Thermodiffusion of latex beads studied with a microfluidic cell

Investigation of the thermodiffusion requires relatively high temperature gradients. The temperature difference at the same time should be small enough because of the temperature dependence of the effect. This can be achieved by reducing the dimensions of the system. Therefore we developed a microfluidic cell which allows us to observe thermophoresis of colloids in the solution. Unlike many existing optical methods our cell is suitable to study big colloids (up to several micrometers) and complex mixtures. The cell can be also applied for investigation of thermophoretic phenomena in biological systems such as living cell and lipid membranes.Our cell consist of three channels (fig 1A): two relatively big ones for providing high flow rate of hot and cold liquid and a small channel in between them which contains the sample to study. The cell is produced either of PDMS by molding on lithographically made Si/SU-8 master or by micromilling the Plexiglas block with a CNC machine. The central channel is made very flat to prevent convection.To characterize the temperature distribution in our cell we used FLIM [1] with Rhodamine B as a temperature sensitive dye. The temperature distribution in the central channel is shown in fig 1B. The temperature difference across the central channel appeared to be around 2°C (the temperature gradient equals 2•104 K/m) although the temperature difference in the cooling and heating channels was much higher (22°C and 47°C respectively) which indicates large temperature drop in the walls.The cell was applied to investigate thermodiffusion of latex microbeads (sulfate modified, 0.5um) in water. The resulting exponential distribution in equilibrium (fig 1C) could be analyzed according to Zhao et al [2]. In order to validate our new method we perform additional measurements with the Thermal Diffusion Forced Rayleigh Scattering setup. Results will be discussed

How does the chain extension of poly (acrylic acid) scale in aqueous solution? A combined study with light scattering and computer simulation

This work adresses the question of the scaling behaviour of polyelectrolytes in solution for a realistic prototype: We show results of a combined experimental (light scattering) and theoretical (computer simulations) investigation of structural properties of poly (acrylic acid) (PAA). Experimentally, we determined the molecular weight (M_W) and the hydrodynamic radius (R_H) by static light scattering for six different PAA samples in aqueous NaCl-containing solution (0.1-1 mol/L) of polydispersity D_P between 1.5 and 1.8. On the computational side, three different variants of a newly developed mesoscopic force field for PAA were employed to determine R_H for monodisperse systems of the same M_W as in the experiments. The force field effectively incorporates atomistic information and one coarse-grained bead corresponds to one PAA monomer. We find that R_H matches with the experimental data for all investigated samples. The effective scaling exponent for R_H is found to be around 0.55, which is well below its asymptotic value for good solvents. Additionally, data for the radius of gyration (R_G) are presented.Comment: 17 pages, 3 figures, submitted to Macromolecule

Complementary experimental methods to obtain thermodynamic parameters of protein ligand systems

In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying physical effect is still not understood. To gain deeper insight, we investigate whether non-equilibrium coefficients can be related to equilibrium properties. Therefore, we compare thermophoretic data measured by thermal diffusion forced Rayleigh scattering (TDFRS) (which is a non-equilibrium process) with thermodynamic data obtained by isothermal titration calorimetry (ITC) (which is an equilibrium process). As a reference system, we studied chelation reaction between ethylenediaminetetraacetic acid (EDTA) and calcium chloride (CaCl$_2$) to relate the thermophoretic behavior quantified by the Soret coefficient $S_{\mathrm T}$ to the Gibb's free energy $\Delta G$ determined in the ITC experiment using an expression proposed by Eastman [J. Am. Chem. Soc. 50, 283 (1928)]. Finally, we have studied the binding of the protein Bovine Carbonic Anhydrase I (BCA I) to two different benzenesulfonamide derivatives: 4-fluorobenzenesulfonamide (4FBS) and pentafluorobenzenesulfonamide (PFBS). For all three systems, we find that the Gibb' free energies calculated from $S_{\mathrm T}$ agree with $\Delta G$ from the ITC experiment. In addition, we also investigate the influence of fluorescent labeling, which allows measurements in a thermophoretic microfluidic cell. Re-examination of the fluorescently labeled system using ITC showed a strong influence of the dye on the binding behavior

Non-monotonic Soret coefficients of aqueous LiCl solutions with varying concentrations

We investigate the thermodiffusive properties of aqueous solutions of lithium chloride, using thermal diffusion forced Rayleigh scattering in a concentration range of 0.5-2 mole per kg of solvent and a temperature range of 5 to 45 °C. All solutions exhibit non-monotonic variations of the Soret coefficient ST with a concentration exhibiting a minimum at about one mole per kg of solvent. The depth of the minimum decreases with increasing temperature and shifts slightly towards higher concentrations. We compare the experimental data with published data and apply a recent model based on overlapping hydration shells. Additionally, we calculate the ratio of the phenomenological Onsager coefficients using our experimental results and published data to calculate the thermodynamic factor. Simple linear, quadratic and exponential functions can be used to describe this ratio accurately, and together with the thermodynamic factors, the experimental Soret coefficients can be reproduced. The main conclusion from this analysis is that the minimum of the Soret coefficients results from a maximum in the thermodynamic factor, which appears itself at concentrations far below the experimental concentrations. Only after multiplication by the (negative) monotonous Onsager ratio does the minimum move into the experimental concentration window.</p

Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22):9346−9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45–90 d, starting with an initial formamide weight fraction of 10−3 wt % that is typical for concentrations in shallow lakes on early Earth

Thermophoretic Properties of Aqueous Formamide Solutions and Accumulation in Hydrothermal Pores

Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the 'origin-of-life' [1]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infra-Red Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite-element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behaviour of formamide. The accumulation-fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of approximately 85 wt% at large aspect ratios. Time dependent studies show that these high concentrations are reached after 45-90 days, starting with an initial formamide weight fraction of $10-3 wt% that is typical for concentrations in shallow lakes on early earth [2].References1. P. Baaske, F. M. Weinert, S. Duhr, K. H. Lemke, M. J. Russell and D. Braun, et al., P. Natl. Acad. Sci. USA, Vol. 104, No. 22 (2007) pp. 9346-9351.2. D. Niether, D. Afanasenkau, J. K. G. Dhont and S. Wiegand, PNAS, accepted, (2016)

Characterizing decoherence rates of a superconducting qubit by direct microwave scattering

We experimentally investigate a superconducting qubit coupled to the end of an open transmission line, in a regime where the qubit decay rates to the transmission line and to its own environment are comparable. We perform measurements of coherent and incoherent scattering, on- and off-resonant fluorescence, and time-resolved dynamics to determine the decay and decoherence rates of the qubit. In particular, these measurements let us discriminate between non-radiative decay and pure dephasing. We combine and contrast results across all methods and find consistent values for the extracted rates. The results show that the pure dephasing rate is one order of magnitude smaller than the non-radiative decay rate for our qubit. Our results indicate a pathway to benchmark decoherence rates of superconducting qubits in a resonator-free setting

Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations

The human APOBEC3G (A3G) protein is a cellular polynucleotide cytidine deaminase that acts as a host restriction factor of retroviruses, including HIV-1 and various transposable elements. Recently, three NMR and two crystal structures of the catalytic deaminase domain of A3G have been reported, but these are in disagreement over the conformation of a terminal β-strand, β2, as well as the identification of a putative DNA binding site. We here report molecular dynamics simulations with all of the solved A3G catalytic domain structures, taking into account solubility enhancing mutations that were introduced during derivation of three out of the five structures. In the course of these simulations, we observed a general trend towards increased definition of the β2 strand for those structures that have a distorted starting conformation of β2. Solvent density maps around the protein as calculated from MD simulations indicated that this distortion is dependent on preferential hydration of residues within the β2 strand. We also demonstrate that the identification of a pre-defined DNA binding site is prevented by the inherent flexibility of loops that determine access to the deaminase catalytic core. We discuss the implications of our analyses for the as yet unresolved structure of the full-length A3G protein and its biological functions with regard to hypermutation of DNA

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate, and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function, and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate, we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5′ ends, RNA Polymerases II and III, and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins, and DNA replication origins). Interestingly we also find that certain configurations of SWI/SNF subunits are associated with transcripts that have higher levels of expression, whereas other configurations of SWI/SNF factors are associated with transcripts that have lower levels of expression. To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins, we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members, as well as with cellular constituents such as nuclear matrix proteins, key transcription factors, and centromere components, implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated