1,970 research outputs found
Diffusion Dynamics, Moments, and Distribution of First Passage Time on the Protein-Folding Energy Landscape, with Applications to Single Molecules
We study the dynamics of protein folding via statistical energy-landscape
theory. In particular, we concentrate on the local-connectivity case with the
folding progress described by the fraction of native conformations. We obtain
information for the first passage-time (FPT) distribution and its moments. The
results show a dynamic transition temperature below which the FPT distribution
develops a power-law tail, a signature of the intermittency phenomena of the
folding dynamics. We also discuss the possible application of the results to
single-molecule dynamics experiments
Orderly Spanning Trees with Applications
We introduce and study the {\em orderly spanning trees} of plane graphs. This
algorithmic tool generalizes {\em canonical orderings}, which exist only for
triconnected plane graphs. Although not every plane graph admits an orderly
spanning tree, we provide an algorithm to compute an {\em orderly pair} for any
connected planar graph , consisting of a plane graph of , and an
orderly spanning tree of . We also present several applications of orderly
spanning trees: (1) a new constructive proof for Schnyder's Realizer Theorem,
(2) the first area-optimal 2-visibility drawing of , and (3) the best known
encodings of with O(1)-time query support. All algorithms in this paper run
in linear time.Comment: 25 pages, 7 figures, A preliminary version appeared in Proceedings of
the 12th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2001),
Washington D.C., USA, January 7-9, 2001, pp. 506-51
VI-Band Follow-Up Observations of Ultra-Long-Period Cepheid Candidates in M31
The ultra-long period Cepheids (ULPCs) are classical Cepheids with pulsation
periods exceeding days. The intrinsic brightness of ULPCs are ~1
to ~3 mag brighter than their shorter period counterparts. This makes them
attractive in future distance scale work to derive distances beyond the limit
set by the shorter period Cepheids. We have initiated a program to search for
ULPCs in M31, using the single-band data taken from the Palomar Transient
Factory, and identified eight possible candidates. In this work, we presented
the VI-band follow-up observations of these eight candidates. Based on our
VI-band light curves of these candidates and their locations in the
color-magnitude diagram and the Period-Wesenheit diagram, we verify two
candidates as being truly ULPCs. The six other candidates are most likely other
kinds of long-period variables. With the two confirmed M31 ULPCs, we tested the
applicability of ULPCs in distance scale work by deriving the distance modulus
of M31. It was found to be mag. The large error
in the derived distance modulus, together with the large intrinsic dispersion
of the Period-Wesenheit (PW) relation and the small number of ULPCs in a given
host galaxy, means that the question of the suitability of ULPCs as standard
candles is still open. Further work is needed to enlarge the sample of
calibrating ULPCs and reduce the intrinsic dispersion of the PW relation before
re-considering ULPCs as suitable distance indicators.Comment: 13 pages, with 14 Figures and 4 Tables (one online table). AJ
accepte
Effect of Na+ Flow on Cd2+ Block of Tetrodotoxin-resistant Na+ Channels
Tetrodotoxin-resistant (TTX-R) Na+ channels are 1,000-fold less sensitive to TTX than TTX-sensitive (TTX-S) Na+ channels. On the other hand, TTX-R channels are much more susceptible to external Cd2+ block than TTX-S channels. A cysteine (or serine) residue situated just next to the aspartate residue of the presumable selectivity filter “DEKA” ring of the TTX-R channel has been identified as the key ligand determining the binding affinity of both TTX and Cd2+. In this study we demonstrate that the binding affinity of Cd2+ to the TTX-R channels in neurons from dorsal root ganglia has little intrinsic voltage dependence, but is significantly influenced by the direction of Na+ current flow. In the presence of inward Na+ current, the apparent dissociation constant of Cd2+ (∼200 μM) is ∼9 times smaller than that in the presence of outward Na+ current. The Na+ flow–dependent binding affinity change of Cd2+ block is true no matter whether the direction of Na+ current is secured by asymmetrical chemical gradient (e.g., 150 mM Na+ vs. 150 mM Cs+ on different sides of the membrane, 0 mV) or by asymmetrical electrical gradient (e.g., 150 mM Na+ on both sides of the membrane, −20 mV vs. 20 mV). These findings suggest that Cd2+ is a pore blocker of TTX-R channels with its binding site located in a multiion, single-file region near the external pore mouth. Quantitative analysis of the flow dependence with the flux-coupling equation reveals that at least two Na+ ions coexist with the blocking Cd2+ ion in this pore region in the presence of 150 mM ambient Na+. Thus, the selectivity filter of the TTX-R Na+ channels in dorsal root ganglion neurons might be located in or close to a multiion single-file pore segment connected externally to a wide vestibule, a molecular feature probably shared by other voltage-gated cationic channels, such as some Ca2+ and K+ channels
Higher-order solutions to non-Markovian quantum dynamics via hierarchical functional derivative
Solving realistic quantum systems coupled to an environment is a challenging
task. Here we develop a hierarchical functional derivative (HFD) approach for
efficiently solving the non-Markovian quantum trajectories of an open quantum
system embedded in a bosonic bath. An explicit expression for arbitrary order
HFD equation is derived systematically. Moreover, it is found that for an
analytically solvable model, this hierarchical equation naturally terminates at
a given order and thus becomes exactly solvable. This HFD approach provides a
systematic method to study the non-Markovian quantum dynamics of an open system
coupled to a bosonic environment.Comment: 5 pages, 2 figure
Dynamical invariants in non-Markovian quantum state diffusion equation
We find dynamical invariants for open quantum systems described by the
non-Markovian quantum state diffusion (QSD) equation. In stark contrast to
closed systems where the dynamical invariant can be identical to the system
density operator, these dynamical invariants no longer share the equation of
motion for the density operator. Moreover, the invariants obtained with from
bi-orthonormal basis can be used to render an exact solution to the QSD
equation and the corresponding non-Markovian dynamics without using master
equations or numerical simulations. Significantly we show that we can apply
these dynamic invariants to reverse-engineering a Hamiltonian that is capable
of driving the system to the target state, providing a novel way to design
control strategy for open quantum systems.Comment: 6 pages, 2 figure
Prevalence of restless legs syndrome in migraine patients with and without aura: a cross-sectional, case-controlled study
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