Static response of Fermi liquids with tensor interactions

We use Landau's theory of a normal Fermi liquid to derive expressions for the static response of a system with a general tensor interaction that conserves the total spin and the total angular momentum of the quasiparticle-quasihole pair. The magnetic susceptibility is calculated in detail, with the inclusion of the center of mass tensor and cross vector terms in addition to the exchange tensor one. We also introduce a new parametrization of the tensor Landau parameters which significantly reduces the importance of high angular harmonic contributions. For nuclear matter and neutron matter we find that the two most important effects of the tensor interaction are to give a contribution from multipair states and to renormalize the magnetic moments. Response to a weak probe may be calculated using similar methods, replacing the magnetic moments with the matrix elements of the weak charges

Design of Force Fields from Data at Finite Temperature

We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs substantially from the ground state. We apply our method to systems modeling proteins and demonstrate that the correct potentials can be recovered even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late

High-pressure structural investigation of several zircon-type orthovanadates

Room temperature angle-dispersive x-ray diffraction measurements on zircon-type EuVO4, LuVO4, and ScVO4 were performed up to 27 GPa. In the three compounds we found evidence of a pressure-induced structural phase transformation from zircon to a scheelite-type structure. The onset of the transition is near 8 GPa, but the transition is sluggish and the low- and high-pressure phases coexist in a pressure range of about 10 GPa. In EuVO4 and LuVO4 a second transition to a M-fergusonite-type phase was found near 21 GPa. The equations of state for the zircon and scheelite phases are also determined. Among the three studied compounds, we found that ScVO4 is less compressible than EuVO4 and LuVO4, being the most incompressible orthovanadate studied to date. The sequence of structural transitions and compressibilities are discussed in comparison with other zircon-type oxides.Comment: 34 pages, 2 Tables, 11 Figure

Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study

The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such frequencies and, consequently, to develop a strategy to include in the calculations correlations due to the spatial proximity of the amino acids and to their overall tendency of being conserved in proteins. Making use of a lattice model to describe protein chains and defining a "true" potential, we test these strategies by selecting a database of folding model sequences, deriving the contact potentials from such sequences and comparing them with the "true" potential. Taking into account correlations allows for a markedly better prediction of the interaction potentials

Competition between Diffusion and Fragmentation: An Important Evolutionary Process of Nature

We investigate systems of nature where the common physical processes diffusion and fragmentation compete. We derive a rate equation for the size distribution of fragments. The equation leads to a third order differential equation which we solve exactly in terms of Bessel functions. The stationary state is a universal Bessel distribution described by one parameter, which fits perfectly experimental data from two very different system of nature, namely, the distribution of ice crystal sizes from the Greenland ice sheet and the length distribution of alpha-helices in proteins.Comment: 4 pages, 3 figures, (minor changes

Simple models of protein folding and of non--conventional drug design

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of a protein whose sequence is known. Using insight obtained from simple model simulations of the folding of proteins, in particular of the fact that this phenomenon is essentially controlled by conserved (native) contacts among (few) strongly interacting ("hot"), as a rule hydrophobic, amino acids, which also stabilize local elementary structures (LES, hidden, incipient secondary structures like $\alpha$--helices and $\beta$--sheets) formed early in the folding process and leading to the postcritical folding nucleus (i.e., the minimum set of native contacts which bring the system pass beyond the highest free--energy barrier found in the whole folding process) it is possible to work out a succesful strategy for reading the native structure of designed proteins from the knowledge of only their amino acid sequence and of the contact energies among the amino acids. Because LES have undergone millions of years of evolution to selectively dock to their complementary structures, small peptides made out of the same amino acids as the LES are expected to selectively attach to the newly expressed (unfolded) protein and inhibit its folding, or to the native (fluctuating) native conformation and denaturate it. These peptides, or their mimetic molecules, can thus be used as effective non--conventional drugs to those already existing (and directed at neutralizing the active site of enzymes), displaying the advantage of not suffering from the uprise of resistance

Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized

Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been center stage in the prediction and design of protein structure and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state -- a necessary component of these potentials -- is an unsolved problem. PMFs are loosely justified by analogy to the reversible work theorem in statistical physics, or by a statistical argument based on a likelihood function. Both justifications are insightful but leave many questions unanswered. Here, we show for the first time that PMFs can be seen as approximations to quantities that do have a rigorous probabilistic justification: they naturally arise when probability distributions over different features of proteins need to be combined. We call these quantities reference ratio distributions deriving from the application of the reference ratio method. This new view is not only of theoretical relevance, but leads to many insights that are of direct practical use: the reference state is uniquely defined and does not require external physical insights; the approach can be generalized beyond pairwise distances to arbitrary features of protein structure; and it becomes clear for which purposes the use of these quantities is justified. We illustrate these insights with two applications, involving the radius of gyration and hydrogen bonding. In the latter case, we also show how the reference ratio method can be iteratively applied to sculpt an energy funnel. Our results considerably increase the understanding and scope of energy functions derived from known biomolecular structures

Initial Results from the Nobeyama Molecular Gas Observations of Distant Bright Galaxies

We present initial results from the CO survey toward high redshift galaxies using the Nobeyama 45m telescope. Using the new wide bandwidth spectrometer equipped with a two-beam SIS receiver, we have robust new detections of three high redshift (z=1.6-3.4) submillimeter galaxies (SXDF 1100.001, SDP9, and SDP17), one tentative detection (SDSS J160705+533558), and one non-detection (COSMOS-AzTEC1). The galaxies observed during the commissioning phase are sources with known spectroscopic redshifts from previous optical or from wide-band submm spectroscopy. The derived molecular gas mass and line widths from Gaussian fits are ~10^11 Msun and 430-530 km/s, which are consistent with previous CO observations of distant submm galaxies and quasars. The spectrometer that allows a maximum of 32 GHz instantaneous bandwidth will provide new science capabilities at the Nobeyama 45m telescope, allowing us to determine redshifts of bright submm selected galaxies without any prior redshift information.Comment: 4 pages, 1 figure, PASJ Letter Accepte