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Dynamic information system for small molecules

Kiran K Telukunta, Xavier Lucas, Kersten Döring, Björn A Grüning, Stefan Günther
2014 Journal of Cheminformatics  
Users can query the system for a given compound and retrieve information on questions such as: • Which other similar compounds exist?  ...  The pursued project is aiming at the integration of existing data resources of small molecules that are combined with tools for the prediction of biological effects based on molecular interactions.  ... 
doi:10.1186/1758-2946-6-s1-p28 pmcid:PMC3980058 fatcat:xtk6keg3ereyzlcrufwxd4ebhm

1SCA-02 Inferring Kinetics Objectively from Single Molecule Time Series with Full Information Content(1SCA Information Dynamics in Biological Systems,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)

Chun-Biu Li
2013 Seibutsu Butsuri  
Recently, we succeeded in visualizing RNA-protein interaction dynamics in single molecule resolution on the designed nanostructure.  ...  役割 Role of Adaptive Dynamics in Stochastic Cellular Sensing Systems Tetsuya Kobayashi (IIS, Univ.  ...  Experimental investigation revealed that our and other organism's sensory systems could detect extremely small signal even though receptor reactions are noisy.  ... 
doi:10.2142/biophys.53.s84_4 fatcat:mgpbb2kcyfhvnechv6blhqjp3e

2SDA-06 Molecular properties and dynamics of single skeletal myosins designed for force generations in ensemble of myosin molecules(2SDA Biological functions derived from cooperation of a small number of molecules,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
2SDA-06 骨格筋ミオシン分子複合体の力発生に特化したミオシン1分子の特性とダイナミクス(2SDA 新学術領域「少数性生物学-個と多数の狭間が織りなす生命現象の探究-」共催,少数個分子の協同が生み出す生命機能のメカニズム,シンポジウム,日本生物物理学会第51回年会(2013年度))

Motoshi Kaya, Hideo Higuchi
2013 Seibutsu Butsuri  
This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ...  While the connected information is formulated globally to include all contributions from the elements, we derive decomposition rules for the connected information to capture local interactions.  ...  This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ... 
doi:10.2142/biophys.53.s95_2 fatcat:srezv7crzvhrhkasrqe67pwpvu

1SCA-01 Information Dynamics in Gene Expression Processes(1SCA Information Dynamics in Biological Systems,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
1SCA-01 遺伝子発現過程の情報ダイナミクス(1SCA 生命システムの情報ダイナミクス,シンポジウム,日本生物物理学会第51回年会(2013年度))

Yuichi Taniguchi
2013 Seibutsu Butsuri  
Recently, we succeeded in visualizing RNA-protein interaction dynamics in single molecule resolution on the designed nanostructure.  ...  役割 Role of Adaptive Dynamics in Stochastic Cellular Sensing Systems Tetsuya Kobayashi (IIS, Univ.  ...  Experimental investigation revealed that our and other organism's sensory systems could detect extremely small signal even though receptor reactions are noisy.  ... 
doi:10.2142/biophys.53.s84_3 fatcat:glkjeyle2ngshhk4rpo3zcy2a4

1SCA-04 Estimating inner-cell dynamics from spatio-temporal data(1SCA Information Dynamics in Biological Systems,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
1SCA-04 細胞内時空間データからの方程式推定(1SCA 生命システムの情報ダイナミクス,シンポジウム,日本生物物理学会第51回年会(2013年度))

Shuji Ishihara, Daisuke Taniguchi, Satoshi Sawai
2013 Seibutsu Butsuri  
Recently, we succeeded in visualizing RNA-protein interaction dynamics in single molecule resolution on the designed nanostructure.  ...  役割 Role of Adaptive Dynamics in Stochastic Cellular Sensing Systems Tetsuya Kobayashi (IIS, Univ.  ...  Experimental investigation revealed that our and other organism's sensory systems could detect extremely small signal even though receptor reactions are noisy.  ... 
doi:10.2142/biophys.53.s84_6 fatcat:odzukscg6fhbtpen4ww66ryy34

Targeting a Rate-Promoting Vibration with an Allosteric Mediator in Lactate Dehydrogenase

Michael W. Dzierlenga, Steven D. Schwartz
2016 Journal of Physical Chemistry Letters  
As a test case for this type of allostery, we chose an enzyme with a well-characterized rate-promoting vibration, lactate dehydrogenase; identified a suitable small molecule for binding; and used transition  ...  The ability of a small-molecule to disrupt enzymatic reactions through alteration of subpicosecond protein motion opens the door for new experimental studies on protein motion coupled to enzymatic reactions  ...  Systems with the bound molecule, called the CPA system, and without the bound molecule, called the control system, were prepared for TPS with explicit solvation, neutralization, minimization, heating,  ... 
doi:10.1021/acs.jpclett.6b01209 pmid:27327209 pmcid:PMC4939807 fatcat:mginqrxkujhkpm3db54sfdjamu

On statistical mechanics of small systems: accurate analytical equation of state for confined fluids

Mehrdad Khanpour, Luis A. Rivera-Rivera, Thomas D. Sewell
2015 Physics and chemistry of liquids (Print)  
This is a comprehensive theoretical research program to investigate the fundamental principles of small-system thermodynamics (a.k.a. nanothermodynamics).  ...  is a comprehensive theoretical research program to investigate the fundamental principles of small-system thermodynamics (a.k.a. nanothermodynamics).  ...  Box 12211 Research Triangle Park, NC 27709-2211 hotspots, small-system thermodynamics, nanoenergetics, molecular dynamics REPORT DOCUMENTATION PAGE 11.  ... 
doi:10.1080/00319104.2015.1006631 fatcat:h6txyb35kzguxnsecbwsm3lwii

Molecular Dynamics—From Small Molecules to Macromolecules

Ki Hyun Nam
2021 International Journal of Molecular Sciences  
All molecular systems, from small molecules to macromolecules, exhibit specific characteristics for a specific environment and time.  ...  Through dynamic studies, using techniques such as spectroscopy, structure determination, and computer analysis, it is possible to collect functional information on molecules at specific times and in specific  ...  Comprehensive molecular dynamics information for pinpointing the functions and properties of molecules can be inferred from information gleaned from multiple snapshots obtained using traditional techniques  ... 
doi:10.3390/ijms22073761 pmid:33916359 fatcat:64f2cdfrg5cnjojxycyeiczdxi

Dynamic and static behaviors of CH4 and CO2 in small and large cavities of hydrate

Tomonori Ida, Kazunaka Endo, Daisuke Matsumoto, Nobuhiko Kato, Motohiro Mizuno, You Suzuki, Makoto Tadokoro
2013 Journal of Molecular Structure  
We investigated the static structures and dynamic behaviors for guest molecules (CH 4 and CO 2 ) in small and large cavities which are composed of 12 pentagonal faces of 20 water molecules (5 12 ), and  ...  For QMD calculations, we used a cluster model containing 73 water molecules, and examined dynamic behavior of guest molecules in the shell cluster model of 39 water molecules which own small and large  ...  Conclusions We studied the static and dynamic behaviors for guest molecules (CH 4 and CO 2 ) in small and For NMR carbon chemical shifts, the calculated carbon NMR chemical shifts of the CO 2 molecule  ... 
doi:10.1016/j.molstruc.2012.10.015 fatcat:n4jyvlrlnjelpes3x5qzr3uw4u

2SDA-05 Imaging of single to a few number of molecules in motion and their enzymatic reactions(2SDA Biological functions derived from cooperation of a small number of molecules,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
2SDA-05 1個から数個の分子が引き起こす運動と酵素反応のイメージング(2SDA 新学術領域「少数性生物学-個と多数の狭間が織りなす生命現象の探究-」共催,少数個分子の協同が生み出す生命機能のメカニズム,シンポジウム,日本生物物理学会第51回年会(2013年度))

Tomoko Masaike, Koji Ikegami, Mitsutoshi Setou, Hiroshi Suzuki, Takayuki Nishizaka
2013 Seibutsu Butsuri  
This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ...  While the connected information is formulated globally to include all contributions from the elements, we derive decomposition rules for the connected information to capture local interactions.  ...  This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ... 
doi:10.2142/biophys.53.s95_1 fatcat:d4wncuw4jjgtrd64pbswhiiz5q

2SDA-07 Toward quantifying higher-order interactions among elements from molecular imaging(2SDA Biological functions derived from cooperation of a small number of molecules,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
2SDA-07 分子イメージングから要素間の高次相互作用の定量化に向けて(2SDA 新学術領域「少数性生物学-個と多数の狭間が織りなす生命現象の探究-」共催,少数個分子の協同が生み出す生命機能のメカニズム,シンポジウム,日本生物物理学会第51回年会(2013年度))

Tamiki Komatsuzaki
2013 Seibutsu Butsuri  
This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ...  While the connected information is formulated globally to include all contributions from the elements, we derive decomposition rules for the connected information to capture local interactions.  ...  This system accomplishes micromolar concentrations by small numbers of molecules. These observation systems will be integrated and thus contribute to understanding of biological systems.  ... 
doi:10.2142/biophys.53.s95_3 fatcat:gmscsia33ncmpbzordbevnnmqa

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water–Na+ system

Dmitry Nerukh, George Karvounis, Robert C. Glen
2002 Journal of Chemical Physics  
The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water-Na ϩ system.  ...  New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.  ...  INTRODUCTION Molecular systems are Hamiltonian nonlinear dynamical systems. They are also large systems consisting of small, relatively simple interacting parts.  ... 
doi:10.1063/1.1518011 fatcat:3ikaeu6dlbegxdwyczrnro2sbu

1SBA-07 Implementation of in vitro intelligence for controlling molecular robots(1SBA The Exploration of the design principle of biomolecular robots based on biophysics,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
1SBA-07 分子ロボットを制御する試験管内知能の実装(1SBA 新学術領域「感覚と知能を備えた分子ロボットの創成」共催,生物物理学による生体分子ロボットの設計原理の探求,シンポジウム,日本生物物理学会第51回年会(2013年度))

Ken Komiya
2013 Seibutsu Butsuri  
Recently, we succeeded in visualizing RNA-protein interaction dynamics in single molecule resolution on the designed nanostructure.  ...  役割 Role of Adaptive Dynamics in Stochastic Cellular Sensing Systems Tetsuya Kobayashi (IIS, Univ.  ...  Experimental investigation revealed that our and other organism's sensory systems could detect extremely small signal even though receptor reactions are noisy.  ... 
doi:10.2142/biophys.53.s84_2 fatcat:iljl66shbnfinkxvipdrb4wbhm

1SBA-06 Synthetic RNA-Protein complexes to construct molecular robot in vitro and in cells(1SBA The Exploration of the design principle of biomolecular robots based on biophysics,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
1SBA-06 人工RNA-Protein複合体による細胞内外で機能する分子ロボットの創出にむけて(1SBA 新学術領域「感覚と知能を備えた分子ロボットの創成」共催,生物物理学による生体分子ロボットの設計原理の探求,シンポジウム,日本生物物理学会第51回年会(2013年度))

Hirohide Saito
2013 Seibutsu Butsuri  
Recently, we succeeded in visualizing RNA-protein interaction dynamics in single molecule resolution on the designed nanostructure.  ...  役割 Role of Adaptive Dynamics in Stochastic Cellular Sensing Systems Tetsuya Kobayashi (IIS, Univ.  ...  Experimental investigation revealed that our and other organism's sensory systems could detect extremely small signal even though receptor reactions are noisy.  ... 
doi:10.2142/biophys.53.s84_1 fatcat:ywpwfxh56nckpo26agzwhr7jem

Channel Capacity of Starch and Glucose Molecular Communications in the Small Intestine Digestive Tract [article]

Dixon Vimalajeewa, Sasitharan Balasubramaniam
2021 arXiv   pre-print
The emerging field of Molecular Communication (MC) aims to characterize biological-based signaling environment through information that are encoded into molecules.  ...  This study proposes a new application and direction for MC, focusing on the digestive system, where we characterize and model the starch and glucose propagation along the small intestine.  ...  in the digestive system dynamics.  ... 
arXiv:2107.12901v1 fatcat:z23jcm6vsrhbla3naabw5zrnoi
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