<div style="margin: 0px; padding: 0px; color: rgb(51, 51, 51); font-family: "Source Serif Pro", serif; font-size: 19.2px; background-color: rgb(252, 252, 252);"><h1 style="font-size: 30.72px; margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: inherit; text-rendering: optimizeLegibility; line-height: 1.2 !important;"><br></h1><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Recently we did some all-atom classical molecular dynamics simulations involving DMPC model membrane, Nogo66 membrane active protein, TIP3P water model and NaCl ions. We used CHARMM36 forcefield and ran the simulations in NAMD software. VMD was the software used to visualize system. (If you are new to these, I have written many previous articles relating to all things which I have just mentioned. Please feel free to dig my previous articles. I will give some links as references.)</p><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: inherit; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;">Lipid defects</h2><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Lipid molecules which form cellular membranes and membranes of other oragnelles are amphipathic (a.k.a amphiphilic) molecules which means they have both hydrophobic(water hating) and hydrophilic(water liking) regions.</p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"><img src="https://steemitimages.com/DQmZXPkVknLeSjHRu2SGs7jpPpQCF7APSEKt3PRuz4eWqUn/image.png" style="border-style: none; display: inline-block; vertical-align: middle; height: auto; width: auto; max-height: none;"><br><em style="line-height: inherit;">The fatty acid legs are hydrophobic,and the head region(other than tail) is hydrophilic. From one of my old articles. <a href="https://www.steemstem.io/#!/@dexterdev/phospholipids-the-unsung-heroes-in-biomoleucles" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">Link here</a></em></p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Lipid defects are those regions in bilayers where the hydrophobic tails get exposed to water, which is energetically very unfavourable. Defects can get get induced by many factors. One being interaction of membrane with particular molecules(I will write more about lipid defects in a future article.)</p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Defects can lead to lipid interdigitation. Means the lipid tails in both leaflets can overlap as shown below:<br><img src="https://steemitimages.com/640x0/https://i.imgur.com/b8skvY2.png" style="border-style: none; display: inline-block; vertical-align: middle; height: auto; width: auto; max-height: none;"><br></p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"><em style="line-height: inherit;">The state with lipid defects is energetically unfavourable. So lipids reorganize themselves to a favourable interdigitated state.[1]</em></p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">So below is a youtube video which I created. This shows defects:</p><p style="color: rgb(0, 0, 0); font-family: "Open Sans", "Helvetica Neue", Arial, Helvetica, sans-serif; font-size: 14px;"><br></p><p style="color: rgb(0, 0, 0); font-family: "Open Sans", "Helvetica Neue", Arial, Helvetica, sans-serif; font-size: 14px;"><br></p><p style="color: rgb(0, 0, 0); font-family: "Open Sans", "Helvetica Neue", Arial, Helvetica, sans-serif; font-size: 14px;">https://www.youtube.com/watch?v=5pYLUgAeLK8</p><p style="color: rgb(0, 0, 0); font-family: "Open Sans", "Helvetica Neue", Arial, Helvetica, sans-serif; font-size: 14px;"><br></p><p style="color: rgb(0, 0, 0); font-family: "Open Sans", "Helvetica Neue", Arial, Helvetica, sans-serif; font-size: 14px;"><br></p><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"><em style="line-height: inherit;">This is a 300ns all-atom classical molecular dynamics simulation of Nogo66 protein (from pdb structure 2KO2) on a model DMPC bilayer patch (144 lipids in each leaflet). This setup is solvated in TIP3P water model + 0.15 M NaCl ion concentration. Only the top monolayer in the bilayer is shown for clearly visualizing the lipid defects. The black voids are defects. Look for it. If you feel the video is very fast, please reduce the speed to 0.5 or so in the youtube settings.</em></p><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;">References</h2><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 23.04px; line-height: 1.2 !important;">Research paper:</h3><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">[1] <a href="https://pubs.acs.org/doi/abs/10.1021/jp035007s" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">Kranenburg, Marieke, Maddalena Venturoli, and Berend Smit. "Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics." The Journal of Physical Chemistry B 107.41 (2003): 11491-11501.</a></p><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 23.04px; line-height: 1.2 !important;">My previous posts:</h3><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">To learn about VMD and PDB file format, see here:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; font-size: 19.2px;"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-2-introduction-to-tcl-scripting-environment-in-vmd-1-sbd-prize-task-inside" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/visualizing-bio-molecules-in-computer-part-2-introduction-to-tcl-scripting-environment-in-vmd-1-sbd-prize-task-inside</a></li></ul><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">To learn about the concepts in All-atom molecular dynamics see articles below:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; font-size: 19.2px;"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-1-the-fundamentals" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-1-the-fundamentals</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-2-the-force-field" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-2-the-force-field</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-3-solving-the-molecular-dynamics-equation" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-3-solving-the-molecular-dynamics-equation</a></li></ul><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">To setup and run simulations in NAMD software, see below:</p><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; font-size: 19.2px;"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4a-let-us-setup-a-simulation-and-run-it" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4a-let-us-setup-a-simulation-and-run-it</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4b-running-small-systems-on-your-computer" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/classical-molecular-dynamics-series-part-4b-running-small-systems-on-your-computer</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="https://www.steemstem.io/#!/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">https://www.steemstem.io/#!/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility</a></li></ul><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 23.04px; line-height: 1.2 !important;">Textbook references for learning theory of Molecular Dynamics:</h3><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; font-size: 19.2px;"><li style="margin: 0px; padding: 0px; font-size: inherit;">"Statistical Mechanics: Theory and Molecular Simulations" by Mark E. Tuckerman</li><li style="margin: 0px; padding: 0px; font-size: inherit;">"Molecular Modelling: Principles and Applications" by Andrew R. Leach</li><li style="margin: 0px; padding: 0px; font-size: inherit;">"Computer Simulation of Liquids" by D. J. Tildesley and M.P. Allen</li></ul><h3 style="margin: 2rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 23.04px; line-height: 1.2 !important;">References specific to NAMD and VMD:</h3><ul style="margin: 0px 0px 1rem 2rem; padding: 0px; list-style-position: outside; line-height: 1.6; font-size: 19.2px;"><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Research/namd/cvs/ug.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">NAMD userguide</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">NAMD tutorial</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">VMD userguide</a></li><li style="margin: 0px; padding: 0px; font-size: inherit;"><a href="http://www.ks.uiuc.edu/Training/TutorialsOverview/vmd/vmd-tutorial.pdf" rel="noopener" title="This link will take you away from steemit.com" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">VMD tutorial</a></li></ul><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;"><a href="https://steemit.com/trending/steemstem" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">#steemSTEM</a></h2><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"><a href="https://steemit.com/trending/steemstem" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">#steemSTEM</a> is a very vibrant community on top of STEEM blockchain for Science, Technology, Engineering and Mathematics (STEM). 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padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"><span style="font-weight: 600; line-height: inherit;"></span></p><center style="font-size: 19.2px;"><span style="font-weight: 600; line-height: inherit;">All images without image sources are my creations :)</span></center><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;"><center>Follow me <a href="https://steemit.com/@dexterdev" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">@dexterdev</a></center></h2><hr style="box-sizing: content-box; overflow: visible; clear: both; max-width: 75rem; margin: 1.25rem auto; border-top: 0px; border-right: 0px; border-left: 0px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238); font-size: 19.2px;"><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><center style="font-size: 19.2px;"><pre style="margin-top: 0px; margin-bottom: 0px; padding: 0px;"><code style="font-family: Consolas, "Liberation Mono", Courier, monospace; font-size: 16.32px; padding: 0.2rem; border: none; background-color: rgb(244, 244, 244); font-weight: inherit; border-radius: 3px; overflow: scroll; display: block;"> ____ _______ ______ _________ ____ ______
/ _ / __\ \//__ __/ __/ __/ _ / __/ \ |\
| | \| \ \ / / \ | \ | \/| | \| \ | | //
| |_/| /_ / \ | | | /_| | |_/| /_| \//
\____\____/__/\\ \_/ \____\_/\_\____\____\__/
</code></pre><h2 style="margin: 2.5rem 0px 0.3rem; padding: 0px; font-family: "Source Sans Pro", "Helvetica Neue", Helvetica, Arial, sans-serif; color: inherit; text-rendering: optimizeLegibility; font-size: 26.88px; line-height: 1.2 !important;"></h2><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><center><img src="https://steemitimages.com/DQmVM9FmLfAYojdB7Ex2ooGhkZMGHht3NzPLUSEvwSvpjTd/dexter.png" style="border-style: none; display: inline-block; vertical-align: middle; height: auto; width: auto; max-height: none;"><br>credit: <a href="https://steemit.com/@mathowl" style="line-height: inherit; color: rgb(31, 191, 143); cursor: pointer; transition: all 0.2s ease-in-out;">@mathowl</a></center><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;"></p><hr style="box-sizing: content-box; overflow: visible; clear: both; max-width: 75rem; margin: 1.25rem auto; border-top: 0px; border-right: 0px; border-left: 0px; border-bottom-style: solid; border-bottom-color: rgb(238, 238, 238);"><p style="margin-bottom: 1.5rem; padding: 0px; font-size: 19.2px; line-height: 28.8px; text-rendering: optimizeLegibility;">Signing off now! I will be back with some interesting topic from my area of research soon.</p></center></div>
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