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. We carry out lattice calculations of the polarizability for the lightest "baryon" states in SU(3) and SU(4) gauge theories using the background field method on quenched configurations. We find the polarizabilities of SU(3) and SU(4) to be comparable (within about 50%) normalized to the stealth baryon mass, which is suggestive for extensions to larger SU(N) groups. The resulting scattering cross sections with a xenon target are shown to be potentially detectable in the dark matter mass range of about 200-700 GeV, where the lower bound is from the existing LUX constraint while the upper bound is the coherent neutrino background. Significant uncertainties in the cross section remain due to the more complicated interaction of the polarizablity operator with nuclear structure; however, the steep dependence on the dark matter mass, 1/m(B)(6), suggests the observable dark matter mass range is not appreciably modified. We briefly highlight collider searches for the mesons in the theory as well as the indirect astrophysical effects that may also provide excellent probes of stealth dark matter.

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. Thus either of these phases exhibits novel behavior.

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.

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 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.

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. Results are presented for the Wilson-Dirac operator of the 2D U(1) Schwinger model.

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. The method thus can be applied to the equations of motion of molecular dynamics (MD) or its Langevin or Brownian variants. For example, in Langevin MD simulations our acceleration technique permits a straightforward spectral decomposition of forces so that the long-wavelength modes are integrated with a longer time step, thereby reducing the time required to reach equilibrium or to decorrelate the system in equilibrium. Speedup factors of up to 30 are observed relative to pure (unaccelerated) Langevin MD. As with acceleration of critical lattice models, even further gains relative to the unaccelerated method are expected for larger systems. Preliminary results for Fourier-accelerated molecular dynamics are presented in order to illustrate the basic concepts. Possible extensions of the method and further lines of research are discussed.

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. However, nanosecond explicit solvent molecular dynamics simulations of misfolded surface side chains from the independently solved structures of barstar, bovine pancreatic trypsin inhibitor, and lysozyme show that even before any receptor-ligand interaction, key side chains frequently visit the rotamer conformations seen in the complex. We show that these simple structural motifs can reconcile most of the binding affinity required for a rapid and highly specific association process. Side chains amenable to induced fit are also identified. These results corroborate that solvent-side chain interactions play a critical role in the recognition process. Our findings are also supported by crystallographic data.

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. Modeling neutrophil degranulation, we examined the effect of PLD (Streptomyces chromofuscus) hydrolysis on the aggregation and fusion of liposomes in the presence and absence of annexin I. We found that PLD-mediated conversion of PC to PA lowered the [Ca2+] required for fusion. Annexin I increased the rate of fusion in the presence of PA, although it did not lower threshold [Ca2+], which remained above the physiological range. However, after hydrolysis by PLD, annexin I lowered the [Ca2+] required for aggregation by almost three orders of magnitude, to near physiological concentrations. These studies indicate that the activation of PLD and the production of PA may play a role in annexin-mediated membrane-membrane apposition.

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). We observed reciprocal inhibition with respect to chemotaxis. We demonstrated that homologous desensitization, with respect to the mobilization of intracellular calcium stores, lasted approximately 15 min. Heterologous desensitization between the fMLP receptor and the C5a receptor was reciprocal; either stimulant would diminish the cells' response to stimulation by the other for approximately 3-5 min. However, we observed a unidirectional heterologous desensitization of the IL-8 receptor by both the fMLP and the C5a receptor. This unidirectional heterologous desensitization was observed with respect to both calcium mobilization and arachidonic acid production (i.e., prestimulation of the IL-8 receptor had no effect on subsequent stimulation by either fMLP or C5a).

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. Furthermore, although lysophospholipids inhibited fusion, the incorporation of arachidonic acid into liposome membranes overcame the inhibitory effects of the lysophospholipids. Thus with PLA2 and annexins we were able to obtain fusion of complex liposomes at concentrations of Ca2+ that are close to physiological. Our data suggest that the activation of PLA2 and the generation of arachidonic acid may be the major fusion-promoting event mediating neutrophil degranulation.

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. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvation energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the nonelectrostatic contributions with estimates of hydrophobic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations. We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydrogen-bonding terms.

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. This is in distinct contrast to estimates in the literature of the number of peptide-MHC complexes required for activity, which is necessarily larger. The analysis also predicted that activity is potentiated by interaction between class I molecules, even if one member of the pair is not bound by antigen. The analytical approach used in this paper may be applicable to other activation systems.

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. On the basis of the observed exponential increase in folding time of the standard SA algorithms, it is imperative that better algorithms be found for minimizing longer chains.

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. These problems are general. Although they are greatly mitigated by experimental information, they become increasingly severe as empirical constraints are reduced. We review the difficulties involved in the general problem of protein structure prediction and discuss the impact of increased computer power in the context of new approaches to solvation and parallel algorithm design. A general focus of our discussion is the need to understand the theoretical basis for effective theories and to accommodate in numerical methods the interplay of different temporal and spatial scales.