scholarly journals Coarse-Grained Simulation of Myosin-V Movement

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Zoe Katsimitsoulia ◽  
William R. Taylor
Keyword(s):  
Molecular Motor ◽  
Current Model ◽  
Coarse Grained ◽  
Myosin V ◽  
Biomolecular Systems ◽  
Bounding Volumes ◽  
Different Levels ◽  
Structure Domain ◽  
Hierarchic Model ◽  
Good Agreement

We describe the development of a hierarchic modelling method applied to simulating the processive movement of the myosin-V molecular motor protein along an actin filament track. In the hierarchic model, three different levels of protein structure resolution are represented: secondary structure, domain, and protein, with the level of detail changing according to the degree of interaction among the molecules. The integrity of the system is maintained using a tree of spatially organised bounding volumes and distance constraints. Although applied to an actin-myosin system, the hierarchic framework is general enough so that it may easily be adapted to a number of other large biomolecular systems containing in the order of 100 proteins. We compared the simulation results with biophysical data, and despite the lack of atomic detail in our model, we find good agreement and can even suggest some refinements to the current model of myosin-V motion.

An Analytical Drain Current Model for Dual-material Gate Graded - channel and Dual-oxide Thickness Cylindrical Gate (DMG-GC-DOT) MOSFET

2019 ◽  
Vol 9 (2) ◽  
pp. 291-297
Author(s):  
Hind Jaafar ◽  
Abdellah Aouaj ◽  
Ahmed Bouziane ◽  
Benjamin Iñiguez
Keyword(s):  
Current Model ◽  
Drain Current ◽  
Oxide Thickness ◽  
Subthreshold Current ◽  
The Poisson Equation ◽  
Strong Inversion ◽  
Cylindrical Form ◽  
Silvaco Atlas ◽  
Dual Material ◽  
Good Agreement

Background: A novel Dual Material Gate Graded Channel and Dual Oxide Thickness Cylindrical Gate (DMG-GC-DOT) MOSFET is presented in this paper. Methods: Analytical model of drain current is developed using a quasi-two-dimensional cylindrical form of the Poisson equation and is expressed as a function of the surface potential, which is calculated using the expressions of the current density. Results: Comparison of the analytical results with 3D numerical simulations using Silvaco Atlas - TCAD software presents a good agreement from subthreshold to strong inversion regime and for different bias voltages. Conclusion: Two oxide thicknesses with different permittivity can effectively improve the subthreshold current of DMG-GC-DOT MOSFET.

scholarly journals Computation of vortex sheet roll-up in the Trefftz plane

1987 ◽  
Vol 184 ◽  
pp. 123-155 ◽  
Author(s):  
Robert Krasny
Keyword(s):  
Mesh Size ◽  
Vortex Sheet ◽  
Smoothing Parameter ◽  
Tip Vortex ◽  
Tip Vortices ◽  
Time Calculation ◽  
Long Time ◽  
Principal Value ◽  
Different Levels ◽  
Good Agreement

Two vortex-sheet evolution problems arising in aerodynamics are studied numerically. The approach is based on desingularizing the Cauchy principal value integral which defines the sheet's velocity. Numerical evidence is presented which indicates that the approach converges with respect to refinement in the mesh-size and the smoothing parameter. For elliptic loading, the computed roll-up is in good agreement with Kaden's asymptotic spiral at early times. Some aspects of the solution's instability to short-wavelength perturbations, for a small value of the smoothing parameter, are inferred by comparing calculations performed with different levels of computer round-off error. The tip vortices’ deformation, due to their mutual interaction, is shown in a long-time calculation. Computations for a simulated fuselage-flap configuration show a complicated process of roll-up, deformation and interaction involving the tip vortex and the inboard neighbouring vortices.

Coupling of Sloshing and Ship Motions

2003 ◽  
Vol 47 (03) ◽  
pp. 208-221 ◽  
Author(s):  
Olav F. Rognebakke ◽  
Odd M. Faltinsen
Keyword(s):  
Steady State ◽  
Transient Behavior ◽  
Frequency Domain Analysis ◽  
Ship Motions ◽  
Steady State Motion ◽  
Constant Coefficients ◽  
Incident Waves ◽  
Violent Sloshing ◽  
Different Levels ◽  
Good Agreement

The coupled effect between ship motions and sloshing is studied. Two-dimensional experiments of a hull section containing tanks filled with different levels of water excited in sway by regular waves have been conducted. Steady-state results are obtained for the sway amplitude. Even if violent sloshing occurs in the tanks, the steady-state motion is almost linear and sinusoidal with the frequency of the linear incident waves. This implies that higher-order harmonics of the sloshing force are filtered out by the system. Simulations of the modeled case are performed using a linear and a nonlinear sloshing model and mainly assuming linear external flow. For steady-state motion, a convolution formulation does not improve the results relative to using constant coefficients in the equation of motion. However, in order to properly model the transient behavior in an irregular sea, a convolution formulation must be included. The treatment of the retardation function for the external problem is discussed in detail. A good agreement between experiments and computations is reported. The calculated coupled motion is sensitive to the damping of the sloshing motion in a certain frequency range where the coupled sloshing and ship motions cause resonant ship motions. A quasilinear frequency domain analysis is used to explain this by introducing the sloshing loads as a frequency dependent spring.

scholarly journals Structure of the poleward wall of the trough and the inclination of the geomagnetic field above the EISCAT radar

1997 ◽  
Vol 15 (6) ◽  
pp. 740-746 ◽  
Author(s):  
D. G. Jones ◽  
I. K. Walker ◽  
L. Kersley
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Time Scale ◽  
Geomagnetic Field ◽  
Energy Input ◽  
Current Model ◽  
Soft Particle ◽  
Dynamic Feature ◽  
Eiscat Radar ◽  
Good Agreement

Abstract. A special high-resolution routine of the EISCAT radar has been used to investigate the structure and development of the poleward wall of a deep trough in electron density. The feature was tracked by the radar during a 7-hour period under very quiet geomagnetic conditions. The field-aligned nature of the structure enabled an estimate to be made of the inclination of the geomagnetic field above EISCAT that was in good agreement with the current model. Observations of narrow field-aligned enhancements in electron temperature demonstrated that the wall of this trough is a dynamic feature, reforming regularly as the electron density responds on a time scale of tens of minutes to energy input from soft-particle precipitation.

The metrical parse is guided by gradient phonotactics

Phonology ◽  
2018 ◽  
Vol 35 (3) ◽  
pp. 367-405
Author(s):  
Paul Olejarczuk ◽  
Vsevolod Kapatsinski
Keyword(s):  
Coarse Grained ◽  
Stress Assignment ◽  
Fine Grained ◽  
Gradient Phonotactics ◽  
Different Levels

Phonotactic generalisations can be computed at different levels of granularity, from a coarse-grained legal/illegal dichotomy (blick,dwick≻ *bnick, *lbick) to a fine-grained gradient of acceptability (blick≻dwick≻bnick≻lbick). This article investigates the sensitivity of the English metrical parse to the granularity of medial onset phonotactics. We present two experiments that feature pseudo-words with medial consonants and CC clusters varying in word-edge frequency and sonority (e.g.vatablick,vatadwick,vatabnick,vatalbick). The metrical parse is inferred from a hyphenation experiment and an online stress-assignment experiment. The results of both studies indicate that the parse is stochastic, and guided by relatively fine-grained phonotactic dependencies. Vocabulary simulations suggest that this level of granularity may arise because the gradient parser consistently outperforms the coarse-grained alternative across the developing lexicon.

scholarly journals 1P-138 Role of the lever arm in the subunit coordination in myosin V(Molecular motor, The 47th Annual Meeting of the Biophysical Society of Japan)

2009 ◽  
Vol 49 (supplement) ◽  
pp. S84
Author(s):  
Yusuke Oguchi ◽  
Sergey V. Mikhailenko ◽  
Takashi Ohki ◽  
Adrian O. Olivares ◽  
Enrique M. De La Cruz ◽  
...  
Keyword(s):  
Annual Meeting ◽  
Molecular Motor ◽  
Myosin V ◽  
Lever Arm ◽  
Biophysical Society

Tailoring of Stress Development in MEMS Packaging Systems

2002 ◽  
Vol 741 ◽  
Author(s):  
Satyajit S. Walwadkar ◽  
Junghyun Cho ◽  
P.W. Farrell ◽  
Lawrence E. Felton
Keyword(s):  
Microelectromechanical Systems ◽  
Inertial Sensors ◽  
Thermal Exposure ◽  
Origin And Evolution ◽  
Mems Packaging ◽  
Operation Conditions ◽  
Die Attach ◽  
Device Operation ◽  
Different Levels ◽  
Good Agreement

ABSTRACTA better understanding of the origin and evolution of the stresses is a crucial step in improving reliability of packaging systems for microelectromechanical systems (MEMS). Given its importance, we examine the stresses developed in hermetically packaged MEMS inertial sensors. For this purpose, an optical surface profilometer is employed to assess the stresses by measuring the curvature of dummy silicon dies (3.5×3.5 mm2) assembled in different types of packages and die attach adhesives. We also explore a temporal evolution of stresses during thermal exposure of the test packages in an effort to emulate actual packaging processes and device operation conditions. The result shows different levels of stresses generated from various adhesives and package types, and also a stress evolution during packaging processes. The mechanical stress data also show a good agreement with MEMS performance data obtained from actual accelerometers. Therefore, the stress data will not only be useful in better understanding performance of MEMS packages, but the testing protocol can also provide a diagnostic tool for very small packaging systems.

The gated gait of the processive molecular motor, myosin V

2001 ◽  
Vol 4 (1) ◽  
pp. 59-65 ◽  
Author(s):  
Claudia Veigel ◽  
Fei Wang ◽  
Marc L. Bartoo ◽  
James R. Sellers ◽  
Justin E. Molloy
Keyword(s):  
Molecular Motor ◽  
Myosin V

POWER AND EFFICIENCY OF F1-ATPase MOLECULAR MOTOR

2012 ◽  
Vol 11 (01) ◽  
pp. 1240003
Author(s):  
J. M. SANCHO ◽  
RUBEN PEREZ-CARRASCO
Keyword(s):  
Experimental Data ◽  
Angular Velocity ◽  
Molecular Motor ◽  
Transition Rates ◽  
Motor Power ◽  
F1 Atpase ◽  
Flashing Ratchet ◽  
Model Predictions ◽  
Good Agreement ◽  
Ratchet Potential

We present the study of the energetics of the F1-ATPase rotatory molecular motor. The dynamics of this machine are described by a overdamped Langevin equation with a dichotomous flashing ratchet potential whose transition rates are controlled by an analysis of the chemical and physical steps. The model predictions on the observable angular velocity are in good agreement with the experimental data. Inspired by these results we extend our approach to study the energetics of this motor. Power and efficiency are analyzed for different experimental situations which can be tested in experiments.

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