From Transient to Stationary Transport in Porous Networks under Various Adsorption Conditions and Kinetics.

We investigate the interplay between adsorption and transport in a two-dimensional porous medium by means of an extended Lattice Boltzmann technique within the Two-Relaxation-Time framework. We focus on two canonical adsorption thermodynamics and kinetics formalisms: (1) the Henry model in which the adsorbed amount scales linearly with the free adsorbate concentration and (2) the Langmuir model that accounts for surface saturation upon adsorption. We simulate transport of adsorbing and nonadsorbing particles to investigate the effect of the adsorption/desorption ratio k, initial free adsorbate concentration c0, surface saturation Γ∞, and Peclet numbers Pe on their dispersion behavior. In all cases, despite marked differences between the different adsorption models, the three following transport regimes are observed: diffusion-dominated regime, transient regime and Gaussian or nearly Gaussian dispersion regime. On the one hand, at short times, the intermediate transient regime strongly depends on the system's parameters with the shape of the concentration field at a given time being dependent on the amount of particles adsorbed shortly after injection. On the other hand, at longer times, the influence of the initial condition attenuates as particles sample sufficiently the adsorbed and nonadsorbed states. Once such dynamical equilibrium is reached, transport becomes Gaussian (i.e., normal) or nearly Gaussian in the asymptotic regime. Interestingly, the characteristic time scale to reach equilibrium, which varies drastically with the system's parameters, can be much longer than the actual simulation time. In practice, such results reflect many experimental situations such as in water treatment where dispersion is found to remain anomalous (non-Gaussian), even if transport is considered over long macroscopic times.

Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix.

Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.

Lattice Boltzmann method for adsorption under stationary and transient conditions: Interplay between transport and adsorption kinetics in porous media.

A numerical method based on the Lattice Boltzmann formalism is presented to capture the effect of adsorption kinetics on transport in porous media. Through the use of a general adsorption operator, canonical models such as Henry and Langmuir adsorption as well as more complex adsorption mechanisms involving collective behavior with lateral interactions and surface aggregation can be investigated using this versatile model. By extending the description of adsorption phenomena to kinetic regimes with any underlying adsorption model, this effective technique allows assessing the coupled dynamics resulting from advection, diffusion, and adsorption in pores not only in stationary conditions but also under transient conditions (i.e., in regimes where the adsorbed amount evolves with time due to diffusion and advection). As illustrated in this paper, the development of such an approach provides a simple tool to determine the reciprocal effect of molecular flow and dispersion on adsorption kinetics. In this context, the use of a Lattice Boltzmann-based approach is important as it allows considering porous media of any morphology and topology. Beyond fundamental implications, this efficient method allows treating real engineering conditions such as pollutant dispersion or surfactant injection in a flowing liquid in soils and porous rocks.

Cooperative Effects Dominating the Thermodynamics and Kinetics of Surfactant Adsorption in Porous Media: From Lateral Interactions to Surface Aggregation.

Surfactant adsorption in porous media remains poorly understood, as the microscopic collective behavior of these amphiphilic molecules leads to nonconventional phenomena with complex underlying kinetics/structural organization. Here, we develop a simple thermodynamic model, which captures this rich behavior by including cooperative effects to account for lateral interactions between adsorbed molecules and the formation of ordered or disordered self-assemblies. In more detail, this model relies on a kinetic approach, involving adsorption/desorption rates that depend on the surfactant surface concentration to account for facilitated or hindered adsorption at different adsorption stages. Using different surfactants/porous solids, adsorption on both strongly and weakly adsorbing surfaces is found to be accurately described with parameters that are readily estimated from available adsorption experiments. The validity of our physical approach is confirmed by showing that the inferred adsorption/desorption rates obey the quasi-chemical approximation for lateral adsorbate interactions. Such cooperative effects are shown to lead to adsorption kinetics that drastically depart from conventional frameworks (e.g., Henry, Langmuir, and Sips models).

Photodynamic performance of amphiphilic chlorin e6 derivatives with appropriate properties: A comparison between different-type liposomes as delivery systems.

BACKGROUND: Many aspects are currently being investigated, with the aim of improving the application of PDT in the clinic by rendering it more effective. One of the current trends focuses on the use of nanocarriers. The aim of this study is to describe novel photosensitizers among polyol amide chlorin e6 derivatives for photodynamic therapy (PDT) using liposomes. METHODS: In addition to their intracellular localization and antiproliferative activity against HCT116 cells, appropriate photophysical features have been determined (especially high 1O2 quantum yield production). RESULTS AND CONCLUSIONS: Fluorescent microscopy demonstrated that the compounds entered the endoplasmic reticulum (ER), lysosomes, mitochondria and partially the cytoplasm. All of the chlorins showed no dark cytotoxicity; however, high phototoxicity was observed. Using optical and electron microscopy, we investigated the impact of chlorin-based PDT upon cell damage leading to cell death. Chl ara 3 was identified as the most promising compound among polyol amide chlorin e6 derivatives and improved phototoxicity was observed as compared with a clinically approved temoporfin. Our results indicate that newly-synthesized chlorins seem to be promising candidates for PDT application, and two of them (chl ara 3 and chl mme 2) may create promising new drugs, both in the form of a free compound and as a liposomal formulation.

Insight into Kinetics and Mechanisms of AOT Vesicle Adsorption on Silica in Unfavorable Conditions.

The structure of adsorbed surfactant layers at the equilibrium state has already been investigated using various experimental techniques. However, the comprehension of the formation of structural intermediates in nonequilibrium states and the resulting adsorption kinetics still remain a challenging task. The temporal characterization of these intermediate structures provides further understanding of the layer structure at equilibrium and of the main interactions involved in the adsorption process. In this article, we studied the adsorption kinetics of AOT vesicles on silica at different pHs at ambient temperature. The AOT vesicles were formed in a brine solution. Quartz crystal microbalance with dissipation monitoring (QCM-D) was used to obtain information on the kinetics of surfactant adsorption and on the structure of the adsorbed layer at the equilibrium state. Additionally, neutron reflectivity experiments were performed to provide a detailed description of the mean surfactant concentration profile normal to the surface at equilibrium. Results suggest that vesicles in the bulk influence the adsorption mechanisms. In acidic conditions, after a time-dependent structural rearrangement step, followed by the rupture of initially adsorbed vesicles, the formation of a bilayer was observed. At an intermediate and basic pH, in spite of the electrostatic repulsion between the negatively charged surfactants and silica, results demonstrated the existence of an adsorbed layer composed of AOT vesicles. Vesicles are more or less closely packed depending on the pH of the solution. Results show a non-negligible influence of NaCl addition at pH values where adsorption is initially inhibited. Vesicle adsorption at the intermediate and basic pH is probably due to the combination of attractive van der Waals interactions promoted in high ionic strength systems and the formation of hydrogen bonds. Interpretation of adsorption kinetics gave insight into adsorption mechanisms in an electrostatic repulsion environment.

Bioorthogonal protein-DNA conjugation methods for force spectroscopy.

Accurate and stable site-specific attachment of DNA molecules to proteins is a requirement for many single-molecule force spectroscopy techniques. The most commonly used method still relies on maleimide chemistry involving cysteine residues in the protein of interest. Studies have consequently often focused on model proteins that either have no cysteines or with a small number of cysteines that can be deleted so that cysteines can then be introduced at specific sites. However, many proteins, especially in eukaryotes, contain too many cysteine residues to be amenable to this strategy, and therefore there is tremendous need for new and broadly applicable approaches to site-specific conjugation. Here we present bioorthogonal approaches for making DNA-protein conjugates required in force spectroscopy experiments. Unnatural amino acids are introduced site-specifically and conjugated to DNA oligos bearing the respective modifications to undergo either strain-promoted azidealkyne cycloaddition (SPAAC) or inverse-electron-demand Diels-Alder (IE-DA) reactions. We furthermore show that SPAAC is compatible with a previously published peptide-based attachment approach. By expanding the available toolkit to tag-free methods based on bioorthogonal reactions, we hope to enable researchers to interrogate the mechanics of a much broader range of proteins than is currently possible.

An Active, Ligand-Responsive Pulling Geometry Reports on Internal Signaling between Subdomains of the DnaK Nucleotide-Binding Domain in Single-Molecule Mechanical Experiments.

Single-molecule mechanical experiments have proven to be ideal tools for probing the energetics and mechanics of large proteins and domains. In this paper, we investigate the nucleotide-dependent unfolding mechanics of the nucleotide-binding domain (NBD) of the Hsp70 chaperone DnaK. The NBD binds ADP or ATP in the binding cleft formed by lobe I and lobe II, which consists of two subdomains each. When force is applied to the termini of the NBD, the observed unfolding forces are independent of the nucleotide state. In contrast, when force is applied across the nucleotide-binding pocket, the unfolding forces report specifically on the nucleotide-phosphate state. In this active, ligand-responsive pulling geometry, we observed a bifurcation of the unfolding pathway; the pathway proceeds either through a cooperative "coupled pathway" or through a noncooperative "uncoupled pathway". The partitioning between individual unfolding pathways can be effectively tuned by mutation or by the nucleotide exchange factor GrpE, i.e., by the factors affecting the strength of the lobe I-lobe II interactions within the native NBD. These experiments provide important insight into the molecular origin of the internal signaling between the subdomains of the nucleotide-binding domain of Hsp70 proteins and how signals are efficiently transferred inside the protein molecule.

A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy.

The folding pathways of large proteins are complex, with many of them requiring the aid of chaperones and others folding spontaneously. Along the folding pathways, partially folded intermediates are frequently populated; their role in the driving of the folding process is unclear. The structures of these intermediates are generally not amenable to high-resolution structural techniques because of their transient nature. Here we employed single-molecule force measurements to scrutinize the hierarchy of intermediate structures along the folding pathway of the nucleotide binding domain (NBD) of Escherichia coli Hsp70 DnaK. DnaK-NBD is a member of the sugar kinase superfamily that includes Hsp70s and the cytoskeletal protein actin. Using optical tweezers, a stable nucleotide-binding competent en route folding intermediate comprising lobe II residues (183-383) was identified as a critical checkpoint for productive folding. We obtained a structural snapshot of this folding intermediate that shows native-like conformation. To assess the fundamental role of folded lobe II for efficient folding, we turned our attention to yeast mitochondrial NBD, which does not fold without a dedicated chaperone. After replacing the yeast lobe II residues with stable E. coli lobe II, the obtained chimeric protein showed native-like ATPase activity and robust folding into the native state, even in the absence of chaperone. In summary, lobe II is a stable nucleotide-binding competent folding nucleus that is the key to time-efficient folding and possibly resembles a common ancestor domain. Our findings provide a conceptual framework for the folding pathways of other members of this protein superfamily.

Iron Chelators and Exogenic Photosensitizers. Synergy through Oxidative Stress Gene Expression.

In non-invasive anticancer photodynamic therapy (PDT), a nontoxic photosensitizer (PS), which is activated by visible light, is used as a magic bullet that selectively destroys cancer cells. Recently, we described the combined therapy of 5-aminolevulinic acid (ALA-PDT) with thiosemicarbazone (TSC), i.e. an iron-chelating agent. This resulted in a strong synergistic effect. Herein, we investigated a novel strategy using a combination of PDT consist of the xenobiotic-porphyrin type PS with TSC. We observed a synergistic effect for all of the pairs of TSC-PS. This approach can be rationalized by the fact that both chlorin and TSC can affect the generation of reactive oxygen species (ROS). In order to elucidate the plausible mechanism of action, we also combined the investigated PSs with DFO, which forms complexes that are redox inactive. We detected a slight antagonism or additivity for this combination. This may suggest that the ability of an iron chelator (IC) to participate in the production of ROS and the generation of oxidative stress is important.

Solid-Sampling Electrothermal Vaporization Inductively Coupled Plasma Optical Emission Spectrometry for Direct Determination of Total Oxygen in Coal.

A new analytical method for direct determination of total oxygen contents in eight coal samples of the Argonne Premium Coal (APC) series and in the NIST SRM 1632d is presented. The development of a suitable calibration procedure, optimization of measurement conditions, and the application of a tailored data processing for handling of plasma effects and high blanks enable the quantification of oxygen simultaneously with other trace, minor, or major elements in whole coal samples by means of electrothermal vaporization inductively coupled plasma optical emission spectrometry (ETV-ICP OES). For comparison, the oxygen contents were determined by a direct oxygen analyzer. The obtained oxygen values of the APC and the reference material NIST SRM 1632d were compared to data in the literature. The precision of the ETV-ICP OES was within ±3.5%, and the recovery better than 92%. With this good accuracy, the developed direct solid sampling method ETV-ICP OES is well suited for the fast determination of oxygen in coals, varying in rank from lignite to semianthracite, in a content range of about 100 ppm up to 27% using 1.5 mg sample weight. This direct analysis method represents an accurate, advantageous alternative to currently used methods for estimation of total oxygen contents in coals.

Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.

The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.

Direct determination of sulfur species in coals from the Argonne premium sample program by solid sampling electrothermal vaporization inductively coupled plasma optical emission spectrometry.

A new direct solid sampling method for speciation of sulfur in coals by electrothermal vaporization inductively coupled plasma optical emission spectrometry (ETV-ICP OES) is presented. On the basis of the controlled thermal decomposition of coal in an argon atmosphere, it is possible to determine the different sulfur species in addition to elemental sulfur in coals. For the assignment of the obtained peaks from the sulfur transient emission signal, several analytical techniques (reflected light microscopy, scanning electron microscopy with energy dispersive X-ray spectroscopy and X-ray diffraction) were used. The developed direct solid sampling method enables a good accuracy (relative standard deviation ≤ 6%), precision and was applied to determine the sulfur forms in the Argonne premium coals, varying in rank. The generated method is time- and cost-effective and well suited for the fast characterization of sulfur species in coal. It can be automated to a large extent and is applicable for process-accompanying analyses.

Model to interpret pulsed-field-gradient NMR data including memory and superdispersion effects.

We propose a versatile model specifically designed for the quantitative interpretation of NMR velocimetry data. We use the concept of mobile or immobile tracer particles applied in dispersion theory in its Lagrangian form, adding two mechanisms: (i) independent random arrests of finite average representing intermittent periods of very low velocity zones in the mean flow direction and (ii) the possibility of unexpectedly long (but rare) displacements simulating the occurrence of very high velocities in the porous medium. Based on mathematical properties related to subordinated Lévy processes, we give analytical expressions of the signals recorded in pulsed-field-gradient NMR experiments. We illustrate how to use the model for quantifying dispersion from NMR data recorded for water flowing through a homogeneous grain pack column in single- and two-phase flow conditions.

On the determination of a generalized Darcy equation for yield-stress fluid in porous media using a Lattice-Boltzmann TRT scheme.

Simulating flow of a Bingham fluid in porous media still remains a challenging task as the yield stress may significantly alter the numerical stability and precision. We present a Lattice-Boltzmann TRT scheme that allows the resolution of this type of flow in stochastically reconstructed porous media. LB methods have an intrinsic error associated to the boundary conditions. Depending on the schemes this error might be directly linked to the effective viscosity. As for non-Newtonian fluids viscosity varies in space the error becomes inhomogeneous and very important. In contrast to that, the TRT scheme does not present this deficiency and is therefore adequate to be used for simulations of non-Newtonian fluid flow. We simulated Bingham fluid flow in porous media and determined a generalized Darcy equation depending on the yield stress, the effective viscosity, the pressure drop and a characteristic length of the porous medium. By evaluating the flow in the porous structure, we distinguished three different scaling regimes. Regime I corresponds to the situation where fluid is flowing in only one channel. Here, the relation between flow rate and pressure drop is given by the non-Newtonian Poiseuille law. During Regime II an increase in pressure triggers the opening of new paths and the relation between flow rate and the difference in pressure to the critical yield pressure becomes quadratic: [Formula: see text]. Finally, Regime III corresponds to the situation where all the fluid is flowing. In this case, [Formula: see text].

RAPPORT: running scientific high-performance computing applications on the cloud.

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.

Photoprocesses of chlorin e6 glucose derivatives.

The ground and excited state processes of chlorin e6, the monomethyl ester C1, the glucose derivative C2 and the 3-heptylchlorin-glucose C3, were studied in solvents of lower and higher polarity. The excited singlet and lowest triplet states of C1-C3 were characterized by spectroscopic methods for several conditions. The quantum yields of formation of singlet molecular oxygen and the other triplet properties of the three chlorins and chlorin e6 are similar, whereas the fluorescence quantum yield decreases on going from C1 to C3. Time-resolved optoacoustic experiments revealed a ca. 30 kJ mol(-1) higher triplet level for C3 with respect to C1/2.