Biomedical subjects

W J Briels

Publications and source records attributed to W J Briels.

At least 19 recordsLinked to original sources

PubMed2006

Simulations of the dynamics of thermal undulations in lipid bilayers in the tensionless state and under stress.

The relaxation processes of height undulations and density fluctuations in a membrane have been studied by molecular dynamics simulations of a coarse grained amphiphilic bilayer model. We observe a double exponential decay in their time correlations, with relaxation rates in good quantitative agreement with the theory by Seifert and Langer [Europhys. Lett. 23, 71 (1993)]. Intermonolayer friction due to slippage between the two monolayers is shown to be the dominant dissipative mechanism at the high wave numbers, q>10 mum(-1), typically encountered in computer simulations. We briefly discuss the ramifications of the slow undulatory relaxation process for the calculation of bending rigidities from the static undulation structure factors. The relaxation rates are sensitive to the surface tension, and at high elongations an oscillatory contribution is observed in the time correlation of the undulations.

Algorithms↗

PubMed2006

Periodic orientational motions of rigid liquid-crystalline polymers in shear flow.

The collective periodic motions of liquid-crystalline polymers in a nematic phase in shear flow have, for the first time, been simulated at the particle level by Brownian dynamics simulations. A wide range of parameter space has been scanned by varying the aspect ratio L/D between 10 and 60 at three different scaled volume fractions Lphi/D and an extensive series of shear rates. The influence of the start configuration of the box on the final motion has also been studied. Depending on these parameters, the motion of the director is either characterized as tumbling, kayaking, log-rolling, wagging, or flow-aligning. The periods of kayaking and wagging motions are given by T=4.2(Lphi/D)gamma(-1) for high aspect ratios. Our simulation results are in agreement with theoretical predictions and recent shear experiments on fd viruses in solution. These calculations of elongated rigid rods have become feasible with a newly developed event-driven Brownian dynamics algorithm.

Algorithms↗

PubMed2006

Thermal undulations of lipid bilayers relax by intermonolayer friction at submicrometer length scales.

The time correlation functions of the thermal undulations of a lipid membrane have been studied by molecular dynamics simulations of a coarse-grained bilayer model. We observe a double-exponential decay, with relaxation rates in good agreement with the theory by Seifert and Langer, [Europhys. Lett. 23, 71 (1993)]. Intermonolayer friction resulting from local velocity differences between the two monolayers is shown to be the dominant dissipative mechanism for fluctuations with wave lengths below approximately -0.1 microm.

Friction↗

PubMed2006

Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations.

Atomistic molecular dynamics simulations of a lipid bilayer were performed to calculate the free energy of a trans-membrane pore as a function of its radius. The free energy was calculated as a function of a reaction coordinate using a potential of mean constraint force. The pore radius was then calculated from the reaction coordinate using Monte Carlo particle insertions. The main characteristics of the free energy that comes out of the simulations are a quadratic shape for a radius less than about 0.3 nm, a linear shape for larger radii than this, and a rather abrupt change without local minima or maxima between the two regions. In the outer region, a line tension can be calculated, which is consistent with the experimentally measured values. Further, this line tension can be rationalized and understood in terms of the energetic cost for deforming a part of the lipid bilayer into a hydrophilic pore. The region with small radii can be described and understood in terms of statistical mechanics of density fluctuations. In the region of crossover between a quadratic and linear free energy there was some hysteresis associated with filling and evacuation of the pore with water. The metastable prepore state hypothesized to interpret the experiments was not observed in this region.

Computer Simulation↗

PubMed2006

Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations.

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new event-driven algorithm that takes the excluded volume interactions between particles into account as instantaneous collisions, but neglects the hydrodynamic interactions. This algorithm is applied to dense systems of highly elongated rods and proves to be efficient. The calculated isotropic-nematic spinodals lie between the previously established binodals in the phase diagram and extrapolate for infinitely long rods to Onsager's [Ann. N. Y. Acad. Sci. 51, 627 (1949)] theoretical predictions. Moreover, we investigate the shear induced shifts of the spinodals, qualitatively confirming the theoretical prediction of the critical shear rate at which the two spinodals merge and the isotropic-nematic phase transition ceases to exist.

Journal Article↗

PubMed2005

Scaling of mesoscale simulations of polymer melts with the bare friction coefficient.

Both the Rouse and reptation model predict that the dynamics of a polymer melt scale inversely proportional with the Langevin friction coefficient xi. Mesoscale Brownian dynamics simulations of polyethylene validate these scaling predictions, providing the reptational friction xi(R)=xi+xi(C) is used, where xi(C) reflects the fundamental difference between a deterministic and a stochastic propagator even in the limit of xi to zero. The simulations have been performed with Langevin background friction and with pairwise friction, as in dissipative particle dynamics. Both simulation methods lead to equal scaling behavior with xi(C) having almost the same value in both cases. The scaling is tested for the diffusion g(t), the shear relaxation modulus G(t), and the Rouse mode autocorrelations of melts of C(120)H(242), C(400)H(802), and C(1000)H(2002). The derived dynamical scaling procedure is very useful to reduce run-time in mesoscale computer simulations, especially if pairwise friction is applied.

Chemistry, Physical↗

PubMed2005

Kayaking and wagging of rods in shear flow.

For the first time, we have simulated the periodic collective orientational motions performed by rigid liquid-crystalline polymers with large aspect ratio in the nematic state in shear flow. In order to be able to do so, we developed a new, event-driven Brownian dynamics technique. We present the results of simulations of rods with aspect ratios L/d ranging from 20 to 60 at volume fractions phi given by Lphi/d = 3.5 and 4.5. By studying the path of the director, i.e., the average direction of the rods, we observe kayaking, wagging, flow aligning, and log-rolling type of orbits, depending on the parameters of the simulation and the initial orientation. We find that the tumbling periods depend on Lphi/d and the shear rate but not on the type of motion. Our simulation results qualitatively confirm theoretical predictions and are in good agreement with the experimental measurements of tumbling times of fd viruses.

Journal Article↗

PubMed2005

Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations.

We use simulations to predict the stability and mechanical properties of two amphiphilic bilayer membranes. We carry out atomistic MD simulations and investigate whether it is possible to use an existing coarse-grained (CG) surfactant model to map the membrane properties. We find that certain membranes can be represented well by the CG model, whereas others cannot. Atomistic MD simulations of the erucate membrane yield a headgroup area per surfactant a(0) of 0.26 nm(2), an elastic modulus K(A) of 1.7 N/m, and a bending rigidity kappa of 5 k(B)T. We find that the CG model, with the right choice for the size and potential well depth of the head, correctly reproduces a(0), kappa, as well as the fluctuation spectrum over the whole range of q values. Atomistic MD simulations of EHAC, on the other hand, suggest that this membrane is unstable. This is indicated by the fact that kappa is of the order of k(B)T, which means that the interface is extremely flexible and diffuse, and K(A) is close to zero, which means that the surface tension is zero. We argue that the CG model can be used if the headgroups are uncharged, dipolar, or effectively dipolar due to headgroup charge screening induced by counterion condensation.

Journal Article↗

PubMed2005

Isotropic-nematic spinodal decomposition kinetics.

The initial stage of isotropic-nematic spinodal demixing kinetics of suspensions of very long and thin, stiff, repulsive rods is analyzed on the basis of the N-particle Smoluchowski equation. Equations of motion for the reduced probability density function of the position and orientation of a rod are expanded up to second order in spatial gradients and leading order in orientational order parameter. The resulting equation of motion is solved analytically, from which the temporal evolution of light-scattering patterns are calculated. It is shown that inhomogeneities in number density are enslaved by the temporal development of inhomogeneities in orientational order. Furthermore, demixing due to rotational diffusion is shown to be much faster as compared to translational diffusion. This results in an instable mode that is rotational, for which the corresponding eigenvector remains finite at zero wave vector. The scattered intensity nevertheless exhibits a maximum at a finite wave vector due to the wave-vector dependence of time-exponential prefactors. The wave vector where the intensity exhibits a maximum is therefore predicted to be a function of time even during the initial stage of demixing.

Journal Article↗

PubMed2005

Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods.

Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here this theory is put to the test by comparing it against computer simulations. A Brownian dynamics simulation program was developed to follow the dynamics of the rods, with a length over a diameter ratio of 60, on the Smoluchowski time scale. The model accounts for excluded volume interactions between rods, but neglects hydrodynamic interactions. The self-rotational diffusion coefficients D(r)(phi) of the rods were calculated by standard methods and by a new, more efficient method based on calculating average restoring torques. Collective decay of orientational order was calculated by means of equilibrium and nonequilibrium simulations. Our results show that, for the currently accessible volume fractions, the decay times in both cases are virtually identical. Moreover, the observed decay of diffusion coefficients with volume fraction is much quicker than predicted by the theory, which is attributed to an oversimplification of dynamic correlations in the theory.

Journal Article↗

PubMed2005

Surface viscosity, diffusion, and intermonolayer friction: simulating sheared amphiphilic bilayers.

The flow properties of an amphiphilic bilayer are studied in molecular dynamics simulations, by exposing a coarse grained model bilayer to two shear flows directed along the bilayer surface. The first field, with a vorticity perpendicular to the bilayer, induces a regular shear deformation, allowing a direct calculation of the surface viscosity. In experiments this property is measured indirectly, by relating it to the diffusion coefficient of a tracer particle through the Saffman-Einstein expression. The current calculations provide an independent test of this relation. The second flow field, with a vorticity parallel to the bilayer, causes the two constituent monolayers to slide past one another, yielding the interlayer friction coefficient.

Computer Simulation↗

PubMed2004

Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations.

The formation of a pore in a membrane requires a considerable rearrangement of the amphiphilic molecules about to form the bilayer edge surrounding the pore, and hence is accompanied by a steep increase of the free energy. Recent rupture and conductance experiments suggest that this reshuffling process is also responsible for a small energy barrier that stabilizes "prepores" with diameters of less than 1 nm, rendering both the opening and closing of pores an activated process. We use the potential of mean constraint force method to study this free energy profile, as a function of pore radius, in a coarse grained bilayer model. The calculations show that the free energy rises by (15-20) kT during pore opening, making it an extremely rare nucleation event. Although we do not observe a barrier to pore closure, the results do make the existence of such a barrier plausible. For larger pores we find a smooth transition to Litster's model, from which a line tension coefficient of about 3.7 x 10(-11) J m(-1) is deduced.

Journal Article↗

PubMed2004

Simulations of stable pores in membranes: system size dependence and line tension.

Amphiphilic bilayers with a pore were simulated using a coarse grained model. By stretching the bilayer to 70% beyond its equilibrium surface area, we established the phase diagram of pores, identifying regions where pores are stable, metastable, or unstable. A simple theoretical model is proposed to explain the phase diagram, and to calculate the critical and equilibrium relative stretches. Interestingly, these are found to scale with the inverse cubic root of the number of amphiphiles in the bilayer, thus explaining the order of magnitude difference between the simulated and the measured values. Three different methods are used to calculate a line tension coefficient of (3.5-4.0) x 10(-11) J/m, in good agreement with experimental data.

Computer Simulation↗

PubMed2004

Molecular-dynamics simulation of amphiphilic bilayer membranes and wormlike micelles: a multi-scale modelling approach to the design of viscoelastic surfactant solutions.

Bilayer membranes and wormlike micelles have been studied using molecular-dynamics simulations. The structure of the worm is analysed in terms of radial density distribution functions, and mechanical properties such as the elastic modulus are calculated. From an analysis of the fluctuation spectra of the tensionless states, we have calculated bending rigidities. Micelles consisting of coarse-grained (CG) model surfactants are studied in order to map the properties of the atomistic micelle. We optimize the CG model with respect to the structure factor of the atomistic micelle. The mechanical properties thus obtained will be used as input for a mesoscopic model of wormlike micelles where the persistence length is the smallest length-scale.

Colloids↗

PubMed2004

Combined discrete particle and continuum model predicting solid-state fermentation in a drum fermentor.

The development of mathematical models facilitates industrial (large-scale) application of solid-state fermentation (SSF). In this study, a two-phase model of a drum fermentor is developed that consists of a discrete particle model (solid phase) and a continuum model (gas phase). The continuum model describes the distribution of air in the bed injected via an aeration pipe. The discrete particle model describes the solid phase. In previous work, mixing during SSF was predicted with the discrete particle model, although mixing simulations were not carried out in the current work. Heat and mass transfer between the two phases and biomass growth were implemented in the two-phase model. Validation experiments were conducted in a 28-dm3 drum fermentor. In this fermentor, sufficient aeration was provided to control the temperatures near the optimum value for growth during the first 45-50 hours. Several simulations were also conducted for different fermentor scales. Forced aeration via a single pipe in the drum fermentors did not provide homogeneous cooling in the substrate bed. Due to large temperature gradients, biomass yield decreased severely with increasing size of the fermentor. Improvement of air distribution would be required to avoid the need for frequent mixing events, during which growth is hampered. From these results, it was concluded that the two-phase model developed is a powerful tool to investigate design and scale-up of aerated (mixed) SSF fermentors.

Aspergillus oryzae↗

PubMed2004

A time-integrated estimate of the entanglement mass in polymer melts in agreement with the one determined by time-resolved measurements.

We make a critical examination of how the entanglement molecular mass Me is determined from various measurable quantities. We are guided by reptation theory, where it is assumed that characteristic relaxations abruptly change and become equal to those of a chain moving in a Gaussian tube, as soon as the corresponding length scales surpass the tube diameter d or similarly as soon as the corresponding mass surpasses a critical value. Taking this critical mass as a definition of the "reptational" entanglement mass, we observe that all methods based on time-resolved quantities, such as the single-chain dynamic structure factor S(q,t) and the zero-shear relaxation modulus G(t), give the same result. We observe that such a value differs, beyond error bars, from that obtained from the plateau modulus, which is a time-integrated quantity. We have investigated an alternative definition of entanglement mass in terms of time-integrated quantities and observe that the value of this specific entanglement mass is consistent with that obtained from the time-resolved observables. We comment on possible reasons for the plateau modulus discrepancy.

Journal Article↗

PubMed2004

Impact of the solvent on the conformational isomerism of calix[4]arenes: a study based on continuum solvation models.

The influence of solvation on the conformational isomerism of calix[4]arene and p-tert-butylcalix[4]arene has been investigated by using the continuum model reported by Miertus, Scrocco, and Tomasi (MST). The quantum mechanical (QM) and semiclassical (SC) formalisms of the MST model have been considered for two different solvents (chloroform and water). The suitability of the QM-MST and SC-MST methods has been examined by comparison with previous results derived from classical molecular dynamics (MD) simulations with explicit solvent molecules. The application of the continuum model to the solute configurations generated by using in vacuo classical MD simulations provides a fast strategy to evaluate the effects of the solvent on the conformational preferences of calixarenes. These encouraging results allow us to propose the use of continuum models to solutes with complex molecular structures, which are traditionally studied by MD simulations.

Journal Article↗

PubMed2003

Numerical simulation and PEPT measurements of a 3D conical helical-blade mixer: a high potential solids mixer for solid-state fermentation.

Helical-blade solids mixers have a large potential as bioreactors for solid-state fermentation (SSF). Fundamental knowledge of the flow and mixing behavior is required for robust operation of these mixers. In this study predictions of a discrete particle model were compared to experiments with colored wheat grain particles and positron emission particle tracking (PEPT) measurements. In the discrete particle model individual movements of particles were calculated from interaction forces. It was concluded that the predicted overall flow behavior matched well with the PEPT measurements. Differences between the model predictions and the experiments with wheat grains were found to be due to the assumption that substrate particles were spherical, which was in the model. Model simulations and experiments with spherical green peas confirmed this. The mixing in the helical-blade mixer could be attributed to (1) the transport of particles up and down in the interior of the mixer, and (2) dispersion or micro-mixing of particles in the top region of the mixer. It appeared that the mixing rate scaled linearly with the rotation rate of the blade, although the average particle velocity did not scale proportionally. It may be that the flow behavior changes as a function of the rotation rate (e.g., changing thickness of the top region); further study is required to confirm this. To increase the mixing performance of the mixer, a larger blade or a change in the shape of the mixer (larger top surface/volume ratio) is recommended.

Bioreactors↗