The antigenic index: a novel algorithm for predicting antigenic determinants

In this paper, we introduce a computer algorithm which can be used to predict the topological features of a protein directly from its primary amino acid sequence. The computer program generates values for surface accessibility parameters and combines these values with those obtained for regional backbone flexibility and predicted secondary structure. The output of this algorithm, the antigenic index, is used to create a linear surface contour profile of the protein. Because most, if not all, antigenic sites are located within surface exposed regions of a protein, the program offers a reliable means of predicting potential antigenic determinants. We have tested the ability of this program to generate accurate surface contour profiles and predict antigenic sites from the linear amino acid sequences of well-characterized proteins and found a strong correlation between the predictions of the antigenic index and known structural and biological data

Contact mechanics of and Reynolds flow through saddle points: On the coalescence of contact patches and the leakage rate through near-critical constrictions

We study numerically local models for the mechanical contact between two solids with rough surfaces. When the solids softly touch either through adhesion or by a small normal load $L$, contact only forms at isolated patches and fluids can pass through the interface. When the load surpasses a threshold value, $L_c$, adjacent patches coalesce at a critical constriction, i.e., near points where the interfacial separation between the undeformed surfaces forms a saddle point. This process is continuous without adhesion and the interfacial separation near percolation is fully defined by scaling factors and the sign of $L_c-L$. The scaling factors lead to a Reynolds flow resistance which diverges as $(L_c-L)^\beta$ with $\beta = 3.45$. Contact merging and destruction near saddle points becomes discontinuous when either short-range adhesion or specific short-range repulsion are added to the hard-wall repulsion. These results imply that coalescence and break-up of contact patches can contribute to Coulomb friction and contact aging.Comment: 6 pages, 6 figures, submitted to Euro. Phys. Let

Towards time-dependent, non-equilibrium charge-transfer force fields: Contact electrification and history-dependent dissociation limits

Force fields uniquely assign interatomic forces for a given set of atomic coordinates. The underlying assumption is that electrons are in their quantum-mechanical ground state or in thermal equilibrium. However, there is an abundance of cases where this is unjustified because the system is only locally in equilibrium. In particular, the fractional charges of atoms, clusters, or solids tend to not only depend on atomic positions but also on how the system reached its state. For example, the charge of an isolated solid -- and thus the forces between atoms in that solid -- usually depends on the counterbody with which it has last formed contact. Similarly, the charge of an atom, resulting from the dissociation of a molecule, can differ for different solvents in which the dissociation took place. In this paper we demonstrate that such charge-transfer history effects can be accounted for by assigning discrete oxidation states to atoms. With our method, an atom can donate an integer charge to another, nearby atom to change its oxidation state as in a redox reaction. In addition to integer charges, atoms can exchange "partial charges" which are determined with the split charge equilibration method.Comment: 11 pages, 7 figure

Systematic analysis of Persson's contact mechanics theory of randomly rough elastic surfaces

We systematically check explicit and implicit assumptions of Persson's contact mechanics theory. It casts the evolution of the pressure distribution ${\rm Pr}(p)$ with increasing resolution of surface roughness as a diffusive process, in which resolution plays the role of time. The tested key assumptions of the theory are: (a) the diffusion coefficient is independent of pressure $p$, (b) the diffusion process is drift-free at any value of $p$, (c) the point $p=0$ acts as an absorbing barrier, i.e., once a point falls out of contact, it never reenters again, (d) the Fourier component of the elastic energy is only populated if the appropriate wave vector is resolved, and (e) it no longer changes when even smaller wavelengths are resolved. Using high-resolution numerical simulations, we quantify deviations from these approximations and find quite significant discrepancies in some cases. For example, the drift becomes substantial for small values of $p$, which typically represent points in real space close to a contact line. On the other hand, there is a significant flux of points reentering contact. These and other identified deviations cancel each other to a large degree, resulting in an overall excellent description for contact area, contact geometry, and gap distribution functions. Similar fortuitous error cancellations cannot be guaranteed under different circumstances, for instance when investigating rubber friction. The results of the simulations may provide guidelines for a systematic improvement of the theory.Comment: 27 pages, 16 figures, accepted for publication by Journal of Physics: Condensed Matte

Supersymmetric features of the Maxwell fish-eye lens

We provide a supersymmetric analysis of the Maxwell fisheye (MF) wave problem at zero energy. Working in the so-called $R_{0}=0$ sector, we obtain the corresponding superpartner (fermionic) MF effective potential within Witten's one-dimensional (radial) supersymmetric procedure.Comment: 5 pages in Latex, one figure not included has been published as Fig. 2 in Phys. Lett. A 208 (1995) 33-3