Relevant bibliographies by topics / DNA motion modeling

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'DNA motion modeling'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "DNA motion modeling"

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Johnson, David A. "DNA in Motion." American Biology Teacher 83, no. 7 (September 1, 2021): 458–63. http://dx.doi.org/10.1525/abt.2021.83.7.458.

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Students often struggle to understand the full implications of some basic chemical concepts of DNA structure and function, especially how DNA’s directionality and antiparallel nature determine key functional features of replication and molecular recombination. Visualizing the complexities of these processes requires a working knowledge of how DNA’s nucleotides are assembled and how these components interact. This article describes a simple activity that can be used to visualize how nucleotides join together, how base pairs form, and, most importantly, how the active processes of replication and recombination are related to DNA chemistry. In this activity, students model DNA structure, with each student representing a single nucleotide, then join together to form a polynucleotide with 5′ to 3′ directionality. Two chains then pair to form the antiparallel DNA duplex. The activity not only illustrates the basic chemistry of DNA but also allows students to participate in active modeling of leading-strand and lagging-strand replication and in the formation of the Holliday junction molecule, the basic intermediate of recombination events including crossing over and gene conversion. The demonstrations can be videotaped from above to make a permanent copy of these events for teaching and study purposes. Example illustrations and links to videos are included.
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Rapino, Stefania, and Francesco Zerbetto. "Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface." Langmuir 21, no. 6 (March 2005): 2512–18. http://dx.doi.org/10.1021/la047091o.

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Якушевич, Л. В., and L. V. Yakushevich. "On the DNA Kink Motion Under the Action of Constant Torque." Mathematical Biology and Bioinformatics 11, no. 1 (April 18, 2016): 81–90. http://dx.doi.org/10.17537/2016.11.81.

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The influence of the torsion moment on the DNA kink motion is studied by the methods of mathematical modeling. Time dependence of the kink coordinate, velocity, size, and energy on the different values of the parameters of the external torsion moment have been found. It has been shown that by changing the parameters, by switching on and off of the external action, one could regulate the velocity and the direction of the kink movement. Estimation of the torque value necessary for the kink (open state) movement with the velocity comparable to the transcription velocity, has been made.
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Huang, Chao-Min, Anjelica Kucinic, Jenny V. Le, Carlos E. Castro, and Hai-Jun Su. "Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis." Nanoscale 11, no. 4 (2019): 1647–60. http://dx.doi.org/10.1039/c8nr06377j.

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We report a hybrid computational framework combining coarse-grained modeling with kinematic variance analysis for predicting uncertainties in the motion pathway of a multi-component DNA origami mechanism.
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Zakirianov, F. K., V. Yu Melnikov, G. T. Zakirianova, G. K. Galina, and L. F. Zakirianova. "MODELING OF MOTION OF CONFORMATIONAL PERTURBATIONS IN DNA MOLECULE WITH ACCOUNT OF RNA POLYMERASE." Vestnik Bashkirskogo universiteta 7, no. 1 (2018): 14. http://dx.doi.org/10.33184/bulletin-bsu-2018.1.3.

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Blatt, Simon, and Philipp Reiter. "Modeling repulsive forces on fibres via knot energies." Computational and Mathematical Biophysics 2, no. 1 (January 1, 2014): 56–72. http://dx.doi.org/10.2478/mlbmb-2014-0004.

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Abstract Modeling of repulsive forces is essential to the understanding of certain bio-physical processes, especially for the motion of DNA molecules. These kinds of phenomena seem to be driven by some sort of “energy” which especially prevents the molecules from strongly bending and forming self-intersections. Inspired by a physical toy model, numerous functionals have been defined during the past twenty-five years that aim at modeling self-avoidance. The general idea is to produce “detangled” curves having particularly large distances between distant strands. In this survey we present several families of these so-called knot energies. It turns out that they are quite similar from an analytical viewpoint. We focus on proving self-avoidance and existence of minimizers in every knot class. For a suitable subfamily of these energies we show how to prove that these minimizers are even infinitely differentiable.
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Faraji, Elham, Roberto Franzosi, Stefano Mancini, and Marco Pettini. "Transition between Random and Periodic Electron Currents on a DNA Chain." International Journal of Molecular Sciences 22, no. 14 (July 8, 2021): 7361. http://dx.doi.org/10.3390/ijms22147361.

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By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.
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Chen, Y. H., X. J. Li, X. F. Zhou, Jia Lin Sun, W. H. Huang, and J. Hu. "Determining the Radial Modulus of DNA Measured by VPSFM." Key Engineering Materials 295-296 (October 2005): 83–88. http://dx.doi.org/10.4028/www.scientific.net/kem.295-296.83.

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Mechanical properties of DNA, for example the elastic modulus, are of vital importance for its biological function. Previously, the modulus is mainly obtained by bending, stretching and twisting DNA using various techniques and tools. By applying vibrating mode scanning polarization force microscopy (VPSFM), deformations of DNA under ultra-small indentation forces can be measured and so the radial modulus can be computed. In this paper, modeling of the VPSFM measuring system is presented. The system is modeled as a spring-mass-damper oscillator under various force fields, such as van der Waals force, attractive electrical force and repulsive interactions between the tip and sample. The electrical polarization force is described by using uniformly charged line model and the DNA is considered to be a simple elastic rod. By numerically integrating the equation of tip motion, the contact force and the radial modulus of DNA under different deformation can be calculated. We found that in measuring radial modulus of DNA, the existence of substrate cannot be neglected, especially when the relative large deformation is reached.
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Fialko, Nadezhda, Maxim Olshevets, and Victor Lakhno. "Charge Transfer in Dimer with Dissipation." EPJ Web of Conferences 224 (2019): 03006. http://dx.doi.org/10.1051/epjconf/201922403006.

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The study of the charge transfer processes in biomacromolecules such as DNA is essential for the development of nanobioelectronics, design and construction of DNA-based nanowires, memory devices, logical elements, etc. Mathematical and computer modeling of charge transfer in biopolymer chains is an important part of these investigations. Some properties of charge transfer can be demonstrated by modeling of two-site chain. Based on the semi-classical Holstein model we consider a system of two sites and charged particle (electron or hole) in which the oscillations of the first site are not related to the charge motion, and the parameters of the second site correspond to a small-radius polaron. The system steady states depending on the electron energy H at the second site are studied numerically. The dynamics of the charge initially localized at the first site is modeled. Various modes depending on H are demonstrated: charge tunneling, resonant transfer, and lack of transfer.
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Socol, Marius, Renjie Wang, Daniel Jost, Pascal Carrivain, Cédric Vaillant, Eric Le Cam, Vincent Dahirel, et al. "Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes." Nucleic Acids Research 47, no. 12 (May 22, 2019): 6195–207. http://dx.doi.org/10.1093/nar/gkz374.

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Abstract DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of –0.3 to –0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in ‘theta’ conditions, in which they are poised for compartmentalization and phase separation.
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Dissertations / Theses on the topic "DNA motion modeling"

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David, Regis Agenor. "Modeling and Testing of DNA Motion for Nanoinjection." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2693.

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A new technique, called nanoinjection, is being developed to insert foreign DNA into a living cell. Such DNA transfection is commonly used to create transgenic organisms vital to the study of genetics, immunology, and many other biological sciences. In nanoinjection, DNA, which has a net negative charge, is electrically attracted to a micromachined lance. The lance then pierces the cell membranes, and the voltage on the lance is reversed, repelling the DNA into the cell. It is shown that DNA motion is strongly correlated to ion transport through a process called electrophoresis. Gel electrophoresis is used to move DNA using an electric field through a gel matrix (electrolytic solution). Understanding and using electrophoretic principals, a mathematical model was created to predict the motion (trajectory) of DNA particles as they are attracted to and repulsed from the nanoinjector lance. This work describes the protocol and presents the results for DNA motion experiments using fabricated gel electrophoresis devices. Electrophoretic systems commonly use metal electrodes in their construction. This work explores and reports the differences in electrophoretic motion of DNA (decomposition voltage, electrical field, etc.) when one electrode is constructed from a semiconductor, silicon rather than metal. Experimental results are used to update and validate the mathematical model to reflect the differences in material selection. Accurately predicting DNA motion is crucial for nanoinjection. The mathematical model allows investigation of the attraction/repulsion process by varying specific parameters. Result show that the ground electrode placement, lance orientation and lance penetration significantly affect attraction or repulsion efficiency while the gap, lance direction, lance tip width, lance tip half angle and lance tip height do not. It is also shown that the electric field around the lance is sufficient to cause localized electroporation of cell membranes, which may significantly improve the efficiency of transport.
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Book chapters on the topic "DNA motion modeling"

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Briki, Fatma, Jean Ramstein, Richard Lavery, and Daniel Genest. "Rotational Motions of Bases in DNA." In Modelling of Biomolecular Structures and Mechanisms, 231–39. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0497-5_19.

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Bagi, Katalin. "The DDA Method." In Computational Modeling of Masonry Structures Using the Discrete Element Method, 90–102. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0231-9.ch004.

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“DDA” stands for “Discontinuous Deformation Analysis”, suggesting that the displacement field of the analyzed domain shows abrupt changes on the element boundaries in the model. This chapter introduces the theoretical fundaments of DDA: mechanical characteristics of the elements together with the basic degrees of freedom, contact behavior, the equations of motion and their numerical integration with the help of Newmark's beta-method taking into account contact creation, loss and sliding with the help of an open-close iteration technique. Finally, a short overview on practical and scientific applications for masonry structures is given.
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Ferziger, Joel H. "Large Eddy Simulation." In Simulation and Modeling of Turbulent Flows. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195106435.003.0007.

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Over a decade ago, the author (Ferziger, 1983) wrote a review of the then state-of-the-art in direct numerical simulation (DNS) and large eddy simulation (LES). Shortly thereafter, a second review was written by Rogallo and Moin (1984). In those relatively early days of turbulent flow simulation, it was possible to write comprehensive reviews of what had been accomplished. Since then, the widespread availability of supercomputers has led to an explosion in this field so, although the subject is undoubtedly overdue for another review, it is not clear that the task can be accomplished in anything less than a monograph. The author therefore apologizes in advance for omissions (there must be many) and for any bias toward the accomplishments of people on the west coast of North America. In the earlier review, the author listed six approaches to the prediction of turbulent flow behavior. The list included: correlations, integral methods, single-point Reynolds-averaged closures, two-point closures, large eddy simulation and direct numerical simulation. Even then the distinction between these methods was not always clear; if anything, it is less clear today. It was possible in the earlier review to give a relatively complete overview of what had been accomplished with simulation methods. Since then, simulation techniques have been applied to an ever expanding range of flows so a thorough review of simulation results is no longer possible in the space available here. Simulation techniques have become well established as a means of studying turbulent flows and the results of simulations are best presented in combination with experimental data for the same flow. There is also a danger that the success of simulation methods will lead to attempts to apply them too soon to flows which the models and techniques are not ready to handle. To some extent, this is already happening. Direct numerical simulation (DNS) is a method in which all of the scales of motion of a turbulent flow are computed. A DNS must include everything from the large energy-containing or integral scales to the dissipative scales; the latter is usually taken to be the viscous or Kolmogoroff scales.
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Churchland, Patricia S., and Terrence J. Sejnowski. "Concluding and Beyond." In The Computational Brain. The MIT Press, 2016. http://dx.doi.org/10.7551/mitpress/9780262533393.003.0007.

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This concluding chapter explores future avenues for research and what remains to be done if the computer-modeling projects aimed at understanding the mysteries of the brain are to progress. In particular, it considers the problem of constructing synthetic brains and the reasons why the long-range project of understanding how the brain works should engender such constructive ambitions. It also discusses three ways of addressing the constructive problem: Carver Mead's strategy of building artificial neural structures, such as retinas and cochleas, using silicon-based CMOS VLSI technology; Dana Ballard's method of integrating perception with motor control; and Rodney Brook's method which involves making mobots capable of getting around in the world using limited reflex repertoires. The chapter concludes with an assessment of theoretical and ethical questions about what to do with the knowledge gained from computational neuroscience.
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Conference papers on the topic "DNA motion modeling"

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David, Regis A., Justin L. Black, Brian D. Jensen, and Sandra H. Burnett. "Modeling and Experimental Validation of DNA Motion During Electrophoresis." In ASME 2010 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/detc2010-28541.

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This paper describes the protocol and presents the results for DNA motion experiments using fabricated macroscale gel electrophoresis devices. Gel electrophoresis is a process used to separate/move DNA, RNA or protein molecules using an electric field through a gel matrix (electrolytic solution). In electrolytic solutions, the current conduction is due to a transport of ions (anions and cations). A better understanding of electrophoretic fundamentals allows for modeling the motion of DNA during electrophoresis. The model is validated through comparison with the experimental results. The model and experimental validation will be used to improve the process of cellular nanoinjection of DNA, currently in development in our lab.
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David, Regis A., and Brian D. Jensen. "Modeling DNA Motion Under Electrostatic Repulsion Within a Living Cell." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-87413.

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We are developing a new technique, called nanoinjection, to insert foreign DNA into a living cell. Such DNA transfection is commonly used to create transgenic organisms vital to the study of genetics, immunology, and many other biological sciences. In nanoinjection, DNA, which has a net negative charge, is electrostatically attracted to a micromachined lance. The lance then pierces the cell membranes, and the voltage on the lance is reversed, repelling the DNA into the cell. This paper presents a mathematical model to predict the motion (trajectory) of DNA particles within a cell in the presence of the electric field developed by the lance and the substrate. The model is used to predict the scattering of DNA through the cell due to electrostatic repulsion. We are currently preparing experiments which will be used to validate the model.
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Raghavan, Sunitha, D. Roy Maahapatra, and Arnab Samanta. "Modeling and Simulation of Hydrodynamic Interaction of DNA in a Micro-Fluidic Channel." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93127.

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The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young’s modulus, Poisson’s ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.
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Schaffer, W. M., and T. V. Bronnikova. "Modeling Peroxidase-Oxidase Interactions." In ASME 2011 Dynamic Systems and Control Conference and Bath/ASME Symposium on Fluid Power and Motion Control. ASMEDC, 2011. http://dx.doi.org/10.1115/dscc2011-5946.

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Reactive oxygen species (ROS) and peroxidase-oxidase (PO) reactions are Janus-faced contributors to cellular metabolism. At low concentrations, reactive oxygen species serve as signaling molecules; at high concentrations, as destroyers of proteins, lipids and DNA. Correspondingly, PO reactions are both sources and consumers of ROS. In the present paper, we study a well-tested model of the PO reaction based on horseradish peroxidase chemistry. Our principal predictions are these: 1. Under hypoxia, the PO reaction can emit pulses of hydrogen peroxide at apparently arbitrarily long intervals. 2. For a wide range of input rates, continuing infusions of ROS are transduced into bounded dynamics. 3. The response to ROS input is hysteretic. 4. With sufficient input, regulatory capacity is exceeded and hydrogen peroxide, but not superoxide, accumulates. These results are discussed with regard to the episodic nature of neurodevelopmental and neurodegenerative diseases that have been linked to oxidative stress and to downstream interactions that may result in positive feedback and pathology of increasing severity.
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Haghshenas-Jaryani, Mahdi, and Alan Bowling. "Multiscale Dynamic Modeling of Flexibility in Myosin V." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-13154.

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This paper presents a multiscale dynamic model for the simulation and analysis of flexibility in myosin V. A three dimensional (3D) flexible multibody model is developed to mechanically model the biological structure of myosin V. Experimental studies have shown that myosin’s neck domain can be considered as three pairs of tandem elements which can bend at junctures between them. Therefore, each neck is modeled by three rigid bodies connected by flexible spherical joints. One of the most important issues in dynamic modeling of micro-nanoscale sized biological structures, likes DNA and motor proteins, is the long simulation run time due to the disproportionality between physical parameters involved in their dynamics such as mass, drag coefficient, and stiffness. In order to address this issue, the mostly used models, based on the famous overdamped Langevin dynamics, omit the inertial terms in the equations of motion; that leads to a first order model which is inconsistent with the Newton’s second law. However, the proposed model uses the concept of the method of multiple scales (MMS) that brings all terms of the equations of motion into proportion with each other that helps to retain the inertia terms. This keeps consistency of the model with the physical laws and increases time step size of numerical integration from commonly used sub-femto seconds to sub-milli seconds. Therefore, simulation run time will be many orders of magnitude less than ones based on the other approaches. The simulation results obtained by the proposed multiscale model show more realistic dynamic behavior of myosin V in compared with other models.
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Haghshenas-Jaryani, Mahdi, Nguyen T. Tran, Alan P. Bowling, James A. Drake, and Samarendra Mohanty. "Multiscale Modeling and Simulation of a Microbead in an Optical Trapping Process." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93059.

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The purpose of this work is to generate a theoretical model for the dynamics of a polystyrene microsphere under the influence of Gaussian beam optical tweezers (OTs) in the ray-optics regime. OTs use the radiation pressure from a focused laser beam to manipulate microscopic objects as small as atoms [1]. They have been used in the biological sciences to measure nanometer-range displacements, apply picoNewton-range forces, and determine the mechanical properties of DNA, cell membranes, whole cells, and microtubules. The proposed model takes into account the forces and moments imparted onto the microbead by the OTs beam, and uses a Newton-Euler Dynamics framework to generate the equations of motion. Although examination of dimensionless numbers and other indicators including, Reynolds number 10−9 ≤ Re ≤ 10−4, Knudsen number 0.0001875, and the disproportionality between the mass and the viscous drag co-efficients O(10−4), does not clearly indicate whether this is a multiscale problem or not; but, a numerical integration of the original model leads to a long simulation run-time, a few days. Moreover, investigation of the step size showed that the adaptive numerical integrator was proceeding with a picosecond step size in order to achieve the requested accuracy. This situation implies a multiscale feature involved in the dynamics of optical trapping process of the small bead. To address this issue, a multiscale model is developed that helps to significantly reduce the simulation run-time and reveals underdamped behavior of the bead. In order to verify the theoretical model, experiments were carried out on a microsphere bead with 1.6μm diameter. A comparison of experimental data and simulation data indicate that this approach closely models microparticle behavior to the accuracy of the experiment under Gaussian beam optical tweezers.
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Khan, Imad M., and Kurt S. Anderson. "A Robust Framework for Adaptive Multiscale Modeling of Biopolymers Using Highly Parallelizable Methods." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93099.

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For many biopolymers (RNA, DNA, enzymes and proteins) the nature of the molecules interaction within the cell has been determined to be highly a function of its conformational structure. Understanding how to influence and control this structure thus is of critical importance if one wishes to manipulate the intercellular processes of which these biopolymers play such a central role. In molecular dynamics (MD) simulations, a fully atomistic model represents the system at the finest scale and as such captures all the dynamics of the system. If the simulation is permitted to run sufficiently long important emergent behaviors can develop and show themselves. Such MD simulations represent a direct applications of Newton’s Laws of Motion to the individual atoms in the system, and are conceptually the easiest to implement. An advantage of this procedure is that the simulation yields important information not only about the intermediate states and the mechanisms which produced them, but also provides the rates at which these processes occur. These intermediate conformational states have repeatedly been implicated in many known biological function [1], [2]. Unfortunately, this albeit correct, but naive approach quickly leads to intractable models and prohibitive computational expense when applied to systems involving many atoms. As a result, researcher often grossly over simplify the system move to non-deterministic methods such as Monte Carlo, which effectively remove dynamics from the system, or use undesirably gross model simplification. Because of these forward dynamics performance difficulties, potentially important mechanisms governing biopolymer structure have not been adequately explored and/or identified. The methods and algorithms described in this paper are intended to extend the capabilities of the simulation techniques for such systems so that the forward dynamics can better predict the non-equilibrium behavior of these systems, thus complementing Monte Carlo, while retaining much useful intermediate process and temporal information.
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Rahmann, Sven, Tobias Marschall, Frank Behler, and Oliver Kramer. "Modeling evolutionary fitness for DNA motif discovery." In the 11th Annual conference. New York, New York, USA: ACM Press, 2009. http://dx.doi.org/10.1145/1569901.1569933.

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Mynderse, James A., Ann M. Whitney, and George T. C. Chiu. "Improved Modeling of a Dynamic Mirror With Antagonistic Piezoelectric Stack Actuation." In ASME 2011 Dynamic Systems and Control Conference and Bath/ASME Symposium on Fluid Power and Motion Control. ASMEDC, 2011. http://dx.doi.org/10.1115/dscc2011-6104.

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An enhanced model of a dynamic mirror actuator (DMA) for laser beam steering is presented. The DMA is driven by an antagonistic pair of piezoelectric stack actuators (PESA). The proposed model of the DMA employs explicit PESA charging dynamics and an adjustable PESA shunt circuit to address the frequency-dependent effective mechanical compliance term in several previous models from literature. The proposed DMA model with shunt circuit accurately predicts the first damped natural frequency of the DMA with a shunt circuit across each PESA. Simulation and experimental data are presented. Good agreement is shown between the predicted and measured damped first natural frequencies.
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Benke, M., E. Shapiro, and D. Drikakis. "FALCO: Fast Linear Corrector for Modelling DNA-Laden Flows." In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2008. http://dx.doi.org/10.1115/icnmm2008-62131.

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The paper concerns the development of a numerical algorithm for improving the efficiency of computational fluid dynamics simulations of transport of biomolecules in microchannels at low number densities. For this problem, the continuum approach based on the concentration field model becomes invalid, whereas time scales involved make purely molecular simulations prohibitively computationally expensive. In this context, meta-models based on coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of biomolecules provide a viable alternative. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical DNA model. Particle-corrector algorithms are not sufficiently robust, thus resulting in slow convergence. A new geometrical particle corrector algorithm — called FALCO — is proposed in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. It is shown that the new corrector can be related to the SHAKE algorithm by an appropriate choice of Lagrangian multipliers. Validation of the new particle corrector against a simple analytic solution is performed and the improved convergence is demonstrated for a macromolecule motion in a micro-cavity. This work has been supported in part by the European Commission under the 6th Framework Program (Project: DINAMICS, NMP4-CT-2007-026804).
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