An Overview of Backtrack Search Satisfiability Algorithms

Propositional Satisfiability (SAT) is often used as the underlying model for a significan

Effective Lower Bounding Techniques for Pseudo-Boolean Optimization

Linear Pseudo-Boolean Optimization (PBO) is a widely used modeling framework in Electronic Design Automation (EDA). Due to significant advances in Boolean Satisfiability (SAT), new algorithms for PBO have emerged, which are effective on highly constrained instances. However, these algorithms fail to handle effectively the information provided by the cost function of PBO. This paper addresses the integration of lower bound estimation methods with SAT-related techniques in PBO solvers. Moreover, the paper shows that the utilization of lower bound estimates can dramatically improve the overall performance of PBO solvers for most existing benchmarks from EDA. 1

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

GRASP: A New Search Algorithm for Satisfiability

This paper introduces GRASP (Generic search Algorithm J3r the Satisfiabilily Problem), an integrated algorithmic J3amework 30r SAT that unifies several previously proposed searchpruning techniques and jcilitates identification of additional ones. GRASP is premised on the inevitability of conflicts during search and its most distinguishingjature is the augmentation of basic backtracking search with a powerful conflict analysis procedure. Analyzing conflicts to determine their causes enables GRASP to backtrack non-chronologically to earlier levels in the search tree, potentially pruning large portions of the search space. In addition, by 'ecording" the causes of conflicts, GRASP can recognize and preempt the occurrence of similar conflicts later on in the search. Einally, straighrward bookkeeping of the causali y chains leading up to conflicts a/lows GRASP to identij) assignments that are necessary jr a solution to be found. Experimental results obtained jom a large number of benchmarks, including many J3om the field of test pattern generation, indicate that application of the proposed conflict analysis techniques to SAT algorithms can be extremely ejctive jr a large number of representative classes of SAT instances

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

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