We simulated the Brownian diffusion and reaction-diffusion processes to study molecular rebinding’s influence on the reaction rates of bimolecular reactions. We found that the number of rebindings, Nreb , is proportional to the target’s size and inversely proportional to the diffusion coefficient D and simulation time-step ∆t.

Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure–function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus.

Metabolic reactions in living cells are limited by diffusion of reagents in the cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in the cytosol should be preceded by careful measurements of the physical properties of the cellular interior.

To find a facile way to produce a hydrophobic sponge that can effectively absorb oils is urgent to resolve the environmental pollution and ecological disaster caused by oil spillage. Here, alkylated carbon dots (C dots) were prepared from pyrolysis of a mixture of dodecylamine and citric acid followed by purification through silica gel column chromatography.

Rheology of polymer solutions suffers from lack of universal model of viscosity applicable across wide range of concentrations. Here we build such a model on the basis of measured viscosity of polydimethylosiloxane (PDMS) in ethyl acetate in a wide range of polymer concentrations: from dilute up to highly concentrated solutions.

Cell lysates (cellular extracts) constitute a perfect imitation of the intracellular environment that can provide insight into cellular response to external stimuli. However, most of the presented results are performed for diluted lysates that do not reflect the actual properties of a crowded cellular environment.

We report the assembly of four imidazolium bromides, each of which bears a naphthyl on one side of the imidazolium cation and a branched alkyl chain on the other. This design creates a new type of amphiphilic ionic liquid with an apolar–polar–apolar structure and a low melting point, which has not been achieved by reported counterparts bearing linear alkyl chains.

Intrinsic molecular brightness (MB) is a number of emitted photons per second per molecule. When a substrate labeled by a fluorophore and a second unlabeled substrate form a complex in solution, the MB of the fluorophore changes. Here we use this change to determine the equilibrium constant (K) for the formation of the complex at pM concentrations.

Thermal motion of particles and molecules in liquids underlies many chemical and biological processes. Liquids, especially in biology, are complex due to structure at multiple relevant length scales. While diffusion in homogeneous simple liquids is well understood through the Stokes–Einstein relation, this equation fails completely in describing diffusion in complex media.

The efficient delivery of drugs to cells depends on their diffusion through the extracellular matrix (ECM) of tissues. Here we present a study of diffusion of nanoprobes of radius from 1 nm to over 100 nm in the ECM of spheroids of three cell types (HeLa, MCF-7 and fibroblasts).

Biochemistry in living cells is an emerging field of science. Current quantitative bioassays are performed ex vivo, thus equilibrium constants and reaction rates of reactions occurring in human cells are still unknown. To address this issue, we present a non-invasive method to quantitatively characterize interactions directly within the cytosol of living cells.

One of the main players in the process of mitochondrial fragmentation is dynamin-related protein 1 (Drp1), which assembles into a helical ring-like structure on the mitochondria and facilitates fission. The fission mechanism is still poorly understood and detailed information concerning oligomeric form of Drp1, its cellular distribution and the size of the fission complex is missing.

This work, based on in vivo and in vitro measurements, as well as in silico simulations, provides a consistent analysis of diffusion of polydisperse nanoparticles in the cytoplasm of living cells. Using the example of fluorescence correlation spectroscopy (FCS), we show the effect of polydispersity of probes on the experimental results.

We measured macroscopic viscosity as well as nanoviscosity experienced by molecular probes diffusing in solutions containing two polymer species vastly differing in the molecular weight. On this basis we postulated a scaling equation for viscosity of complex liquids characterized by two distinct length-scales.

We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales—from diffusion of molecular probes to macroscopic viscous flow—we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions.

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles.

This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model.

A fluorescent supramolecular hydrogel was prepared by α-cyclodextrin (α-CD) and Tyloxapol, which can be considered as an oligomer of the nonionic surfactant polyoxyethylene tert-octylphenyl ether (Triton X-100, TX-100) with a polymerization degree below 7.

The structural dynamics of proteins is crucial to their biological functions. A precise and convenient method to determine the structural changes of a protein is still urgently needed. Herein, we employ fluorescence correlation spectroscopy (FCS) to track the structural transition of bovine serum albumin (BSA) in low concentrated cationic (CTAC), anionic (SDS), and nonionic.

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa).

We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10−3–0.56).

We developed a laser-based method to quantify the double labeling efficiency of double-stranded DNA (dsDNA) in a fluorescent dsDNA pool with fluorescence correlation spectroscopy (FCS). Though, for quantitative biochemistry, accurate measurement of this parameter is of critical importance, before our work it was almost impossible to quantify what percentage of DNA is doubly labeled with the same dye.

We present a method of prediction of in vivo association rate constants between proteins from in vitro rate constants. This model accounts for the changes in length-scale dependent viscosity of the cytoplasm of a living cell and interaction potential between proteins.

A detailed study of the reverse vesicles formed by a salt-free catanionic surfactant system in toluene was carried out by confocal fluorescence microscopy observations, dye-solubilizing tests, UV–vis measurements and cryo-TEM observations. When tetradecyltrimethyl ammonium laurate (TTAL) and lauric acid (LA) were mixed in the binary solution of water and toluene, reverse vesicular phase formed spontaneously.

We measure the activation energy Ea for the diffusion of molecular probes (dyes and proteins of radii from 0.52 to 6.9 nm) and for macroscopic flow in a model complex liquid—aqueous solutions of polyethylene glycol. We cover a broad range of polymer molecular weights, concentrations, and temperatures.

Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3′ or 5′) end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye.

A carbon nanotube/inorganic hybrid material has been fabricated by coupling Eu(III) complexes onto multi-walled carbon nanotubes (MWCNTs). Successful coupling has been verified by X-ray photoelectron spectroscopy (XPS) measurement where a clear signal from Eu3d has been identified.

Controlled formation of gene delivery complexes (DNA and a vector, usually a cationic polymer) is one of the key challenges in developing efficient gene delivery systems. The researchers focused their procedures on the ratio of vector to DNA, neglecting the influence of concentration on the complex formation process.

The viscosity in soft matter systems is a scale dependent quantity. In polymer solutions the viscosity of nanoprobes of size R approaches the macroscopic viscosity when R exceeds the radius of gyration of the polymer, Rg. The nano to macroviscosity crossover occurs for R ∼ Rg. Here we analyze diffusion in a polymer solution of nanoparticles in the crossover regime.

We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells.

There is experimental evidence that in solutions of low ionic strength, charged nanoparticles adsorbing onto an oppositely charged substrate cannot form dense monolayers due to the electrostatic repulsion. Here, we investigated the adsorption onto negatively charged substrates occurring in solutions containing positively charged NPs and salt for a wide range of ionic strengths.

Aggregate transitions in salt-free catanionic surfactant mixtures of tetradecyltrimethylammonium hydroxide (TTAOH)/fatty acid were investigated as a function of surfactant concentration and temperature. Lauric acid (LA), myristic acid (MA), and palmitic acid (PA) were chosen for the current study. The TTAOH/LA mixture exhibited rich phase behavior at room temperature.

We give a detailed confocal fluorescence microscopy study on reverse vesicles from a salt-free catanionic surfactant system. When tetradecyltrimethylammonium laurate (TTAL) and lauric acid (LA) are mixed in cyclohexane at the presence of a small amount of water, stable reverse vesicular phases form spontaneously.

We study the separation in the binary and ternary mixtures of the water/surfactant C12E5/polymer PEG system. The phase separation in the mixtures at late stages is governed by two distinct mechanisms: the coalescence-induced coalescence and the droplet evaporation mechanism.

We studied mixing in the initially separated binary mixture of polystyrene/5CB liquid crystal and ternary mixtures of water/surfactant C12E5/polymer PEG system. In both systems the domains of one phase were characterized by a much higher viscosity than the solvent matrix.