Detecting Stealth Dark Matter Directly through Electromagnetic Polarizability.

We calculate the spin-independent scattering cross section for direct detection that results from the electromagnetic polarizability of a composite scalar "stealth baryon" dark matter candidate, arising from a dark SU(4) confining gauge theory-"stealth dark matter." In the nonrelativistic limit, electromagnetic polarizability proceeds through a dimension-7 interaction leading to a very small scattering cross section for dark matter with weak-scale masses. This represents a lower bound on the scattering cross section for composite dark matter theories with electromagnetically charged constituents.

Two-color gauge theory with novel infrared behavior.

Using lattice simulations, we study the infrared behavior of a particularly interesting SU(2) gauge theory, with six massless Dirac fermions in the fundamental representation. We compute the running gauge coupling derived nonperturbatively from the Schrödinger functional of the theory, finding no evidence for an infrared fixed point up through gauge couplings g(2) of order 20. This implies that the theory either is governed in the infrared by a fixed point of considerable strength, unseen so far in nonsupersymmetric gauge theories, or breaks its global chiral symmetries producing a large number of composite Nambu-Goldstone bosons relative to the number of underlying degrees of freedom.

Parity doubling and the S parameter below the conformal window.

We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N(f)=2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N(f) is increased from 2 to 6, motivating study of these trends as N(f) is increased further, toward the critical value for transition from confinement to infrared conformality.

Adaptive multigrid algorithm for the lattice Wilson-Dirac operator.

We present an adaptive multigrid solver for application to the non-Hermitian Wilson-Dirac system of QCD. The key components leading to the success of our proposed algorithm are the use of an adaptive projection onto coarse grids that preserves the near null space of the system matrix together with a simplified form of the correction based on the so-called γ5-Hermitian symmetry of the Dirac operator. We demonstrate that the algorithm nearly eliminates critical slowing down in the chiral limit and that it has weak dependence on the lattice volume.

Toward TeV conformality.

We study the chiral properties of an SU(3) gauge theory with N{f} massless Dirac fermions in the fundamental representation when N{f} is increased from 2 to 6. For N{f}=2, our lattice simulations lead to a value of psi psi/F{3}, where F is the Nambu-Goldstone-boson decay constant and psi psi is the chiral condensate, which agrees with the measured QCD value. For N{f}=6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{f} increases further, toward the critical value for transition from confinement to infrared conformality.

Adaptive multigrid algorithm for lattice QCD.

We present a new multigrid solver that is suitable for the Dirac operator in the presence of disordered gauge fields. The key behind the success of the algorithm is an adaptive projection onto the coarse grids that preserves the near null space. The resulting algorithm has weak dependence on the gauge coupling and exhibits very little critical slowing down in the chiral limit.

Fourier acceleration of Langevin molecular dynamics.

Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in a continuum. Although our method is based on a mapping of the particles' dynamics to a regular grid so that discrete Fourier transforms may be taken, it should be emphasized that the introduction of the grid is a purely algorithmic device and that no smoothing, coarse-graining, or mean-field approximations are made.

Dynamical view of the positions of key side chains in protein-protein recognition.

When a complex is constructed from the separately determined rigid structures of a receptor and its ligand, some key side chains are usually in wrong positions. These distortions of the interface yield an apparent loss in affinity and would unfavorably affect the kinetics of association. It is generally assumed that the interacting proteins should drive the appropriate conformational changes, leading to their complementarity, but this hypothesis does not explain their fast association rates.

Phospholipase D activity facilitates Ca2+-induced aggregation and fusion of complex liposomes.

Phospholipase D (PLD) activation in stimulated neutrophils results in the conversion of membrane phosphatidylcholine (PC) to phosphatidic acid (PA). This change in membrane phospholipid composition has two potentially positive effects on degranulation. It 1) replaces a nonfusogenic phospholipid with a fusogenic one and 2) increases the potential for interactions between membranes and the annexins.

Unidirectional heterologous receptor desensitization between both the fMLP and C5a receptor and the IL-8 receptor.

During inflammation neutrophils receive multiple signals that are integrated, allowing a single modified response. One mechanism for this discrimination is receptor desensitization, a process whereby ligand-receptor binding is disassociated from cell activation. We examined the effect of heterologous receptor desensitization on neutrophil chemotaxis, calcium mobilization, and arachidonic acid production, using interleukin-8 (IL-8), C5a, and N-formyl-methionyl-leucyl-phenylalanine (fMLP).

PLA2 promotes fusion between PMN-specific granules and complex liposomes.

Neutrophil stimulation results in the activation of a variety of phospholipases, including phospholipase A2 (PLA2), which releases arachidonic acid from the 2 position of membrane phospholipids, leaving a lysophospholipid. Because arachidonic acid is known to be a potent fusogen in vitro, we examined the effect of metabolism by PLA2 on the fusion of complex liposomes (liposomes prepared with a phospholipid composition similar to that found in neutrophil plasma membrane). We observed that PLA2 augmented the fusion of complex liposomes with each other as well as with specific granules isolated from human neutrophils, lowering the Ca2+ requirement for fusion by three orders of magnitude.

Effective water model for Monte Carlo simulations of proteins.

We present an effective theory for water. Our goal is to formulate an accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self-interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms.

Minimal requirements for peptide mediated activation of CD8+ CTL.

A physical chemical model of T cell stimulation by class I-peptide complexes was developed and used to analyse in vitro studies of gamma-interferon release as a function of the number of peptide and MHC molecules. The analysis provided reasonable estimates of well identified parameters, including equilibrium constants and the minimum number of T cell receptor-class I-peptide ternary complexes on a presenting cell required to activate T cells. The latter number was estimated as 3-5 per T cell.

Exhaustive conformational search and simulated annealing for models of lattice peptides.

We consider simple lattice models for short peptide chains whose states can be exhaustively enumerated to find the lowest energy conformation. Using these exact results and numerical simulations, we compute the distributions for the mean time tN, required to find the global minimum energy state by simulated annealing (SA), as a function of N, the number of units in the chain. On the basis of scaling arguments, the time tN, to find the global minimum energy of longer chains, beyond the range covered by exhaustive enumeration, can be estimated.

Impact of massively parallel computation on protein structure determination.

For the past two decades, an important paradigm in protein chemistry has been the assertion that a biologically active protein is at thermodynamic equilibrium and therefore adopts its minimum free energy structure. Although some evidence now suggests that not all proteins conform to this notion, it is true often enough to remain an important guiding principle in structure determination, whether by direct computation or by the computationally assisted approaches of diffraction and resonance. Among the difficulties in predicting structure from sequence are the lack of a useful potential function incorporating the influence of solvent and the inability to sample the phase space efficiently or even to determine whether a free energy minimum is, in fact, the global minimum.