scholarly journals A bacterial size law revealed by a coarse-grained model of cell physiology

2020 ◽  
Vol 16 (9) ◽  
pp. e1008245 ◽  
Author(s):  
François Bertaux ◽  
Julius von Kügelgen ◽  
Samuel Marguerat ◽  
Vahid Shahrezaei
Keyword(s):  
Coarse Grained ◽  
Cell Physiology ◽  
Coarse Grained Model

scholarly journals A bacterial size law revealed by a coarse-grained model of cell physiology

2016 ◽  
Author(s):  
François Bertaux ◽  
Julius von Kügelgen ◽  
Samuel Marguerat ◽  
Vahid Shahrezaei
Keyword(s):  
Growth Rate ◽  
Cell Size ◽  
Mass Fraction ◽  
Structural Model ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Cell Physiology ◽  
Bacterial Physiology ◽  
Coarse Grained Model ◽  
Growth Laws

AbstractUniversal observations in Biology are sometimes described as “laws”. InE. coli, experimental studies performed over the past six decades have revealed major growth laws relating ribosomal mass fraction and cell size to the growth rate. Because they formalize complex emerging principles in biology, growth laws have been instrumental in shaping our understanding of bacterial physiology. Here, we discovered a novel size law that connects cell size to the inverse of the metabolic proteome mass fraction and the active fraction of ribosomes. We used a simple whole-cell coarse-grained model of cell physiology that combines the proteome allocation theory and the structural model of cell division. The model captures all available experimental data connecting the cell proteome composition, ribosome activity, division size and growth rate in response to nutrient quality, antibiotic treatment and increased protein burden. Finally, a stochastic extension of the model explains non-trivial correlations observed in single cell experiments including the adder principle. This work provides a simple and robust theoretical framework for studying the fundamental principles of cell size determination in unicellular organisms.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

scholarly journals Molecular Dynamics Study of Ganglioside GM3/DPPC Membrane by Using Coarse-Grained Model

2016 ◽  
Vol 110 (3) ◽  
pp. 323a
Author(s):  
Kento Inoue ◽  
Eiji Ymamoto ◽  
Daisuke Takaiwa ◽  
Kenji Yasuoka ◽  
Masuhiro Mikami
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Ganglioside Gm3 ◽  
Coarse Grained Model

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

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