10,633 research outputs found
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
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