Session A2: Biological and Complex Systems

Interplay between protein folding and its physicochemical properties probed by VUV and X-ray action spectroscopy

Understanding the correlation between proteins folding and its electronic structures and physicochemical properties could possibly lead to a more efficient prediction of protein functions in living organisms. We report on the recent experimental results obtained from both VUV and X-ray gas-phase action spectroscopy of multiply protonated protein ions formed by electrospray. The experiment has been performed by coupling a commercial linear quadrupole ion trap, fitted with an electrospray ion source (ESI), to the DESIRS (VUV) and PLEIADES (X-ray) beamlines at the SOLEIL facility, France. The series of charge states that could be formed by ESI for different proteins have been studied both in the valence shell and around the C-, N- and O-edges, with some control on their three-dimensional structure provided by their level of protonation. We found that both valence and core ionization energies of a protonated protein are strongly correlated to its tertiary structure, which influences its effective Coulomb field. On the other hand, the electronic core-to-valence shell transition energies are not markedly affected by the unfolding of the protein.   

Multicomponent model of deformation and detachment of a blood clot under fluid flow

A novel model derived by using the Energetic Variational Approach coupled with the phase field method, is developed for simulating deformation and detachment of blood clot under flow. Volume fractions of components of the blood clot, namely, fibrin, platelets and the plasma are denoted by phase field functions. Interactions among these components are included in the model by using different mixed energy and elasticities of the platelets and fibrin network are both considered in the model. Rheological property of blood clot under flow is determined by mechanical properties of components of the blood clot. An energy stable numerical scheme based on the energy split method is implemented for solving the coupling system. Model simulations predict that higher viscosity, elasticity and surface tension proved greater resistance to the deformation and removal by the flow. Moreover, the higher elasticity of the blood clot also causes lower pressure inside the blood clot, which contributes to its contraction.   

\textbf{Formation of Multiple-Oxide/Hydroxide Species on GaP(111) Surface tracked by Near-Ambient Pressure XPS}

A photoelectrochemical (PEC) solar cell can convert solar energy into chemical energy and store it in the form of hydrogen via water splitting, a promising route to generate sustainable and clean fuels. PEC solar cells consisted of phosphide-based III-V semiconductors have a higher solar to hydrogen (STH) conversion efficiency than other materials. They are, however, usually limited by practical drawbacks such as photocorrosion or decreased electron extraction efficiency due to the formation of surface oxide species. Therefore, it is desirable to understand the interfacial processes of water/O$_{\mathrm{2}}$ interactions with semiconductors, and to elucidate possible oxidation and reduction mechanisms at the H$_{\mathrm{2}}$O(O$_{\mathrm{2}})$/semiconductor interface, especially under near realistic conditions. In this study, H$_{\mathrm{2}}$O(O$_{\mathrm{2}})$ dissociative adsorption onto a GaP (111) surface was investigated using near ambient pressure X-ray photoelectron spectroscopy (NAP XPS) at various pressures and temperatures. The interfacial chemistry was tracked by recording high-resolution photoemission spectra of Ga 2p$_{\mathrm{3/2}}$, O 1s, and P 2p. The formation of Ga and P oxide/hydroxide networks was suggested and a "phase diagram" that demonstrates the distribution of different chemical species under various experimental conditions has been generated.   

Sorption mechanisms of metals to multi-layer graphene oxide.

Environmental toxic metal contamination remediation and prevention is an ongoing issue. Graphene oxide is highly sorptive for many heavy metals over a wide pH range under different ionic strength conditions. We present x-ray absorption fine structure (XAFS) spectroscopy results investigating the binding environment of Pb(II), Cd(II) and U(VI) ions onto multi-layered graphene oxide (MLGO). Analysis indicates that the dominant sorption mechanism of Pb to MLGO changes as a function of pH, with increasing inner sphere contribution as pH increases. In contrast, the sorption mechanism of Cd to MLGO remains constant under the studied pH range. This adsorption mechanism is an electrostatic attraction between the hydrated Cd$^{\mathrm{+2}}$ ion and the MLGO surface. The U(VI), present as a uranyl ion, changes only subtly as a function of pH and is bound to the surface via an inner sphere bond. Since each metal exhibits unique binding properties, it might be possible to cater the MLGO in order to best adsorb specific metal ions and optimize the environmental remediation or prevention in filtration systems.   

Core-periphery structure of brain cortical networks

The first step towards understanding how the brain works is to describe its structure, its wiring and the guiding principles behind it. With the use of retrograde tracing experiments, which yield reliable directed and weighted connectivity data, the mouse and macaque monkey cortex was mapped at the level of functional areas. Although very dense, these interareal networks have strong structural specificity. We show that this is governed by an exponential cost to wiring, the probability of connecting two areas decreases exponentially with the distance between them. To define the importance of this rule, we constructed a single-parameter random graph model, which indeed predicted several weighted and binary properties of the networks. Using a non-traditional clique-based method we show the existence of a core-periphery structure in the experimental data, a key property of any functional network, which was found by the model as well. To emphasize the validity of this structure we used various binary and weighted importance measures (spectral and path based centralities, hierarchical decomposition, clique distribution analysis), which result in consistent outcomes. These findings underline the importance of the exponential cost to wiring, as a guiding principle in brain formation.