Biomedical subjects
Publications and source records attributed to Kurt Kremer.
Using atomistic molecular dynamics simulations we study solid and liquid crystalline columnar discotic phases formed by alkyl-substituted hexabenzocoronene mesogens. Correlations between the molecular structure, packing, and dynamical properties of these materials are established.
We develop a generalized hyperdynamics method that 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 slow nucleation processes of a Lennard-Jones gas and show that our method can generate correct long-time dynamics without prior knowledge.
The adaptive resolution scheme (AdResS) for efficient hybrid particle-based atomistic/mesoscale molecular dynamics (MD) simulations recently introduced by us, [J. Chem. Phys. 123, 224106 (2005)] is extended to high density molecular liquids with spherical boundaries between the atomistic and mesoscale regions. The key feature of this approach is that it allows for a dynamical change of the number of molecular degrees of freedom during the course of a MD simulation by an on-the-fly switching between the atomistic and mesoscopic levels of detail. Pressure and density variations occurring at the atomistic/mesoscale boundary in the original version are considerably reduced employing the improved methodology presented here.
We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics 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 levels 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, and 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 hybrid and the atomistically resolved systems have the same statistical properties at the same physical conditions.
Using the phenol-terminated polycarbonate blend as an example, we demonstrate that the hydrodynamic boundary conditions for a flow of an adsorbing polymer melt are extremely sensitive to the structure of the epitaxial layer. Under shear, the adsorbed parts (chain ends) of the polymer melt move along the equipotential lines of the surface potential whereas the adsorbed additives serve as the surface defects. In response to the increase of the number of the adsorbed additives the surface layer becomes thinner and solidifies. This results in a gradual transition from the slip to the no-slip boundary condition for the melt flow, with a nonmonotonic dependence of the slip length on the surface concentration of the adsorbed ends.
We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.
We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head bead 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 (e.g., 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(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.
Employing molecular dynamics simulations of a coarse-grained model, the equilibrium swelling behavior of a cross-linked polyelectrolyte gel has been investigated with a bead-spring defect-free network with diamond-like topology under good solvent conditions and close to the theta-point, the counterions were treated explicitly. To examine the validity range of simple scaling arguments we varied the amount of charges in the system, the length of the network chains, the strength of the electrostatic interactions for both solvent qualities over a wide range of parameters. We find that classical theories only apply in the limit of weak electrostatics and suggest corrections based on the microscopic interplay of the systems' components accessible in a simulation, which model successfully our measured data.
Forces across polymer melts are poorly understood despite their importance for adhesion and fabricating composite materials. Using an atomic force microscope (AFM), this interaction was measured for poly(dimethyl siloxane) (PDMS). The structure of the polymer at the surface changed during the first approximately 10 h. Afterward, short-range attractive forces were observed with short-chain PDMS (M(w) = 4200 g/mol). Using PDMS with a molecular weight (M(w) = 18 000 g/mol) above the entanglement limit, we measured a monotonically decaying repulsive force, which indicates that a quasi-immobilized layer had formed at the solid surface. Due to the small radius of curvature of the tip, forces could be measured in equilibrium.
We extend a previous dual scale modeling approach for the behavior of polymers near a metal surface to a variety of end groups. Our approach combines a coarse-grained polymer model with ab initio DFT calculations. Such a procedure was applied to a melt of phenolic-like terminated Bisphenol A-polycarbonate (BPA-PC) interacting with a (111) nickel surface (Delle Site, L.; Abrams, C. F.; Alavi, A.; Kremer, K. Phys. Rev. Lett. 2002, 89, 156103. Abrams, C. F.; Delle Site, L.; Kremer, K. Phys. Rev. E 2003, 67, 021807). This work extends this study to different chain-end modifications of BPA-PC, p-tert-butylphenolic, p-tetramethylpropylphenolic, and p-cumylphenolic. We show how the interplay between adsorption energies and conformational entropy selects different morphologies for the various melts at the interface. Implications of these results for realistic technical materials are finally discussed.
The viscoelastic properties of high molecular weight polymeric liquids are dominated by topological constraints on a molecular scale. In a manner similar to that of entangled ropes, polymer chains can slide past but not through each other. Tube models of polymer dynamics and rheology are based on the idea that entanglements confine a chain to small fluctuations around a primitive path that follows the coarse-grained chain contour. Here we provide a microscopic foundation for these highly successful phenomenological models. We analyze the topological state of polymeric liquids in terms of primitive paths and obtain parameter-free, quantitative predictions for the plateau modulus, which agree with experiment for all major classes of synthetic polymers.
We discuss dissipative particle dynamics as a thermostat to molecular dynamics, and highlight some of its virtues: (i) universal applicability irrespective of the interatomic potential; (ii) correct and unscreened reproduction of hydrodynamic correlations; (iii) stabilization of the numerical integration of the equations of motion; and (iv) the avoidance of a profile bias in boundary-driven nonequilibrium simulations of shear flow. Numerical results on a repulsive Lennard-Jones fluid illustrate our arguments.
We present a dual-resolution coarse-graining scheme for efficient molecular dynamics simulations of bisphenol-A-polycarbonate (BP-A-PC) liquids in contact with a (111) nickel surface. The essential feature of this model is the strong adsorption of phenoxy chain ends, and the absence of adsorption by other parts of the chains. Details of how phenoxy chain ends interact with the nickel surface were extracted from Car-Parrinello molecular dynamics calculations of adsorption of phenol on nickel. These calculations show that phenol adsorption on nickel is short ranged (<3 A) and strongly dependent on the C1-C4 orientation of the ring. The structure of BP-A-PC prevents internal phenylene groups from interacting with the surface, due to steric hindrances from the noninteracting isopropylidenes. These dependencies are incorporated in the coarse-grained model of the BP-A-PC chain by resolving chain-terminating carbonate groups with atomistic detail, while the rest of the chain is represented by coarsened "beads." This allows specification of the C1-C4 orientation of the terminal phenoxy groups, while overall allowing for system equilibration with reasonable computer time. We simulate liquids of up to 240 chains of ten chemical repeat units, confined in a slit pore formed by two frozen (111) planes of atoms with the lattice spacing of nickel. We find that the strong adsorption of chain ends has a large effect on the liquid structure through a distance of more than two bulk radii of gyration from the surface. These effects are explained by a competition among single- and double-end adsorption, and dense packing. The structure of the interface less than 10 A from the wall is greatly sensitive to the orientational dependence of the phenoxy adsorption.
We study the shear-induced alignment transition from transverse to the shear plane to parallel and perpendicular in a lamellar or smectics system. A recently proposed simple continuum model for amphiphiles is studied by large-scale nonequilibrium molecular dynamics simulation. We find a shear-rate dependence of the alignment transition under shear flow, parallel at low and perpendicular alignment at high shear rates. To identify the alignment and degree of order of these shear-induced orientations by scattering, a 3D analysis of the scattering data is needed.
We report results from a molecular dynamics simulation on the conformations of a long flexible polyelectrolyte complexed to a charged sphere, both negatively charged, in the presence of neutralizing counterions in the strong Coulomb coupling regime. The structure of this complex is very sensitive to the charge density of the polyelectrolyte. For a fully charged polyelectrolyte the polymer forms a dense two-dimensional "disk," whereas for a partially charged polyelectrolyte the monomers are spread over the colloidal surface. A mechanism involving the overcharging of the polyelectrolyte by counterions is proposed to explain the observed conformations.