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MGOS: A library for molecular geometry and its operating system

Deok-Soo Kim, Joonghyun Ryu, Youngsong Cho, Mokwon Lee, Jehyun Cha, Chanyoung Song, Sangwha Kim, Roman A. Laskowski, Kokichi Sugihara, Jong Bhak, Seong Eon Ryu
2019 Computer Physics Communications  
Solution method: Molecular Geometry (MG) is a general framework of mathematical/computational methods for solving molecular structure problems using a geometry-priority philosophy and is implemented by  ...  The geometry of atomic arrangement underpins the structural understanding of molecules in many fields.  ...  Acknowledgments This work was in part supported by the National Research  ... 
doi:10.1016/j.cpc.2019.107101 fatcat:qs6zzmmfrbew7gnxaedwmab6m4

Beta-complex vs. Alpha-complex: Similarities and Dissimilarities

Donguk Kim, Mokwon Lee, Youngsong Cho, Deok-Soo Kim
2018 IEEE Transactions on Visualization and Computer Graphics  
The beta-complex is a generalization of the alpha-complex.  ...  The beta-complex is a construct derived from the Voronoi diagram of spherical balls of arbitrary radii and has proven a powerful capability for proximity reasoning among spherical balls in three-dimensional  ...  In the beta-complex approach to solve the problem, it is obvious and easy as follows.  ... 
doi:10.1109/tvcg.2018.2873633 pmid:30334798 fatcat:vcnggud4zvannlawwypvyrlwp4

Spatial Modeling of Cell Signaling Networks [chapter]

Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, Leslie M. Loew
2012 Methods in Cell Biology  
The shape of a cell, the sizes of subcellular compartments and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior.  ...  The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically are then described and some guidance is provided in how to set up and run simulations.  ...  Acknowledgments We are grateful to the Ed Boyce and Frank Morgan for their help in visualizing the volumetric simulations presented in Figure 1 .  ... 
doi:10.1016/b978-0-12-388403-9.00008-4 pmid:22482950 pmcid:PMC3519356 fatcat:vonsdgo7pnb5ni53hhcbq6323a

BetaMol: A Molecular Modeling, Analysis and Visualization Software Based on the Beta-Complex and the Quasi-Triangulation

Youngsong CHO, Jae-Kwan KIM, Joonghyun RYU, Chung-In WON, Chong-Min KIM, Donguk KIM, Deok-Soo KIM
2012 Journal of Advanced Mechanical Design, Systems, and Manufacturing  
The powerful features of the BetaMol are solely based on a unified, single framework of the mathematically rigorous and computationally efficient beta-complex theory.  ...  In this paper, we introduce the BetaMol, a molecular modeling, analysis, and visualization software based on the recent theory of the beta-complex and the quasi-triangulation that are derived from the  ...  We claim that the beta-complex will be the ultimate computational tool for the geometry-or shape-related computational/structural biology problems.  ... 
doi:10.1299/jamdsm.6.389 fatcat:j37zcjrebfaopcy35kb33nfxwq

Quantum and Classical Dynamics of Molecular Scale Structures [article]

Eman Nader Almutib
2016 arXiv   pre-print
In this thesis, I investigate the molecular electronic properties of molecular junctions formed from single molecules.  ...  I found that the beta tunneling factor per methyl unit of the alkanes is lower than the beta factor of oligoether.  ...  All the histograms were constructed from more than 400 curves. of single-molecule conductance and the molecule length or number of (-CH2) units as in our case.  ... 
arXiv:1610.04651v1 fatcat:vn5cs5e2k5ahvmpp4v4236zeje

Automatic structure determination for small molecule crystallography

H. Kanda, T. Higashi, M. Maeyama
2011 Acta Crystallographica Section A Foundations of Crystallography  
additional beta domains.  ...  The method has been applied to a large number of protein test structures, showing a good discriminant power with respect to the complexity of the structure, the space group symmetry and the presence of  ...  We can solve the structure of a small molecule several tens of seconds or sometimes in a few seconds.  ... 
doi:10.1107/s0108767311084832 fatcat:uylhv2e4unaanfytpwu3ugadrm

Representation and Misrepresentation in Biomolecular Science

David S. Goodsell
2007 Theoria et Historia Scientiarum  
The widespread, and nearly exclusive, use of these three types of diagrams has influenced the course of biomolecular research and the perception of molecules in the popular media. visual solutions to a  ...  visual problem E.  ...  X-ray crystallography continues this approach, revealing the structure of a single molecule or a complex of two or three.  ... 
doi:10.12775/ths.2002.026 fatcat:tgdw5funynfgpp64hkprxckzgu

Structural and computational analysis of 3,6-dioctyloxiphenyl-2,5-dimethyl-1,4-diketopyrrolo[3,4-c]pyrrole-1,4-dione

B. Şen, R. Sevinçek, S. Çelik, M. Aygün, S. Alp
2011 Acta Crystallographica Section A Foundations of Crystallography  
additional beta domains.  ...  The method has been applied to a large number of protein test structures, showing a good discriminant power with respect to the complexity of the structure, the space group symmetry and the presence of  ...  We can solve the structure of a small molecule several tens of seconds or sometimes in a few seconds.  ... 
doi:10.1107/s0108767311084844 fatcat:dswse4nr4rhhxphudoiujimxtu

Virtual Cell modelling and simulation software environment

I.I. Moraru, F. Morgan, Y. Li, L.M. Loew, J.C. Schaff, A. Lakshminarayana, B.M. Slepchenko, F. Gao, M.L. Blinov
2008 IET Systems Biology  
available for reactiondiffusion-advection simulations in complex cell geometries including 3D geometries derived from microscope images.  ...  The Virtual Cell (VCell; is a problem solving environment, built on a central database, for analysis, modeling and simulation of cell biological processes.  ...  Acknowledgments This work is supported by NIH Roadmap Award for a National Technology Center for Networks and Pathways (#U54RR022232) and grant # P41RR013186 from the NIH National Center for Research Resources  ... 
doi:10.1049/iet-syb:20080102 pmid:19045830 pmcid:PMC2711391 fatcat:wql4fuivczgo7jakavcffuszgi

A computational chemistry approach to modelling conducting polymers in ionic liquids for next generation batteries

Ben Craig, Chris-Kriton Skylaris, Theresa Schoetz, Carlos Ponce de León
2020 Energy Reports  
An overview of modern quantum chemical methods is presented followed by a discussion of their application in the field of conducting organic polymers (COPs), with a view towards modelling the cathodic  ...  A comprehensive specification of these elements appears well suited to the determination of many relevant parameters including molecular geometry, bandgap of oligomers and energies for systems including  ...  Acknowledgements The authors acknowledge support from the International Consortium of Nanotechnologies (ICoN) funded by Lloyd's Register Foundation, UK [G0086], a charitable foundation which helps to protect  ... 
doi:10.1016/j.egyr.2020.03.025 fatcat:smxwbwhsqvhhldqpblhkeozxku

Application of neutron imaging-plate system to crystal structure analysis of deuterated polymers

M. Hanesaka, K. Tashiro, Y. Yoshizawa, T. Kitano, T. Nishu, T. Ohhara, I. Tanaka, N. Niimura, K. Kurihara, R. Kuroki, T. Tamada, S. Fujiwara (+1 others)
2008 Acta Crystallographica Section A Foundations of Crystallography  
The sites of the halide ions in the complex crystals are similar to those of the water molecules in the hydrated form.  ...  The unit cell constants are a = 9.299(9), b = 9.504(8), c(fiber axis) = 10.41(1) Å and beta = 106.93(8) deg, and a = 9.46(2), b = 9.79(2), c(fiber axis) = 10.33(2) Å and beta = 105.1(2) deg for HBr and  ...  In 1990, crystal structure of actin-DNase I complex was solved by Holmes group. Since then, a lot of crystal structures of actin were solved.  ... 
doi:10.1107/s0108767308081865 fatcat:kia2sehuozejnpczfkv3xoyrgu

Small-Scale Dosimetry: Challenges and Future Directions

John C. Roeske, Bulent Aydogan, Manuel Bardies, John L. Humm
2008 Seminars in nuclear medicine  
The increased specificity of targeting agents has resulted in an interest in the use of radionuclides that emit particulate radiation: alpha particles, beta particles and Auger electrons.  ...  However, the dosimetry of these radionuclides is challenging because the dose must be characterized on a scale that is comparable to the range of these emissions, ie, millimeters for beta particles, micrometers  ...  of complex geometries.  ... 
doi:10.1053/j.semnuclmed.2008.05.003 pmid:18662558 fatcat:dlqhrixgh5dzfjzdygfwsb6gr4

On a method for the absolute scaling of refined atomic B factors

H. Botti, L. Bonilla, F. Trajtenberg, R. Radi, A. Buschiazzo
2011 Acta Crystallographica Section A Foundations of Crystallography  
As part of the EPSRC grant "Age Concern" we developed a companion library, the Small Molecule Toolbox (smtbx).  ...  It provides tools covering the whole workflow of small molecule work but we will focus on refinement in this talk.  ...  One can ask then a question whether it is possible to refine single crystal X-ray diffraction data only in such a way as to mimic the geometry of molecules obtained from single crystal neutron diffraction  ... 
doi:10.1107/s0108767311084960 fatcat:e4lsfhzqxbebblzydz4nqh4ofy

Copper(II) and nickel(II) complexes with N′-[(Z)-phenyl(pyridin-2-yl)methylidene]acetohydrazide: Synthesis, crystal structures, DFT calculations and antioxidant effects

Ram N. Patel, Yogendra Singh, Yogendra Pratap Singh, Raymond J. Butcher, Arti Kamal, I.P. Tripathi
2016 Polyhedron  
Complex 1 has hexacoordinated geometry with 1:2 metals to ligand ratio whereas complex 2 has pentacoordinated with two ligand and Schiff base and neocuproine donors sites.  ...  Both complexes were structurally characterized using single crystal X-ray diffraction studies and belonging to space group P2 1 /n for 1 and P 1 for 2 respectively.  ...  Matthias Zeller in the collection of diffraction data and NSF Grant CHE 0087210, Ohio Board of Regents Grant CAP-491 and by Youngstown State University for funds to purchase the X-ray diffractometer.  ... 
doi:10.1016/j.poly.2016.05.036 fatcat:gsmfsjgiqrbolkfcr5sp3t4s64

Electrostatic complementarity in pseudoreceptor modeling based on drug molecule crystal structures: the case of loxistatin acid (E64c)

Ming W. Shi, Alexandre N. Sobolev, Tanja Schirmeister, Bernd Engels, Thomas C. Schmidt, Peter Luger, Stefan Mebs, Birger Dittrich, Yu-Sheng Chen, Joanna M. Bąk, Dylan Jayatilaka, Charles S. Bond (+4 others)
2015 New Journal of Chemistry  
A combination of pseudoreceptor modeling and electrostatic complementarity maps properties of a native pocket for an enzyme ligand.  ...  approach (Figure 4a , showing a single molecule), and (ii) calculated from an isolated-molecule wavefunction for the experimental geometry (Figure 4b , showing two neighboring molecules).  ...  Overall, the arrangement of pairs of antiparallel molecules exemplified in Figure 3c is reminiscent of two antiparallel peptides in a beta-pleated sheet.  ... 
doi:10.1039/c4nj01503g fatcat:7yol24xrhjayvgmix4t4wuci5u
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