Coupling Methods for Continuum Model with Molecular Model

2003 ◽  
Vol 1 (1) ◽  
pp. 12 ◽  
Author(s):  
Ted Belytschko ◽  
S. P. Xiao
Keyword(s):  
Continuum Model ◽  
Molecular Model ◽  
Coupling Methods

A PERIDYNAMICS FORMULATION BASED HIERARCHICAL MULTISCALE MODELING APPROACH BETWEEN CONTINUUM SCALE AND ATOMISTIC SCALE

2012 ◽  
Vol 01 (03) ◽  
pp. 1250029 ◽  
Author(s):  
R. RAHMAN ◽  
A. HAQUE
Keyword(s):  
Multiscale Modeling ◽  
Continuum Model ◽  
Molecular Model ◽  
Multiscale Simulation ◽  
Coupling Method ◽  
Fine Scale ◽  
Modeling Framework ◽  
Multiscale Modeling Framework ◽  
Hierarchical Multiscale ◽  
Nonlocal Force

In this paper, a multiscale modeling framework has been established between peridynamics and atomistic models. Peridynamics (PD) formulation is based on continuum theory implying nonlocal force based interactions. Peridynamics (PD) and molecular dynamics (MD) have similarities since both use nonlocal force based interaction. It means continuum points in PD and MD atoms are separated by finite distance and exert force upon each other. In this work PD based continuum model of epoxy polymer is defined by meshless Lagrangian particles. MD is coupled with PD based continuum model through a hierarchical multiscale modeling framework. In this framework, PD particles at coarse scale interact with fine scale PD particles by transferring pressure, displacements and velocities among each other. Based on the same hierarchical coupling method, fine scale PD model is seamlessly interfaced with molecular model through an intermediate mesoscale region i.e. coarse-grain atomic model. At the end of this hierarchical downscaling, the information — such as deformation, energy and other important parameters — were captured in the atomistic region under the applied force at micro and macro regions. A two-dimensional plate of neat epoxy was considered for demonstration of such multiscale simulation platform. The region of interest in the 2D plate was interfaced with atomistic model by applying the proposed hierarchical coupling method. The results show reasonable consistency between PD and MD simulations.

Toward an alignment of the actin molecule within the actin filament

1983 ◽  
Vol 41 ◽  
pp. 450-451
Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi
Keyword(s):  
Actin Filament ◽  
Diffraction Data ◽  
Quantitative Estimate ◽  
Molecular Model ◽  
Quantitative Comparison ◽  
Regulatory Proteins ◽  
Essential Information ◽  
X Ray ◽  
Maximum Resolution ◽  
Lack Of Information

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.

Exploration of cell wall architecture with the rapid-freeze deep-etch technique

1993 ◽  
Vol 51 ◽  
pp. 128-129
Author(s):  
Béatrice Satiat-Jeunemaitre ◽  
Chris Hawes
Keyword(s):  
Plant Cell ◽  
Cell Walls ◽  
Cell Biology ◽  
Molecular Model ◽  
Three Dimensional ◽  
Secretory Activity ◽  
Wall Structure ◽  
Specimen Preparation ◽  
Molecular Architecture ◽  
Plant Cell Walls

The comprehension of the molecular architecture of plant cell walls is one of the best examples in cell biology which illustrates how developments in microscopy have extended the frontiers of a topic. Indeed from the first electron microscope observation of cell walls it has become apparent that our understanding of wall structure has advanced hand in hand with improvements in the technology of specimen preparation for electron microscopy. Cell walls are sub-cellular compartments outside the peripheral plasma membrane, the construction of which depends on a complex cellular biosynthetic and secretory activity (1). They are composed of interwoven polymers, synthesised independently, which together perform a number of varied functions. Biochemical studies have provided us with much data on the varied molecular composition of plant cell walls. However, the detailed intermolecular relationships and the three dimensional arrangement of the polymers in situ remains a mystery. The difficulty in establishing a general molecular model for plant cell walls is also complicated by the vast diversity in wall composition among plant species.

The development of a molecular model of lung

1970 ◽  
Vol 126 (3) ◽  
pp. 491-495
Author(s):  
H. G. Boren
Keyword(s):  
Molecular Model

Structural Studies of Fibrinolysis by Electron and Light Microscopy

1999 ◽  
Vol 82 (08) ◽  
pp. 277-282 ◽  
Author(s):  
Yuri Veklich ◽  
Jean-Philippe Collet ◽  
Charles Francis ◽  
John W. Weisel
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Plasminogen Activator ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Degradation Products ◽  
Molecular Model ◽  
Three Dimensional ◽  
Tissue Type ◽  
Type Plasminogen Activator

IntroductionMuch is known about the fibrinolytic system that converts fibrin-bound plasminogen to the active protease, plasmin, using plasminogen activators, such as tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator. Plasmin then cleaves fibrin at specific sites and generates soluble fragments, many of which have been characterized, providing the basis for a molecular model of the polypeptide chain degradation.1-3 Soluble degradation products of fibrin have also been characterized by transmission electron microscopy, yielding a model for their structure.4 Moreover, high resolution, three-dimensional structures of certain fibrinogen fragments has provided a wealth of information that may be useful in understanding how various proteins bind to fibrin and the overall process of fibrinolysis (Doolittle, this volume).5,6 Both the rate of fibrinolysis and the structures of soluble derivatives are determined in part by the fibrin network structure itself. Furthermore, the activation of plasminogen by t-PA is accelerated by the conversion of fibrinogen to fibrin, and this reaction is also affected by the structure of the fibrin. For example, clots made of thin fibers have a decreased rate of conversion of plasminogen to plasmin by t-PA, and they generally are lysed more slowly than clots composed of thick fibers.7-9 Under other conditions, however, clots made of thin fibers may be lysed more rapidly.10 In addition, fibrin clots composed of abnormally thin fibers formed from certain dysfibrinogens display decreased plasminogen binding and a lower rate of fibrinolysis.11-13 Therefore, our increasing knowledge of various dysfibrinogenemias will aid our understanding of mechanisms of fibrinolysis (Matsuda, this volume).14,15 To account for these diverse observations and more fully understand the molecular basis of fibrinolysis, more knowledge of the physical changes in the fibrin matrix that precede solubilization is required. In this report, we summarize recent experiments utilizing transmission and scanning electron microscopy and confocal light microscopy to provide information about the structural changes occurring in polymerized fibrin during fibrinolysis. Many of the results of these experiments were unexpected and suggest some aspects of potential molecular mechanisms of fibrinolysis, which will also be described here.

m-[o-(2-Chloro-5-Fluorosulfonylphenylureido)Phenoxybutoxy]Benzamidine: Affinity Labeling Reagent Which Can Identify Secondary Binding Sites of Coagulation Complement and Fibrinolytic Serine Proteases

1979 ◽  
Author(s):  
D Bing ◽  
D Robison ◽  
J Andrews ◽  
R Laura
Keyword(s):  
Binding Sites ◽  
Serine Proteases ◽  
Enzyme Inhibitor ◽  
Molecular Model ◽  
Factor Xa ◽  
Affinity Labeling ◽  
Catalytic Center ◽  
Inhibitor Complex ◽  
Polypeptide Chains ◽  
Kinetics Of

We have determined that m-[o-(2-chloro-5-fluorosulfonylphenylureido)phenoxybutoxy]benza-midine [mCP(PBA)-F] is an affinity labeling reagent which labels both polypeptide chains of thrombin, factor Xa, complement component CIS and plasmin. As this means it is reacting outside of the catalytic center, we have called this reagent an exo-site affinity labeling reagent. Progressive irreversible inhibition of these enzymes by this reagent is rapid (k1st 2.5-4.6 x 10-3sec-1), the kinetics of inactivation are consistent with inhibition proceding via formation of a specific enzyme-inhibitor complex analogous to a Michaelis-Menton complex (KL - 115-26 μM), and diisopropylfluorophosphate or p-amidino-phenylmethanesulfonyfluoride Prevent labeling by [3H]mCP(PBA)-F. A molecular model of mCP(PBA)-F shows that the reactive SO2F group can be 17 A from the cationic amidine. The data are consistent with the hypothesis that both peptide chains are required for the specific proteolytic activity exhibited by these proteases and that the peptide chain which does not contain the active site serine is close to the catalytic center. (Supported by NIH and AHA grants

Synchronization of Chaotic Quantum Dot Light Emitting Diodes under Optical Feedback Effect

2020 ◽  
pp. 144-148
Keyword(s):  
Quantum Dot ◽  
Delay Time ◽  
Chaos Synchronization ◽  
Optical Feedback ◽  
Light Emitting Diode ◽  
Feedback Effect ◽  
Complete Synchronization ◽  
Light Emitting ◽  
Coupling Methods ◽  
Coupling Parameters

Chaos synchronization of delayed quantum dot light emitting diode has been studied theortetically which are coupled via the unidirectional and bidirectional. at synchronization of chaotic, The dynamics is identical with delayed optical feedback for those coupling methods. Depending on the coupling parameters and delay time the system exhibits complete synchronization, . Under proper conditions, the receiver quantum dot light emitting diode can be satisfactorily synchronized with the transmitter quantum dot light emitting diode due to the optical feedback effect.

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