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Kurt Kremer

Publications and source records attributed to Kurt Kremer.

At least 73 records · Page 4Linked to original sources
arXiv2009

Coupling different levels of resolution in molecular simulations

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures thermodynamic equilibrium among the molecules of different representation. The robustness of the algorithm is tested for two examples, namely an adaptive resolution simulation, atomistic/coarse-grained, for a liquid of tetrahedral molecules and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

cond-mat.stat-mech↗
arXiv2009

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water

We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic model owing to the conservation of linear momentum by the adaptive resolution forces. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under non-equilibrium conditions.

cond-mat.soft↗
arXiv2009

Comparison of a Microgel Simulation to Poisson-Boltzmann Theory

We have investigated a single charged microgel in aqueous solution with a combined simulational model and Poisson-Boltzmann theory. In the simulations we use a coarse-grained charged bead-spring model in a dielectric continuum, with explicit counterions and full electrostatic interactions under periodic and non-periodic boundary conditions. The Poisson-Boltzmann model is that of a single charged colloid confined to a spherical cell where the counterions are allowed to enter the uniformly charged sphere. We compare the simulational results to those of the Poisson-Boltzmann solution and find good agreement, i.e., for the number of confined counterions within the gel. We then proceed to investigate the origin of the differences between the results these two models give, and performed a variety of simulations which were designed to test for the influence of charge correlations, excluded volume interactions, and thermal fluctuations in the strands of the gel. Our results support the applicability of the Poisson-Boltzman cell model to study ionic properties of small microgels under dilute conditions.

cond-mat.soft↗
arXiv2008

Quantitative Study of Polymer Dynamics Through Hierarchical Multi-scale Dynamic Simulations

The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal with specific chemistries. In this letter we present a hierarchical approach that combines atomistic and coarse-grained simulations to quantitatively study polymer dynamics. As an example we predict diffusion coefficients of atactic polystyrene melts of molecular weights relevant to polymer processing (up to 50kDa) without any adjustable parameter and compare the results to experiment.

cond-mat.soft↗
arXiv2007

Modeling Diffusive Dynamics in Adaptive Resolution Simulation of Liquid Water

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice-versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of essential thermodynamic, structural and dynamical properties of liquid water at ambient conditions.

cond-mat.soft↗
arXiv2007

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e.g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosity of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.

cond-mat.soft↗
arXiv2007

A Macromolecule in a Solvent: Adaptive Resolution Molecular Dynamics Simulation

We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on-the-fly. We show that our approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

cond-mat.soft↗
arXiv2006

Adaptive Resolution Simulation of Liquid Water

We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct description of all essential thermodynamic and structural properties of liquid water.

cond-mat.soft↗
arXiv2006

Adaptive molecular resolution via a continuous change of the phase space dimensionality

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being developed for many applications. However in almost all cases, the regions of different resolution are fixed and not in a true equilibrium with each other. We here give the theoretical framework for an efficient and flexible coupling of the different regimes. The approach leads to an analog of a geometry induced phase transition and a counterpart of the equipartition theorem for fractional degrees of freedom. This provides a rather general formal basis for advanced computer simulation methods applying different levels of resolution.

cond-mat.stat-mech↗
arXiv2006

Hyperdynamics for entropic systems: time-space compression and pair correlation function approximation

We develop a generalized hyperdynamics method, which is able to simulate slow dynamics in atomistic general (both energy and entropy-dominated) systems. We show that a few functionals of the pair correlation function, involving two-body entropy, form a low-dimensional collective space, which is a good approximation that is able to distinguish stable and transitional conformations. A bias potential, which raises the energy in stable regions, is constructed on the fly. We examine the slowly nucleation processes of a Lennard-Jones gas and show that our new method can generate correct long time dynamics without a prior knowledge.

cond-mat.stat-mech↗
arXiv2005

Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.

cond-mat.soft↗
arXiv2005

Efficient tunable generic model for fluid bilayer membranes

We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a wide range of parameters, without the need for an explicit solvent. The model shows the expected elastic behavior on large length scales, and its physical properties (eg fluidity or bending stiffness) can be widely tuned via a single parameter. In particular, bending rigidities in the experimentally relevant range are obtained, at least within $3-30 k_{\text{B}}T$. The model is naturally suited to study many physical topics, including self-assembly, fusion, bilayer melting, lipid mixtures, rafts, and protein-bilayer interactions.

cond-mat.soft↗
arXiv2004

Thermal Fluctuations in a Lamellar Phase of a Binary Amphiphile-Solvent Mixture: A Molecular Dynamics Study

We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by bead-and-spring tetramers. At a solvent bead fraction of 20 % and sufficiently low temperature, the amphiphiles self-assemble into a highly oriented lamellar phase. Our study aims at comparing the structure of this phase with the predictions of the elastic theory of thermally fluctuating fluid membrane stacks [Lei et al., J. Phys. II 5, 1155 (1995)]. We suggest a method which permits to calculate the bending rigidity and compressibility modulus of the lamellar stack from the simulation data. The simulation results are in reasonable agreement with the theory.

cond-mat.soft↗
arXiv2003

Polyelectrolyte Multilayering on a Charged Sphere

The adsorption of highly \textit{oppositely} charged flexible polyelectrolytes onto a charged spherical surface is investigated by means of Monte Carlo simulations in a fashion which resembles the layer-by-layer deposition technique introduced by Decher. Electroneutrality is insured at each step by the presence of monovalent counterions (anions and cations). We study in detail the structure of the \textit{equilibrium} complex. Our investigations of the first few layer formations strongly suggest that multilayering in spherical geometry is not possible as an equilibrium process with purely electrostatic interactions. We especially focus on the influence of specific (non-electrostatic) short range attractive interactions (e.g., Van der Waals) on the stability of the multilayers.

cond-mat.soft↗
arXiv2003

Equilibration of Long Chain Polymer Melts in Computer Simulations

Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the simulation cell and introduces the excluded volume rapidly, leads to deformation on short length scales. This deformation is strongest for long chains and relaxes only after the chains have moved their own size. Two methods are shown to overcome this local deformation of the chains. One method is to first pre-pack the Gaussian chains, which reduces the density fluctuations in the system, followed by a gradual introduction of the excluded volume. The second method is a double-pivot algorithm in which new bonds are formed across a pair of chains, creating two new chains each substantially different from the original. We demonstrate the effectiveness of these methods for a linear bead spring polymer model with both zero and nonzero bending stiffness, however the methods are applicable to more complex architectures such as branched and star polymer.

cond-mat.soft↗
arXiv2002

Structure of Polyelectrolytes in Poor Solvent

We present simulations on charged polymers in poor solvent. First we investigate in detail the dilute concentration range with and without imposed extension constraints. The resulting necklace polymer conformations are analyzed in detail. We find strong fluctuations in the number of pearls and their sizes leading only to small signatures in the form factor and the force-extension relation. The scaling of the peak in the structure factor with the monomer density shows a pertinent different behavior from good solvent chains.

cond-mat.soft↗
arXiv2002

Corrections to Scaling in the Hydrodynamic Properties of Dilute Polymer Solutions

We discuss the hydrodynamic radius $R_H$ of polymer chains in good solvent, and show that the leading order correction to the asymptotic law $R_H \propto N^ν$ ($N$ degree of polymerization, $ν\approx 0.59$) is an ``analytic'' term of order $N^{-(1 - ν)}$, which is directly related to the discretization of the chain into a finite number of beads. This result is further corroborated by exact calculations for Gaussian chains, and extensive numerical simulations of different models of good--solvent chains, where we find a value of $1.591 \pm 0.007$ for the asymptotic universal ratio $R_G / R_H$, $R_G$ being the chain's gyration radius. For $Θ$ chains the data apparently extrapolate to $R_G / R_H \approx 1.44$, which is different from the Gaussian value 1.5045, but in accordance with previous simulations. We also show that the experimentally observed deviations of the initial decay rate in dynamic light scattering from the asymptotic Benmouna--Akcasu value can partly be understood by similar arguments.

cond-mat.soft↗