Quantum Electrodynamics of the Helium Atom

Using singlet S states of the helium atom as an example, I describe precise calculation of energy levels in few-electron atoms. In particular, a complete set of effective operators is derived which generates O(m*alpha^6) relativistic and radiative corrections to the Schr"odinger energy. Average values of these operators can be calculated using a variational Schr"odinger wave function.Comment: 23 pages, revte

Theory of Anomalous Hall Effect in a Heavy fermion System with a Strong Anisotropic Crystal Field

In a heavy fermion system, there exists the anomalous Hall effect caused by localized $f$-orbital freedom, in addition to the normal Hall effect due to the Lorentz force. In 1994, we found that the Hall coefficient caused by the anomalous Hall effect ($R_H^{AHE}$) is predominant and the relation $R_H^{AHE} \propto \rho^2$ ($\rho$ is the electrical resistivity) holds at low temperatures in many compounds. In this work, we study the system where the magnetic susceptibility is highly anisotropic due to the strong crystalline electric field on $f$-orbitals. Interestingly, we find that $R_H^{AHE}$ is nearly isotropic in general. This tendency is frequently observed experimentally, which has casted suspicion that the anomalous Hall effect may be irrelevant in real materials. Our theory corresponds to corrections and generalizations of the pioneering work on ferromagnetic metals by Karplus and Luttinger.Comment: 4 pages, revtex, to be published in J. Phys. Soc. Jpn. (No.8

Sequencing of folding events in Go-like proteins

We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It is shown that folding is dominated by a well-defined sequencing of events as determined by establishment of particular contacts. The order of events depends primarily on the geometry of the native state. Variations in temperature, coupling strengths and viscosity affect the sequencing scenarios to a rather small extent. The sequencing is strongly correlated with the distance of the contacting aminoacids along the sequence. Thus $\alpha$-helices get established first. Crambin is found to behave like a single-route folder, whereas in CI2 and SH3 the folding trajectories are more diversified. The folding scenarios for CI2 and SH3 are consistent with experimental studies of their transition states.Comment: REVTeX, 12 pages, 11 EPS figures, J. Chem. Phys (in press

Design Equation: A Novel Approach to Heteropolymer Design

A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of the proposed approach is the use of soft spins (fuzzy monomers) that leads to a design equation, which is an analog of the Boltzmann machine learning equation in the design problem. We implement an algorithm based on the design equation for the generalized HP model on the 3x3x3 cubic lattice and check its performance.Comment: 7 pages, 3 tables, 1 figures, uses jpsj.sty, jpsjbs1.sty, epsf.sty, Submitted to J. Phys. Soc. Jp

Free energies of crystalline solids: a lattice-switch Monte Carlo method

We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through atomic-displacement-space, leading from one structure to the other by way of an intervening transformation that switches one set of lattice vectors for another. The configurations of both structures can thus be sampled within a single Monte Carlo process, and the difference between their free energies evaluated directly from the ratio of the measured probabilities of each. The method is used to determine the difference between the free energies of the fcc and hcp crystalline phases of a system of hard spheres.Comment: 5 pages Revtex, 3 figure

Collapse of Randomly Self-Interacting Polymers

We use complete enumeration and Monte Carlo techniques to study self--avoiding walks with random nearest--neighbor interactions described by $v_0q_iq_j$, where $q_i=\pm1$ is a quenched sequence of ``charges'' on the chain. For equal numbers of positive and negative charges ($N_+=N_-$), the polymer with $v_0>0$ undergoes a transition from self--avoiding behavior to a compact state at a temperature $\theta\approx1.2v_0$. The collapse temperature $\theta(x)$ decreases with the asymmetry $x=|N_+-N_-|/(N_++N_-)$Comment: 8 pages, TeX, 4 uuencoded postscript figures, MIT-CMT-

Protein structures and optimal folding emerging from a geometrical variational principle

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is found that, irrespective of the sequence, the native state of a protein has exceedingly large number of conformations with a given amount of structural overlap compared to other compact artificial backbones; moreover the conformational entropies of unrelated proteins of the same length are nearly equal at any given stage of folding. These results are suggestive of an extremality principle underlying protein evolution, which, in turn, is shown to be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed

One-loop self-energy correction to the 1s and 2s hyperfine splitting in H-like systems

The one-loop self-energy correction to the hyperfine splitting of the 1s and 2s levels in H-like low-Z atoms is evaluated to all orders in Z\alpha. The results are compared to perturbative calculations. The residual higher-order contribution is evaluated. Implications to the specific difference of the hyperfine structure intervals 8\Delta \nu_2 - \Delta \nu_1 in He^+ are investigated.Comment: 17 pages, RevTeX, 3 figure