Variational Principles in Quantum Monte Carlo: The Troubled Story of Variance Minimization.

We investigate the use of different variational principles in quantum Monte Carlo, namely, energy and variance minimization, prompted by the interest in the robust and accurate estimation of electronic excited states. For two prototypical, challenging molecules, we readily reach the accuracy of the best available reference excitation energies using energy minimization in a state-specific or state-average fashion for states of different or equal symmetry, respectively. On the other hand, in variance minimization, where the use of suitable functionals is expected to target specific states regardless of the symmetry, we encounter severe problems for a variety of wave functions: as the variance converges, the energy drifts away from that of the selected state.

Coarse-Grained Simulations of Three-Armed Star Polymer Melts and Comparison with Linear Chains.

Melts of three-armed star polymers have been simulated using a coarse-grained model parameterized by atomistic simulations of polyethylene. The bonds between the highly coarse-grained, and hence soft, polymer beads are explicitly prevented from crossing by the TWENTANGLEMENT algorithm. The three melts of symmetric stars, differing in the lengths of the arms, are compared against five melts of linear polymers with comparable dimensions to study the impact of branched architecture on self-diffusion and bulk rheological properties.

Physical Networks from Multifunctional Telechelic Star Polymers: A Rheological Study by Experiments and Simulations.

The equilibrium mechanical properties of a cross-linked gel of telechelic star polymers are studied by rheology and Brownian dynamics simulations. The Brownian dynamics model consists of cores to which Rouse arms are attached. Forces between the cores are obtained from a potential of mean force model developed by Likos and co-workers.

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations.

Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril.

Red-shifting and blue-shifting OH groups on metal oxide surfaces - towards a unified picture.

We analyse the OH vibrational signatures of 56 structurally unique water molecules and 34 structurally unique hydroxide ions in thin water films on MgO(001) and CaO(001), using DFT-generated anharmonic potential energy surfaces. We find that the OH stretching frequencies of intact water molecules on the surface are always downshifted with respect to the gas-phase species while the OH- groups are either upshifted or downshifted. Despite these differences, the main characteristics of the frequency shifts for all three types of surface OH groups (OHw, OsH and OHf) can be accounted for by one unified expression involving the in situ electric field from the surrounding environment, and the gas-phase molecular properties of the vibrating species (H2O or OH-).

The attachment of α-synuclein to a fiber: A coarse-grain approach.

We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet.

Clathrin Assembly Regulated by Adaptor Proteins in Coarse-Grained Models.

The assembly of clathrin triskelia into polyhedral cages during endocytosis is regulated by adaptor proteins (APs). We explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a Monte Carlo click interaction, to simulate their collective aggregation behavior. The phase diagrams indicate that a crucial role is played by the mechanical properties of the disordered linker segment of AP.

A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation.

Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics--like sequences of amino acids or even an entire protein--are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level.

An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles.

Brownian Dynamics is the designated technique to simulate the collective dynamics of colloidal particles suspended in a solution, e.g., the self-assembly of patchy particles.

A computational and experimental study of the linear and nonlinear response of a star polymer melt with a moderate number of unentangled arms.

We present from simulations and experiments results on the linear and nonlinear rheology of a moderate functionality, low molecular weight unentangled polystyrene (PS) star melt. The PS samples were anionically synthesized and close to monodisperse while their moderate functionality ensures that they do not display a pronounced core effect. We employ a highly coarse-grained model known as Responsive Particle Dynamics where each star polymer is approximated as a point particle.

Rotational Brownian dynamics simulations of clathrin cage formation.

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics.

The generation of curved clathrin coats from flat plaques.

Flat clathrin lattices or 'plaques' are commonly believed to be the precursors to clathrin-coated buds and vesicles. The sequence of steps carrying the flat hexagonal lattice into a highly curved polyhedral cage with exactly 12 pentagons remains elusive, however, and the large numbers of disrupted interclathrin connections in previously proposed conversion pathways make these scenarios rather unlikely. The recent notion that clathrin can make controlled small conformational transitions opens new avenues.

Translational and rotational coupling in Brownian rods near a solid surface.

An anisotropic macromolecule confined between two surfaces displays Brownian motion predominantly in the plane parallel to these surfaces. It can be expected that both the rotational and translational diffusion coefficients are strongly affected by hydrodynamic interactions with the walls. This work studies the more extreme case in which a rodlike particle comes into contact with a wall or in very close proximity (order of 100 nm).

Calculation of anharmonic OH phonon dispersion curves for the Mg(OH)2 crystal.

Anharmonic OH phonon dispersion curves have been calculated for the Mg(OH)(2) crystal. A crystal Hamiltonian was set up for the vibrational problem, where the coordinates consists of the bond lengths of two hydroxide ions in the central unit cell. Its two-dimensional potential energy surface was constructed from first principle calculations within the density functional theory approximation.

Flow of wormlike micelles in an expansion-contraction geometry.

Recently there has been a great deal of attention, from researchers both in academia and in industry, focused on the rheological properties of solutions of viscoelastic wormlike micelles formed by surfactants. It is particularly vital to understand the properties of these solutions with regard to their flow in porous media, given their application to the recovery of hydrocarbons from subterranean formations. In this study a realistic mesoscopic Brownian dynamics model has been utilized to investigate the flow of viscoelastic surfactant (VES) fluid through individual pores with sizes of around one micron.