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

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-

Breit interaction correction to the hyperfine constant of an external s-electron in many-electron atom

Correction to the hyperfine constant $A$ of an external s-electron in many-electron atom caused by the Breit interaction is calculated analytically: $\delta A/A =0.68 Z\alpha^2$. Physical mechanism for this correction is polarization of the internal electronic shells (mainly $1s^2$ shell) by the magnetic field of the external electron. This mechanism is similar to the polarization of vacuum considered by Karplus and Klein long time ago. The similarity is the reason why in both cases (Dirac sea polarization and internal atomic shells polarization) the corrections have the same dependence on the nuclear charge and fine structure constant. In conclusion we also discuss $Z\alpha^2$ corrections to the parity violation effects in atoms.Comment: 8 pages, 2 figure

One Loop Multiphoton Helicity Amplitudes

We use the solutions to the recursion relations for double-off-shell fermion currents to compute helicity amplitudes for $n$-photon scattering and electron-positron annihilation to photons in the massless limit of QED. The form of these solutions is simple enough to allow {\it all}\ of the integrations to be performed explicitly. For $n$-photon scattering, we find that unless $n=4$, the amplitudes for the helicity configurations (+++...+) and (-++...+) vanish to one-loop order.Comment: 27 pages + 4 uuencoded figures (included), Fermilab-Pub-93/327-T, RevTe

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

Radiative Corrections to the Muonium Hyperfine Structure. I. The α2(Zα)\alpha^2 (Z\alpha) Correction

This is the first of a series of papers on a systematic application of the NRQED bound state theory of Caswell and Lepage to higher-order radiative corrections to the hyperfine structure of the muonium ground state. This paper describes the calculation of the $\alpha^2 (Z\alpha)$ radiative correction. Our result for the complete $\alpha^2 (Z\alpha)$ correction is 0.424(4) kHz, which reduces the theoretical uncertainty significantly. The remaining uncertainty is dominated by that of the numerical evaluation of the nonlogarithmic part of the $\alpha (Z\alpha )^2$ term and logarithmic terms of order $\alpha^4$.Comment: 56 pages, Rev.tex V3.0 and epsf.tex. 12 postscript files are called in the text. Version accepted by Phys. Rev. D. A new table is adde

Thermodynamically Important Contacts in Folding of Model Proteins

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.Comment: 5 pages, 5 figures; to be published in PR

Thermal Diffusion of a Two Layer System

In this paper thermal conductivity and thermal diffusivity of a two layer system is examined from the theoretical point of view. We use the one dimensional heat diffusion equation with the appropriate solution in each layer and boundary conditions at the interfaces to calculate the heat transport in this bounded system. We also consider the heat flux at the surface of the samle as boundary condition instead of using a fixed tempertaure. From this, we obtain an expression for the efective thermal diffusivity of the composite sample in terms of the thermal diffusivity of its constituent materials whithout any approximations.Comment: 16 pages, 1 figure, RevTeX v. 3.0 macro packag

Many-body-QED perturbation theory: Connection to the Bethe-Salpeter equation

The connection between many-body theory (MBPT)--in perturbative and non-perturbative form--and quantum-electrodynamics (QED) is reviewed for systems of two fermions in an external field. The treatment is mainly based upon the recently developed covariant-evolution-operator method for QED calculations [Lindgren et al. Phys. Rep. 389, 161 (2004)], which has a structure quite akin to that of many-body perturbation theory. At the same time this procedure is closely connected to the S-matrix and the Green's-function formalisms and can therefore serve as a bridge between various approaches. It is demonstrated that the MBPT-QED scheme, when carried to all orders, leads to a Schroedinger-like equation, equivalent to the Bethe-Salpeter (BS) equation. A Bloch equation in commutator form that can be used for an "extended" or quasi-degenerate model space is derived. It has the same relation to the BS equation as has the standard Bloch equation to the ordinary Schroedinger equation and can be used to generate a perturbation expansion compatible with the BS equation also for a quasi-degenerate model space.Comment: Submitted to Canadian J of Physic

Parity nonconservation in heavy atoms: The radiative correction enhanced by the strong electric field of the nucleus

Parity nonconservation due to the nuclear weak charge is considered. We demonstrate that the radiative corrections to this effect due to the vacuum fluctuations of the characteristic size larger than the nuclear radius $r_0$ and smaller than the electron Compton wave-length $\lambda_C$ are enhanced because of the strong electric field of the nucleus. The parameter that allows one to classify the corrections is the large logarithm $\ln(\lambda_C/r_0)$. The vacuum polarization contribution is enhanced by the second power of the logarithm. Although the self-energy and the vertex corrections do not vanish, they contain only the first power of the logarithm. The value of the radiative correction is 0.4% for Cs and 0.9% for Tl, Pb, and Bi. We discuss also how the correction affects the interpretation of the experimental data on parity nonconservation in atoms.Comment: 4 pages, 3 figures, RevTe