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VIA-MD: Visual Interactive Analysis of Molecular Dynamics [article]

Robin Skånberg, Mathieu Linares, Carolin König, Patrick Norman, Daniel Jönsson, Ingrid Hotz, Anders Ynnerman
2018 Workshop on Molecular Graphics and Visual Analysis of Molecular Data  
The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations  ...  The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes.  ...  The prototype of this project has been implemented using the visualization framework Inviwo [Inv] and immediate mode GUI Dear ImGui [Cor].  ... 
doi:10.2312/molva.20181102 dblp:conf/molva-ws/SkanbergLKNJHY18 fatcat:cwtzkbsrovdk3gut3k6c352ndi

Cooperative binding of DNA and CBF to the Runt domain of the CBF studied via MD simulations

B. Habtemariam
2005 Nucleic Acids Research  
Here, we report results from molecular dynamics (MD) simulations of RD alone, as a dimer in complexes with DNA and CBFb and in a ternary complex with DNA and CBFb.  ...  Consistent with the experimental findings, in the presence of CBFb the estimated free energy of binding of RD to the DNA is more favorable, which is shown to be due to more favorable intermolecular interactions  ...  Program, Department of Defense Aeronautical Systems Center Major Shared Resource Computing, and the Pittsburgh Supercomputing Center Terascale Computing for computational support.  ... 
doi:10.1093/nar/gki724 pmid:16049027 pmcid:PMC1180745 fatcat:7bkjsdf4zvbjvlyps37vkyab2u

Structural aspects of the O‐glycosylation linkage in glycopeptides via MD simulations and comparison with NMR experiments

Aysegül Turupcu, Matthias Diem, Lorna Smith, Chris Oostenbrink
2019 ChemPhysChem  
A powerful conformational searching and enhanced sampling simulation method, and unbiased molecular dynamics simulations have been used along with NMR spectroscopic observables to provide a detailed structural  ...  view of O-glycosylation.  ...  Acknowledgement This work was supported by the Austrian Science Fund in the context of the Doctoral Program BioToP (Grant W 1224).  ... 
doi:10.1002/cphc.201900079 pmid:30920077 pmcid:PMC6563056 fatcat:ipryaaazlzaszavn4p4pkdaini

MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures

Robin Skånberg, Mathieu Linares, Martin Falk, Ingrid Hotz, Anders Ynnerman
2019 Workshop on Molecular Graphics and Visual Analysis of Molecular Data  
Selecting components and observing changes of properties and configurations over time is an important step in the analysis of molecular dynamics (MD) data.  ...  The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events.  ...  [PSCO09] This is also true for the analysis of molecular dynamics (MD) data and the generation of expressive visualization.  ... 
doi:10.2312/molva.20191096 dblp:conf/molva-ws/SkanbergLFHY19 fatcat:rojxri6va5ajnbvidtqo7d2rpm

Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions

Robin Skanberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz
2021 IEEE Transactions on Visualization and Computer Graphics  
In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time.  ...  For the computation of meaningful distribution functions, the definition of molecular reference structures is essential.  ...  VIA-MD [2] , [25] , short for Visual Interactive Analysis of MD, supports interactive filtering to effectively find and select spatial, temporal, and statistical patterns.  ... 
doi:10.1109/tvcg.2021.3051632 pmid:33444141 fatcat:w26oyymzyben3iehccqihruyii

Diffusion mechanisms in lithium disilicate melt by molecular dynamics simulation

Luis G.V. Gonçalves, José P. Rino
2014 Journal of Non-Crystalline Solids  
Additionally, an analysis on the dynamical behavior of slow-diffusing atoms reveals explicitly the presence of dynamical heterogeneities.  ...  in materials once a realistic interaction potential is applied.  ...  Thus, the Eyring relation does not hold at any temperature using diffusion and relaxation calculated via MD.  ... 
doi:10.1016/j.jnoncrysol.2014.05.018 fatcat:e7o3qbjsmfarfbfrdoyxotnpoy

Employing Hybrid Lennard-Jones and Axilrod-Teller Potentials to Parametrize Force Fields for the Simulation of Materials' Properties

Danilo de Camargo Branco, Gary J. Cheng
2021 Materials  
Because this parametrization process is simple and computationally inexpensive, it allows users to predict materials' behaviors under close-to-ambient conditions in molecular dynamics, independent of pre-existing  ...  Quantum mechanics and molecular dynamics simulations have been valuable options for material properties determination.  ...  Parameters Set Validation through Molecular Dynamics Properties Determination After the parametrization was finished, we tested the parameters set by determining mechanical and thermal properties via MD  ... 
doi:10.3390/ma14216352 pmid:34771878 pmcid:PMC8585255 fatcat:pk7aczx5ivhjbjj757i3aearha

Physisorption of bio oil nitrogen compounds onto montmorillonite

Maisa I Vuorte, Susanna Kuitunen, Maria Sammalkorpi
2021 Physical Chemistry, Chemical Physics - PCCP  
We assess computationally the adsorption of a series of nitrogen containing heterocycles and fatty acid amides from bio oil on a model clay surface, Na-montmorillonite.  ...  via MD simulations and DFT electronic structure calculations.  ...  was studied in terms of adsorption conformation and free energy changes accompanying adsorption events via MD simulations.  ... 
doi:10.1039/d1cp01880a pmid:34554171 fatcat:qnqxlf46qbhavb2nxfruwnprma

Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics

Juraj Palenik, Jan Byska, Stefan Bruckner, Helwig Hauser
2019 IEEE Transactions on Visualization and Computer Graphics  
Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures.  ...  In order to drill into these aggregate values, we propose a multi-scale visual exploration technique.  ...  Sérgio Marques from Loschmidt Laboratories and Hanif Muhammad Khan from Computational Biology Unit at University of Bergen, for providing us with the data and their invaluable feedback.  ... 
doi:10.1109/tvcg.2019.2934258 pmid:31403429 fatcat:47bnsp26d5b4bafbluq3eeyrvu

Molecular Dynamics Simulation of Crack Propagation in Nanoscale Polycrystal Nickel Based on Different Strain Rates

Yanqiu Zhang, Shuyong Jiang
2017 Metals  
Based on the strain rates of 2 × 10 8 s −1 and 2 × 10 10 s −1 , molecular dynamics simulation was conducted so as to study mechanisms of crack propagation in nanoscale polycrystal nickel.  ...  Orientation difference between adjacent grains leads to the slipping of dislocations along the different directions, which results in the initiation of a void near the triple junction of grain boundaries  ...  Acknowledgments: The work was financially supported by National Natural Science Foundation of China (No. 51475101 and 51305091).  ... 
doi:10.3390/met7100432 fatcat:t5pj64q47zgyrmbxmxsaxxauku

A Molecular Dynamics Study of the Stability and Mechanical Properties of a Nano-Engineered Fuzzy Carbon Fiber Composite

Hassan Almousa, Qing Peng, Abduljabar Q. Alsayoud
2022 Journal of Composites Science  
We have investigated the impact of introducing different carbon nanotube loadings to the surfaces of carbon fibers and characterized the interfacial properties by molecular dynamics simulations.  ...  The mechanical properties of the CF models were calculated through uniaxial tensile simulations.  ...  Conflicts of Interest: There are no conflicts of interest to declare.  ... 
doi:10.3390/jcs6020054 fatcat:c3vqxwboezflhexd65ue3lrxjq

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

Benjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock, Qiang Cui
2014 PLoS Computational Biology  
The behavior of the system is then studied via MD simulation. Since minimization puts the molecular system at a low energy state, it is necessary to ''reheat'' it to physiological temperature.  ...  Two sections of the tutorial are devoted to running dynamics: Molecular Dynamics and Langevin Dynamics.  ... 
doi:10.1371/journal.pcbi.1003719 pmid:25057988 pmcid:PMC4109840 fatcat:avvmair5s5egjh37wxkwk7lfie

Neon Atoms Oscillating Inside Carbon and Boron-Nitride Nanotubes: A Fully Atomistic Molecular Dynamics Investigation [article]

Karl M. Garcez, David L. Azevedo, Douglas S. Galvão
2007 arXiv   pre-print
In the present work we discuss based on extensive fully atomistic molecular dynamics simulations the dynamics of Neon atoms oscillating inside (5,5)single-walled carbon nanotubes (CNTs) and boron-nitride  ...  Our results also show that the general features of the oscillations are quite similar to CNT and BNNT, in contrast with some speculations in previous work literature about the importance of broken symmetry  ...  [7] studied the behavior of oscillator damping via MD and they showed that the damping depends on the inverse of the CNT length, which is in good agreement with the prediction of analytical models  ... 
arXiv:0707.3392v1 fatcat:nk2cchcfcjbx5badi7dddzpgyy

Physicochemical properties of blue fluorescent protein determined via molecular dynamics simulation

Veera Krasnenko, Alan H. Tkaczyk, Eric R. Tkaczyk, Koit Mauring
2008 Biopolymers  
BFP Physicochemical Properties via MD Method 1139 FIGURE 6 6 Mean square displacement of BFP center of mass vs. time. FIGURE 7 7 Dependence of BFP diffusion coefficient on temperature.  ...  BFP Physicochemical Properties via MD Method 1137 calculated with Gaussian 03 20 using the density functional method up to the B3LYP/6-31G(d) level.  ... 
doi:10.1002/bip.21065 pmid:18690664 fatcat:ewxjkipj7bf2hoebjspulxg5ya

Low Molecular Weight Oligomers of Poly(alkylene succinate) Polyesters as Plasticizers in Poly(vinyl alcohol) Based Pharmaceutical Applications

Artemis Palamidi, Afroditi Kapourani, Evi Christodoulou, Panagiotis A. Klonos, Konstantinos N. Kontogiannopoulos, Apostolos Kyritsis, Dimitrios N. Bikiaris, Panagiotis Barmpalexis
2021 Polymers  
Furthermore, molecular interactions between PVA and the prepared poly(alkylene succinate) polyesters were revealed by DSC, ATR-FTIR, and molecular dynamics simulations.  ...  Hence, according to findings of the present work, only the use of low molecular weight PPSu is suitable in order to reduce processing temperature of PVA and improve its melt flow properties (plasticizing  ...  via MD simulations.  ... 
doi:10.3390/polym13010146 pmid:33401411 fatcat:mshc3x2ldjdmxeikfmhzwp6nxi
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