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Mikko Karttunen

Publications and source records attributed to Mikko Karttunen.

At least 73 records · Page 4Linked to original sources
arXiv2004

Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers

Extensive microscopic molecular dynamics simulations have been performed to study the effects of short-chain alcohols, methanol and ethanol, on two different fully hydrated lipid bilayer systems in the fluid phase at 323 K. It is found that ethanol has a stronger effect on the structural properties of the membranes. In particular, the bilayers become more fluid and permeable: Ethanol molecules are able to penetrate through the membrane in typical time scales of about 200 ns whereas for methanol that time scale is considerably longer, at least of the order of microseconds. We find good agreement with NMR and micropipette studies. We have also measured partitioning coefficients and the rate of crossing events for alcohols, i.e., typical time scale it takes for a molecule to cross the lipid bilayer and to move from one leaflet to the other. For structural properties, two-dimensional centre of mass radial-distribution functions indicate the possibility for quasi long-range order for ethanol-ethanol correlations in contrast to liquid-like behaviour for all other combinations.

cond-mat.soft↗
arXiv2004

Structural Effects of Small Molecules on Phospholipid Bilayers Investigated by Molecular Simulations

We summarize and compare recent Molecular Dynamics simulations on the interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid crystalline phase with a number of small molecules including trehalose, a disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar molecules tend to stabilize the structure of the bilayer as they bridge adjacent lipid headgroups. They do not strongly change the structure of the bilayer. Alcohols and DMSO destabilize the bilayer as they increase its area per molecule in the bilayer plane and decrease the order parameter. Alcohols have a stronger detrimental effect than DMSO. The observables which we compare are the area per molecule in the plane of the bilayer, the membrane thickness, and the NMR order parameter of DPPC hydrocarbon tails. The area per molecule and the order parameter are very well correlated whereas the bilayer thickness is not necessarily correlated with them.

physics.bio-ph↗
arXiv2004

Coarse-Grained Model for Phospholipid/Cholesterol Bilayer

We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by point-like particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speed-up of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the novel coarse-grained model, and discuss the general validity and applicability of the present approach.

cond-mat.soft↗
arXiv2004

Nonlinear alternating current responses of dipolar fluids

The frequency-dependent nonlinear dielectric increment of dipolar fluids in nonpolar fluids is often measured by using a stationary relaxation method in which two electric fields are used: The static direct current (DC) field of high strength causing the dielectric nonlinearity, and the probing alternating current (AC) field of low strength and high frequency. When a nonlinear composite is subjected to a sinusoidal electric field, the electric response in the composite will, in general, consist of AC fields at frequencies of higher-order harmonics. Based on the Froehlich model, we present a theory to investigate nonlinear AC responses of dipolar fluids containing both polarizable monomers and dimers. In the case of monomers only, our theory reproduces the known results. We obtain the fundamental, second-, and third-order harmonics of the Froehlich field by performing a perturbation expansion. The even-order harmonics are induced by the coupling between the AC and DC fields although the system under consideration has a cubic nonlinearity only. The harmonics of the Froehlich field can be affected by the field frequency, temperature, dispersion strength and the characteristic frequency of the dipolar fluid, as well as the dielectric constant of the nonpolar fluid. The results are found to be in agreement with recent experimental observations.

cond-mat.soft↗
arXiv2004

Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers

We employ 100 ns molecular dynamics simulations to study the influence of cholesterol on structural and dynamic properties of dipalmitoylphosphatidylcholine (DPPC) bilayers in the fluid phase. The effects of the cholesterol content on the bilayer structure are considered by varying the cholesterol concentration between 0 and 50%. We concentrate on the free area in the membrane and investigate quantities that are likely to be affected by changes in the free area and free volume properties. It is found that cholesterol has a strong impact on the free area properties of the bilayer. The changes in the amount of free area are shown to be intimately related to alterations in molecular packing, ordering of phospholipid tails, and compressibility. Further, the behavior of the lateral diffusion of both DPPC and cholesterol molecules with an increasing amount of cholesterol can in part be understood in terms of free area. Summarizing, our results highlight the central role of free area in comprehending the structural and dynamic properties of membranes containing cholesterol.

cond-mat.soft↗
arXiv2003

Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study

Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the composition of the bilayers affects their structural and electrostatic properties in the liquid-crystalline phase. By varying the mole fraction of DMTAP, we have found that the area per lipid has a pronounced non-monotonic dependence on the DMTAP concentration, with a minimum around the point of equimolar mixture. We show that this behavior has an electrostatic origin and is driven by the interplay between positively charged TAP headgroups and the zwitterionic PC heads. This interplay leads to considerable re-orientation of PC headgroups for an increasing DMTAP concentration, and gives rise to major changes in the electrostatic properties of the lipid bilayer, including a significant increase of total dipole potential across the bilayer and prominent changes in the ordering of water in the vicinity of the membrane. Moreover, chloride counter-ions are bound mostly to PC nitrogens implying stronger screening of PC heads by Cl ions compared to TAP head groups. The implications of these findings are briefly discussed.

cond-mat.soft↗
arXiv2003

Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions

We present a theory to investigate electro-kinetic behavior, namely, electrorotation and dielectrophoresis under alternating current (AC) applied fields for a pair of touching inhomogeneous colloidal particles and biological cells. These inhomogeneous particles are treated as graded ones with physically motivated model dielectric and conductivity profiles. The mutual polarization interaction between the particles yields a change in their respective dipole moments, and hence in the AC electrokinetic spectra. The multipolar interactions between polarized particles are accurately captured by the multiple images method. In the point-dipole limit, our theory reproduces the known results. We find that the multipolar interactions as well as the spatial fluctuations inside the particles can affect the AC electrokinetic spectra significantly.

cond-mat.soft↗
arXiv2003

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties

In this paper we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium and, to a lesser extent, chloride translate into large differences in the computed radial-distribution functions. This uncertainty reflects the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity.We discuss possible implications on the computation of potential of mean force and effective potentials.

physics.chem-ph↗
arXiv2003

Crumpling of a stiff tethered membrane

first-principles numerical simulation model for crumpling of a stiff tethered membrane is introduced. In our model membranes, wrinkles, ridge formation, ridge collapse, as well as the initiation of stiffness divergence, are observed. The ratio of the amplitude and wave length of the wrinkles, and the scaling exponent of the stiffness divergence, are consistent with both theory and experiment. We observe that close to the stiffness divergence there appears a crossover beyond which the elastic behavior of a tethered membrane becomes similar to that of dry granular media. This suggests that ridge formation in membranes and force-chain network formation in granular packings are different manifestations of a single phenomenon.

cond-mat.soft↗
arXiv2003

Dimensionality effects in Turing pattern formation

The problem of morphogenesis and Turing instability are revisited from the point of view of dimensionality effects. First the linear analysis of a generic Turing model is elaborated to the case of multiple stationary states, which may lead the system to bistability. The difference between two- and three-dimensional pattern formation with respect to pattern selection and robustness is discussed. Preliminary results concerning the transition between quasi-two-dimensional and three-dimensional structures are presented and their relation to experimental results are addressed.

cond-mat.soft↗
arXiv2003

Connectivity of Turing structures

It is well-known that in two dimensions Turing systems produce spots, stripes and labyrinthine patterns, and in three dimensions lamellar and spherical structures or their combinations are observed. We study transitions between these states in both two and three dimensions by first analytically deriving a control parameter and a scaling function for the number of clusters. Then, we apply large scale computer simulations to study the effect of nonlinearities on clustering, the appearance of topological defects and morphological changes in Turing structures. In the two-dimensional real space spotty structures we find some evidence of twin domain formation, of the kind seen in crystalline materials. With the help of reciprocal space analysis we find indication of other more general forms of order accommodation, i.e., eutactic local structures. Also a mechanism for the observed ``connectivity transition'' is proposed.

cond-mat.stat-mech↗
arXiv2002

Electrorotation in graded colloidal suspensions

Biological cells can be treated as composites of graded material inclusions. In addition to biomaterials, graded composites are important in more traditional materials science. In this article, we investigate the electrorotation (ER) spectrum of a graded colloidal suspension in an attempt to discuss its dielectric properties. For that, we use the recently obtained differential effective dipole approximation (DEDA) and generalize it for non-spherical particles. We find that variations in the conductivity profile may make the characteristic frequency red-shifted and have also an effect on the rotation peak. On the other hand, variations in the dielectric profile may enhance the rotation peak, but do not have any significant effect on the characteristic frequency. In the end, we apply our theory to fit experimental data obtained for yeast cells and find good agreement.

cond-mat.soft↗
arXiv2002

Integration Schemes for Dissipative Particle Dynamics Simulations: From Softly Interacting Systems Towards Hybrid Models

We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often studied in simulations. Specifically we clarify the performance of integration schemes in hybrid models, which combine microscopic and meso-scale descriptions of different particles using both soft and hard interactions. We find that in all three model systems many commonly used integrators may give rise to surprisingly pronounced artifacts in physical observables such as the radial distribution function, the compressibility, and the tracer diffusion coefficient. The artifacts are found to be strongest in systems, where interparticle interactions are soft and predominated by random and dissipative forces, while in systems governed by conservative interactions the artifacts are weaker. Our results suggest that the quality of any integration scheme employed is crucial in all cases where the role of random and dissipative forces is important, including hybrid models where the solvent is described in terms of soft potentials.

cond-mat.soft↗
arXiv2002

A new dimension to Turing patterns

It is well known that simple reaction-diffusion systems can display very rich pattern formation behavior. Here we have studied two examples of such systems in three dimensions. First we investigate the morphology and stability of a generic Turing system in three dimensions and then the well-known Gray-Scott model. In the latter case, we added a small number of morphogen sources in the system in order to study its robustness and the formation of connections between the sources. Our results raise the question of whether Turing patterning can produce an inductive signaling mechanism for neuronal growth.

cond-mat.stat-mech↗
arXiv2002

Instabilities and resistance fluctuations in thin accelerated superconducting rings

The non-equilibrium properties of a driven quasi-one dimensional superconducting ring subjected to a constant electromotive force ({\it emf}) is studied. The {\it emf} accelerates the superconducting electrons until the critical current is reached and a dissipative phase slip occurs that lowers the current. The phase slip phenomena is examined as a function of the strength of the {\it emf}, thermal noise, and normal state resistivity. Numerical and analytic methods are used to make detailed predictions for the magnitude of phase slips and subsequent dissipation.

cond-mat.supr-con↗
arXiv2002

Dielectrophoresis of charged colloidal suspensions

We present a theoretical study of dielectrophoretic (DEP) crossover spectrum of two polarizable particles under the action of a nonuniform AC electric field. For two approaching particles, the mutual polarization interaction yields a change in their respective dipole moments, and hence, in the DEP crossover spectrum. The induced polarization effects are captured by the multiple image method. Using spectral representation theory, an analytic expression for the DEP force is derived. We find that the mutual polarization effects can change the crossover frequency at which the DEP force changes sign. The results are found to be in agreement with recent experimental observation and as they go beyond the standard theory, they help to clarify the important question of the underlying polarization mechanisms.

physics.chem-ph↗
arXiv2002

Stability of charge inversion, Thomson problem and application to electrophoresis

We analyse charge inversion in colloidal systems at zero temperature using stability concepts, and connect this to the classical Thomson problem of arranging electrons on sphere. We show that for a finite microion charge, the globally stable, lowest energy state of the complex formed by the colloid and the oppositely charged microions is always overcharged. This effect disappears in the continuous limit. Additionally, a layer of at least twice as many microions as required for charge neutrality is always locally stable. In an applied external electric field the stability of the microion cloud is reduced. Finally, this approach is applied to a system of two colloids at low but finite temperature.

physics.chem-ph↗