Two-dimensional Superfluidity and Localization in the Hard-Core Boson Model: a Quantum Monte Carlo Study

Quantum Monte Carlo simulations are used to investigate the two-dimensional superfluid properties of the hard-core boson model, which show a strong dependence on particle density and disorder. We obtain further evidence that a half-filled clean system becomes superfluid via a finite temperature Kosterlitz-Thouless transition. The relationship between low temperature superfluid density and particle density is symmetric and appears parabolic about the half filling point. Disorder appears to break the superfluid phase up into two distinct localized states, depending on the particle density. We find that these results strongly correlate with the results of several experiments on high-$T_c$ superconductors.Comment: 10 pages, 3 figures upon request, RevTeX version 3, (accepted for Phys. Rev. B

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

Enhanced stability of layered phases in parallel hard-spherocylinders due to the addition of hard spheres

There is increasing evidence that entropy can induce microphase separation in binary fluid mixtures interacting through hard particle potentials. One such phase consists of alternating two dimensional liquid-like layers of rods and spheres. We study the transition from a uniform miscible state to this ordered state using computer simulations and compare results to experiments and theory. We conclude that (1) there is stable entropy driven microphase separation in mixtures of parallel rods and spheres, (2) adding spheres smaller then the rod length decreases the total volume fraction needed for the formation of a layered phase, therefore small spheres effectively stabilize the layered phase; the opposite is true for large spheres and (3) the degree of this stabilization increases with increasing rod length.Comment: 11 pages, 9 figures. Submitted to Phys. Rev. E. See related website http://www.elsie.brandeis.ed

Neutron matter at zero temperature with auxiliary field diffusion Monte Carlo

The recently developed auxiliary field diffusion Monte Carlo method is applied to compute the equation of state and the compressibility of neutron matter. By combining diffusion Monte Carlo for the spatial degrees of freedom and auxiliary field Monte Carlo to separate the spin-isospin operators, quantum Monte Carlo can be used to simulate the ground state of many nucleon systems (A\alt 100). We use a path constraint to control the fermion sign problem. We have made simulations for realistic interactions, which include tensor and spin--orbit two--body potentials as well as three-nucleon forces. The Argonne $v_8'$ and $v_6'$ two nucleon potentials plus the Urbana or Illinois three-nucleon potentials have been used in our calculations. We compare with fermion hypernetted chain results. We report results of a Periodic Box--FHNC calculation, which is also used to estimate the finite size corrections to our quantum Monte Carlo simulations. Our AFDMC results for $v_6$ models of pure neutron matter are in reasonably good agreement with equivalent Correlated Basis Function (CBF) calculations, providing energies per particle which are slightly lower than the CBF ones. However, the inclusion of the spin--orbit force leads to quite different results particularly at relatively high densities. The resulting equation of state from AFDMC calculations is harder than the one from previous Fermi hypernetted chain studies commonly used to determine the neutron star structure.Comment: 15 pages, 15 tables and 5 figure

First principles simulations of liquid Fe-S under Earth's core conditions

First principles electronic structure calculations, based upon density functional theory within the generalized gradient approximation and ultra-soft Vanderbilt pseudopotentials, have been used to simulate a liquid alloy of iron and sulfur at Earth's core conditions. We have used a sulfur concentration of $\approx 12$wt, in line with the maximum recent estimates of the sulfur abundance in the Earth's outer core. The analysis of the structural, dynamical and electronic structure properties has been used to report on the effect of the sulfur impurities on the behavior of the liquid. Although pure sulfur is known to form chains in the liquid phase, we have not found any tendency towards polymerization in our liquid simulation. Rather, a net S-S repulsion is evident, and we propose an explanation for this effect in terms of the electronic structure. The inspection of the dynamical properties of the system suggests that the sulfur impurities have a negligible effect on the viscosity of Earth's liquid core.Comment: 24 pages (including 8 figures

Twist-averaged Boundary Conditions in Continuum Quantum Monte Carlo

We develop and test Quantum Monte Carlo algorithms which use a``twist'' or a phase in the wave function for fermions in periodic boundary conditions. For metallic systems, averaging over the twist results in faster convergence to the thermodynamic limit than periodic boundary conditions for properties involving the kinetic energy with the same computational complexity. We determine exponents for the rate of convergence to the thermodynamic limit for the components of the energy of coulomb systems. We show results with twist averaged variational Monte Carlo on free particles, the Stoner model and the electron gas using Hartree-Fock, Slater-Jastrow, three-body and backflow wavefunction. We also discuss the use of twist averaging in the grand canonical ensemble, and numerical methods to accomplish the twist averaging.Comment: 8 figures, 12 page

Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such diverse length, and also time scales, requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach