Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of (irreversible) expected coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the ``coarse molecular dynamics'' approach, we combine multiple short (0.5-ps) replica simulations to map the free energy surface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000 ps) rate of interconversion between the two stable configurational basins corresponding to the alpha-helical and extended minima.Comment: The article has been submitted to "The Journal of Chemical Physics.

New classical properties of quantum coherent states

A noncommutative version of the Cramer theorem is used to show that if two quantum systems are prepared independently, and if their center of mass is found to be in a coherent state, then each of the component systems is also in a coherent state, centered around the position in phase space predicted by the classical theory. Thermal coherent states are also shown to possess properties similar to classical ones

Migration of semiflexible polymers in microcapillary flow

The non-equilibrium structural and dynamical properties of a semiflexible polymer confined in a cylindrical microchannel and exposed to a Poiseuille flow is studied by mesoscale hydrodynamic simulations. For a polymer with a length half of its persistence length, large variations in orientation and conformations are found as a function of radial distance and flow strength. In particular, the polymer exhibits U-shaped conformations near the channel center. Hydrodynamic interactions lead to strong cross-streamline migration. Outward migration is governed by the polymer orientation and the corresponding anisotropy in its diffusivity. Strong tumbling motion is observed, with a tumbling time which exhibits the same dependence on Peclet number as a polymer in shear flow.Comment: 6 pages, 7 figures, accepted by EP

Vertical Product Differentiation When Quality is Unobservable to Buyers

We analyze vertical product differentiation in a model where a good’s quality is unobservable to buyers before purchase, a continuum of quality levels is technologically feasible, and minimum quality is supplied under competitive conditions. After purchase the true quality of the good is revealed with positive probability. To provide firms with incentives to actually deliver promised quality, prices must exceed marginal cost. We derive sufficient conditions for these incentive constraints to determine equilibrium prices, and show that under certain conditions only one or both of the extreme levels of quality, minimum and maximum quality, are available in the market.experience goods, product differentiation, product quality, asymmetric information

A fully discrete evolving surface finite element method

In this paper we consider a time discrete evolving surface finite element method for the advection and diffusion of a conserved scalar quantity on a moving surface. In earlier papers using a suitable variational formulation in time dependent Sobolev space we proposed and analyzed a finite element method using surface finite elements on evolving triangulated surfaces [IMA J. Numer Anal., 25 (2007), pp. 385--407; Math. Comp., to appear]. Optimal order L2(Γ(t)) and H1(Γ(t)) error bounds were proved for linear finite elements. In this work we prove optimal order error bounds for a backward Euler time discretization

Flow-Induced Helical Coiling of Semiflexible Polymers in Structured Microchannels

The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the narrow high-velocity region into the wide low-velocity region of the channel. The transient helix formation is the result of a non-equilibrium and non-stationary buckling transition of the semiflexible polymer, which is subjected to a compressive force originating from the fluid-velocity variation in the channel. The helix properties depend on the diameter ratio of the channel, the polymer bending rigidity, and the flow strength.Comment: Accepted in Phys. Rev. Let

Physics of Microswimmers - Single Particle Motion and Collective Behavior

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.Comment: 54 pages, 59 figures, review article, Reports of Progress in Physics (to appear