NEXUS/Physics: An interdisciplinary repurposing of physics for biologists

In response to increasing calls for the reform of the undergraduate science curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a repurposing of an introductory physics curriculum for the life sciences. The curriculum interacts strongly and supportively with introductory biology and chemistry courses taken by life sciences students, with the goal of helping students build general, multi-discipline scientific competencies. In order to do this, our two-semester NEXUS/Physics course sequence is positioned as a second year course so students will have had some exposure to basic concepts in biology and chemistry. NEXUS/Physics stresses interdisciplinary examples and the content differs markedly from traditional introductory physics to facilitate this. It extends the discussion of energy to include interatomic potentials and chemical reactions, the discussion of thermodynamics to include enthalpy and Gibbs free energy, and includes a serious discussion of random vs. coherent motion including diffusion. The development of instructional materials is coordinated with careful education research. Both the new content and the results of the research are described in a series of papers for which this paper serves as an overview and context.Comment: 12 page

Light scattering spectra of supercooled molecular liquids

The light scattering spectra of molecular liquids are derived within a generalized hydrodynamics. The wave vector and scattering angle dependences are given in the most general case and the change of the spectral features from liquid to solidlike is discussed without phenomenological model assumptions for (general) dielectric systems without long-ranged order. Exact microscopic expressions are derived for the frequency-dependent transport kernels, generalized thermodynamic derivatives and the background spectra.Comment: 12 page

Reorientational relaxation of a linear probe molecule in a simple glassy liquid

Within the mode-coupling theory (MCT) for the evolution of structural relaxation in glass-forming liquids, correlation functions and susceptibility spectra are calculated characterizing the rotational dynamics of a top-down symmetric dumbbell molecule, consisting of two fused hard spheres immersed in a hard-sphere system. It is found that for sufficiently large dumbbell elongations, the dynamics of the probe molecule follows the same universal glass-transition scenario as known from the MCT results of simple liquids. The $\alpha$-relaxation process of the angular-index-j=1 response is stronger, slower and less stretched than the one for j=2, in qualitative agreement with results found by dielectric-loss and depolarized-light-scattering spectroscopy for some supercooled liquids. For sufficiently small elongations, the reorientational relaxation occurs via large-angle flips, and the standard scenario for the glass-transition dynamics is modified for odd-j responses due to precursor phenomena of a nearby type-A MCT transition. In this case, a major part of the relaxation outside the transient regime is described qualitatively by the $\beta$-relaxation scaling laws, while the $\alpha$-relaxation scaling law is strongly disturbed.Comment: 40 pages. 10 figures as GIF-files, to be published in Phys. Rev.

The Dreyfus model of clinical problem-solving skills acquisition: a critical perspective

Context: The Dreyfus model describes how individuals progress through various levels in their acquisition of skills and subsumes ideas with regard to how individuals learn. Such a model is being accepted almost without debate from physicians to explain the ‘acquisition’ of clinical skills. Objectives: This paper reviews such a model, discusses several controversial points, clarifies what kind of knowledge the model is about, and examines its coherence in terms of problem-solving skills. Dreyfus’ main idea that intuition is a major aspect of expertise is also discussed in some detail. Relevant scientific evidence from cognitive science, psychology, and neuroscience is reviewed to accomplish these aims. Conclusions: Although the Dreyfus model may partially explain the ‘acquisition’ of some skills, it is debatable if it can explain the acquisition of clinical skills. The complex nature of clinical problem-solving skills and the rich interplay between the implicit and explicit forms of knowledge must be taken into consideration when we want to explain ‘acquisition’ of clinical skills. The idea that experts work from intuition, not from reason, should be evaluated carefully

Simulation-based analysis of micro-robots swimming at the center and near the wall of circular mini-channels

Swimming micro robots have great potential in biomedical applications such as targeted drug delivery, medical diagnosis, and destroying blood clots in arteries. Inspired by swimming micro organisms, micro robots can move in biofluids with helical tails attached to their bodies. In order to design and navigate micro robots, hydrodynamic characteristics of the flow field must be understood well. This work presents computational fluid dynamics (CFD) modeling and analysis of the flow due to the motion of micro robots that consist of magnetic heads and helical tails inside fluid-filled channels akin to bodily conduits; special emphasis is on the effects of the radial position of the robot. Time-averaged velocities, forces, torques, and efficiency of the micro robots placed in the channels are analyzed as functions of rotation frequency, helical pitch (wavelength) and helical radius (amplitude) of the tail. Results indicate that robots move faster and more efficiently near the wall than at the center of the channel. Forces acting on micro robots are asymmetrical due to the chirality of the robot’s tail and its motion. Moreover, robots placed near the wall have a different flow pattern around the head when compared to in-center and unbounded swimmers. According to simulation results, time-averaged for-ward velocity of the robot agrees well with the experimental values measured previously for a robot with almost the same dimensions

Dynamics at a smeared phase transition

We investigate the effects of rare regions on the dynamics of Ising magnets with planar defects, i.e., disorder perfectly correlated in two dimensions. In these systems, the magnetic phase transition is smeared because static long-range order can develop on isolated rare regions. We first study an infinite-range model by numerically solving local dynamic mean-field equations. Then we use extremal statistics and scaling arguments to discuss the dynamics beyond mean-field theory. In the tail region of the smeared transition the dynamics is even slower than in a conventional Griffiths phase: the spin autocorrelation function decays like a stretched exponential at intermediate times before approaching the exponentially small equilibrium value following a power law at late times.Comment: 10 pages, 8eps figures included, final version as publishe

Isomorphs in model molecular liquids

Isomorphs are curves in the phase diagram along which a number of static and dynamic quantities are invariant in reduced units. A liquid has good isomorphs if and only if it is strongly correlating, i.e., the equilibrium virial/potential energy fluctuations are more than 90% correlated in the NVT ensemble. This paper generalizes isomorphs to liquids composed of rigid molecules and study the isomorphs of two systems of small rigid molecules, the asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for both systems we find that the isochoric heat capacity, the excess entropy, the reduced molecular center-of-mass self part of the intermediate scattering function, the reduced molecular center-of-mass radial distribution function to a good approximation are invariant along an isomorph. In agreement with theory, we also find that an instantaneous change of temperature and density from an equilibrated state point to another isomorphic state point leads to no relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be more approximative than those of the asymmetric dumbbell model, which is consistent with the OTP model being less strongly correlating. For both models we find "master isomorphs", i.e., isomorphs have identical shape in the virial/potential energy phase diagram.Comment: 20 page

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

The crossover from propagating to strongly scattered acoustic modes of glasses observed in densified silica

Spectroscopic results on low frequency excitations of densified silica are presented and related to characteristic thermal properties of glasses. The end of the longitudinal acoustic branch is marked by a rapid increase of the Brillouin linewidth with the scattering vector. This rapid growth saturates at a crossover frequency Omega_co which nearly coincides with the center of the boson peak. The latter is clearly due to additional optic-like excitations related to nearly rigid SiO_4 librations as indicated by hyper-Raman scattering. Whether the onset of strong scattering is best described by hybridization of acoustic modes with these librations, by their elastic scattering (Rayleigh scattering) on the local excitations, or by soft potentials remains to be settled.Comment: 14 pages, 6 figures, to be published in a special issue of J. Phys. Condens. Matte

Fluid transport at low Reynolds number with magnetically actuated artificial cilia

By numerical modeling we investigate fluid transport in low-Reynolds-number flow achieved with a special elastic filament or artifical cilium attached to a planar surface. The filament is made of superparamagnetic particles linked together by DNA double strands. An external magnetic field induces dipolar interactions between the beads of the filament which provides a convenient way of actuating the cilium in a well-controlled manner. The filament has recently been used to successfully construct the first artificial micro-swimmer [R. Dreyfus at al., Nature 437, 862 (2005)]. In our numerical study we introduce a measure, which we call pumping performance, to quantify the fluid transport induced by the magnetically actuated cilium and identify an optimum stroke pattern of the filament. It consists of a slow transport stroke and a fast recovery stroke. Our detailed parameter study also reveals that for sufficiently large magnetic fields the artificial cilium is mainly governed by the Mason number that compares frictional to magnetic forces. Initial studies on multi-cilia systems show that the pumping performance is very sensitive to the imposed phase lag between neighboring cilia, i.e., to the details of the initiated metachronal wave.Comment: 12 pages, 10 figures. To appear in EPJE, available online at http://dx.doi.org/10.1140/epje/i2008-10388-