8,492 research outputs found
A Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision
Mesoscopic 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
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