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. Here, we report for the first time the measurement of the viscosity and shear storage modulus of highly concentrated Escherichia coli (E. coli) lysates with and without adenosine triphosphate (ATP). By cleavage of DNA content, we showed the value of shear storage modulus G′G′ decreases by 19–31% in comparison to control samples. The addition of molecules that provides energy (ATP) allowed to rebuild the structure of the lysate by reversibly increasing viscous properties over elastic ones. When the energy delivered in the form of ATP is consumed by the unliving bacterial lysate, the system returns to its initial state.

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 (m_p, <−20 °C), which has not been achieved by reported counterparts bearing linear alkyl chains. In solvent-free states, microphase segregation occurs where polar and apolar domains arrange bicontinuously as proved by molecular dynamics (MD) simulations. When dispersed in water, self-stabilized giant aggregates formed with ultrahigh colloidal stability (up to years). MD simulations provide clues of discrete bicontinuous phases within the giant aggregates. These newly discovered self-assemblies provide a heterogeneous reservoir that can accommodate guest molecules including the highly apolar fullerene C₆₀, paving the way for a wide range of potential applications.

We study a quantity T defined as the energy U, stored in non-equilibrium steady states (NESS) over its value in equilibrium U0 , ΔU=U−U0 divided by the heat flow JU going out of the system. A recent study suggests that T is minimized in steady states (Phys.Rev.E.99, 042118 (2019)). We evaluate this hypothesis using an ideal gas system with three methods of energy delivery: from a uniformly distributed energy source, from an external heat flow through the surface, and from an external matter flow. By introducing internal constraints into the system, we determine T with and without constraints and find that T is the smallest for unconstrained NESS. We find that the form of the internal energy in the studied NESS follows U=U0∗f(JU) . In this context, we discuss natural variables for NESS, define the embedded energy (an analog of Helmholtz free energy for NESS), and provide its interpretation.

The majority of analytical chemistry methods requires presence of target molecules directly at a sensing surface. Diffusion of analyte from the bulk towards the sensing layer is random and might be extremely lengthy, especially in case of low concentration of molecules to be detected. Thus, even the most sensitive transducer and the most selective sensing layer are limited by the efficiency of deposition of molecules on sensing surfaces. However, rapid development of new sensing technologies is rarely accompanied by new protocols for analyte deposition. To bridge this gap, we propose a method for fast and efficient deposition of variety of molecules (e.g. proteins, dyes, drugs, biomarkers, amino acids) based on application of the alternating electric field. We show the dependence between frequency of the applied electric field, the intensity of the surface enhanced Raman spectroscopy (SERS) signal and the mobility of the studied analyte. Such correlation allows for a priori selection of parameters for any desired compound without additional optimization. Thanks to the application of the electric field, we improve SERS technique by decrease of time of deposition from 20 h to 5 min, and, at the same time, reduction of the required sample volume from 2 ml to 50 μl. Our method might be paired with number of analytical methods, as it allows for deposition of molecules on any conductive surface, or a conductive surface covered with dielectric layer.

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. To illustrate this method, we used a reaction of DNA hybridization, where only one of the strands was fluorescently labeled. We determined K at the substrate concentrations from 80 pM to 30 nM. We validated this method against Förster resonance energy transfer (FRET). This method is much simpler than FRET as it requires only one fluorophore in the complex with a very small (a f̃ew percent) change in MB.

We study periodic steady states of a lattice system under external cyclic energy supply using simulation. We consider different protocols for cyclic energy supply and examine the energy storage. Under the same energy flux, we found that the stored energy depends on the details of the supply, period, and amplitude of the supply. Further, we introduce an adiabatic wall as an internal constraint into the lattice and examine the stored energy with respect to different positions of the internal constrain. We found that the stored energy for constrained systems is larger than its unconstrained counterpart. We also observe that the system stores more energy through large and rare energy delivery, comparing to small and frequent delivery.

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. Modeling, understanding, engineering and controlling processes at the nanoscale, most importantly inside living cells, requires a theoretical framework for the description of viscous response to allow predictions of diffusion rates in complex fluids. Here we use a general framework with the viscosity η(k) described by a function of wave vector in reciprocal space. We introduce a formulation that allows one to relate the rotational and translational diffusion coefficients and determine the viscosity η(k) directly from experiments. We apply our theory to provide a database for rotational diffusion coefficients of proteins/protein complexes in the bacterium E. coli. We also provide a database for the diffusion coefficient of proteins sliding along major grooves of DNA in E. coli. These parameters allow predictions of rate constants for association of proteins. In addition to constituting a theoretical framework for description of diffusion of probes and viscosity in complex fluids, the formulation that we propose should decrease substantially the cost of numerical simulations of transport in complex media by replacing the simulation of individual crowding particles with a continuous medium characterized by a wave-length dependent viscosity η(k).

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). We quantified nanoparticle transport in spheroids’ proliferating zone. We determined the size-dependent viscosity of the ECM. We revealed that nanoobjects up to 10 nm in radius exhibited unobstructed diffusion in the ECM, regardless of the spheroid type. Presented length-scale dependent viscosity profiles for spheroids pave the way for advanced modelling of drug administration through tissue.
Journal: Nanoscale
Publisher: The Royal Society of Chemistry