148 research outputs found
hTOP3B systems with covalently and non-covalently bound DNA and RNA substrates
No full text<p>hTOP3 simulations for both covalently and non-covalently bound DNA and RNA substrates. Simulation times = 300ns, with 1/ns per frame = 300 frames each.</p>
The thermodynamics and statistical mechanics of protein folding
No full textThe physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding
SPNS2 Simulation files
No full text<p>This list contains the pdb, psf and dcd files for two different systems of SPNS2 in inward-facing conformation: 1) with glucose and S1P and 2) with glucose only (no S1P). The trajectories uploaded here are saved at 1 ns/frame (i.e. 1000 frames = 1000 ns). The trajectories are not pbc-wrapped or aligned. Trajectories saved more frequently (at 0.2 ns/frame) are available upon request.</p>
<p>To load the trajectories in VMD:</p>
<p><code>mol new md_IF_1G_1S1p_input.psf </code></p>
<p><code>mol addfile md_IF_1G_1S1p.dcd waitfor all</code></p>
Firewood management practice by hoteliers and non-hoteliers in Langtang valley, Nepal Himalayas
No full textLangtang Region is the third largest trekking destination in Nepal. The annual tourist flow was about 8000 by 2000. However, after 2000, the number of tourists were increased to about 15000 annually. Out of it, one third tourists visit to the Langtang Valley. With increasing number of tourists, the number of hotels and lodges are also rapidly increased there. Firewood has been the major source of energy for both hoteliers and non-hoteliers for a long time and its demand has been abruptly increased with increasing number of hotels and lodges. Both hoteliers and non-hoteliers collect firewood from nearby forest and also transport from the valley bottom to Langtang village and Kyanjing. However, there are major differences in collection places, and collection strategy especially in terms of distance, preference of tree species, purpose, and relation to nature.The Geographical Journal of Nepal Vol. 10: 55-72, 2017 </jats:p
CG simulations of eVP40-Membrane systems
No full text<p>This list contains the .xtc (compressed trajectory) and .gro (coordinate) files for five different coarse-grained systems: </p>
<p>1) eVP40 & membrane (without PA) </p>
<p>2) eVP40 & membrane (with 2% PA)</p>
<p>3) eVP40 & membrane (with 7% PA)</p>
<p>4) membrane only (without PA)</p>
<p>5) membrane only (with 7% PA)</p>
<p>The trajectories uploaded here are saved at 0.006 microseconds/frame (i.e., 3335 frames = 20.01 microseconds). The trajectories for the protein-membrane systems are compacted and centered. </p>
<p>To load the trajectories on VMD, type the following in Tk console (7% PA trajectory for example):</p>
<pre><code> mol new eVP40_7%PA_coords.gro
mol addfile eVP40_7%PA_traj.xtc waitfor all</code></pre>
Multiphysics machine learning framework for on-demand multi-functional nano pattern design by light-controlled capillary force lithography
No full textNature finds ways to realize multi-functional surfaces by modulating nano-scale patterns on their surfaces, enjoying transparent, bactericidal, and/or anti-fogging features. Therein height distributions of nanopatterns play a key role. Recent advancements in nanotechnologies can reach that ability via chemical, mechanical, or optical fabrications. However, they require laborious complex procedures, prohibiting fast mass manufacturing. This paper presents a computational framework to help design multi-functional nano patterns by light. The framework behaves as a surrogate model for the inverse design of nano distributions. The framework’s hybrid (i.e., human and artificial) intelligence-based approach helps learn plausible rules of multi-physics processes behind the UV-controlled nano patterning and enriches training data sets. Then the framework’s inverse machine learning (ML) model can describe the required UV doses for the target heights of liquid in nano templates. Thereby, the framework can realize multiple functionalities including the desired nano-scale color, frictions, and bactericidal properties. Feasibility test results demonstrate the promising capability of the framework to realize the desired height distributions that can potentially enable multi-functional nano-scale surface properties. This computational framework will serve as a multi-physics surrogate model to help accelerate fast fabrications of nanopatterns with light and ML.This article is published as Chapagain, Ashish, and In Ho Cho. "Multiphysics machine learning framework for on-demand multi-functional nano pattern design by light-controlled capillary force lithography." Communications Physics 7, no. 1 (2024): 213. doi: https://doi.org/10.1038/s42005-024-01703-9. © The Author(s) 2024. This Open Access article is licensed under a Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)
Globalisation of water: Opportunities and threats of virtual water trade
No full textMore information: http://www.taylorandfrancis.co.ukCivil Engineering and Geoscience
Entrepreneurship in the Peripheral Regions: A Case of Tourism in the Himalayan Village Manang, Nepal
No full textEntrepreneurship in the Peripheral Regions: A Case of Tourism in the Himalayan Village Manang, Nepal
No full textThis study attempts to describe the impact of tourism on the Himalayan village Manang in Western Nepal. The people of Manang have been famous for their international trading since the 1960s and those who experienced success in international trading began to migrate to Kathmandu and buy real estate. Manang is located along the trekking routes of the Annapurna Circuit and has had many trekkers since the 1980s. Since Nepali democracy in 1990, the trading business has become more competitive, so some residents decided to enter the tourism industry in Kathmandu or Manang. Compared with the situation in Kathmandu, in the peripheral region such like Manang they needed to put more effort into providing modern facilities and services to meet the demands of tourists because of its remote location. Some hotel owners introduced eco-friendly and advanced technology to provide modern facilities. However, tourists who prefer to visit peripheral regions regret such development, and start to look for other ‘hidden’ villages. Although tourism development is beset by these contradictions, the people of Manang have accepted the situation and just appropriated the entrepreneurship that have ever developed their livelihoods including international trade.Article【論文／Article】departmental bulletin pape
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