Lattice model for cold and warm swelling of polymers in water

We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact conformation at low temperature; as the temperature grows, there is a sharp transition towards a compact state, then, at higher temperatures, the polymer swells again. This behaviour closely reminds that of proteins, that are unfolded at both low and high temperatures.Comment: REVTeX, 5 pages, 2 EPS figure

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press

A refined hydrogen bond potential for flexible protein models

One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical restrictions or energetic contributions are defined into the system.We have efficiently overcome this problem, for chains of adequate size in a relevant temperature range, with a refined coarse-grained hydrogen bond potential. With it, we have been able to obtain nativelike alpha-helices and beta-sheets in peptidic systems, and successfully reproduced the competition between the populations of these secondary structure elements by the effect of temperature and concentration changes. In this manuscript we detail the design of the interaction potential and thoroughly examine its applicability in energetic and structural terms, considering factors such as chain length, concentration, and temperature

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

Response of the Brazilian gravitational wave detector to signals from a black hole ringdown

It is assumed that a black hole can be disturbed in such a way that a ringdown gravitational wave would be generated. This ringdown waveform is well understood and is modelled as an exponentially damped sinusoid. In this work we use this kind of waveform to study the performance of the SCHENBERG gravitational wave detector. This first realistic simulation will help us to develop strategies for the signal analysis of this Brazilian detector. We calculated the signal-to-noise ratio as a function of frequency for the simulated signals and obtained results that show that SCHENBERG is expected to be sensitive enough to detect this kind of signal up to a distance of $\sim 20\mathrm{kpc}$.Comment: 5 pages, 4 figures, Amaldi 5 Conference Proceedings contribution. Submitted to Class. Quantum Gra

Black Hole Area in Brans-Dicke Theory

We have shown that the dynamics of the scalar field $\phi (x)= ``G^{-1}(x)"$ in Brans-Dicke theories of gravity makes the surface area of the black hole horizon {\it oscillatory} during its dynamical evolution. It explicitly explains why the area theorem does not hold in Brans-Dicke theory. However, we show that there exists a certain non-decreasing quantity defined on the event horizon which is proportional to the black hole entropy for the case of stationary solutions in Brans-Dicke theory. Some numerical simulations have been demonstrated for Oppenheimer-Snyder collapse in Brans-Dicke theory.Comment: 12 pages, latex, 5 figures, epsfig.sty, some statements clarified and two references added, to appear in Phys. Rev.

Phase Transitions of Single Semi-stiff Polymer Chains

We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth Method" (PERM). It is very efficient both for relatively open configurations at high temperatures and for compact and frozen-in low-T states. This allows us to study in detail the phase diagram as a function of nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a transition from open coils to molten compact globules (large epsilon) and a freezing transition toward a state with orientational global order (large stiffness x). Qualitatively this is similar to a recently studied mean field theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are important differences. In contrast to the mean field theory, the theta-temperature increases with stiffness x. The freezing temperature increases even faster, and reaches the theta-line at a finite value of x. For even stiffer chains, the freezing transition takes place directly without the formation of an intermediate globule state. Although being in contrast with mean filed theory, the latter has been conjectured already by Doniach et al. on the basis of low statistics Monte Carlo simulations. Finally, we discuss the relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 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