Figure 18 - uploaded by Martin O. Steinhauser
Content may be subject to copyright.
Master curves for a) the radius of gyration and b) the expansion factor α 2 vs. the rescaled chain length.
Source publication
During the last decade, computer simulation has become indispensable as a research tool in many branches of science. The numerical simulation of structural properties using a variety of methods and underlying theories has emerged as a new field of research called Computational Physicsor Computational Materials Science(CMS). Typical methods used rou...
Citations
... For our purposes, we use a simple representation of the atomic structure of the lipids where many atoms are lumped into CG soft particles which are connected by entropic springs. This type of generic bead-spring model where several atoms (i.e., atomic degrees of freedom) are mapped onto a specific particle in order to gain computational speed-up is very common in computational polymer physics [17][18][19]. ...
... This situation has led to the increasing use of CG models of biomembranes during the last ten years [17,30,[54][55][56][57][58][59][60]. CG models constitute a class of mesoscale models, in which many atoms are treated by grouping them together into new particles which act as individual interaction sites connected by entropic springs [19,43,55,57,61,62]. ...
... Our approach to coarse-graining lipids is based on a standard CG polymer model, Eqs.(1)-(3), that has successfully been used in several studies of polymers [17][18][19]. In order to model the specific hydrophobic effect of lipids, we use an additional potential in Eq. (4), akin to one, that was introduced originally by Steinhauser in computational polymer physics to account for the effects of different solvent qualities in polymer solutions [65]. ...
We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction \(h_\mathrm{c}\) of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli \(K_\mathrm{A}\) and bending stiffnesses \(\kappa _\mathrm{B}\) for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol–gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity \(h_\mathrm{c}\) of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self-repairing membranes (reducing their damage after impact) and permanent (irreversible) damage, depending on the shock front speed. The here presented idea of using coarse-grained (CG) particle models for soft matter systems in combination with the investigation of shock-wave effects in these systems is a quite new approach.
... Second, due to usually wider potential wells, CG simulations allow the use of much larger timesteps (100– 500 fs) compared to 10 to 40 fs used in purely atomistic simulations. Together, these factors make CG simulations highly efficient compared to their atomistic counterpart [38]. Hence, by using this simplified modeling of polymer-solvent interactions results in a computational speed-up, making simulations of large-scale membrane structures possible. ...
... We perform constant temperature molecular dynamics simulations using the MD simulation software package MD-CUBE which was originally developed by Steinhauser [36], [38] for coarse-grained (CG) macromolecular simulations of single polymers and melts of almost arbitrarily branched monomer connectivity. For studying lipid bilayer membranes, many different CG implicit-solvent models based on either MD [42], [57], [62][63][64][65][66]or Monte Carlo (MC) procedures [9], [52][53][54][55], [58], [67], [68] have been developed, each one capturing molecular details at different levels of resolution. ...
... Our approach to coarse-graining lipids is based on a standard CG polymer model, Eqs. (1) to (3), that has been used in several studies of polymers [22], [38], [40] . In order to model the particular hydrophobic effect of lipids, we use an additional potential in Eq. (4), akin to one, that was introduced originally by Steinhauser to account for the effects of different solvent qualities in polymer solutions [36]. ...
Equations of convection in a gas are analyzed and a computational algorithm that is efficient when the condition mugh/RT≪1 is satisfied for an arbitrary (fairly large) temperature drop is proposed. Calculations of convection occurring in steady nonuniform heating of walls are performed for axisymmetric argoncontaining volumes of different shape. Results of these calculations demonstrate the establishment of steady and periodic motions of the gas.
The idea of the book is to provide a comprehensive overview of computational physics methods and techniques, that are used for materials modeling on different length and time scales. Each chapter first provides an overview of the physical basic principles which are the basis for the numerical and mathematical modeling on the respective length-scale.
The book includes the micro-scale, the meso-scale and the macro-scale. The chapters follow this classification. The book will explain in detail many tricks of the trade of some of the most important methods and techniques that are used to simulate materials on the perspective levels of spatial and temporal resolution. Case studies are occasionally included to further illustrate some methods or theoretical considerations. Example applications for all techniques are provided, some of which are from the author’s own contributions to some of the research areas. Methods are explained, if possible, on the basis of the original publications but also references to standard text books established in the various fields are mentioned.
A molecular dynamics study of the effect of increasing molecular chain stiffness on the dynamic properties of single linear chains and polymer melts is presented. The chain stiffness is controlled by a bending potential. By means of a normal mode analysis the systematic crossover behavior of coarse-grained linear polymer systems from Rouse modes to bending modes with increasing mode number p is presented systematically for the first time via simulation data. The magnitude and the onset of the region where crossover behavior occurs is investigated in dependence of a systematic variation of the chains’ persistence lengths. For long wavelength modes the well-known p
−2 behavior is observed which represents the Rouse scaling, whereas for the bending modes one observes a distinct p
−4 scaling of the mean square mode amplitudes and the relaxation times. Additionally, the effect of this crossover behavior on the monomer dynamics given by their mean square displacements is investigated. The findings are contrasted with previous simulation studies of semiflexible chain behavior and it is shown that those studies—due to too small persistence lengths L
p
—were actually limited to the crossover regime where both, Rouse and bending modes contribute to the chain dynamics, and no distinct p
−4 scaling can be observed. Using an expansion of the monomer position vector, a simple theory of the observed scaling behavior is proposed which allows for deriving analytic expressions that describe the presented simulation data very well.
We present results of high-speed impact experiments on aluminum oxide (Al2O3) and silicon carbide (SiC) ceramics and propose a mesoscopic way to model the fracture behavior of these brittle materials based on discrete particles. The two-dimensional model used here has only three adjustable parameters, but is able of reproducing many salient features of the investigated ceramics under compressive, tensile and shock impact load. We discuss our particle model in detail and then consider strain and shear load simulations. In particular, we model explicitly the macroscopic experimental set-up of the edge-on impact experiment and show that the experimentally observed crack patterns can in principle be explained by the random distribution of particle overlaps and the thereby generated differences in the local strength of the material.
NOx emissions characteristic of vehicle engine fueled with LPG (liquid petrol gas) was studied. A numerical simulation model was established by GT-POWER and was validated by experimental data. Based on the model, the variable parameters study including air-fuel radio, compression radio and ignition advance angle were carried out. The model results showed that the compression radio and the air-fuel radio played an important role during the NOx emissions characteristic. There is a significant improvement of the NOx emissions with the compression ratio increases. The cylinder pressure and temperature increased with the improvement of the compression ratio brought out the NOx emissions rise. With the improvement of the air-fuel ratio, NOx emissions increased first and then decreased. A larger ignition advance angle can decrease the NOx emissions, at the same time the danger of knock corresponding increased. So the ignition advance angle must be appropriate selected.
This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment.
