-
Notifications
You must be signed in to change notification settings - Fork 0
/
background.html
executable file
·117 lines (107 loc) · 6.46 KB
/
background.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
<!doctype html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>MEDYAN - Background</title>
<link rel="icon" href="images/favicon.gif" type="image/x-icon"/>
<!--[if lt IE 9]>
<script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<link rel="shortcut icon" href="images/favicon.gif" type="image/x-icon"/>
<link rel="stylesheet" type="text/css" href="css/styles.css"/>
<link rel="canonical" href="https://medyan.org/background.html" />
</head>
<body>
<div class="bg">
<!--start container-->
<div id="container">
<!--start header-->
<header>
<!--start logo-->
<a href="#" id="logo"><img src="images/Striking.png" width="200" height="130" alt="logo"/></a>
<!--end logo-->
<!--start menu-->
<nav>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="documentation.html">Documentation</a></li>
<li><a href="download.html">Download</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="gallery.html">Gallery</a></li>
<li><a href="contact.html">Contact</a></li>
</ul>
</nav>
<!--end menu-->
<!--end header-->
</header>
<!--start intro-->
<section id="intro">
<hgroup>
<h1><b><i>MEDYAN</b></i> Overview <!--<span>- Leonardo da Vinci</span>--></h1>
<h2>A brief overview of the motivation and development of MEDYAN. A <a href="modeltable.html" style="color: #CC0000"> comparison table</a> of current cytoskeletal models in literature is also provided. </h2>
</hgroup>
</section>
<!--end intro-->
<!--start holder-->
<div class="holder_content2">
<section class="group2">
<p> The cell cytoskeleton plays a key role in human biology and disease, contributing ubiquitously
to such important processes as embryonic development, wound repair and cancer
metastasis. The Papoian laboratory is interested in gaining deeper understanding of the
physical chemistry behind these complex, far-from-equilibrium mechanochemical
processes. Their approach and model, named Mechanochemical Dynamics of Active Networks
(<i>MEDYAN</i>), is based on combining stochastic reaction-diffusion treatment
of cellular biochemical processes with polymer physics of cytoskeletal filament network
growth, while explicitly coupling chemistry and mechanics.</p>
<br>
<p>       While most cytoskeletal models in literature emphasize either reaction-diffusion modeling of cytoskeletal chemistry or semi-flexible polymer chain mechanics of the constituent filaments,
the <i>MEDYAN</i> model intimately couples the chemical processes of an active cytoskeletal
network with its underlying polymer mechanics by iteratively swtiching between stochastic reaction-diffusion
simulation and network mechanical equilibration (Fig 1), producing an efficient yet detailed cytoskeletal network evolution. With chemical and mechanical representations of semi-flexible polymers, cross-linking molecules, molecular motors, as well as polymer branching and severing molecules, <i>MEDYAN</i> allows for an explicit treatment of the key elements involved in cytoskeletal evolution (Fig 2). For a detailed description of the methodology and assumptions of this model, as well as its current capabilities, see its <a href="publications.html" style="color: #CC0000">original paper</a> in PLoS Computational Biology. </p>
<br>
<p>       Papoian laboratory has developed a third-generation software package based on
the <i>MEDYAN</i> model, to simulate growth dynamics of actin based filamentous networks in vitro and
in vivo. Recent papers where <i>MEDYAN</i> or its predecessor, StochTools, were used
can be found on the publication section of the <a href="http://papoian.chem.umd.edu/" style="color: #CC0000">Papoian lab page</a> or in the <a href="publications.html" style="color: #CC0000">publications</a> section of this site.
This package can also be extended to simulate the dynamics of any active
matter network. This webpage contains <a href="documentation.html" style="color: #CC0000"> documentation</a> in usage and installation of the software, as well as source code <a href="download.html" style="color: #CC0000"> download</a>. See the above links for more useful information.</p>
<br>
<br>
</section>
<section class="group5">
<a><img src="images/protocol.png" width="420" height="220"/></a>
<p> Fig 1: The <i>MEDYAN</i> simulation protocol iterates between stochastic reaction-diffusion simulation and network mechanical equilibration while updating force-dependent reaction rates.</p>
<br><br>
<a><img src="images/model.png" width="380" height="300"/></a>
<p> Fig 2: A schematic of cytoskeletal species that can be included in the <i>MEDYAN</i> description. The polymer network is overlaid onto a compartment-based reaction-diffusion scheme. </p>
</section>
</div>
<!--end holder-->
<!--start holder-->
<!--<div class="holder_content">
<section class="group4">
<h3>Latest article</h3>
<article>
<h4>22.08.2011 - Design to express </h4>
<p>Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec molestie. Sed aliquam sem ut arcu. Phasellus sollicitudin. Vestibulum condimentum facilisis nulla. In hac habitasse platea dictumst. Nulla nonummy. Cras quis libero.</p>
<p>Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec molestie. Sed aliquam sem ut arcu. Phasellus sollicitudin. Vestibulum condimentum facilisis nulla. In hac habitasse platea dictumst. Nulla nonummy. Cras quis libero.</p>
<p>Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec molestie. Sed aliquam sem ut arcu. Phasellus sollicitudin. Vestibulum condimentum facilisis nulla. In hac habitasse platea dictumst.</p>
</article>
</section>
</div>-->
<!--end holder-->
</div>
<!--end container-->
<!--start footer-->
<footer>
<div class="container">
<div id="FooterTwo"> © 2019 Papoian Lab at University of Maryland </div>
<!--<div id="FooterTree"> Valid html5, design and code by <a href="http://www.marijazaric.com">marija zaric - creative simplicity</a> </div> -->
</div>
</footer>
<!--end footer-->
</div>
<!--end bg-->
<!-- Free template distributed by http://freehtml5templates.com -->
</body>
</html>