Confinement in Nuclei and the Expanding Proton.

High-precision knowledge of electromagnetic form factors of nuclei is an important current activity in nuclear and atomic physics. Such precision mandates that effects of the nonzero spatial extent of the constituent nucleons be treated carefully. A series of simple, Poincaré-invariant, composite-proton models that respect the Ward-Takahashi identity and in which quarks are confined are used to study such effects.

Electrophobic Scalar Boson and Muonic Puzzles.

A new scalar boson which couples to the muon and proton can simultaneously solve the proton radius puzzle and the muon anomalous magnetic moment discrepancy. Using a variety of measurements, we constrain the mass of this scalar and its couplings to the electron, muon, neutron, and proton. Making no assumptions about the underlying model, these constraints and the requirement that it solve both problems limit the mass of the scalar to between about 100 keV and 100 MeV.

Electromagnetic self-energy contribution to M(p)-M(n) and the isovector nucleon magnetic polarizability.

We update the determination of the isovector nucleon electromagnetic self-energy, valid to leading order in QED. A technical oversight in the literature concerning the elastic contribution to Cottingham's formula is corrected, and modern knowledge of the structure functions is used to precisely determine the inelastic contribution. We find δM(p-n)(γ) = 1.

Taming the pion cloud of the nucleon.

We present a light-front determination of the pionic contribution to the nucleon self-energy, Σ(π), to second order in pion-baryon coupling constants that allows the pion-nucleon vertex function to be treated in a model-independent manner constrained by experiment. The pion mass μ dependence of Σ(π) is consistent with chiral perturbation theory results for small values of μ and is also linearly dependent on μ for larger values, in accord with the results of lattice QCD calculations. The derivative of Σ(π) with respect to μ(2) yields the dominant contribution to the pion content, which is consistent with the d[over ¯]-u[over ¯] difference observed experimentally in the violation of the Gottfried sum rule.

Neutron properties in the medium.

We demonstrate that for small values of momentum transfer Q2 the in-medium change of the GE/GM form factor ratio for a bound neutron is dominated by the change in the electric charge radius and predict within stated assumptions that the in-medium ratio will increase relative to the free result. This effect will act to increase the predicted cross section for the neutron recoil polarization transfer process 4He(e-vector,e'n-vector)3He. This is in contrast with medium modification effects on the proton GE/GM form factor ratio, which act to decrease the predicted cross section for the 4He(e-vector,e'p-vector)3H reaction.

Proton electromagnetic-form-factor ratios at low Q2.

We study the ratio R identical with muG_{E}(Q2)/G_{M}(Q2) of the proton at very small values of Q2. Radii commonly associated with these form factors are not moments of charge or magnetization densities. We show that the form factor F2 is correctly interpretable as the two-dimensional Fourier transformation of a magnetization density.

Charge densities of the neutron and proton.

A model-independent analysis of the infinite-momentum-frame charge density of partons in the transverse plane is presented for the nucleon. We find that the neutron-parton charge density is negative at the center, so that the square of the transverse charge radius is positive, in contrast with many expectations. Additionally, the proton's central d quark charge density is larger than that of the u quark by about 30%.

Quantitative model for binary measurements of protein-protein interactions.

We develop a stochastic model for quantifying the binary measurements of protein-protein interactions. A key concept in the model is the binary response function (BRF) which represents the conditional probability of successfully detecting a protein-protein interaction with a given number of the protein complexes. A popular form of the BRF is introduced and the effect of the sharpness (Hill's coefficient) of this function is studied.

Clustering coefficients of protein-protein interaction networks.

The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k other vertices determines all measurable properties. We study hidden variable models and find an averaging approximation that enables us to obtain a general analytical result for the propagator.

Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences.

Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein-protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power law shows only the surface of the rich information harbored by these high-throughput data.

Quantum opacity, the RHIC Hanbury Brown-Twiss puzzle, and the chiral phase transition.

We present a relativistic quantum-mechanical treatment of opacity and refractive effects that allows reproduction of observables measured in two-pion Hanbury Brown-Twiss (HBT) interferometry and pion spectra at RHIC. The inferred emission duration is substantial. The results are consistent with the emission of pions from a system that has a restored chiral symmetry.

Chiral solitons in nuclei: saturation, EMC effect, and Drell-Yan experiments.

The chiral quark-soliton model of the nucleon contains a mechanism for an attractive interaction between nucleons. This, along with the exchange of vector mesons between nucleons, is used to compute the saturation properties of infinite nuclear matter. This provides a new way to assess the effects of the nuclear medium on a nucleon that includes valence and sea quarks.