Reaction rate theory for supramolecular kinetics: application to protein aggregation

ABSTRACT

Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements.     

Determining the effective density of airborne nanoparticles using multiple charging correction in a tandem DMA/ELPI setup

The cysteamine-modified hyaluronic acid (HA) polymer was employed to coat quantum dots (QDs) through a convenient one-step reverse micelle method, with the final QDs hydrodynamic size of around 22.6 nm. The HA coating renders the QDs with very good stability in PBS for more than 140 days and resistant to large pH range of 2–12. Besides, the HA-coated QDs also show excellent fluorescence stability in BSA-containing cell culture medium. In addition, the cell culture assay indicates no significant cytotoxicity for MD-MB-231 breast cancer cells, and its targeting ability to cancer receptor CD44 has been demonstrated on two breast cancer cell lines. The targeting mechanism was further proved by the HA competition experiment. This work has established a new approach to help solve the stability and toxicity problems of QDs, and moreover render the QDs cancer targeting property. The current results indicate that the HA polymer-coated QDs hold the potential application for both in vitro and in vivo cancer imaging researches.     

Radiation-driven hydrodynamics of high- hohlraums on the national ignition facility

The first hohlraum experiments on the National Ignition Facility (NIF) using the initial four laser beams tested radiation temperature limits imposed by plasma filling. For a variety of hohlraum sizes and pulse lengths, the measured x-ray flux shows signatures of filling that coincide with hard x-ray emission from plasma streaming out of the hohlraum. These observations agree with hydrodynamic simulations and with an analytical model that includes hydrodynamic and coronal radiative losses. The modeling predicts radiation temperature limits with full NIF (1.8 MJ), greater, and of longer duration than required for ignition hohlraums.     

Drag reduction in bubbly Taylor-Couette turbulence

In Taylor-Couette flow the total energy dissipation rate and therefore the drag can be determined by measuring the torque on the system. We do so for Reynolds numbers between Re=7 x 10(4) and Re=10(6) after having injected (i) small bubbles (R=1 mm) up to a volume concentration of alpha=5% and (ii) buoyant particles (rhop/rhol=0.14) of comparable volume concentration. In case (i) we observe a crossover from little drag reduction at smaller Re to strong drag reduction up to 20% at Re=10(6). In case (ii) we observe at most little drag reduction throughout. Several theoretical models for bubbly drag reduction are discussed in view of our findings.     

On the barriers to planarity and the isotope effect in cyclobutane and cyclobutane-d8

The infrared and Raman data on the ring-puckering vibration in cyclobutane and cyclobutane-d₈ have been reexamined including the coordinate dependence of the reduced mass in the Hamiltonian. This was done for the purpose of estimating the importance of these small terms in the determination of barrier heights for four-membered rings and also on the determination of the dihedral angle corresponding to the potential minimum.The conclusions reached are that there is an isotopic dependence of the barriers to planarity in cyclobutane and cyclobutane-d₈ yielding a difference of ～14 cm^?1, but the precise value of the difference in barrier heights is ill determined. The higher-order kinetic energy terms in the Hamiltonian can account for a spread of ～3 cm^?1 in each of the barriers derived for cyclobutane and cyclobutane-d₈, depending on the details of the model used for the vibration, but not a difference of 14 cm^?1, which undoubtedly indicates the effects of coupling with other vibrational modes. It is also found that the derived values of the dihedral angles are quite sensitive to the details of the vibrational model, in fact, much more so than to the uncertainties in the bond distances and bond angles. A relationship between the potential constants derived for cyclobutane and cyclobutane-d₈ assuming an effective constant reduced mass and those derived for a semirigid model is demonstrated.     

Hybrid measurement of auditory steady-state responses and distortion product otoacoustic emissions using an amplitude-modulated primary tone

A maximum auditory steady-state response (ASSR) amplitude is yielded when the ASSR is elicited by an amplitude-modulated tone (f(c)) with a fixed modulation frequency (f(m) = 40 Hz), whereas the maximum distortion product otoacoustic emission (DPOAE) level is yielded when the DPOAE is elicited using a fixed frequency ratio of the primary tones (f2/f1 = 1.2). When eliciting the DPOAE and ASSR by the same tone pair, optimal stimulation is present for either DPOAE or ASSR and thus adequate simultaneous DPOAE/ASSR measurement is not possible across test frequency f2 or f(c), respectively. The purpose of the present study was to determine whether the ASSR and DPOAE can be measured simultaneously without notable restrictions using a DPOAE stimulus setting in which one primary tone is amplitude modulated. A DPOAE of frequency 2f1-f2 and ASSR of modulation frequency 41 Hz were measured in ten normal hearing subjects at a test frequency between 0.5 and 8 kHz (f2 = f(c)). The decrease in the DPOAE level and the loss in ASSR amplitude during hybrid mode stimulation amounted, on average, to only 2.60 dB [standard deviation (SD) = 1.38 dB] and 1.83 dB (SD = 2.38 dB), respectively. These findings suggest simultaneous DPOAE and ASSR measurements to be feasible across all test frequencies when using a DPOAE stimulus setting where the primary tone f2 is amplitude modulated.     

Laser ultrasonic receivers based on organic photorefractive polymer composites

We present two laser ultrasonic receivers based on organic photorefractive polymer composites with 2-[4-bis(2-methoxyethyl)aminobenzylidene]malononitrile (AODCST) or 2-dicyanomethylen-3-cyano-5,5-dimethyl-4-(4′-dihexylaminophenyl)-2,5-dihydrofuran nonlinear optical chromophores. Experimental results show sensitivities of the ultrasonic receivers of ~9.5 × 10^?8 nm (W/Hz)^0.5 for both composites, and a faster response time (~60 ms) for the AODCST-based laser ultrasonic receiver. We show that such LUS detectors are highly suitable for contactless thickness measurements of aluminum, steel sheets and defect detection with an accuracy of 100 μm.