Single-molecule thermodynamics: the heat distribution function of a charged particle in a static magnetic field

Interest in the applicability of fluctuation theorems to the thermodynamics of single molecules in external potentials has recently led to calculations of the work and total entropy distributions of Brownian oscillators in static and time-dependent electromagnetic fields. These calculations, which are based on solutions to a Smoluchowski equation, are not easily extended to a consideration of the other thermodynamic quantity of interest in such systems-the heat exchanges of the particle alone-because of the nonlinear dependence of the heat on a particle's stochastic trajectory. In this paper, we show that a path integral approach provides an exact expression for the distribution of the heat fluctuations of a charged Brownian oscillator in a static magnetic field. This approach is an extension of a similar path integral approach applied earlier by our group to the calculation of the heat distribution function of a trapped Brownian particle, which was found, in the limit of long times, to be consistent with experimental data on the thermal interactions of single micron-sized colloids in a viscous solvent.

Theory of polymer breaking under tension

We consider the breaking of a polymer molecule which is fixed at one end and is acted upon by a force at the other. The polymer is assumed to be a linear chain joined together by bonds which satisfy the Morse potential. The applied force is found to modify the Morse potential so that the minimum becomes metastable. Breaking is just the decay of this metastable bond, by causing it to go over the barrier. Increasing the force causes the potential to become more and more distorted and eventually leads to the disappearance of the barrier. The limiting force at which the barrier disappears is D(e)a/2,D-e with a the parameters characterizing the Morse potential. The rate of breaking is first calculated using multidimensional quantum transition state theory. We use the harmonic approximation to account for vibrations of all the units. It includes tunneling contributions to the rate, but is valid only above a certain critical temperature. It is possible to get an analytical expression for the rate of breaking. We have calculated the rate of breaking for a model, which mimics polyethylene. First we calculate the rate of breaking of a single bond, without worrying about the other bonds. Inclusion of other bonds under the harmonic approximation is found to lower this rate by at the most one order of magnitude. Quantum effects are found to increase the rate of breaking and are significant only at temperatures less than 150 K. At 300 K, the calculations predict a bond in polyethylene to have a lifetime of only seconds at a force which is only half the limiting force. Calculations were also done using the Lennard-Jones potential. The results for Lennard-Jones and Morse potentials were rather different, due to the different long-range behaviors of the two potentials. A calculation including friction was carried out, at the classical level, by assuming that each atom of the chain is coupled to its own collection of harmonic oscillators. Comparison of the results with the simulations of Oliveira and Taylor [J. Chem. Phys. 101, 10 118 (1994)] showed the rate to be two to three orders of magnitude higher. As a possible explanation of discrepancy, we consider the translational motion of the ends of the broken chains. Using a continuum approximation for the chain, we find that in the absence of friction, the rate of the process can be limited by the rate at which the two broken ends separate from one another and the lowering of the rate is at the most a factor of 2, for the parameters used in the simulation (for polyethylene). In the presence of friction, we find that the rate can be lowered by one to two orders of magnitude, making our results to be in reasonable agreement with the simulations.

Capturing higher modes of vibration of micromachined resonators

MEMS resonators have potential applications in the areas of RF-MEMS, clock oscillators, ultrasound transducers, etc. The important characteristics of a resonator are its resonant frequency and Q-factor (a measure of damping). Usually large damping in macro structures makes it difficult to excite and measure their higher modes. In contrast, MEMS resonators seem amenable to excitation in higher modes. In this paper, 28 modes of vibration of an electrothermal actuator are experimentally captured–perhaps the highest number of modes experimentally captured so far. We verify these modes with FEM simulations and report that all the measured frequencies are within 5% of theoretically predicted values.

Two-Stage Extended Kalman Filters with Derivative-Free Local Linearizations

This paper proposes a derivative-free two-stage extended Kalman filter (2-EKF) especially suited for state and parameter identification of mechanical oscillators under Gaussian white noise. Two sources of modeling uncertainties are considered: (1) errors in linearization, and (2) an inadequate system model. The state vector is presently composed of the original dynamical/parameter states plus the so-called bias states accounting for the unmodeled dynamics. An extended Kalman estimation concept is applied within a framework predicated on explicit and derivative-free local linearizations (DLL) of nonlinear drift terms in the governing stochastic differential equations (SDEs). The original and bias states are estimated by two separate filters; the bias filter improves the estimates of the original states. Measurements are artificially generated by corrupting the numerical solutions of the SDEs with noise through an implicit form of a higher-order linearization. Numerical illustrations are provided for a few single- and multidegree-of-freedom nonlinear oscillators, demonstrating the remarkable promise that 2-EKF holds over its more conventional EKF-based counterparts. DOI: 10.1061/(ASCE)EM.1943-7889.0000255. (C) 2011 American Society of Civil Engineers.

A perturbed martingale approach to global optimization

A new global stochastic search, guided mainly through derivative-free directional information computable from the sample statistical moments of the design variables within a Monte Carlo setup, is proposed. The search is aided by imparting to the directional update term additional layers of random perturbations referred to as `coalescence' and `scrambling'. A selection step, constituting yet another avenue for random perturbation, completes the global search. The direction-driven nature of the search is manifest in the local extremization and coalescence components, which are posed as martingale problems that yield gain-like update terms upon discretization. As anticipated and numerically demonstrated, to a limited extent, against the problem of parameter recovery given the chaotic response histories of a couple of nonlinear oscillators, the proposed method appears to offer a more rational, more accurate and faster alternative to most available evolutionary schemes, prominently the particle swarm optimization. (C) 2014 Elsevier B.V. All rights reserved.

A non-resonant mass sensor to eliminate the ``missing mass'' effect during mass measurement of biological materials

Resonant sensors and crystal oscillators for mass detection need to be excited at very high natural frequencies (MHz). Use of such systems to measure mass of biological materials affects the accuracy of mass measurement due to their viscous and/or viscoelastic properties. The measurement limitation of such sensor system is the difficulty in accounting for the ``missing mass'' of the biological specimen in question. A sensor system has been developed in this work, to be operated in the stiffness controlled region at very low frequencies as compared to its fundamental natural frequency. The resulting reduction in the sensitivity due to non-resonant mode of operation of this sensor is compensated by the high resolution of the sensor. The mass of different aged drosophila melanogaster (fruit fly) is measured. The difference in its mass measurement during resonant mode of operation is also presented. That, viscosity effects do not affect the working of this non-resonant mass sensor is clearly established by direct comparison. (C) 2014 AIP Publishing LLC.

Weakly corrected numerical solutions to stochastically driven nonlinear dynamical systems

A method to weakly correct the solutions of stochastically driven nonlinear dynamical systems, herein numerically approximated through the Eule-Maruyama (EM) time-marching map, is proposed. An essential feature of the method is a change of measures that aims at rendering the EM-approximated solution measurable with respect to the filtration generated by an appropriately defined error process. Using Ito's formula and adopting a Monte Carlo (MC) setup, it is shown that the correction term may be additively applied to the realizations of the numerically integrated trajectories. Numerical evidence, presently gathered via applications of the proposed method to a few nonlinear mechanical oscillators and a semi-discrete form of a 1-D Burger's equation, lends credence to the remarkably improved numerical accuracy of the corrected solutions even with relatively large time step sizes. (C) 2015 Elsevier Inc. All rights reserved.