Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm Douglas Ridgway, Gordon Broderick, Ana Lopez-Campistrous,

Slides:

Advertisements

Similar presentations

Tethered Polymer-Supported Planar Lipid Bilayers for Reconstitution of Integral Membrane Proteins: Silane-Polyethyleneglycol-Lipid as a Cushion and Covalent.

Advertisements

Development of a Novel GFP-based Ratiometric Excitation and Emission pH Indicator for Intracellular Studies Ranieri Bizzarri, Caterina Arcangeli, Daniele.

Picosecond Fluorescence of Intact and Dissolved PSI-LHCI Crystals Bart van Oort, Alexey Amunts, Jan Willem Borst, Arie van Hoek, Nathan Nelson, Herbert.

Creep Function of a Single Living Cell Nicolas Desprat, Alain Richert, Jacqueline Simeon, Atef Asnacios Biophysical Journal Volume 88, Issue 3, Pages

How Do Thermophilic Proteins and Proteomes Withstand High Temperature? Lucas Sawle, Kingshuk Ghosh Biophysical Journal Volume 101, Issue 1, Pages

Quantitative Characterization of the Large-Scale Association of ErbB1 and ErbB2 by Flow Cytometric Homo-FRET Measurements Ágnes Szabó, Gábor Horváth, János.

Water Dependent Properties of Cutinase in Nonaqueous Solvents: A Computational Study of Enantioselectivity Nuno M. Micaelo, Vitor H. Teixeira, António.

Conformational Changes in Actin Filaments Induced by Formin Binding to the Barbed End Gábor Papp, Beáta Bugyi, Zoltán Ujfalusi, Szilvia Barkó, Gábor Hild,

A New FRAP/FRAPa Method for Three-Dimensional Diffusion Measurements Based on Multiphoton Excitation Microscopy Davide Mazza, Kevin Braeckmans, Francesca.

On the Thermodynamic Efficiency of Ca2+-ATPase Molecular Machines Anders Lervik, Fernando Bresme, Signe Kjelstrup, J. Miguel Rubí Biophysical Journal Volume.

Light-Scattering Studies of Protein Solutions: Role of Hydration in Weak Protein-Protein Interactions A. Paliwal, D. Asthagiri, D. Abras, A.M. Lenhoff,

Analysis of Kinetic Intermediates in Single-Particle Dwell-Time Distributions Daniel L. Floyd, Stephen C. Harrison, Antoine M. van Oijen Biophysical Journal.

Counter-Intuitive Stochastic Behavior of Simple Gene Circuits with Negative Feedback Tatiana T. Marquez-Lago, Jörg Stelling Biophysical Journal Volume.

Kinetic Properties of the Cardiac L-Type Ca2+ Channel and Its Role in Myocyte Electrophysiology: A Theoretical Investigation Gregory M. Faber, Jonathan.

Liposomes, Disks, and Spherical Micelles: Aggregate Structure in Mixtures of Gel Phase Phosphatidylcholines and Poly(Ethylene Glycol)-Phospholipids Markus.

Determination of the Interfacial Water Content in Protein-Protein Complexes from Free Energy Simulations Peter Monecke, Thorsten Borosch, Jürgen Brickmann,

Structure and Dynamics of ER: Minimal Networks and Biophysical Constraints Congping Lin, Yiwei Zhang, Imogen Sparkes, Peter Ashwin Biophysical Journal.

The Dynamics and Mechanics of Endothelial Cell Spreading Cynthia A. Reinhart-King, Micah Dembo, Daniel A. Hammer Biophysical Journal Volume 89, Issue 1,

Calibration of Optical Tweezers for In Vivo Force Measurements: How do Different Approaches Compare? Yonggun Jun, Suvranta K. Tripathy, Babu R.J. Narayanareddy,

High-Resolution Waveguide THz Spectroscopy of Biological Molecules N. Laman, S. Sree Harsha, D. Grischkowsky, Joseph S. Melinger Biophysical Journal Volume.

Rigidification of Neutral Lipid Bilayers in the Presence of Salts Georg Pabst, Aden Hodzic, Janez Štrancar, Sabine Danner, Michael Rappolt, Peter Laggner.

Molecular Model of a Cell Plasma Membrane With an Asymmetric Multicomponent Composition: Water Permeation and Ion Effects Robert Vácha, Max L. Berkowitz,

Intrinsic Disorder and Functional Proteomics Predrag Radivojac, Lilia M. Iakoucheva, Christopher J. Oldfield, Zoran Obradovic, Vladimir N. Uversky, A.

Three-Color Alternating-Laser Excitation of Single Molecules: Monitoring Multiple Interactions and Distances Nam Ki Lee, Achillefs N. Kapanidis, Hye Ran.

Thermal Fluctuations of Red Blood Cell Membrane via a Constant-Area Particle- Dynamics Model Gianluca Marcelli, Kim H. Parker, C. Peter Winlove Biophysical.

Secondary-Structure Analysis of Denatured Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy Koichi Matsuo, Yoshie Sakurada, Ryuta Yonehara,

Packaging of a Polymer by a Viral Capsid: The Interplay between Polymer Length and Capsid Size Yufang Hu, Roya Zandi, Adriana Anavitarte, Charles M. Knobler,

Structure of the Alamethicin Pore Reconstructed by X-Ray Diffraction Analysis Shuo Qian, Wangchen Wang, Lin Yang, Huey W. Huang Biophysical Journal Volume.

X-Ray Absorption Spectroscopy of Dinuclear Metallohydrolases David L. Tierney, Gerhard Schenk Biophysical Journal Volume 107, Issue 6, Pages

Domain Registration in Raft-Mimicking Lipid Mixtures Studied Using Polymer-Tethered Lipid Bilayers Sumit Garg, Jürgen Rühe, Karin Lüdtke, Rainer Jordan,

The Nuclear Pore Complex Mystery and Anomalous Diffusion in Reversible Gels Thomas Bickel, Robijn Bruinsma Biophysical Journal Volume 83, Issue 6, Pages.

Both MHC Class II and its GPI-Anchored Form Undergo Hop Diffusion as Observed by Single-Molecule Tracking Yasuhiro M. Umemura, Marija Vrljic, Stefanie.

Contrast Inversion in the Epifluorescence of Cholesterol-Phospholipid Monolayers T.M. Okonogi, H.M. McConnell Biophysical Journal Volume 86, Issue 2, Pages.

A Hydrodynamic Model for Hindered Diffusion of Proteins and Micelles in Hydrogels Ronald J. Phillips Biophysical Journal Volume 79, Issue 6, Pages

Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part I: Methods and Power Analysis Douglas F. Levinson, Matthew D. Levinson, Ricardo Segurado,

Dissecting Streptavidin-Biotin Interaction with a Laminar Flow Chamber Anne Pierres, Dominique Touchard, Anne-Marie Benoliel, Pierre Bongrand Biophysical.

Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation Shigehiko Hayashi, Emad Tajkhorshid, Klaus.

Lever-Arm Mechanics of Processive Myosins Yujie Sun, Yale E. Goldman Biophysical Journal Volume 101, Issue 1, Pages 1-11 (July 2011) DOI: /j.bpj

Spatiotemporal Image Correlation Spectroscopy (STICS) Theory, Verification, and Application to Protein Velocity Mapping in Living CHO Cells Benedict Hebert,

Mesoscale Simulation of Blood Flow in Small Vessels Prosenjit Bagchi Biophysical Journal Volume 92, Issue 6, Pages (March 2007) DOI: /biophysj

Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies.

Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation Sonya M. Hanson, Simon Newstead, Kenton J. Swartz, Mark S.P.

The Importance of the Hook Region of the Cochlea for Bone-Conduction Hearing Namkeun Kim, Charles R. Steele, Sunil Puria Biophysical Journal Volume 107,

Analytical Solutions of Poisson's Equation for Realistic Geometrical Shapes of Membrane Ion Channels Serdar Kuyucak, Matthew Hoyles, Shin-Ho Chung Biophysical.

The Interrelations among Stochastic Pacing, Stability, and Memory in the Heart Hila Dvir, Sharon Zlochiver Biophysical Journal Volume 107, Issue 4, Pages.

Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanism for the A- to-B Transition in DNA Kelly M. Knee, Surjit B. Dixit, Colin Echeverría.

Cell Traction Forces Direct Fibronectin Matrix Assembly Christopher A. Lemmon, Christopher S. Chen, Lewis H. Romer Biophysical Journal Volume 96, Issue.

Quantifying the Rheological and Hemodynamic Characteristics of Sickle Cell Anemia Huan Lei, George Em Karniadakis Biophysical Journal Volume 102, Issue.

Design of Superior Spider Silk: From Nanostructure to Mechanical Properties Ning Du, Xiang Yang Liu, Janaky Narayanan, Lian Li, Matthew Lek Min Lim, Daiqin.

Mechanical Properties of Spider Dragline Silk: Humidity, Hysteresis, and Relaxation T. Vehoff, A. Glišović, H. Schollmeyer, A. Zippelius, T. Salditt Biophysical.

Agarose-Dextran Gels as Synthetic Analogs of Glomerular Basement Membrane: Water Permeability Jeffrey A. White, William M. Deen Biophysical Journal Volume.

Phospholipid-Cholesterol Bilayers under Osmotic Stress Emma Sparr, Linda Hallin, Natalia Markova, Håkan Wennerström Biophysical Journal Volume 83, Issue.

Charged Polymers Modulate Retrovirus Transduction via Membrane Charge Neutralization and Virus Aggregation Howard E. Davis, Matthew Rosinski, Jeffrey R.

Nonlinear Poisson Equation for Heterogeneous Media Langhua Hu, Guo-Wei Wei Biophysical Journal Volume 103, Issue 4, Pages (August 2012) DOI: /j.bpj

Defining the Physical Gate of a Mechanosensitive Channel, MscL, by Engineering Metal-Binding Sites Irene Iscla, Gal Levin, Robin Wray, Robert Reynolds,

Phenol Red Interacts with the Protofibril-Like Oligomers of an Amyloidogenic Hexapeptide NFGAIL through Both Hydrophobic and Aromatic Contacts Chun Wu,

Metallic Nanoparticles Used to Estimate the Structural Integrity of DNA Motifs Jiwen Zheng, Philip S. Lukeman, William B. Sherman, Christine Micheel, A.

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy Peng Zheng, Hongbin Li.

Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids Johan Elf, Måns Ehrenberg Biophysical Journal Volume 88,

Probing the Role of Dynamics in Hydride Transfer Catalyzed by Lactate Dehydrogenase Nickolay Zhadin, Miriam Gulotta, Robert Callender Biophysical Journal.

Different Effects of Trifluoroethanol and Glycerol on the Stability of Tropomyosin Helices and the Head-to-Tail Complex Fernando Corrêa, Chuck S. Farah.

Mehdi Bagheri Hamaneh, Matthias Buck Biophysical Journal

Electroosmosis in Transdermal Iontophoresis: Implications for Noninvasive and Calibration-Free Glucose Monitoring Anke Sieg, Richard H. Guy, M. Begoña.

Henry van den Bedem, Ellen Kuhl Biophysical Journal

The Complex Kinetics of Protein Folding in Wide Temperature Ranges

On Imposing Detailed Balance in Complex Reaction Mechanisms

Volume 69, Issue 12, Pages (June 2006)

A Superresolution Census of RNA Polymerase

Systems Biophysics: Multiscale Biophysical Modeling of Organ Systems

Alice S. Whittemore, Jerry Halpern

Presentation transcript:

Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm Douglas Ridgway, Gordon Broderick, Ana Lopez-Campistrous, Melania Ru’aini, Philip Winter, Matthew Hamilton, Pierre Boulanger, Andriy Kovalenko, Michael J. Ellison Biophysical Journal Volume 94, Issue 10, Pages (May 2008) DOI: /biophysj Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 1 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 2 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 3 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 4 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 5 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 6 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions

Figure 7 Biophysical Journal , DOI: ( /biophysj ) Copyright © 2008 The Biophysical Society Terms and Conditions Terms and Conditions