Rotational Diffusion Research Articles

Dispersion of run-and-tumble microswimmers through disordered media.

Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.

Four-Phase Lags in a Generalized Thermoelastic Rotational Diffusive Plate with Laser Pulse Emission

Four-Phase Lags in a Generalized Thermoelastic Rotational Diffusive Plate with Laser Pulse Emission

First coarse grain then scale: How to estimate diffusion coefficients of confined molecules.

An approach for approximating position and orientation dependent translational and rotational diffusion coefficients of rigid molecules of any shape suspended in a viscous fluid under geometric confinement is proposed. It is an extension of the previously developed scheme for evaluating near-wall diffusion of macromolecules, now applied to any geometry of boundaries. The method relies on shape based coarse-graining combined with scaling of mobility matrix components by factors derived based on energy dissipation arguments for Stokes flows. Tests performed for a capsule shaped molecule and its coarse-grained model, a dumbbell, for three different types of boundaries (a sphere, an open cylinder, and two parallel planes) are described. An almost perfect agreement between mobility functions of the detailed and coarse-grained models, even close to boundary surfaces, is obtained. The proposed method can be used to simplify hydrodynamic calculations and reduce errors introduced due to coarse-graining of molecular shapes.

The interplay between bulk flow and boundary conditions on the distribution of microswimmers in channel flow

While previous experimental and numerical studies of dilute microswimmer suspensions have focused on the behaviours of swimmers in the bulk flow and near boundaries, models typically do not account for the interplay between bulk flow and the choice of boundary conditions imposed in continuum models. In our work, we highlight the effect of boundary conditions on the bulk flow distributions, such as through the development of boundary layers or secondary peaks of cell accumulation in bulk-flow swimmer dynamics. For the case of a dilute swimmer suspension in Poiseuille flow, we compare the distribution (in physical and orientation space) obtained from individual-based stochastic models with those from continuum models, and identify under what conditions it is mathematically sensible to use specific continuum boundary conditions to capture different physical scenarios (i.e. specular reflection, uniform random reflection and absorbing boundaries). We identify that the spread of preferred cell orientations is dependent on the interplay between rotation driven by the shear flow (Jeffery orbits) and rotational diffusion. We find that in the absence of hydrodynamic wall interactions, swimmers preferentially approach the walls perpendicular to the surface in the presence of high rotational diffusion, and that the preferential approach of swimmers to the walls is shape-dependent at low rotational diffusion (when suspensions tend towards a fully deterministic case). In the latter case, the preferred orientations are nearly parallel to the surface for elongated swimmers and nearly perpendicular to the surface for near-spherical swimmers. Furthermore, we highlight the effects of swimmer geometries and shear throughout the bulk-flow on swimmer trajectories and show how the full history of bulk-flow dynamics affects the orientation distributions of microswimmer wall incidence.

Nanoswimmers in a ratchet potential: Effects of a transverse rocking force

We study the dynamics of a chemical nanoswimmer in a ratchet potential, which is periodically rocked in the transverse direction. As a result of the mechanochemical coupling, the self-propulsion velocity becomes force-dependent and particle trajectories are rectified in the direction of the ratchet modulation. The magnitude and direction of the nanoswimmer mean velocity depend upon both the rocking amplitude and the frequency. Remarkably, for frequencies larger than the inverse correlation time of the rotational diffusion, the velocity exhibits oscillatory behaviour as a function of the amplitude and the frequency with multiple reversals of the sign. These findings suggest that mechanochemical coupling can be utilized for controlling the motion of chemically active particles at the nanoscale.

Rotational diffusion of shape-switching particles dissolved in biaxial liquid crystals

ABSTRACT The interpretation of many experimental or computational studies on the orientational dynamics of molecules dissolved in liquid crystals relies on assuming some stochastic model for their time evolution. The Rotational Diffusion model is typically employed for this purpose, representing the molecules being monitored as rigid particles. However, this is not a realistic assumption for many molecules or nanoparticles in solution, and we have previously proposed a model to describe the rotational diffusion of a shape-changing particle dissolved in uniaxial fluids. Here, we extend the model allowing the host medium to be of biaxial symmetry, and we apply the theory to a simple example case, as well as exploring its general features.

The solid effect of dynamic nuclear polarization in liquids - accounting for g-tensor anisotropy at high magnetic fields.

In spite of its name, the solid effect of dynamic nuclear polarization (DNP) is also operative in viscous liquids, where the dipolar interaction between the polarized nuclear spins and the polarizing electrons is not completely averaged out by molecular diffusion on the timescale of the electronic spin-spin relaxation time. Under such slow-motional conditions, it is likely that the tumbling of the polarizing agent is similarly too slow to efficiently average the anisotropies of its magnetic tensors on the timescale of the electronic . Here we extend our previous analysis of the solid effect in liquids to account for the effect of -tensor anisotropy at high magnetic fields. Building directly on the mathematical treatment of slow tumbling in electron spin resonance , we calculate solid-effect DNP enhancements in the presence of both translational diffusion of the liquid molecules and rotational diffusion of the polarizing agent. To illustrate the formalism, we analyze high-field (9.4 T) DNP enhancement profiles from nitroxide-labeled lipids in fluid lipid bilayers. By properly accounting for power broadening and motional broadening, we successfully decompose the measured DNP enhancements into their separate contributions from the solid and Overhauser effects.

Study of factors affecting some properties of hydrophilic suppository base

The aim. To study the effect of the composition of hydrophilic suppository bases on the physicochemical and osmotic properties of suppositories made from them.
 Materials and methods. The bases were studied with varying compositions of excipients. The microstructure of the bases was evaluated, and the disintegration time and resistance to rupture of suppositories made from them were determined. The kinetics of water absorption and solvent release were studied by dialysis. The content of propylene glycol (PG) and macrogol 400 (M400) in the receptor medium was determined by gas chromatography. The melted bases were studied by rotational viscometry. The electron paramagnetic resonance spectra of spin probes in hydrophilic solvents and bases were obtained; the type of spectrum, isotropic constant (AN), rotational correlation times (τ), and anisotropy parameter (ε) were determined.
 Results. The disintegration times and resistance to rupture of suppositories were determined depending on such factors as the content and grade of poloxamers, the ratio between high molecular weight macrogols and the mixed solvent PG-M400 (60 : 40 % m/m), the ratio of nonionic surfactant and cetostearyl alcohol (CSA) and their total content, water and hard fat content. The introduction of solid fat and a mixture of surfactants and CSA provides the uniform structure of the bases. The mass ratio between surfactants and CSA and their total content are important factors that provide acceptable resistance to rupture and disintegration times for suppositories and reduce water absorption and solvent release. As the temperature decreases from 45 °C to 20 °C, the bases transform from Newtonian liquids to solids. At that time, the microviscosity of the environment of the spin probes increased by about 5 times, but the parameters of their rotational diffusion in solid bases and the mixed solvent PG-M400 are comparable. This indicates the dissolved state of the spin probes in the bases and the absence of the formation of mixed associates from molecules of surfactant and CSA.
 Conclusions. By varying the composition of excipients, the properties of hydrophilic suppository bases can be controlled, significantly reducing their osmotic properties. The active substances in these bases may be in a dissolved state due to the high content of non-aqueous solvents

Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics.

This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids.

Orientation Mixing in Active Suspensions

We study a popular kinetic model introduced by Saintillan and Shelley for the dynamics of suspensions of active elongated particles where the particles are described by a distribution in space and orientation. The uniform distribution of particles is the stationary state of incoherence which is known to exhibit a phase transition. We perform an extensive study of the linearised evolution around the incoherent state. We show (i) in the non-diffusive regime corresponding to spectral (neutral) stability that the suspensions experience a mixing phenomenon similar to Landau damping and we provide optimal pointwise in time decay rates in weak topology. Further, we show (ii) in the case of small rotational diffusion ν\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ u $$\\end{document} that the mixing estimates persist up to time scale ν-1/2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ u ^{-1/2}$$\\end{document} until the exponential decay at enhanced dissipation rate ν1/2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ u ^{1/2}$$\\end{document} takes over. The interesting feature is that the usual velocity variable of kinetic models is replaced by an orientation variable on the sphere. The associated orientation mixing leads to limited algebraic decay for macroscopic quantities. For the proof, we start with a general pointwise decay result for Volterra equations that may be of independent interest. While, in the non-diffusive case, explicit formulas on the sphere allow to conclude the desired decay, much more work is required in the diffusive case: here we prove mixing estimates for the advection-diffusion equation on the sphere by combining an optimized hypocoercive approach with the vector field method. One main point in this context is to identify good commuting vector fields for the advection-diffusion operator on the sphere. Our results in this direction may be useful to other models in collective dynamics, where an orientation variable is involved.

Understanding the influence of ethylene glycol on the microscopic behavior of imidazolium-based monocationic and dicationic ionic liquid

In the present work, the influence of a molecular co-solvent, ethylene glycol (EG) on the microscopic behaviour of an imidazolium-based dicationic ionic liquid (DIL) is analysed by employing time-resolved fluorescence anisotropy (TRFA) and nuclear magnetic resonance (NMR) spectroscopic techniques. In order to have a clear understanding of the specific role of DIL, a mono-cationic ionic liquid (MIL) containing an alkyl side chain unit, same as the alkyl spacer chain length of DIL, has also been investigated. The rotational diffusion of two fluorescent probes 9-PA and R110 have been carried out in both neat MIL and DIL and their mixtures with various fractions of EG. The analysis of the results has demonstrated that, within the studied concentration range, the microstructure of MIL encompassing both polar and nonpolar domains gets disrupted as the mole fraction of EG increases. However, a similar investigation in DIL has revealed that the micro-structure of DIL gets affected slightly when similar proportions of EG are added to DIL. This behaviour of DIL is attributed to the enhanced rigidity of the DIL structure due to its folded structural arrangements. Furthermore, NMR studies have provided additional insights into the interactions between the components of ILs and the added solvent. It has been observed that EG can form strong hydrogen-bonding interactions with the imidazolium-ring and alkyl chain protons of MIL. However, such interaction has not been observed in DIL. Moreover, the translational diffusion coefficient (Dt) value for the cationic moiety of both MIL and DIL, measured through NMR, has depicted that in the presence of EG, the change in Dtvalue is much higher for MIL than that for DIL. Overall, the outcome of the combined fluorescence and NMR studies have pointed out that the behaviour of DIL and MIL in the presence of a co-solvent is very different from one another and thus the individual mixture (IL+solvent) can be used for various targeted industrial applications.

Photophysical properties of Radachlorin photosensitizer in solutions of different pH, viscosity and polarity

We present a thorough experimental investigation of fluorescence properties of Radachlorin photosensitizer in solutions of different acidity, viscosity and polarity. Experiments were performed using time-resolved fluorescence lifetime imaging and time-resolved analysis of polarized fluorescence. Variations of solution acidity resulted in considerable changes of Radachlorin fluorescence quantum yield and lifetime in the pH range from 4 to 7, but did not affect the rotational diffusion time, and almost did not change the quantum yield and characteristic times of singlet oxygen phosphorescence. Variations of solution polarity and viscosity were achieved by changing ethanol or methanol fraction in aqueous solution. The decrease of solution polarity resulted in nonlinear rise of Radachlorin fluorescence quantum yield and lifetime up to alcohol concentration of 50%–65%, as well as in considerable rise of singlet oxygen quantum yield and significant changes in characteristic times of its phosphorescence. Variations of solution viscosity resulted in changes of rotational diffusion time of Radachlorin molecules, which appeared to be in perfect correlation with methanol solution viscosity. Good correspondence with ethanol solution viscosity was observed only up to 50% alcohol fraction. Deviations of rotational diffusion time of Radachlorin molecules from direct proportionality with solution viscosity at higher ethanol concentrations were suggested to be due to different solvation conditions. The data obtained can give important reference points for analysis of microenvironment of Radachlorin molecules, their intracellular localization and performance in singlet oxygen generation.

The Debye's model for the dielectric relaxation of liquid water and the role of cross-dipolar correlations. A MD-simulations study.

By means of massive (more than 1.2 · 106 molecules) molecular dynamics simulations at 300K we have disentangled self- and cross-dipolar contributions to the dielectric relaxation of liquid water that cannot be experimentally resolved. We have demonstrated that cross dipolar correlations are of paramount importance. They amount for almost a 60% of the total dielectric amplitude. The corresponding relaxation function is a one-step Debye-like function with a characteristic time, τcross, of the order of the phenomenological Debye time, τD. In contrast, the relaxation function corresponding to the self-contribution is rather complex and contains a fast decay related to dipolar librations and a second relaxation step that can be well described by two exponentials: a low-amplitude fast process (τ0 = 0.31ps) and a main slow process (τself = 5.4ps) that fully randomizes the dipolar orientation. In addition to dipolar relaxation functions, we have also calculated scattering-like magnitudes characterizing translation and rotation of water molecules. Although these processes can be considered as "jump" processes in the short time range, at the time scale of about τD-τcross, at which the cross-dipolar correlations decay to zero, the observed behavior cannot be distinguished from that corresponding to uncoupled Brownian translational and rotational diffusion. We propose that this is the reason why the Debye model, which does not consider intermolecular dipolar interactions, seems to work at time t ≳ τD.

Role of translational noise on current reversals of active particles on ratchet

In this study, we explore using Langevin dynamics simulations, the role of thermal fluctuations on the rectification of non-interacting inertial active (self-propelled) particles in a rocking ratchet setup in the absence and in the presence of the external time periodic drive. The system is first studied in the absence of the external drive. It is found that the average velocity is always positive and a peaked function of the translational noise, indicating that the asymmetry effects dominate at intermediate values of the strength of the thermal noise. In the second part of this work, we study the effect of the external drive on the dynamics of the system by exploring a phase diagram in the parameter space of translational noise and driving frequency for two different strengths of rotational diffusion. For a given constant amplitude of the active force and amplitude of external drive less than the maximum force due to the potential, the average velocity magnitude as well as the direction (+ {hat{x}}/- {hat{x}}) is found to depend on the rotational diffusion, frequency of the external drive and the strength of the translational noise. We discover certain critical parameters in the phase space at which current reversals happen. It is found that when the average particle energy is lower than the potential energy of the barrier, symmetry breaking dominates and the currents are in the ‘easy’ direction of the ratchet. On the other hand, when the energy available per particle crosses the potential energy of the barrier, the competition between inertial effects and diffusion effects decides the direction of currents. We explain our findings by constructing phase difference datum, velocity probability distribution, and current probability analyses. Our results provide a novel method for controlling the direction of transport of inertial active particles.

Resonance Light-Scattering Correlation Spectroscopy and Its Application in Analytical Chemistry for Life Science.

Resonance light-scattering correlation spectroscopy (RLSCS) is a new single-particle detection method with its working principle being like fluorescence correlation spectroscopy (FCS). RLSCS is obtained by autocorrelation function analysis on the measured fluctuation of the resonance light scattering (RLS) intensity occurring within a subfemtoliter volume when a single nanoparticle (such as gold nanoparticles (NPs) or silver (SNPs)) freely diffuses through the volume. The RLSCS technique can detect such parameters as concentration, diffusion coefficient (translation and rotation), etc. Compared with the FCS technique, the correlated fluorescence intensity signal in RLSCS is replaced with the RLS signal of the nanoparticles, overcoming some limits of the fluorescent probes such as photobleaching under high-intensity or long-term illumination. In this Account, we showcase RLSCS methods, theoretical models at different optical configurations, and some key applications. First, the RLSCS optical detection system was constructed based on the confocal optics, its theoretical model was proposed, and the diffusion behaviors of the nanoparticles in the solution were studied including the rotational and translational diffusion. And, methods were developed to measure the concentration, size, aspect ratio, and size distribution of the NPs. Second, based on the RLSCS methods, some detection strategies were developed for homogeneous DNA detection, immunoassay, apoptosis assay, self-thermophoresis of the nanomotor, and quantitative assay in single living cells. Meanwhile, a new fluorescence/scattering cross-correlation spectroscopy (FSCCS) method was proposed for monitoring the molecule-particle interaction. This method enriched the conventional fluorescence/fluorescence cross-correlation spectroscopy (FCCS) method. Third, using the EMCCD with high sensitivity and rapid response as an optical detector, two temporospatially resolved scattering correlation spectroscopy methods and their theoretical models were developed: total internal reflection (TIR) configuration-based spatially resolved scattering correlation spectroscopy (SRSCS) and dark-field illumination-based scattering correlation spectroscopy (DFSCS). These methods extended single-spot confocal RLSCS to imaging RLSCS, which makes RLSCS have the ability for multiple channel detection with temporospatial resolution. The method was successfully used for investigating the dynamic behaviors of gold NPs in live cells and obtained its temporospatial concentration distribution and diffusion behaviors. The final section of this Account outlines future directions in the development of RLSCS.

Lithium Ion Battery Electrolytes Based on Deep Eutectic Solvents

Deep eutectic solvents (DESs) have emerged as an alternative to both common organic solvents and ionic liquids (ILs). DESs share physicochemical properties with ILs such as low vapor pressure, high thermal stability, while offering advantages such as low toxicity, lower cost, and ease of preparation. Moreover, DESs are attractive candidates for electrochemical applications due to their large voltage windows and solubility properties. DESs as a solvent class share a general composition of a hydrogen bond donor (HBD), typically a polyol, amide, or acid, and a hydrogen bond acceptor (HBA), usually a quaternary ammonium or phosphonium salt. At a specific molar composition of a HBD and HBA, the DES forms a eutectic mixture resulting in a large melting point depression.Despite being widely studied, the microscopic structures of DESs have remained largely uncharacterized. Herein, we present a multitechnique NMR study of ethaline (ethylene glycol + choline chloride). Pulsed field gradient diffusion, nuclear Overhauser effect spectroscopy (NOESY), 13C NMR relaxation experiments are deployed to sample a range of frequencies and modes of motion of the polyol and choline components of the DES. Generally, translational and rotational diffusion of polyols are more rapid than those of choline while short-range rotational motions observed from 13C relaxation indicate slow local motion of ethylene glycol at low choline chloride (ChCl) content.Additionally, we have investigated the solubility properties of several lithium salts (LiTFSI, LiFSI, LiBF4, and LiOAc) in these DESs and utilized the same suite of NMR techniques to understand how they act as solvents. One interesting observation is that the Li+ diffusivity exceeds that of the counterion for TFSI-, but not for FSI-. Finally, large changes in the structural organization of DESs that result from the presence of lithium salts may serve as a guide to the design of a new class of electrolytes for lithium-ion batteries.

Comparison of Friction Parametrization from Dynamics and Material Properties for a Coarse-Grained Polymer Melt.

In this work, we extend an approach to coarse-grained (CG) modeling for polymer melts in which the conservative potential is parametrized using the iterative Boltzmann inversion (IBI) method and the accelerated dynamics inherent to IBI are corrected using the dissipative Langevin thermostat with a single tunable friction parameter (J. Chem. Phys. 2021, 154, 084114). Diffusive measures from picoseconds to nanoseconds are used to determine the Langevin friction factor to apply to the CG model to recover all-atom (AA) dynamics; the resulting friction factors are then compared for consistency. Here, we additionally parametrize the CG dynamics using a material property, the zero-shear viscosity, which we measure using the Green-Kubo (GK) method. Two materials are studied, squalane as a function of temperature and the same polystyrene oligomers previously studied as a function of chain length. For squalane, the friction derived from the long-time diffusive measures and the viscosity all strongly increase with decreasing temperature, showing an Arrhenius-like dependence, and remain consistent with each other over the entire temperature range. In contrast, the friction required for the picosecond diffusive measurement, the Debye-Waller factor, is somewhat lower than the friction from long-time measures and relatively insensitive to temperature. A time-dependent friction would be required to exactly reproduce the AA measurements during the caging transition connecting these two extremes over the entire timespan at this level of coarse-graining. For the polystyrene oligomers for which we previously characterized the diffusive friction, the viscosity-parametrized frictions are consistent with the diffusive measures for the smallest chain length. However, for the longer chains, we find different trends based on measurement method with friction derived from rotational diffusion remaining nearly constant, friction derived from translational diffusion showing a modestly increasing trend, and viscosity-derived friction showing a modest decreasing trend. This seems to indicate that there is some sensitivity of the friction measurement method for systems with increased relaxation times and that in particular, the unsteady dynamics of the individual parametrization schemes plays a role in this. Increased difficulty in applying the GK method with increasing relaxation time of the longer chain systems is also discussed. Overall, we find that when the material is in a high-temperature melt state and the viscosity measurement is reliable, the friction parametrization from the diffusive friction measures is consistent and the lower cost diffusive parametrization is a reliable means for modeling viscosity. Our data give insight into the time-dependent friction one might compute using a non-Markovian approach to enable the recovery of AA dynamics over a wider range of time scales than can be computed using a single friction.

Intracellular environment can change protein conformational dynamics in cells through weak interactions.

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules.

The Brownian dynamics (BD) simulation technique is widely used to model the diffusive and conformational dynamics of complex systems comprising biological macromolecules. For the diffusive properties of macromolecules to be described correctly by BD simulations, it is necessary to include hydrodynamic interactions (HIs). When modeled at the Rotne-Prager-Yamakawa (RPY) level of theory, for example, the translational and rotational diffusion coefficients of isolated macromolecules can be accurately reproduced; when HIs are neglected, however, diffusion coefficients can be underestimated by an order of magnitude or more. The principal drawback to the inclusion of HIs in BD simulations is their computational expense, and several previous studies have sought to accelerate their modeling by developing fast approximations for the calculation of the correlated random displacements. Here, we explore the use of an alternative way to accelerate the calculation of HIs, i.e., by replacing the full RPY tensor with an orientationally averaged (OA) version which retains the distance dependence of the HIs but averages out their orientational dependence. We seek here to determine whether such an approximation can be justified in application to the modeling of typical proteins and RNAs. We show that the use of an OA-RPY tensor allows translational diffusion of macromolecules to be modeled with very high accuracy at the cost of rotational diffusion being underestimated by ∼25%. We show that this finding is independent of the type of macromolecule simulated and the level of structural resolution employed in the models. We also show, however, that these results are critically dependent on the inclusion of a non-zero term that describes the divergence of the diffusion tensor: when this term is omitted from simulations that use the OA-RPY model, unfolded macromolecules undergo rapid collapse. Our results indicate that the orientationally averaged RPY tensor is likely to be a useful, fast, approximate way of including HIs in BD simulations of intermediate-scale systems.

Orientational dynamics and rheology of active suspensions in weakly viscoelastic flows

Microswimmer suspensions in Newtonian fluids exhibit unusual macroscale properties, such as a superfluidic behavior, which can be harnessed to perform work at microscopic scales. Since most biological fluids are non-Newtonian, here we study the rheology of a microswimmer suspension in a weakly viscoelastic shear flow. At the individual level, we find that the viscoelastic stresses generated by activity substantially modify the Jeffery orbits well-known from Newtonian fluids. The orientational dynamics depends on the swimmer type; especially pushers can resist flow-induced rotation and align at an angle with the flow. To analyze its impact on bulk rheology, we study a dilute microswimmer suspension in the presence of random tumbling and rotational diffusion. Strikingly, swimmer activity and its elastic response in polymeric fluids alter the orientational distribution and substantially amplify the swimmer-induced viscosity. This suggests that pusher suspensions reach the superfluidic regime at lower volume fractions compared to a Newtonian fluid with identical viscosity.