scholarly journals The Longitudinal Superdiffusive Motion of Block Copolymer in a Tight Nanopore

Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 2931
Author(s):  
Waldemar Nowicki
Keyword(s):  
Dynamic Properties ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Ballistic Motion ◽  
The Monte Carlo Method ◽  
Long Time ◽  
The Mean ◽  
Confined Environment ◽  
Unidirectional Motion

The structure and dynamic properties of polymer chains in a confined environment were studied by means of the Monte Carlo method. The studied chains were represented by coarse-grained models and embedded into a simple 3D cubic lattice. The chains stood for two-block linear copolymers of different energy of bead–bead interactions. Their behavior was studied in a nanotube formed by four impenetrable surfaces. The long-time unidirectional motion of the chain in the tight nanopore was found to be correlated with the orientation of both parts of the copolymer along the length of the nanopore. A possible mechanism of the anomalous diffusion was proposed on the basis of thermodynamics of the system, more precisely on the free energy barrier of the swapping of positions of both parts of the chain and the impulse of temporary forces induced by variation of the chain conformation. The mean bead and the mass center autocorrelation functions were examined. While the former function behaves classically, the latter indicates the period of time of superdiffusive motion similar to the ballistic motion with the autocorrelation function scaling with the exponent t5/3. A distribution of periods of time of chain diffusion between swapping events was found and discussed. The influence of the nanotube width and the chain length on the polymer diffusivity was studied.

Computer Simulation of Polymer Chains in Confinement

2008 ◽  
Vol 138 ◽  
pp. 451-475 ◽  
Author(s):  
Andrzej Sikorski
Keyword(s):  
Computer Simulation ◽  
Brownian Dynamics ◽  
Dynamic Properties ◽  
Practical Importance ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Theoretical Treatment ◽  
Narrow Slit ◽  
Exchange Method ◽  
Confined Polymers

Properties of macromolecules confined in a narrow slit, pore or capillary are important due to of their practical importance. Theoretical treatment of such systems is also interesting because the introduction of confinement has an impact on most properties of polymer chains and it gained a longstanding attention. In order to determine the properties of such systems coarse-grained models of confined polymers were designed where macromolecules were represented by united atoms. Lattice approximation was also often introduced. Different macromolecular architectures were studied: linear, cyclic and star-branched chains. Computer simulation techniques (the variants of the Monet Carlo method like the Metropolis algorithm and the Replica Exchange method as well as Molecular Dynamics and Brownian Dynamics methods) applied for studies of such models were reviewed and evaluated. The structure of the polymer film and the dynamic properties were mainly presented and discussed. The influence of the width of the slit, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that a moderate confinement stabilizes folded chains while a strong confinement does not.

Diffusion of Confined Polymer Chains

2005 ◽  
Vol 237-240 ◽  
pp. 169-174 ◽  
Author(s):  
Andrzej Sikorski
Keyword(s):  
Dynamic Properties ◽  
Polymer Chains ◽  
Polymer Systems ◽  
Cubic Lattice ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
Simple Lattice ◽  
The Monte Carlo Method ◽  
A Chain ◽  
Confined Polymer Chains

Simple lattice model of polymer systems was developed and studied using the Monte Carlo method. The model chains were star-branched with f = 3 arms and rings. The number of polymer segments in a chain was varied up to 800. The chains were built on a simple cubic lattice with the excluded volume interactions only (the athermal system). The polymers were confined between two parallel impenetrable walls with a set of irregular obstacles what can be treated as porous media. A Metropolis-like sampling algorithm employing local changes of chain conformation was used. The dynamic properties of the model system were studied. The differences in the mobility of chains with different internal architectures were shown and discussed. The possible mechanisms of motions were presented.

The influence of temperature and density on the microscopic structure and dynamics of long polymer chains: Molecular dynamics and dissipative particle dynamics modeling

2017 ◽  
Vol 06 (03) ◽  
pp. 1750023
Author(s):  
M. Lemaalem ◽  
A. Derouiche ◽  
S. EL Fassi ◽  
H. Ridouane
Keyword(s):  
Molecular Dynamics ◽  
Dynamic Properties ◽  
Dissipative Particle Dynamics ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Polymer Physics ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Dynamics Modeling ◽  
Polymer Simulation

Long polymer chains that mainly exhibit thermoplastic properties are recognized to demonstrate excellent thermal and mechanical features at the molecular level. For the purpose of facilitating its study, we present the results of a coarse-grained Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) simulations under the Canonical ensemble (NVT) conditions. For each simulation method, the structure, static and dynamic properties were analyzed, with particular emphasis on the influence of density and temperature on the equilibrium of the polymer. We find, after correcting the Soft Repulsive Potential (SRP) parameters used in DPD method, that both simulation methods describe the polymer physics with the same accuracy. This proves that the DPD method can simplify the polymer simulation and can reproduce with the same precision the equilibrium obtained in the MD simulation.

The statistical and dynamics properties of hard-sphere polymer chains

2015 ◽  
Vol 29 (18) ◽  
pp. 1550091 ◽  
Author(s):  
Zi-Wen Huang ◽  
Ji-Xuan Hou ◽  
Chun Xie ◽  
Hao Zhang
Keyword(s):  
Relaxation Time ◽  
Chain Length ◽  
Hard Sphere ◽  
Dynamic Properties ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Power Exponent ◽  
Polymer Model ◽  
Time Saving ◽  
Scaling Relationship

We investigated a highly coarse-grained polymer model — hard-sphere (HS) model. This model is characterized by its time-saving computation and strictly guaranteed uncrossability of polymer chains. Regarding the statistical and dynamic properties of HS model, our simulating results perfectly coincide with pre-existing scaling theory. Additionally, we point out that the power exponent of scaling relationship between its relaxation time and chain length is 2.2.

scholarly journals Unveiling the Dynamics of KRAS4b on Lipid Model Membranes

2021 ◽  
Author(s):  
Cesar A. López ◽  
Animesh Agarwal ◽  
Que N. Van ◽  
Andrew G. Stephen ◽  
S. Gnanakaran
Keyword(s):  
Molecular Mechanisms ◽  
Hypervariable Region ◽  
Small Gtpase ◽  
Model Systems ◽  
Coarse Grained ◽  
Regulatory Function ◽  
Limited Information ◽  
Long Time ◽  
Cell Growth And Differentiation ◽  
State Models

AbstractSmall GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms. Graphic Abstract

scholarly journals Biological Risk Assessment of Heavy Metals in Sediments and Health Risk Assessment in Marine Organisms from Daya Bay, China

2020 ◽  
Vol 9 (1) ◽  
pp. 17
Author(s):  
Zexing Kuang ◽  
Yangguang Gu ◽  
Yiyong Rao ◽  
Honghui Huang
Keyword(s):  
Heavy Metals ◽  
Risk Assessment ◽  
Marine Organisms ◽  
Daya Bay ◽  
Ecological Risks ◽  
The Monte Carlo Method ◽  
Accumulation Index ◽  
The Mean ◽  
Primary Pollutant ◽  
Geo Accumulation

The concentrations of heavy metals in sediments and marine organisms in Daya Bay were investigated, and the Monte Carlo method was used to analyze the uncertainty of the results of geo-accumulation characteristics and ecological and health risks. The mean concentrations of metal elements in sediments were in the following order: Zn > Cr > Cu > As > Cd > Hg, while those in marine organisms were Zn > Cu > As > Cr ≈ Cd > Hg. The geo-accumulation index (Igeo) indicated that the primary pollutant was Hg, with 5.46% moderately polluted, and 39.52% for unpolluted to moderately polluted. Potential ecological risks (RI) were between low and high risks, and the contributions of Hg, Cd, and As to ecological risks were 50.85%, 33.92%, and 11.47%, respectively. The total hazard coefficients (THQ) were less than 1, but on the basis of total carcinogenic risks (TCR), the probability of children and adults exceeded the unacceptable risk threshold of 22.27% and 11.19%, respectively. Sensitivity analysis results showed that the concentrations of carcinogenic elements contributed to risk in the order of As > Cd > Cr. Therefore, in order to effectively control heavy metals contamination in Daya Bay, it is necessary to strengthen the management of Hg, Cd, and As emissions.

Relationship between temporal and spatial averages in grid turbulence

2013 ◽  
Vol 730 ◽  
pp. 593-606 ◽  
Author(s):  
L. Djenidi ◽  
S. F. Tardu ◽  
R. A. Antonia
Keyword(s):  
Strong Support ◽  
Statistical Properties ◽  
Grid Turbulence ◽  
Mean Flow ◽  
Lateral Direction ◽  
Ergodic Hypothesis ◽  
Long Time ◽  
The Mean ◽  
Temporal And Spatial ◽  
Boltzmann Method

AbstractA long-time direct numerical simulation (DNS) based on the lattice Boltzmann method is carried out for grid turbulence with the view to compare spatially averaged statistical properties in planes perpendicular to the mean flow with their temporal counterparts. The results show that the two averages become equal a short distance downstream of the grid. This equality indicates that the flow has become homogeneous in a plane perpendicular to the mean flow. This is an important result, since it confirms that hot-wire measurements are appropriate for testing theoretical results based on spatially averaged statistics. It is equally important in the context of DNS of grid turbulence, since it justifies the use of spatial averaging along a lateral direction and over several realizations for determining various statistical properties. Finally, the very good agreement between temporal and spatial averages validates the comparison between temporal (experiments) and spatial (DNS) statistical properties. The results are also interesting because, since the flow is stationary in time and spatially homogeneous along lateral directions, the equality between the two types of averaging provides strong support for the ergodic hypothesis in grid turbulence in planes perpendicular to the mean flow.

Residual Alkaline Phosphatase Activity in Milks Subjected to Various Time-Temperature Treatments

1997 ◽  
Vol 60 (5) ◽  
pp. 525-530 ◽  
Author(s):  
C. J. PAINTER ◽  
R. L. BRADLEY
Keyword(s):  
Alkaline Phosphatase ◽  
Activity Levels ◽  
Milk Product ◽  
Milk Products ◽  
Alp Activity ◽  
High Temperature Short Time ◽  
Thermally Processed ◽  
Long Time ◽  
The Mean ◽  
Fluid Milk

Milk is routinely tested for proper pasteurization. The Scharer and Fluorophos methods, among others, test for residual alkaline phosphatase (ALP) activity to assure proper pasteurization. Until recently there were no tests available to accurately detect residual ALP activity levels below the U.S. legal limit of 1 μg of phenol or 350 mU of ALP per liter of milk. The new Fluorophos method can detect accurately residual ALP activity levels as low as 10 mU/liter. The Fluorophos method was used to investigate residual ALP activity levels in several fluid milk products. The milk products were thermally processed under various time and temperature protocols below, at, and above current U.S. Food and Drug Administration-mandated heat treatments for fluid milk and milk products. The data established values for residual ALP activity in milks pasteurized under high-temperature short-time (HTST) and low-temperature long-time (LTLT) treatments. The mean ALP activities for whole, 2% lowfat, 1% lowfat, skim, half and half, and chocolate-flavored milks thermally processed at the legal minimum HTST pasteurization treatment are 169.7 ± 12.3, 145.2 ± 9.3, 98.6 ± 8.9, 72.5 ± 4.2, 38.4 ± 4.6 and 157.3 ± 6.5 mU/liter, respectively. The mean ALP activities generated at the legal minimum LTLT pasteurization treatment are 81.8 ± 4.8, 66.4 ± 5.9, 56.4 ± 2.1, 39.1 ± 3.9, 35.0 ± 1.2 and 91.3 ± 7.7 mU/liter, respectively. The values for all milks pasteurized at the legal minimum heat treatment were significantly below the current legal cutoff for residual ALP activity of 350 mU/liter of milk or milk product.

A new spectral coarse-graining algorithm based on K-means clustering in complex networks

2019 ◽  
Vol 33 (01) ◽  
pp. 1850421 ◽  
Author(s):  
Lang Zeng ◽  
Zhen Jia ◽  
Yingying Wang
Keyword(s):  
Complex Networks ◽  
Large Scale ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Kuramoto Model ◽  
Coarse Grained ◽  
Original Network ◽  
Topological Information ◽  
Real World Applications ◽  
Large Scale Networks

Coarse-graining of complex networks is one of the important algorithms to study large-scale networks, which is committed to reducing the size of networks while preserving some topological information or dynamic properties of the original networks. Spectral coarse-graining (SCG) is one of the typical coarse-graining algorithms, which can keep the synchronization ability of the original network well. However, the calculation of SCG is large, which limits its real-world applications. And it is difficult to accurately control the scale of the coarse-grained network. In this paper, a new SCG algorithm based on K-means clustering (KCSCG) is proposed, which cannot only reduce the amount of calculation, but also accurately control the size of coarse-grained network. At the same time, KCSCG algorithm has better effect in keeping the network synchronization ability than SCG algorithm. A large number of numerical simulations and Kuramoto-model example on several typical networks verify the feasibility and effectiveness of the proposed algorithm.

COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL

2013 ◽  
Vol 12 (08) ◽  
pp. 1341004
Author(s):  
XUE WU ◽  
TING FU ◽  
ZHI-LONG XIU ◽  
LIU YIN ◽  
JIN-GUANG WANG ◽  
...  
Keyword(s):  
Free Energy ◽  
Prion Protein ◽  
Energy Barrier ◽  
Prion Proteins ◽  
Coarse Grained ◽  
Transmissible Spongiform Encephalopathies ◽  
Free Energy Barrier ◽  
Spongiform Encephalopathies ◽  
Go Model ◽  
Folding Free Energy

Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant α-helical conformation to the abnormal PrP Sc that is rich in β-sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the difference among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the five prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy profile. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from all-atom Gō model confirmed the validity of C α-Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.

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