اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدHydrophobic interactions with coarse-grained model for water
218
0
0.0
(
0
)
تأليف
S. A. Egorov
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Integral equation theory is applied to a coarse-grained model of water to study potential of mean force between hydrophobic solutes. Theory is shown to be in good agreement with the available simulation data for methane-methane and fullerene-fullerene potential of mean force in water; the potential of mean force is also decomposed into its entropic and enthalpic contributions. Mode coupling theory is employed to compute self-diffusion coefficient of water, as well as diffusion coefficient of a dilute hydrophobic solute; good agreement with molecular dynamics simulation results is found.
قيم البحث
اقرأ أيضاً
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is represented by a s
ingle interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the DNA model to perform simulations of the self-assembly kinetics of DNA tetrahedra, an icosahedron, as well as strand displacement operations used in DNA computation.
Water modeling is a challenging problem. Its anomalies are difficult to reproduce, promoting the proliferation of a large number of computational models, among which researchers select the most appropriate for the property they study. In this chapter
, we introduce a coarse-grained model introduced by Franzese and Stanley (FS) that accounts for the many-body interactions of water. We review mean-field calculations and Monte Carlo simulations on water monolayers for a wide range of pressures and temperatures, including extreme conditions. The results show the presence of two dynamic crossovers and explain the origin of diffusion anomalies. Moreover, the model shows that all the different scenarios, proposed in the last decades as alternative explanations of the experimental anomalies of water, can be related by the fine-tuning of the many-body (cooperative) interaction. Once this parameter is set from the experiments, the FS model predicts a phase transition between two liquids with different densities and energies in the supercooled water region, ending in a liquid-liquid critical point. From this critical point stems a liquid-liquid Widom line, i.e., the locus of maxima of the water correlation length, that in the FS model can be directly calculated. The results are consistent with the extrapolations from experiments. Furthermore, they agree with those from atomistic models but make predictions over a much wider thermodynamic region, allowing for a better interpretation of the available experimental data. All these findings provide a coherent picture of the properties of water and confirm the validity of the FS model that has proved to be useful for large-scale simulations of biological systems.
A first-principle multiscale modeling approach is presented, which is derived from the solution of the Ornstein-Zernike equation for the coarse-grained representation of polymer liquids. The approach is analytical, and for this reason is transferable
. It is here applied to determine the structure of several polymeric systems, which have different parameter values, such as molecular length, monomeric structure, local flexibility, and thermodynamic conditions. When the pair distribution function obtained from this procedure is compared with the results from a full atomistic simulation, it shows quantitative agreement. Moreover, the multiscale procedure accurately captures both large and local scale properties while remaining computationally advantageous.
Using concepts from integral geometry, we propose a definition for a local coarse-grained curvature tensor that is well-defined on polygonal surfaces. This coarse-grained curvature tensor shows fast convergence to the curvature tensor of smooth surfa
ces, capturing with accuracy not only the principal curvatures but also the principal directions of curvature. Thanks to the additivity of the integrated curvature tensor, coarse-graining procedures can be implemented to compute it over arbitrary patches of polygons. When computed for a closed surface, the integrated curvature tensor is identical to a rank-2 Minkowski tensor. We also provide an algorithm to extend an existing C++ package, that can be used to compute efficiently local curvature tensors on triangulated surfaces.
When a colloid is mixed with a depletant such as a non-adsorbing polymer, one observes attractive effective interactions between the colloidal particles. If these particles are anisotropic, analysis of these effective interactions is challenging in g
eneral. We present a method for inference of approximate (coarse-grained) effective interaction potentials between such anisotropic particles. Using the example of indented (lock-and-key) colloids, we show how numerical solutions can be used to integrate out the (hard sphere) depletant, leading to a depletion potential that accurately characterises the effective interactions. The accuracy of the method is based on matching of contributions to the second virial coefficient of the colloids. The simplest version of our method yields a piecewise-constant effective potential; we also show how this scheme can be generalised to other functional forms, where appropriate.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
