Transport dynamics of complex fluids.

Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate subdiffusive, and long-time diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitative understanding of thermal motion in complex fluids remains a challenging problem. Here, we present a transport equation and its solutions, which yield a unified quantitative explanation of the mean-square displacement (MSD), the non-Gaussian parameter (NGP), and the displacement distribution of complex fluids. In our approach, the environment-coupled diffusion kernel and its time correlation function (TCF) are the essential quantities that determine transport dynamics and characterize mobility fluctuation of complex fluids; their time profiles are directly extractable from a model-free analysis of the MSD and NGP or, with greater computational expense, from the two-point and four-point velocity autocorrelation functions. We construct a general, explicit model of the diffusion kernel, comprising one unbound-mode and multiple bound-mode components, which provides an excellent approximate description of transport dynamics of various complex fluidic systems such as supercooled water, colloidal beads diffusing on lipid tubes, and dense hard disk fluid. We also introduce the concepts of intrinsic disorder and extrinsic disorder that have distinct effects on transport dynamics and different dependencies on temperature and density. This work presents an unexplored direction for quantitative understanding of transport and transport-coupled processes in complex disordered media.

Stochastic Kinetics of Nanocatalytic Systems.

Catalytic reaction events occurring on the surface of a nanoparticle constitute a complex stochastic process. Although advances in modern single-molecule experiments enable direct measurements of individual catalytic turnover events occurring on a segment of a single nanoparticle, we do not yet know how to measure the number of catalytic sites in each segment or how the catalytic turnover counting statistics and the catalytic turnover time distribution are related to the microscopic dynamics of catalytic reactions. Here, we address these issues by presenting a stochastic kinetics for nanoparticle catalytic systems. We propose a new experimental measure of the number of catalytic sites in terms of the mean and variance of the catalytic event count. By considering three types of nanocatalytic systems, we investigate how the mean, the variance, and the distribution of the catalytic turnover time depend on the catalytic reaction dynamics, the heterogeneity of catalytic activity, and communication among catalytic sites. This work enables accurate quantitative analyses of single-molecule experiments for nanocatalytic systems and enzymes with multiple catalytic sites.

Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics.

Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically, and the frequency spectrum of this chemical fluctuation carries valuable information about the dynamics of the reactions creating these biomolecules. Recent advances in single-cell techniques enable direct monitoring of the time-traces of the protein number in each cell; however, it is not yet clear how the stochastic dynamics of these time-traces is related to the reaction mechanism and dynamics. Here, we derive a rigorous relation between the frequency-spectrum of the product number fluctuation and the reaction mechanism and dynamics, starting from a generalized master equation. This relation enables us to analyze the time-traces of the protein number and extract information about dynamics of mRNA number and transcriptional regulation, which cannot be directly observed by current experimental techniques. We demonstrate our frequency spectrum analysis of protein number fluctuation, using the gene network model of luciferase expression under the control of the Bmal 1a promoter in mouse fibroblast cells. We also discuss how the dynamic heterogeneity of transcription and translation rates affects the frequency-spectra of the mRNA and protein number.

Lifetime and diffusion distance of singlet oxygen in air under everyday atmospheric conditions.

Singlet oxygen is a toxic chemical but powerful oxidant, exploited in many chemical and biological applications. However, the lifetime of singlet oxygen in air under atmospheric conditions is yet to be known. This has limited safe usage of singlet oxygen in air, despite being a strong antimicrobial agent with the unique property of relaxing to breathable oxygen after serving its purpose. Here, we solve this long-standing problem by combining experimental and theoretical research efforts; we generate singlet oxygen using a photosensitizer at a local source and monitor the time-dependent extent of singlet oxygen reaction with probe molecules at a detector, precisely controlling the detector distance from the source. To explain our experimental results, we employ a theoretical model that fully accounts for singlet oxygen diffusion, radiative and nonradiative relaxations, and the bimolecular reaction with probe molecules at the detector. For all cases investigated, our model, with only two adjustable parameters, provides an excellent quantitative explanation of the experiment. From this analysis, we extract the lifetime of singlet oxygen in the air to be 2.80 s at 23 °C under 1 atm, during which time singlet oxygen diffuses about 0.992 cm. The correctness of this estimation is confirmed by a simple mean-first-passage time analysis of the maximum distance singlet oxygen can reach from the source. We also confirm the sterilization effects of singlet oxygen for distances up to 0.6-0.8 cm, depending on the bacteria strain in question, between the bacteria and the singlet oxygen source.

Green's function of the Smoluchowski equation with reaction sink: Application to geminate and bulk recombination reactions.

By applying a recently developed solution method for the Fredholm integral equation of the second kind, we obtain an expression for Green's function of the Smoluchowski equation with a reaction sink. The result is applied to obtain accurate analytical expressions for the time-dependent survival probability of a geminate reactant pair and the rate coefficient of the bulk recombination between reactants undergoing diffusive motions under strong Coulomb interactions. The effects of both repulsive and attractive interactions are considered, and the results are compared with the numerical results obtained by solving the equation for the survival probability and the nonequilibrium pair correlation function. It is shown that the solutions are accurate enough for most reasonable parameter values.

Transport Dynamics of Water Molecules Confined between Lipid Membranes.

Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from that of bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space, quantitatively explaining molecular dynamics simulation results. We find that the unique transport dynamics of water molecules stems from the lateral diffusion coefficient fluctuation caused by their longitudinal motion in the direction perpendicular to the membranes. We also identify an interfacial region where water possesses distinct physical properties, which is unaffected by changes in the intermembrane separation.

Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production.

Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.

Quantitative interpretation of the randomness in single enzyme turnover times.

Fluctuating turnover times of a single enzyme become observable with the advent of modern cutting-edge, single enzyme experimental techniques. Although the conventional chemical kinetics and its modern generalizations could provide a good quantitative description for the mean of the enzymatic turnover times, to our knowledge there has not yet been a successful quantitative interpretation for the variance or the randomness of the enzymatic turnover times. In this review, we briefly review several theories in this field, and compare predictions of these theories to the randomness parameter data reported for ß-galactosidase enzyme. We find the recently proposed kinetics for renewal reaction processes could provide an excellent quantitative interpretation of the randomness parameter data. From the analysis of the randomness parameter data of the single enzyme reaction, one can extract quantitative information about the mean lifetime of enzyme-substrate complex; the success or the failure probability of the catalytic reaction per each formation of ES complex; and the non-Poisson character of the reaction dynamics of the ES complex (which is beyond reach of the long-standing paradigm of the conventional chemical kinetics).

Communication: Propagator for diffusive dynamics of an interacting molecular pair.

We introduce a new method of solution for the Fredholm integral equations of the second kind. The method would be useful when the direct iterative approach leads to a divergent perturbation series solution. By using the method, we obtain an accurate expression of the propagator for diffusive dynamics of a pair of particles interacting via an arbitrary central potential and hydrodynamic interaction. We test the accuracy of the propagator expression by calculating the diffusion-controlled geminate and bimolecular reaction rates. It is shown that our propagator expression provides very accurate results for the whole time region.

High Pressure Deuterium Passivation of Charge Trapping Layer for Nonvolatile Memory Applications.

In this study, the deuterium passivation effect of silicon nitride (Si3N4) on data retention characteristics is investigated in a Metal-Nitride-Oxide-Silicon (MNOS) memory device. To focus on trap passivation in Si3N4 as a charge trapping layer, deuterium (D2) high pressure annealing (HPA) was applied after Si3N4 deposition. Flat band voltage shifts (ΔVFB) in data retention mode were compared by CV measurement after D2 HPA, which shows that the memory window decreases but charge loss in retention mode after program is suppressed. Trap energy distribution based on thermal activated retention model is extracted to compare the trap density of Si3N4. D2 HPA reduces the amount of trap densities in the band gap range of 1.06-1.18 eV. SIMS profiles are used to analyze the D2 profile in Si3N4. The results show that deuterium diffuses into the Si3N4 and exists up to the Si3N4-SiO2 interface region during post-annealing process, which seems to lower the trap density and improve the memory reliability.

Physical and Electrical Analysis of Poly-Si Channel Effect on SONOS Flash Memory.

In this study, polycrystalline silicon (poly-Si) is applied to silicon-oxide-nitride-oxide-silicon (SONOS) flash memory as a channel material and the physical and electrical characteristics are analyzed. The results show that the surface roughness of silicon nitride as charge trapping layer (CTL) is enlarged with the number of interface traps and the data retention properties are deteriorated in the device with underlying poly-Si channel which can be serious problem in gate-last 3D NAND flash memory architecture. To improve the memory performance, high pressure deuterium (D2) annealing is suggested as a low-temperature process and the program window and threshold voltage shift in data retention mode is compared before and after the D2 annealing. The suggested curing is found to be effective in improving the device reliability.

Real-space imaging of nanoparticle transport and interaction dynamics by graphene liquid cell TEM.

Thermal motion of colloidal nanoparticles and their cohesive interactions are of fundamental importance in nanoscience but are difficult to access quantitatively, primarily due to the lack of the appropriate analytical tools to investigate the dynamics of individual particles at nanoscales. Here, we directly monitor the stochastic thermal motion and coalescence dynamics of gold nanoparticles smaller than 5 nm, using graphene liquid cell (GLC) transmission electron microscopy (TEM). We also present a novel model of nanoparticle dynamics, providing a unified, quantitative explanation of our experimental observations. The nanoparticles in a GLC exhibit non-Gaussian, diffusive motion, signifying dynamic fluctuation of the diffusion coefficient due to the dynamically heterogeneous environment surrounding nanoparticles, including organic ligands on the nanoparticle surface. Our study shows that the dynamics of nanoparticle coalescence is controlled by two elementary processes: diffusion-limited encounter complex formation and the subsequent coalescence of the encounter complex through rotational motion, where surface-passivating ligands play a critical role.

Super-Gaussian, superdiffusive transport of multimode active matter.

Living matter often exhibits multimode transport that switches between an active, self-propelled motion and a seemingly passive, random motion. Here, we investigate an exactly solvable model of multimode active matter, such as living cells and motor proteins, which alternatingly undergoes active and passive motion. Our model study shows that the reversible transition between a passive mode and an active mode causes super-Gaussian transport dynamics, observed in various experiments. We find the non-Gaussian character of the matter's displacement distribution is essentially determined by the population ratio between active and passive motion. Interestingly, under a certain population ratio of the active and passive modes, the displacement distribution changes from sub-Gaussian to super-Gaussian as time increases. The mean-square displacement of our model exhibits transient superdiffusive dynamics, yet recovers diffusive behavior at both the short- and long-time limits. We finally generalize our model to encompass complex, multimode active matter in an arbitrary spatial dimension.

Practical model for imperfect conductometric molecular wire sensors.

We present a theoretical model for description of real polyreceptor molecular wire sensors (MWS), whose conductance signal may dramatically reduce upon analyte binding to one of the receptors coupled to the molecular wire but may not vanish as completely as assumed in the ideal MWS model. For the present nonideal MWS model, we establish the exact relationship between analyte concentration and the sensory signal intensity. It turns out that, whereas the Stern-Volmer curve of the ideal MWS always has a positive curvature, the Stern-Volmer curve of the imperfect MWS can have a negative curvature, consistent with experimental data. We find that the MWS still performs better than the corresponding ideal monoreceptor sensor, unless the nonideality of the imperfect MWS is egregiously large. We establish the conditions for the imperfect polyreceptor MWS to have a sensitivity and detection limit superior to the traditional monoreceptor sensor.

Excess grand potential for a system under an external field: effects of external field driven nonextensivity.

We report that an external field can drive inherently extensive systems into nonextensive ones. For the correct grand canonical description of nonextensive systems, it is necessary to take into account the excess grand potential, X, in addition to the conventional grand potential proportional to the thermodynamic pressure, which has long been overlooked in the literature in this field. We present the statistical mechanical expression for X of a system as a functional of the external field imposed on the system, from which we establish the criterion for the external field that drives an inherently extensive macroscopic system into a nonextensive one.

Bandgap engineered reverse type-I CdTe/InP/ZnS core-shell nanocrystals for the near-infrared.

New quantum dots were fabricated with a core/shell/shell structure consisting of CdTe core/InP shell/ZnS shell of which the InP shell causes a red-shift to the NIR region and the ZnS shell imparts photo-stability; toxicity tests on mammalian cells and NIR imaging of a mouse highlight their potential applications in biomedical imaging.

Anomalous Dynamics of in Vivo Cargo Delivery by Motor Protein Multiplexes.

Vesicle transport conducted by motor protein multiplexes (MPMs), which is ubiquitous among eukaryotes, shows anomalous and stochastic dynamics qualitatively different from the dynamics of thermal motion and artificial active matter; the relationship between in vivo vesicle-delivery dynamics and the underlying physicochemical processes is not yet quantitatively understood. Addressing this issue, we perform accurate tracking of individual vesicles, containing upconverting nanoparticles, transported by kinesin-dynein-multiplexes along axonal microtubules. The mean-square-displacement of vesicles along the microtubule exhibits unusual dynamic phase transitions that are seemingly inconsistent with the scaling behavior of the mean-first-passage time over the travel length. These paradoxical results and the vesicle displacement distribution are quantitatively explained and predicted by a multimode MPM model, developed in the current work, where ATP-hydrolysis-coupled motion of MPM has both unidirectional and bidirectional modes.

TOF-2: a large 1D channel thorium organic framework.

A new neutral 1D channel thorium organic framework material (TOF-2) has been synthesized under hydrothermal conditions. TOF-2 exhibits a hexagonal channel structure consisting of eight-coordinate ThO6F2 polyhedra and 1,3,5-benzentricarboxylate ligands. The channels run along the c-axis and are approximately 13 A in diameter. The single-crystal X-ray structure suggests that the amount of void space is 41%. The structure is stable to ca. 400 degrees C. Gas adsorption measurements show deferential gas uptake behavior.

Excluded volume effects on the intrachain reaction kinetics.

On the basis of the recently developed optimized Rouse-Zimm theory of chain polymers with excluded volume interactions, we calculate the long-time first-order rate constant k(1) for end-to-end cyclization of linear chain polymers. We first find that the optimized Rouse-Zimm theory provides the longest chain relaxation times tau(1) of excluded volume chains that are in excellent agreement with the available Brownian dynamics simulation results. In the free-draining limit, the cyclization rate is diffusion-controlled and k(1) is inversely proportional to tau(1), and the k(1) values calculated using the Wilemski-Fixman rate theory are in good agreement with Brownian dynamics simulation results. However, when hydrodynamic interactions are included, noticeable deviations are found. The main sources of errors are fluctuating hydrodynamic interaction and correlation hole effects as well as the non-Markovian reaction dynamic effect. The physical natures of these factors are discussed, and estimates for the magnitudes of required corrections are given. When the corrections are included, the present theory allows the prediction of accurate k(1) values for the cyclization of finite-length chains in good solvents as well as the correct scaling exponent in the long-chain limit.