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.

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.

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.

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.

The Chemical Fluctuation Theorem governing gene expression.

Gene expression is a complex stochastic process composed of numerous enzymatic reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell technologies, the lack of a theory accurately describing the gene expression process has restricted a robust, quantitative understanding of gene expression variability among cells. Here we present the Chemical Fluctuation Theorem (CFT), providing an accurate relationship between the environment-coupled chemical dynamics of gene expression and gene expression variability. Combined with a general, accurate model of environment-coupled transcription processes, the CFT provides a unified explanation of mRNA variability for various experimental systems. From this analysis, we construct a quantitative model of transcription dynamics enabling analytic predictions for the dependence of mRNA noise on the mRNA lifetime distribution, confirmed against stochastic simulation. This work suggests promising new directions for quantitative investigation into cellular control over biological functions by making complex dynamics of intracellular reactions accessible to rigorous mathematical deductions.

Nonclassical Kinetics of Clonal yet Heterogeneous Enzymes.

Enzyme-to-enzyme variation in the catalytic rate is ubiquitous among single enzymes created from the same genetic information, which persists over the lifetimes of living cells. Despite advances in single-enzyme technologies, the lack of an enzyme reaction model accounting for the heterogeneous activity of single enzymes has hindered a quantitative understanding of the nonclassical stochastic outcome of single enzyme systems. Here we present a new statistical kinetics and exactly solvable models for clonal yet heterogeneous enzymes with possibly nonergodic state dynamics and state-dependent reactivity, which enable a quantitative understanding of modern single-enzyme experimental results for the mean and fluctuation in the number of product molecules created by single enzymes. We also propose a new experimental measure of the heterogeneity and nonergodicity for a system of enzymes.

Exchange symmetry, fluctuation-compressibility relation, and thermodynamic potentials of quantum liquids.

Liquid helium does not obey the Gibbs fluctuation-compressibility relation, which was noted more than six decades ago. However, still missing is a clear explanation of the reason for the deviation or the correct fluctuation-compressibility relation for the quantum liquid. Here we present the fluctuation-compressibility relation valid for any grand canonical system. Our result shows that the deviation from the Gibbs formula arises from a nonextensive part of thermodynamic potentials. The particle-exchange symmetry of many-body wave function of a strongly degenerate quantum gas is related to the thermodynamic extensivity of the system; a Bose gas does not always obey the Gibbs formula, while a Fermi gas does. Our fluctuation-compressibility relation works for classical systems as well as quantum systems. This work demonstrates that the application range of the Gibbs-Boltzmann statistical thermodynamics can be extended to encompass nonextensive open systems without introducing any postulate other than the principle of equal a priori probability.