Active noise-driven particles under space-dependent friction in one dimension.

We study a Langevin equation describing the stochastic motion of a particle in one dimension with coordinate x, which is simultaneously exposed to a space-dependent friction coefficient γ(x), a confining potential U(x) and nonequilibrium (i.e., active) noise. Specifically, we consider frictions γ(x)=γ_{0}+γ_{1}|x|^{p} and potentials U(x)∝|x|^{n} with exponents p=1,2 and n=0,1,2. We provide analytical and numerical results for the particle dynamics for short times and the stationary probability density functions (PDFs) for long times. The short-time behavior displays diffusive and ballistic regimes while the stationary PDFs display unique characteristic features depending on the exponent values (p,n). The PDFs interpolate between Laplacian, Gaussian, and bimodal distributions, whereby a change between these different behaviors can be achieved by a tuning of the friction strengths ratio γ_{0}/γ_{1}. Our model is relevant for molecular motors moving on a one-dimensional track and can also be realized for confined self-propelled colloidal particles.

Fractures of the transverse processes of the fourth and fifth lumbar vertebrae in patients with pelvic ring injuries: indicator of biomechanical instability but not shock.

Aims: This study aimed to analyze the correlation between transverse process (TP) fractures of the fourth (L4) and fifth (L5) lumbar vertebrae and biomechanical and haemodynamic stability in patients with a pelvic ring injury, since previous data are inconsistent. Patients and Methods: The study is a retrospective matched-pair analysis of patients with a pelvic fracture according to the modified Tile AO Müller and the Young and Burgess classification who presented to a level 1 trauma centre between January 2005 and December 2014. Results: A total of 728 patients with pelvic ring injuries were included, of whom 183 (25.1%) had a biomechanically unstable pelvic fracture. Of these patients, 84 (45.9%) had a fracture of a TP of L4 and/or L5. A total of 73 patients (13.4%) with a stable pelvic ring injury (p < 0.001) had a fracture of a TP. Patients with a fracture of a TP of L4 and/or L5 had a 5.5-fold risk (odds ratio (OR)) of having a biomechanically unstable pelvic injury. TP fractures (OR 1.6, p = 0.2) could not be confirmed as an independent predictor of haemodynamic instability. Conclusion: This is the first study that has demonstrated a positive correlation between a TP fracture of L4 and/or L5 and a biomechanically unstable pelvic ring injury. The presence of transverse process fractures of L4 and/or L5 indicates increased severity of pelvic injury and therefore can help in the planning of emergency treatment. Cite this article: Bone Joint J 2018;100-B:1214-19.

[Posttraumatic torsional deformities of the forearm : Methods of measurement and decision guidelines for correction]. / Posttraumatische Torsionsfehler am Unterarm : Messmethoden und Entscheidungsleitfaden für die Korrektur.

Forearm fractures are common in all age groups. Even if the adjacent joints are not directly involved, these fractures have an intra-articular character. One of the most common complications of these injuries is a painful limitation of the range of motion and especially of pronation and supination. This is often due to an underdiagnosed torsional deformity; however, in recent years new methods have been developed to make these torsional differences visible and quantifiable through the use of sectional imaging. The principle of measurement corresponds to that of the torsion measurement of the lower limbs. Computed tomography (CT) or magnetic resonance imaging (MRI) scans are created at defined heights. By searching for certain landmarks, torsional angles are measured in relation to a defined reference line. A new alternative is the use of 3D reformation models. The presence of a torsional deformity, especial of the radius, leads to an impairment of the pronation and supination of the forearm. In the presence of torsional deformities, radiological measurements can help to decide if an operation is needed or not. Unlike the lower limbs, there are still no uniform cut-off values as to when a correction is indicated. Decisions must be made together with the patient by taking the clinical and radiological results into account.

Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations.

We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)]PRLTAO0031-900710.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.

Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory.

Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics and has been applied to numerous physical chemistry and biophysics problems. Its essential limitations are in its neglect of correlation effects and fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review, we provide an update on the developments achieved in the self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce a corresponding system of coupled non-linear equations for both continuum electrostatics with a uniform dielectric constant, and a structured solvent-a dipolar Coulomb fluid-including non-local effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows us to include physically relevant effects, as we show for a range of applications of these equations.

Quantitative comparison of polar approach versus fitting method in time domain FLIM image analysis.

We calculate here analytically the performance of the polar approach (or phasor) in terms of signal-to-noise ratio and F values when performing time-domain Fluorescence Lifetime Imaging Microscopy (FLIM) to determine the minimal number of photons necessary for FLIM measurements (which is directly related to the F value), and compare them to those obtained from a well-known fitting strategy using the Least Square Method (LSM). The importance of the fluorescence background on the lifetime measurement precision is also investigated. We demonstrate here that the LSM does not provide the best estimator of the lifetime parameter for fluorophores exhibiting mono-exponential intensity decays as soon as fluorescence background is superior to 5%. The polar approach enables indeed to determine more precisely the lifetime values for a limited range corresponding to usually encountered fluorescence lifetime values. These theoretical results are corroborated with Monte Carlo simulations. We finally demonstrate experimentally that the polar approach allows distinguishing in living cells two fluorophores undetectable with usual time-domain LSM fitting software.

Electrowetting and droplet impalement experiments on superhydrophobic multiscale structures.

The reversible actuation of droplets on superhydrophobic surfaces under ambient conditions is currently an important field of research due to its potential applicability in microfluidic lab-on-a-chip devices. We have recently shown that Si-nanowire (NW) surfaces allow for reversible actuation provided that the surface structures show certain characteristics. In particular it appears that, for such surfaces, the presence of structures with multiple specific length scales is indeed needed to have a robust reversibility of contact angle changes. Here we report on electrowetting (EW) and impalement experiments on double-scale structured surfaces prepared by a combination of silicon micropillars prepared by an association of optical lithography and silicon etching, and nanowire growth on top of these surfaces. We show that while micropillar surfaces have a low impalement threshold and irreversible EW behaviour, a surface with double-scale texture can show both a very high resistance to impalement and a limited reversibility under EW, provided that the roughness of the micro-scale is large enough--i.e. that the pillars are tall enough. The optimal performance is obtained for a space between pillars that is comparable to the height of the nanostructure.

Y-DNA melting: a short tale of three scales.

We address some aspects of the thermal denaturation of Y-DNA-the three-way junction-on three different length scales: the effect of chain concentration on the extrinsic melting behaviour within a simple kinetic approach, the exponent of the loop entropy in intrinsic melting as it appears in statistical mechanics models, and the microscopics of stacking within the junction from molecular dynamics simulations. Our results suggest that a multiscale approach is needed to properly describe the denaturation properties of these systems. We propose experiments which can also shed light on the melting of short and long duplex DNA sequences.

Kicked by Mos and tuned by MPF-the initiation of the MAPK cascade in Xenopus oocytes.

The mitogen-activated protein kinase (MAPK) cascade is a paradigmatic signaling cascade, which plays a crucial role in many aspects of cellular events. The main initiator of the cascade in Xenopus oocytes is the oncoprotein Mos. After activation of the cascade, Mos activity is stabilized by MAPK via a feedback loop. Mos concentration levels are, however, not controlled by MAPK alone. In this paper we show, by imposing either a sustained or a peaked activity of M-phase promoting factor (MPF) (Cdc2-cyclin B), how the latter regulates the dynamics of Mos. Our experiments are supported by a detailed kinetic model for the Mos-MPF-MAPK network, which takes into account the three different phosphorylation states of Mos and, as a consequence, allows us to determine the time evolution of Mos under control of MPF. Our work opens a path toward a more complete and biologically realistic quantitative understanding of the dynamic interdependence of Mos and MPF in Xenopus oocytes.

Mean-field versus stochastic models for transcriptional regulation.

We introduce a minimal model description for the dynamics of transcriptional regulatory networks. It is studied within a mean-field approximation, i.e., by deterministic ODE's representing the reaction kinetics, and by stochastic simulations employing the Gillespie algorithm. We elucidate the different results that both approaches can deliver, depending on the network under study, and in particular depending on the level of detail retained in the respective description. Two examples are addressed in detail: The repressilator, a transcriptional clock based on a three-gene network realized experimentally in E. coli, and a bistable two-gene circuit under external driving, a transcriptional network motif recently proposed to play a role in cellular development.

Kinetic proofreading of gene activation by chromatin remodeling.

Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodelers, and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed interactions of the molecules are in accord with a kinetic proofreading scheme. Our finding could provide a basis for the development of quantitative models for gene regulation in eukaryotes based on the combinatorical interactions of chromatin modifiers.

Stability domains of actin genes and genomic evolution.

In eukaryotic genes, the protein coding sequence is split into several fragments, the exons, separated by noncoding DNA stretches, the introns. Prokaryotes do not have introns in their genomes. We report calculations of the stability domains of actin genes for various organisms in the animal, plant, and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes, all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e., before intron insertion. Common stability boundaries are found in evolutionarily distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general, the boundaries correspond with intron positions in the actins of vertebrates and other animals, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae, and animals have introns in positions separated by one nucleotide only, which identifies a hot spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamically driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for intron insertion in plants and animals.

Fluidics of a nanogap.

We have determined the filling properties of nanogaps with chemically heterogeneous walls. The quantitative criteria we present allow the prediction of the liquid loading of the nanostructure. They can easily be applied in combination with contact-angle measurements on planar substrates of the nanogap materials. We present an application of the theory to a recently developed nanogap biosensor. Chemical force microscopy (CFM) is employed to characterize the initial silanol properties of the gap. The functionality of the complex surface chemistry of the biosensor is demonstrated by the observation of functionalized nanoparticles in the gap with its resulting characteristic current-voltage relationship.

A thin-film model for corotational Jeffreys fluids under strong slip.

We derive a thin-film model for viscoelastic liquids under strong slip which obey the stress tensor dynamics of corotational Jeffreys fluids.

Slip vs. viscoelasticity in dewetting thin films.

Ultrathin polymer films on non-wettable substrates display dynamic features which have been attributed to either viscoelastic or slip effects. Here we show that in the weak- and strong-slip regime, effects of viscoelastic relaxation are either absent or essentially indistinguishable from slip effects. Strong slip modifies the fastest unstable mode in a rupturing thin film, which questions the standard approach to reconstruct the effective interface potential from dewetting experiments.

Regulating chromatin: on code and dynamic models.

In this short comment on the contributions by Arndt Benecke, Francois Fuks and Helmut Schiessel I refer to some recent experimental work which sheds light on the histone code hypothesis. Further, I make some remarks on the role theoretical approaches can play in decoding chromatin regulation.

A thin-film equation for viscoelastic liquids of Jeffreys type.

We derive a novel thin-film equation for linear viscoelastic media describable by generalized Maxwell or Jeffreys models. As a first application of this equation we discuss the shape of a liquid rim near a dewetting front. Although the dynamics of the liquid is equivalent to that of a phenomenological model recently proposed by Herminghaus et al. (S. Herminghaus, R. Seemann, K. Jacobs, Phys. Rev. Lett. 89, 056101 (2002)), the liquid rim profile in our model always shows oscillatory behaviour, contrary to that obtained in the former. This difference in behaviour is attributed to a different treatment of slip in both models.

Chains, dimers, and sandwiches: melting behavior of DNA nanoassemblies.

We have studied, in experiment and theory, the melting behavior of DNA nanoassemblies of perylenediimide-bis-oligonucleotides (PON), in which two short oligonucleotide chains (16- or 24-mers) are attached to the extremities of a spacer molecule. By varying both the sequence orientation (exchange of 3' and 5' ends neighboring the spacer) and the oligomer composition of the solutions, nanoassemblies of different complexity can be generated. Our results show a subtle dependence of the melting behavior on the supramolecular arrangement of the DNA-based assemblies.

Novel formulation of nonlocal electrostatics.

The accurate modeling of the dielectric properties of water is crucial for many applications in physics, computational chemistry, and molecular biology. This becomes possible in the framework of nonlocal electrostatics, for which we propose a novel formulation allowing for numerical solutions for the nontrivial molecular geometries arising in the applications mentioned before. Our approach is based on the introduction of a secondary field psi, which acts as the potential for the rotation free part of the dielectric displacement field D. For many relevant models, the dielectric function of the medium can be expressed as the Green's function of a local differential operator. In this case, the resulting coupled Poisson (-Boltzmann) equations for psi and the electrostatic potential phi reduce to a system of coupled partial differential equations. The approach is illustrated by its application to simple geometries.

Blobs, channels and "cigars": morphologies of liquids at a step.

We have studied the equilibria of liquid droplets wetting a step edge with an opening angle 0 < alpha < pi by a combination of analytical and numerical methods. Depending on the wetting properties of the substrate walls and on the liquid volume, different locally or globally stable liquid morphologies are found. Complete spreading of the liquid along the bottom edge of the step is observed at equilibrium contact angles theta satisfying theta < theta(s) = pi/2 - alpha/2. If the contact angle theta exceeds a threshold value theta(b) the liquid exists in a blob-like configuration. Surprisingly, we find an intermediate regime at a sufficiently high liquid volume and in a range of contact angles theta(s) < theta < theta(b), in which "cigar"-shaped configurations arise in addition to the blob. We close the paper by a detailed discussion of the stability of this novel liquid morphology.