Variational approach to protein design and extraction of interaction potentials

We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature free energy of sequences of amino acids. The knowledge-based technique is simple and straightforward to implement even for realistic off-lattice proteins because it does not entail threading-like procedures. Its validity is assessed in the context of a lattice model by means of a variety of stringent checks.Comment: 5 pages, 3 figure

Holographic field theory models of dark energy in interaction with dark matter

We discuss two lagrangian interacting dark energy models in the context of the holographic principle. The potentials of the interacting fields are constructed. The models are compared with CMB distance information, baryonic acoustic oscilations, lookback time and the Constitution supernovae sample. For both models the results are consistent with a non vanishing interaction between dark sectors - with more than three standard deviations of confidence for one of them. Moreover, in both cases, the sign of coupling is consistent with dark energy decaying into dark matter, alleviating the coincidence problem.Comment: arXiv admin note: substantial text overlap with arXiv:0912.399

Willful Patent Infringement after \u3cem\u3eIn Re Seagate\u3c/em\u3e: Just What is Objectively Reckless Infringement?

Recently the United States Court of Appeals for the Federal Circuit dramatically change the rules for proving willful patent infringement—and justifying enhanced damages—in In re Seagate Technology. A patentee alleging willful infringement must now first prove by clear and convincing evidence that the infringer acted despite an objectively high likelihood that its actions constituted infringement of a valid patent. He must then show that the objectively defined risk was either known or so obvious that it should have been known to the accused infringer. The court expressly delegated substantive development of the new test to future cases. Because district courts have generally struggled to apply the new standard, and because a clearer standard will provide patentees and their competitors increased certainty in business planning, this article proposes a multi-factor test for applying In re Seagate Technology. To determine the objective risk of infringement of a valid patent, courts should at least consider (1) the similarity of the patented invention to the infringing conduct, (2) conclusions of infringement, invalidity, and unenforceability found in pre-litigation opinions of counsel, (3) characteristics of the infringer\u27s commercial market including patent saturation and the pace of innovation, and (3) legitimate defenses to infringement that were raised at trial. To determine whether the infringer knew or should have known of the objectively high risk of infringement, courts should at least consider (1) evidence that the patentee provided the infringer clear notice, (2) whether the infringer obtained an opinion of counsel that communicated a high risk of infringement, (3) whether the patentee and the infringer were in a special relationship, (4) the defendant\u27s level of skill compared to a person having ordinary skill in the art, (5) contemporary publicity of the patentee or its patent, (6) markings on the patented product, and (7) the length of time between patent issuance and commencement of the infringing activity

Surface spin-flop phases and bulk discommensurations in antiferromagnets

Phase diagrams as a function of anisotropy D and magnetic field H are obtained for discommensurations and surface states for a model antiferromagnet in which $H$ is parallel to the easy axis. The surface spin-flop phase exists for all $D$. We show that there is a region where the penetration length of the surface spin-flop phase diverges. Introducing a discommensuration of even length then becomes preferable to reconstructing the surface. The results are used to clarify and correct previous studies in which discommensurations have been confused with genuine surface spin-flop states.Comment: 4 pages, RevTeX, 2 Postscript figure

Depletion effects and loop formation in self-avoiding polymers

Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while, for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.Comment: 4 pages, 3 figure

Surface spin-flop and discommensuration transitions in antiferromagnets

Phase diagrams as a function of anisotropy $D$ and magnetic field $H$ are obtained for discommensurations and surface states for an antiferromagnet in which $H$ is parallel to the easy axis, by modeling it using the ground states of a one-dimensional chain of classical XY spins. A surface spin-flop phase exists for all $D$, but the interval in $H$ over which it is stable becomes extremely small as $D$ goes to zero. First-order transitions, separating different surface states and ending in critical points, exist inside the surface spin-flop region. They accumulate at a field $H'$ (depending on $D$) significantly less than the value $H_{SF}$ for a bulk spin-flop transition. For $H' < H < H_{SF}$ there is no surface spin-flop phase in the strict sense; instead, the surface restructures by, in effect, producing a discommensuration infinitely far away in the bulk. The results are used to explain in detail the phase transitions occurring in systems consisting of a finite, even number of layers.Comment: Revtex 17 pages, 15 figure

Anharmonicity and self-similarity of the free energy landscape of protein G

The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence of salient thermodynamical features. While the quasi-harmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.Comment: revtex, 6 pages, 5 figure