scholarly journals Coarse-grained molecular models of the surface of hair

Author(s):  
Erik Weiand ◽  
James P. Ewen ◽  
Peter H. Koenig ◽  
Yuri Roiter ◽  
Steven H. Page ◽  
...  

We present a coarse-grained molecular model of the surface of human hair, which consists of a lipid monolayer, in the MARTINI framework. Using molecular dynamics simulations, we identify a lipid grafting distance that yields a monolayer thickness consistent with atomistic simulations and experimental measurements of hair surfaces. Coarse-grained models for fully-functionalised, partially damaged, and fully damaged hair surfaces are created by randomly replacing neutral thioesters with anionic sulfonate groups. This mimics the progressive removal of fatty acids from the hair surface by bleaching. We study the structure of the lipid monolayer at different degrees of damage using molecular dynamics simulations in vacuum as well as in polar (water) and non-polar (n-hexadecane) solvents. We also compare the wetting behaviour of water and n-hexadecane on the hair surfaces through contact angle measurements conducted using molecular dynamics simulations and experiments. Our model captures the experimentally-observed transition of the hair surface from hydrophobic (and oleophilic) to hydrophilic (and oleophobic) as the level of bleaching damage increases. By using surfaces with different damage ratios, we obtain contact angles from the simulations that are in good agreement with experiments for both solvents on virgin and bleached human hairs. In both the molecular dynamics simulations and further experiments using biomimetic surfaces, the cosine of the water contact angle increases linearly with the sulfonate group surface coverage. We expect that the proposed systems will be useful for future molecular dynamics simulations of the adsorption and tribological behaviour of hair surfaces.

2018 ◽  
Author(s):  
Xingcheng Lin ◽  
Susmita Roy ◽  
Mohit Kumar Jolly ◽  
Federico Bocci ◽  
Nicholas Schafer ◽  
...  

AbstractProstate-Associated Gene 4 (PAGE4) is a disordered protein implicated in the progression of prostate cancer. PAGE4 can be phosphorylated at two residue sites by Homeodomain-Interacting Protein Kinase 1 (HIPK1) to facilitate its binding to the Activator Protein-1 (AP-1) transcription factor. In contrast, a further hyperphosphorylation of PAGE4 by CDC-Like Kinase 2 (CLK2) reduces its binding affinity to AP-1, thus affecting the androgen receptor (AR) activity. Both SAXS and smFRET experiments have shown a structural expansion of PAGE4 upon hyperphosphorylation and a significant increase in size at its N-terminal half than that at its C-terminus. To understand the molecular mechanism underlying this structural transition, we performed a series of constant temperature molecular dynamics simulations using Atomistic AWSEM — a multi-scale molecular model combining detailed atomistic and coarse-grained simulation approaches. Our simulations show that electrostatic interaction drives a transient formation of an N-terminal loop, which causes the change in size for different phosphorylated forms of PAGE4. Phosphorylation also changes the preference of secondary structure formation of PAGE4, which signifies a transition between states that display different degree of disorder. Finally, we construct a mechanism-based mathematical model that allows us to capture the interactions of different forms of PAGE4 with AP-1 and AR, a key therapeutic target in prostate cancer. Our model predicts intracellular oscillatory dynamics of HIPK1-PAGE4, CLK2-PAGE4 and AR activity, indicating phenotypic heterogeneity in an isogenic cell population. Thus, conformational switching among different forms of PAGE4 may potentially affect the efficiency of therapeutic targeting of AR.


2021 ◽  
Author(s):  
Isa Silveira de Araujo ◽  
◽  
Archana Jagadisan ◽  
Zoya Heidari ◽  
◽  
...  

Reliable quantification of wettability is critical in assessment of fluid distribution, capillary pressure, relative permeability, and flow properties of fluids in reservoirs. Wettability of reservoirs can be affected by chemical composition of rock-fluid system, salinity, and reservoir temperature. Experimental assessment of wettability under reservoir conditions, while gaining control on the aforementioned parameters, may be tedious and challenging. Several published researches have used experimental studies to focus on determining the impact of individual factors on wettability of rock. However, studies on the combined effects of these factors are limited, although critical, for better understanding of wettability of hydrocarbon reservoirs. In this paper we introduce a workflow for assessment of wettability of rocks at reservoir condition using molecular dynamics (MD) simulations. The outcomes include (i) quantifying the wettability of pure minerals, (ii) quantifying the impact of reservoir temperature on wettability of pure mineral. The inputs to the simulation include molecules of pure minerals (quartz, calcite, albite) packed in a cubical simulation box. The molecules are condensed to form a flat surface. Subsequently, water and oil (hexane) molecules are placed on the surface of the mineral. We then perform simulations with constant number of particles, temperature and volume (NVT) on the system till equilibrium is reached. At equilibrium, the contact angle formed by the water droplet is measured. Contact angle is simulated for temperature conditions in the range of 300 to 380 K. The results showed that the contact angle between water-mineral for quartz, calcite, and albite at room temperature (300 K) ranges from 30º to 45º, indicating that the surface of these minerals is hydrophilic, with different degrees of hydrophilicity. This information is essential for reliable fluid flow simulations, which are often overlooked in conventional approaches. We also found that the temperature has a measurable impact on the contact angles formed by water droplet. We found that increase in temperature from 300 to 380 K decreases the contact angles by approximately 30% on quartz surfaces, 20% on albite surfaces, and 24% on calcite surfaces. The results for the hexane-mineral system show that the hexane behaved similarly in the three minerals surface. A thin film of hexane is formed at the surface corresponding to a contact angle of 0º. The method introduced in this paper has application for reliable evaluation of wettability at any reservoir of interest by knowing the molecular structure of clay and non-clay minerals as well as fluid content. Moreover, the challenges of wettability determination under high temperature and pressure conditions can also be efficiently addressed by using molecular dynamics simulations.


2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>


Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...


2020 ◽  
Vol 22 (16) ◽  
pp. 8757-8767
Author(s):  
Tomasz Staszewski ◽  
Małgorzata Borówko

We use coarse-grained molecular dynamics simulations to study the behavior of polymer-tethered particles immersed in fluids of isotropic particles.


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