PBSA or MM-GBSA approaches

Properties of Sobolev-type metrics in the space of curves

©2008 European Mathematical SocietyDOI: 10.4171/IFB/196We define a manifold M where objects c ϵ M are curves, which we parameterize as c : S¹ → R ⁿ (n ≥2, S¹ is the circle). Given a curve c, we define the tangent space TcM of M at c including in it all deformations h : S¹ → R ⁿ of c. We study geometries on the manifold of curves, provided by Sobolev–type Riemannian metrics H[superscript j]. We initially present some mathematical examples to show how the metrics H[superscript j] simplify or regularize gradient flows used in Computer Vision applications. We then provide some basilar results of Hj metrics; and, for the cases j = 1, 2, we characterize the completion of the space of smooth curves; we call this completion(s) “H¹ and H² Sobolev–type Riemannian Manifolds of Curves”. As a byproduct, we prove that the Fréchet distance of curves (see [MM06b]) coincides with the distance induced by the “Finsler L H [superscript ∞] metric” defined in §2.2 in [YM04b]

Light absorption enhancement in thin film hydrgenated amorphus Si solar cells

In this paper, light absorption enhancement in thin film solar cell (SC) is reported and analyzed. The suggested design is based on a nanostructured pattern that increases the diffuse scattered component of radiation and hence the absorption through the active layer. An ion beam sputtering (lBS) approach is used to texture large areas of the glass substrate with high aspect-ratio ripples in order to increase light scattering. Then, thin film SC supported on the textured glass is simulated and analyzed using 3D finite difference time domain (FDTD) method. The suggested SC can offer an ultimate efficiency of 19.26% with short circuit current of 15.76 mA/cm2 with an enhancement of 31.435% over the SC without texturing surface

Probing aqueous ions with non-local Auger relaxation

Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion-water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information

Trace Metals in Soot and PM2.5from Heavy-Fuel-Oil Combustion in a Marine Engine

Heavy fuel oil (HFO) particulate matter (PM) emitted by marine engines is known to contain toxic heavy metals, including vanadium (V) and nickel (Ni). The toxicity of such metals will depend on the their chemical state, size distribution, and mixing state. Using online soot-particle aerosol mass spectrometry (SP-AMS), we quantified the mass of five metals (V, Ni, Fe, Na, and Ba) in HFO-PM soot particles produced by a marine diesel research engine. The in-soot metal concentrations were compared to in-PM2.5measurements by inductively coupled plasma-optical emission spectroscopy (ICP-OES). We found that <3% of total PM2.5metals was associated with soot particles, which may still be sufficient to influence in-cylinder soot burnout rates. Since these metals were most likely present as oxides, whereas studies on lower-temperature boilers report a predominance of sulfates, this result implies that the toxicity of HFO PM depends on its combustion conditions. Finally, we observed a 4-to-25-fold enhancement in the ratio V:Ni in soot particles versus PM2.5, indicating an enrichment of V in soot due to its lower nucleation/condensation temperature. As this enrichment mechanism is not dependent on soot formation, V is expected to be generally enriched within smaller HFO-PM particles from marine engines, enhancing its toxicity

Local electrochemical investigation of copper patina

The patination of copper is known for its complexity and heterogeneous formation. For a deeper investigation, a locally resolved surface analysis was considered. An exact determination of the accessed area and a potentiostatic control in a three-electrode configuration was reached with the use of the electrochemical microcell technique, which enables local electrochemical measurement such as local electrochemical impedance spectroscopy and cyclic voltammetry. Such a technique provides a unique way for performing the investigation of heterogeneities on electrode surfaces. The local electrochemical measurements on the artificially patinated surface have allowed distinguishing areas of different reactivity even when the analysis of the surface revealed a homogenous chemical composition of patina. Local measurements with the electrochemical microcell showed the presence of small defects on the patina layer that can be modelled by considering a hemispherical diffusion process at small active areas surrounded by larger less reactive domains.CAPESSpanish Education Ministr

Tight-binding parameters for charge transfer along DNA

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the $\pi$ molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons, which probably indicates that hole transport along DNA is more favorable than electron transport. Our findings are also compared with existing calculations from first principles.Comment: 15 pages, 3 figures, 7 table

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

Many fundamental cellular processes such as gene expression are tightly regulated by protein allostery. Allosteric signal propagation from the regulatory to the active site requires long-range communication, the molecular mechanism of which remains a matter of debate. A classical example for long-range allostery is the activation of the methionine repressor MetJ, a transcription factor. Binding of its co-repressor SAM increases its affinity for DNA several-fold, but has no visible conformational effect on its DNA binding interface. Our molecular dynamics simulations indicate correlated domain motions within MetJ, and quenching of these dynamics upon SAM binding entropically favors DNA binding. From monitoring conformational fluctuations alone, it is not obvious how the presence of SAM is communicated through the largely rigid core of MetJ and how SAM thereby is able to regulate MetJ dynamics. We here directly monitored the propagation of internal forces through the MetJ structure, instead of relying on conformational changes as conventionally done. Our force distribution analysis successfully revealed the molecular network for strain propagation, which connects collective domain motions through the protein core. Parts of the network are directly affected by SAM binding, giving rise to the observed quenching of fluctuations. Our results are in good agreement with experimental data. The force distribution analysis suggests itself as a valuable tool to gain insight into the molecular function of a whole class of allosteric proteins