Efficient exploration of discrete energy landscapes

Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of dynamics is obtained by partitioning the micro-states of the landscape into macro-states. Since most landscapes of interest are not tractable analytically, the probabilities of transitions between macro-states need to be extracted numerically from the microscopic ones, typically by full enumeration of the state space. Here we propose to approximate transition probabilities by a Markov chain Monte-Carlo method. For landscapes of the number partitioning problem and an RNA switch molecule we show that the method allows for accurate probability estimates with significantly reduced computational cost.Comment: 7 pages, 5 figure

Lattice model refinement of protein structures

To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper we formulate and implement a Constraint Programming method to refine such lattice structure models. We show that the approach is able to provide better quality solutions. The prototype is implemented in COLA and is based on limited discrepancy search. Finally, some promising extensions based on local search are discussed.Comment: In Proceedings of Workshop on Constraint Based Methods for Bioinformatics (WCB 2010); Jul 21, 2010; Edinburgh, UK (co-located with ICLP 2010); 7 page

Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains

Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the hydrophobicity-based energy function applied. We introduce an equivalence relation on protein structures that correlates to the energy function. We discuss the efficient enumeration of optimal representatives of the corresponding equivalence classes and the application of the results.Comment: Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 9 page

Quantum Thermometry

In this review article we revisit and spell out the details of previous work on how Berry phase can be used to construct a precision quantum thermometer. An important advantage of such a scheme is that there is no need for the thermometer to acquire thermal equilibrium with the sample. This reduces measurement times and avoids precision limitations. We also review how such methods can be used to detect the Unruh effect.Comment: 16 pages, 6 figure

Decomposition During Search for Propagation-Based Constraint Solvers

We describe decomposition during search (DDS), an integration of And/Or tree search into propagation-based constraint solvers. The presented search algorithm dynamically decomposes sub-problems of a constraint satisfaction problem into independent partial problems, avoiding redundant work. The paper discusses how DDS interacts with key features that make propagation-based solvers successful: constraint propagation, especially for global constraints, and dynamic search heuristics. We have implemented DDS for the Gecode constraint programming library. Two applications, solution counting in graph coloring and protein structure prediction, exemplify the benefits of DDS in practice.Comment: 20 pages, 9 figures, 2 tables; longer, more detailed versio

Particle Detectors, Cavities, and the Weak Equivalence Principle

We analyze a quantum version of the weak equivalence principle, in which we compare the response of a static particle detector crossed by an accelerated cavity with the response of an accelerated detector crossing a static cavity in (1+1)-dimensional flat spacetime. We show, for both massive and massless scalar fields, that the non-locality of the field is enough for the detector to distinguish the two scenarios. We find this result holds for vacuum and excited field states of different kinds and we clarify the role of field mass in this setup.Comment: 18 pages, 18 figures. RevTeX 4.1. Updated to match published versio

Cavities in curved spacetimes: the response of particle detectors

We introduce a method to compute particle detector transition probability in spacetime regions of general curved spacetimes provided that the curvature is not above a maximum threshold. In particular we use this method to compare the response of two detectors, one in a spherically symmetric gravitational field and the other one in Rindler spacetime to compare the Unruh and Hawking effects: We study the vacuum response of a detector freely falling through a stationary cavity in a Schwarzschild background as compared with the response of an equivalently accelerated detector traveling through an inertial cavity in the absence of curvature. We find that as we set the cavity in further radiuses from the black hole, the thermal radiation measured by the detector approaches the quantity recorded by the detector in Rindler background showing in which way and at what scales the equivalent principle is recovered in the Hawking-Unruh effect. I.e. when the Hawking effect in a Schwarzschild background becomes equivalent to the Unruh effect in Rindler spacetime.Comment: 7 pages, 5 figures. RevTex 4.

Entanglement harvesting and divergences in quadratic Unruh-DeWitt detectors pairs

We analyze correlations between pairs of particle detectors quadratically coupled to a real scalar field. We find that, while a single quadratically coupled detector presents no divergences, when one considers pairs of detectors there emerge unanticipated persistent divergences (not regularizable via smooth switching or smearing) in the entanglement they acquire from the field. We have characterized such divergences, discussed whether a suitable regularization can allow for fair comparison of the entanglement harvesting ability of the quadratic and the linear couplings, and finally we have found a UV-safe quantifier of harvested correlations. Our results are relevant to future studies of the entanglement structure of the fermionic vacuum.Comment: 17 pages, 4 figures. RevTeX 4.

Mode Invisibility and Single Photon Detection

We propose a technique to probe the quantum state of light in an optical cavity without significantly altering it. We minimize the interaction of the probe with the field by arranging a setting where the largest contribution to the transition probability is cancelled. We show that we obtain a very good resolution to measure photon population differences between two given Fock states by means of atomic interferometry.Comment: 12 pages, 5 figures. RevTex 4.1. Added appendix with further mathematical detail. Updated to match published versio

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains

The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice protein structures according to k-local moves in arbitrary lattices. Our declarative description is much more flexible for extensions than standard operational formulations. It enables a generic calculation of k-local neighbors in backbone-only and side chain models. We exemplify the procedure using a simple hierarchical folding scheme.Comment: Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 10 page