A Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision

Mesoscopic $N-$atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. An efficient method for understanding these systems in the friction dominated regime from the underlying N-atom formulation is presented. The method integrates notions of multiscale analysis, Trotter factorization, and a hypothesis that the momenta conjugate to coarse-grained variables can be treated as a stationary random process. The method is demonstrated for Lactoferrin, Nudaurelia Capensis Omega Virus, and Cowpea Chlorotic Mottle Virus to assess its accuracy and scaling with system size.Comment: This is the latest version with improved convergence analysi

Wick's theorem for q-deformed boson operators

In this paper combinatorial aspects of normal ordering arbitrary words in the creation and annihilation operators of the q-deformed boson are discussed. In particular, it is shown how by introducing appropriate q-weights for the associated ``Feynman diagrams'' the normally ordered form of a general expression in the creation and annihilation operators can be written as a sum over all q-weighted Feynman diagrams, representing Wick's theorem in the present context.Comment: 9 page

ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates `GROMACS wrapper' to initiate MD simulations, and `MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md

Servo-controlled intravital microscope system

A microscope system is described for viewing an area of a living body tissue that is rapidly moving, by maintaining the same area in the field-of-view and in focus. A focus sensing portion of the system includes two video cameras at which the viewed image is projected, one camera being slightly in front of the image plane and the other slightly behind it. A focus sensing circuit for each camera differentiates certain high frequency components of the video signal and then detects them and passes them through a low pass filter, to provide dc focus signal whose magnitudes represent the degree of focus. An error signal equal to the difference between the focus signals, drives a servo that moves the microscope objective so that an in-focus view is delivered to an image viewing/recording camera

Reynolds-stress and dissipation rate budgets in a turbulent channel flow

The budgets for the Reynolds stresses and for the dissipation rate of the turbulence kinetic energy are computed using direct simulation data of a turbulent channel flow. The budget data reveal that all the terms in the budget become important close to the wall. For inhomogeneous pressure boundary conditions, the pressure-strain term is split into a return term, a rapid term, and a Stokes term. The Stokes term is important close to the wall. The rapid and return terms play different roles depending on the component of the term. A split of the velocity pressure-gradient term into a redistributive term and a diffusion term is proposed, which should be simpler to model. The budget data is used to test existing closure models for the pressure-strain term, the dissipation rate, and the transport rate. In general, further work is needed to improve the models

Automatically-focusing microscope system for live tissue observation

System includes focus-sensing arrangement which controls servo to keep microscope constantly focused on target. Microscope objective is moved along optical axis. System includes two video cameras that are used as transducers for sensing focus. Incoming visual image is split by beam splitter so that one-half of information is fed to each camera