Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.

Goldilocks Fluctuations: Dynamic Constraints on Loop Formation in Scale-Free Transport Networks.

Adaptive transport networks are known to contain loops when subject to hydrodynamic fluctuations. However, fluctuations are no guarantee that a loop will form, as shown by loop-free networks driven by oscillating flows. We provide a complete stability analysis of the dynamical behavior of any loop formed by fluctuating flows. We find a threshold for loop stability that involves an interplay of geometric constraints and hydrodynamic forcing mapped to constant and fluctuating components. Loops require fluctuation in the relative size of the flux between nodes, not just a temporal variation in the flux at a given node. Hence, there is both a minimum and a maximum amount of fluctuation relative to the constant-flux component where loops are supported.

The Development of Sustainable Polyethylene Terephthalate Glycol-Based (PETG) Blends for Additive Manufacturing Processing-The Use of Multilayered Foil Waste as the Blend Component.

The polymer foil industry is one of the leading producers of plastic waste. The development of new recycling methods for packaging products is one of the biggest demands in today's engineering. The subject of this research was the melt processing of multilayered PET-based foil waste with PETG copolymer. The resulting blends were intended for additive manufacturing processing using the fused deposition modeling (FDM) method. In order to improve the properties of the developed materials, the blends compounding procedure was conducted with the addition of a reactive chain extender (CE) and elastomeric copolymer used as an impact modifier (IM). The samples were manufactured using the 3D printing technique and, for comparison, using the traditional injection molding method. The obtained samples were subjected to a detailed characterization procedure, including mechanical performance evaluation, thermal analysis, and rheological measurements. This research confirms that PET-based film waste can be successfully used for the production of filament, and for most samples, the FDM printing process can be conducted without any difficulties. Unfortunately, the unmodified blends are characterized by brittleness, which makes it necessary to use an elastomer additive (IM). The presence of a semicrystalline PET phase improves the thermal resistance of the prepared blends; however, an annealing procedure is required for this purpose.

Long-term day-by-day tracking of microvascular networks sprouting in fibrin gels: From detailed morphological analyses to general growth rules.

Understanding and controlling of the evolution of sprouting vascular networks remains one of the basic challenges in tissue engineering. Previous studies on the vascularization dynamics have typically focused only on the phase of intense growth and often lacked spatial control over the initial cell arrangement. Here, we perform long-term day-by-day analysis of tens of isolated microvasculatures sprouting from endothelial cell-coated spherical beads embedded in an external fibrin gel. We systematically study the topological evolution of the sprouting networks over their whole lifespan, i.e., for at least 14 days. We develop a custom image analysis toolkit and quantify (i) the overall length and area of the sprouts, (ii) the distributions of segment lengths and branching angles, and (iii) the average number of branch generations-a measure of network complexity. We show that higher concentrations of vascular endothelial growth factor (VEGF) lead to earlier sprouting and more branched networks, yet without significantly affecting the speed of growth of individual sprouts. We find that the mean branching angle is weakly dependent on VEGF and typically in the range of 60°-75°, suggesting that, by comparison with the available diffusion-limited growth models, the bifurcating tips tend to follow local VEGF gradients. At high VEGF concentrations, we observe exponential distributions of segment lengths, which signify purely stochastic branching. Our results-due to their high statistical relevance-may serve as a benchmark for predictive models, while our new image analysis toolkit, offering unique features and high speed of operation, could be exploited in future angiogenic drug tests.

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.

Narcissus' belief about his body: Aspects of narcissism, body image, and eating disorder symptoms.

OBJECTIVE: Narcissism may play a role in shaping body image concerns. Here we examined the relationships between narcissism (i.e., agentic extraversion, antagonism, narcissistic neuroticism, leadership/authority, exhibitionism/entitlement) and body image concerns and disturbances (i.e., drive for thinness, drive for muscularity, eating disorder symptoms, body mass index, current/desired fat, and current/desired muscularity). METHODS: Mechanical Turk workers from the USA (N = 430; 64% male) completed the Narcissistic Admiration and Rivalry Questionnaire, the Hypersensitive Narcissism Scale, the Narcissistic Personality Inventory, the Drive for Muscularity Scale, the Drive for Thinness Scale, the Eating Disorder Examination Questionnaire-Short, and the Sex-Specific Somatomorphic Matrixes. RESULTS: All narcissistic factors were associated with a greater drive for thinness (except for leadership/authority) and for muscularity, more eating disorder symptoms, a greater desired body fat (except for leadership/authority), and a greater current muscularity. Greater agentic extraversion and exhibitionism/entitlement were associated with lower levels of current body fat, and greater antagonism was associated with a greater desired muscularity. DISCUSSION: Notably, individual differences in narcissism appeared to be important in understanding body image concerns, broadly speaking. We found that narcissism may be associated with body image concerns among both sexes differently, and especially that drive for thinness was more related to narcissism in men. Our results emphasize the importance of narcissism in formulating and treating body image-related disorders for both men and women. Ultimately, narcissistic features of personality may be risk factors for developing and perpetuating body image concerns, and therefore should be considered in assessment, formulation, diagnosis, and treatment of eating disorders.

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.

DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.

DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.

Stochastic model of translocation of knotted proteins.

Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model of this process with a time-periodic potential that mimics the action of a molecular motor. We calculate the translocation time as a function of the period of the pulling force, discuss the asymptotic limits and biological relevance of the results.

Through history to growth dynamics: deciphering the evolution of spatial networks.

Many ramified, network-like patterns in nature, such as river networks or blood vessels, form as a result of unstable growth of moving boundaries in an external diffusive field. Here, we pose the inverse problem for the network growth-can the growth dynamics be inferred from the analysis of the final pattern? We show that by evolving the network backward in time one can not only reconstruct the growth rules but also get an insight into the conditions under which branch splitting occurs. Determining the growth rules from a single snapshot in time is particularly important for growth processes so slow that they cannot be directly observed, such as growth of river networks and deltas or cave passages. We apply this approach to analyze the growth of a real river network in Vermont, USA. We determine its growth rule and argue that branch splitting events are triggered by an increase in the tip growth velocity.

Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules.

We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid. In our approach, the position- and orientation-dependent mobility matrix of a body suspended near a no-slip plane is calculated numerically using a coarse-grained molecular model and the Rotne-Prager-Yamakawa description of hydrodynamics. Effects of the boundary are accounted for via Blake's image construction. The matrix components are scaled using ratios of the corresponding bulk values evaluated for the detailed representation of the molecule and its coarse-grained model, leading to accurate values of the near-wall diffusion coefficients. We assess the performance of the approach for two biomolecules at different levels of coarse-graining.

Correction: Stokesian dynamics of sedimenting elastic rings.

Correction for 'Stokesian dynamics of sedimenting elastic rings' by Magdalena Gruziel-Slomka et al., Soft Matter, 2019, 15, 7262-7274, https://doi.org/10.1039/C9SM00598F.

Generalized Rotne-Prager-Yamakawa approximation for Brownian dynamics in shear flow in bounded, unbounded, and periodic domains.

Inclusion of hydrodynamic interactions is essential for a quantitatively accurate Brownian dynamics simulation of colloidal suspensions or polymer solutions. We use the generalized Rotne-Prager-Yamakawa (GRPY) approximation, which takes into account all long-ranged terms in the hydrodynamic interactions, to derive the complete set of hydrodynamic matrices in different geometries: unbounded space, periodic boundary conditions of Lees-Edwards type, and vicinity of a free surface. The construction is carried out both for non-overlapping as well as for overlapping particles. We include the dipolar degrees of freedom, which allows one to use this formalism to simulate the dynamics of suspensions in a shear flow and to study the evolution of their rheological properties. Finally, we provide an open-source numerical package, which implements the GRPY algorithm in Lees-Edwards periodic boundary conditions.

Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods.

We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid-fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. We discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.

Ions in an AC Electric Field: Strong Long-Range Repulsion between Oppositely Charged Surfaces.

Two oppositely charged surfaces separated by a dielectric medium attract each other. In contrast we observe a strong repulsion between two plates of a capacitor that is filled with an aqueous electrolyte upon application of an alternating potential difference between the plates. This long-range force increases with the ratio of diffusion coefficients of the ions in the medium and reaches a steady state after a few minutes, which is much larger than the millisecond timescale of diffusion across the narrow gap. The repulsive force, an order of magnitude stronger than the electrostatic attraction observed in the same setup in air, results from the increase in osmotic pressure as a consequence of the field-induced excess of cations and anions due to lateral transport from adjacent reservoirs.

Reactive-infiltration instability in radial geometry: From dissolution fingers to star patterns.

We consider the process of chemical erosion of a porous medium infiltrated by a reactive fluid in a thin-front limit, in which the width of the reactive front is negligible with respect to the diffusive length. We show that in the radial geometry the advancing front becomes unstable only if the flow rate in the system is sufficiently high. The existence of such a stable region in parameter space is in contrast to the Saffman-Taylor instability in radial geometry, where for a given flow rate the front always eventually becomes unstable, after reaching a certain critical radius. We also examine the similarities between the reactive-infiltration instability and the similar instability in the heat transfer, which is driving the formation of star-like patterns on frozen lakes.

Stokesian dynamics of sedimenting elastic rings.

We consider elastic microfilaments which form closed loops. We investigate how the loops change shape and orientation while settling under gravity in a viscous fluid. Loops are circular at the equilibrium. Their dynamics are investigated numerically based on the Stokes equations for the fluid motion and the bead-spring model of the microfilament. The Rotne-Prager approximation for the bead mobility is used. We demonstrate that the relevant dimensionless parameter is the ratio of the bending resistance of the filament to the gravitation force corrected for buoyancy. The inverse of this ratio, called the elasto-gravitation number B, is widely used in the literature for sedimenting elastic linear filaments. We assume that B is of the order of 104-106, which corresponds to easily deformable loops. We find out that initially tilted circles evolve towards different sedimentation modes, depending on B. Very stiff or stiff rings attain almost planar, oval shapes, which are vertical or tilted, respectively. More flexible loops deform significantly and converge towards one of several characteristic periodic motions. These sedimentation modes are also detected when starting from various shapes, and for different loop lengths. In general, multi-stability is observed: an elastic ring converges to one of several sedimentation modes, depending on the initial conditions. This effect is pronounced for very elastic loops. The surprising diversity of long-lasting periodic motions and shapes of elastic rings found in this work gives a new perspective for the dynamics of more complex deformable objects at micrometer and nanometer scales, sedimenting under gravity or rotating in a centrifuge, such as red blood cells, ring polymers or circular DNA.

Periodic Motion of Sedimenting Flexible Knots.

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwined loops, oscillating periodically around each other. We then recover this motion numerically and find out that it is accompanied by a very slow rotation around the vertical symmetry axis. We analyze the dependence of the characteristic timescales on the chain flexibility and aspect ratio. It is observed in the experiments that this oscillating mode of the dynamics can spontaneously form even when starting from a qualitatively different initial configuration. In numerical simulations, the oscillating modes are usually present as transients or final stages of the evolution, depending on chain aspect ratio and flexibility, and the number of loops.

GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.

Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.

Effect of mobility ratio on interaction between the fingers in unstable growth processes.

We investigate interactions between thin fingers formed as a result of an instability of an advancing front in growth processes. We show that the fingers can both attract and repel each other, depending on their lengths and the mobility ratio between the invading and displaced phase. To understand the origin of these interactions we introduce a simple resistor model of the fingers. The predictions of the model are then compared to the numerical simulations of two unstable growth processes: dissolution of partially cemented rock fracture and viscous fingering in a regular network of channels.