4,002 research outputs found
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation
Exploring Temporal Networks with Greedy Walks
Temporal networks come with a wide variety of heterogeneities, from
burstiness of event sequences to correlations between timings of node and link
activations. In this paper, we set to explore the latter by using greedy walks
as probes of temporal network structure. Given a temporal network (a sequence
of contacts), greedy walks proceed from node to node by always following the
first available contact. Because of this, their structure is particularly
sensitive to temporal-topological patterns involving repeated contacts between
sets of nodes. This becomes evident in their small coverage per step as
compared to a temporal reference model -- in empirical temporal networks,
greedy walks often get stuck within small sets of nodes because of correlated
contact patterns. While this may also happen in static networks that have
pronounced community structure, the use of the temporal reference model takes
the underlying static network structure out of the equation and indicates that
there is a purely temporal reason for the observations. Further analysis of the
structure of greedy walks indicates that burst trains, sequences of repeated
contacts between node pairs, are the dominant factor. However, there are larger
patterns too, as shown with non-backtracking greedy walks. We proceed further
to study the entropy rates of greedy walks, and show that the sequences of
visited nodes are more structured and predictable in original data as compared
to temporally uncorrelated references. Taken together, these results indicate a
richness of correlated temporal-topological patterns in temporal networks
The Barrier Method: A Technique for Calculating Very Long Transition Times
In many dynamical systems there is a large separation of time scales between
typical events and "rare" events which can be the cases of interest. Rare-event
rates are quite difficult to compute numerically, but they are of considerable
practical importance in many fields: for example transition times in chemical
physics and extinction times in epidemiology can be very long, but are quite
important. We present a very fast numerical technique that can be used to find
long transition times (very small rates) in low-dimensional systems, even if
they lack detailed balance. We illustrate the method for a bistable
non-equilibrium system introduced by Maier and Stein and a two-dimensional (in
parameter space) epidemiology model.Comment: 20 pages, 8 figure
Beyond Worst-Case Analysis for Joins with Minesweeper
We describe a new algorithm, Minesweeper, that is able to satisfy stronger
runtime guarantees than previous join algorithms (colloquially, `beyond
worst-case guarantees') for data in indexed search trees. Our first
contribution is developing a framework to measure this stronger notion of
complexity, which we call {\it certificate complexity}, that extends notions of
Barbay et al. and Demaine et al.; a certificate is a set of propositional
formulae that certifies that the output is correct. This notion captures a
natural class of join algorithms. In addition, the certificate allows us to
define a strictly stronger notion of runtime complexity than traditional
worst-case guarantees. Our second contribution is to develop a dichotomy
theorem for the certificate-based notion of complexity. Roughly, we show that
Minesweeper evaluates -acyclic queries in time linear in the certificate
plus the output size, while for any -cyclic query there is some instance
that takes superlinear time in the certificate (and for which the output is no
larger than the certificate size). We also extend our certificate-complexity
analysis to queries with bounded treewidth and the triangle query.Comment: [This is the full version of our PODS'2014 paper.
An Overview of Backtrack Search Satisfiability Algorithms
Propositional Satisfiability (SAT) is often used as the underlying model for a significan
Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations
Polymerases are protein enzymes that move along nucleic acid chains and
catalyze template-based polymerization reactions during gene transcription and
replication. The polymerases also substantially improve transcription or
replication fidelity through the non-equilibrium enzymatic cycles. We briefly
review computational efforts that have been made toward understanding
mechano-chemical coupling and fidelity control mechanisms of the polymerase
elongation. The polymerases are regarded as molecular information motors during
the elongation process. It requires a full spectrum of computational approaches
from multiple time and length scales to understand the full polymerase
functional cycle. We keep away from quantum mechanics based approaches to the
polymerase catalysis due to abundant former surveys, while address only
statistical physics modeling approach and all-atom molecular dynamics
simulation approach. We organize this review around our own modeling and
simulation practices on a single-subunit T7 RNA polymerase, and summarize
commensurate studies on structurally similar DNA polymerases. For multi-subunit
RNA polymerases that have been intensively studied in recent years, we leave
detailed discussions on the simulation achievements to other computational
chemical surveys, while only introduce very recently published representative
studies, including our own preliminary work on structure-based modeling on
yeast RNA polymerase II. In the end, we quickly go through kinetic modeling on
elongation pauses and backtracking activities. We emphasize the fluctuation and
control mechanisms of the polymerase actions, highlight the non-equilibrium
physical nature of the system, and try to bring some perspectives toward
understanding replication and transcription regulation from single molecular
details to a genome-wide scale
Topological Properties of Citation and Metabolic Networks
Topological properties of "scale-free" networks are investigated by
determining their spectral dimensions , which reflect a diffusion process
in the corresponding graphs. Data bases for citation networks and metabolic
networks together with simulation results from the growing network model
\cite{barab} are probed. For completeness and comparisons lattice, random,
small-world models are also investigated. We find that is around 3 for
citation and metabolic networks, which is significantly different from the
growing network model, for which is approximately 7.5. This signals a
substantial difference in network topology despite the observed similarities in
vertex order distributions. In addition, the diffusion analysis indicates that
whereas the citation networks are tree-like in structure, the metabolic
networks contain many loops.Comment: 11 pages, 3 figure
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