CParty: hierarchically constrained partition function of RNA pseudoknots.

Motivation: Biologically relevant RNA secondary structures are routinely predicted by efficient dynamic programming algorithms that minimize their free energy. Starting from such algorithms, one can devise partition function algorithms, which enable stochastic perspectives on RNA structure ensembles. As the most prominent example, McCaskill's partition function algorithm is derived from pseudoknot-free energy minimization.

Observation of Bose-Einstein condensation of dipolar molecules.

Ensembles of particles governed by quantum mechanical laws exhibit intriguing emergent behaviour. Atomic quantum gases, liquid helium and electrons in quantum materials all exhibit distinct properties because of their composition and interactions. Quantum degenerate samples of ultracold dipolar molecules promise the realization of new phases of matter and new avenues for quantum simulation and quantum computation.

Developing Complex RNA Design Applications in the Infrared Framework.

Applications in biotechnology and bio-medical research call for effective strategies to design novel RNAs with very specific properties. Such advanced design tasks require support by computational tools but at the same time put high demands on their flexibility and expressivity to model the application-specific requirements. To address such demands, we present the computational framework Infrared.

LocARNA 2.0: Versatile Simultaneous Alignment and Folding of RNAs.

Generating accurate alignments of non-coding RNA sequences is indispensable in the quest for understanding RNA function. Nevertheless, aligning RNAs remains a challenging computational task. In the twilight-zone of RNA sequences with low sequence similarity, sequence homologies and compatible, favorable (a priori unknown) structures can be inferred only in dependency of each other.

Infrared: a declarative tree decomposition-powered framework for bioinformatics.

Motivation: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.

Methods: We introduce the Infrared framework to overcome such hindrances for a large class of problems.

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.

Motivation: Computational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions. These methods find the structure with the minimum free energy (MFE) among exponentially many possible structures and have a restrictive time and space complexity ( time and space for pseudoknot-free structures) for longer RNA sequences. Furthermore, accurate free energy calculations, including dangle contributions can be difficult and costly to implement, particularly when optimizing for time and space requirements.

Resilience in rural health system.

Introduction: Current literature emphasises the importance of resilience in health care. Studies have shown that lack of resilience not only leads to adverse clinical outcomes but is also associated with burnout and long-term stress in clinicians. Resource-limited rural settings in the United States often impose unique stressors, and thus, it is critical to examine resilience of health care providers practicing rural medicine.

A planar cloverleaf antenna for circularly polarized microwave fields in atomic and molecular physics experiments.

We report on the design and characterization of a compact microwave antenna for atomic and molecular physics experiments. The antenna is comprised of four loop antennas arranged in a cloverleaf shape, allowing for precise adjustment of polarization by tuning the relative phase of the loops. We optimize the antenna for left-circularly polarized microwaves at 3.

3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations.

The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction predictions provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction.

Automated design of dynamic programming schemes for RNA folding with pseudoknots.

Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since the prediction of pseudoknotted structures by minimizing (realistically modelled) energy is NP-hard, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. To achieve good performance, these methods rely on specific and carefully hand-crafted DP schemes.

Laser Scheme for Doppler Cooling of the Hydroxyl Cation (OH).

We report on a cycling scheme for Doppler cooling of trapped OH ions using transitions between the electronic ground state Σ and the first excited triplet state Π. We have identified relevant transitions for photon cycling and repumping, have found that coupling into other electronic states is strongly suppressed, and have calculated the number of photon scatterings required to cool OH to a temperature where Raman sideband cooling can take over. In contrast to the standard approach, where molecular ions are sympathetically cooled, our scheme does not require co-trapping of another species and opens the door to the creation of pure samples of cold molecular ions with potential applications in quantum information, quantum chemistry, and astrochemistry.

Ultracold Gas of Dipolar NaCs Ground State Molecules.

We report on the creation of bosonic NaCs molecules in their absolute rovibrational ground state via stimulated Raman adiabatic passage. We create ultracold gases with up to 22 000 dipolar NaCs molecules at a temperature of 300(50) nK and a peak density of 1.0(4)×10^{12}  cm^{-3}.

Bi-alignments with affine gaps costs.

Background: Commonly, sequence and structure elements are assumed to evolve congruently, such that homologous sequence positions correspond to homologous structural features. Assuming congruent evolution, alignments based on sequence and structure similarity can therefore optimize both similarities at the same time in a single alignment. To model incongruent evolution, where sequence and structural features diverge positionally, we recently introduced bi-alignments.

Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.

As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently.

Advanced Design of Structural RNAs Using RNARedPrint.

RNA design addresses the need to build novel RNAs, e.g., for biotechnological applications in synthetic biology, equipped with desired functional properties.

The SARS-CoV-2 subgenome landscape and its novel regulatory features.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate negative subgenomes (subgenomic RNAs [sgRNAs]) through transcription-regulating sequence (TRS)-dependent template switching, but the global dynamic landscapes of coronaviral subgenomes and regulatory rules remain unclear. Here, using next-generation sequencing (NGS) short-read and Nanopore long-read poly(A) RNA sequencing in two cell types at multiple time points after infection with SARS-CoV-2, we identified hundreds of template switches and constructed the dynamic landscapes of SARS-CoV-2 subgenomes.

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.

Motivation: Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solves the theoretical problem exactly with a complexity of [Formula: see text] in the full energy model. Over the last two decades, several variants and improvements of the Sankoff algorithm have been proposed to reduce its extreme complexity by proposing simplified energy models or imposing restrictions on the predicted alignments.

Relation between riding pleasure and vehicle dynamics - Results from a motorcycle field test.

Powered two-wheelers are a common means of transport all over the world. In several countries, primary motorcycles with high displacement involve another purpose, namely motorcycling is a leisure activity. Motorcycles are used as tools of transport pleasure as opposed to being purely used for individual commuting purposes.

Resonant Dipolar Collisions of Ultracold Molecules Induced by Microwave Dressing.

We demonstrate microwave dressing on ultracold, fermionic ^{23}Na^{40}K ground-state molecules and observe resonant dipolar collisions with cross sections exceeding 3 times the s-wave unitarity limit. The origin of these interactions is the resonant alignment of the approaching molecules' dipoles along the intermolecular axis, which leads to strong attraction. We explain our observations with a conceptually simple two-state picture based on the Condon approximation.

The locality dilemma of Sankoff-like RNA alignments.

Motivation: Elucidating the functions of non-coding RNAs by homology has been strongly limited due to fundamental computational and modeling issues. While existing simultaneous alignment and folding (SA&F) algorithms successfully align homologous RNAs with precisely known boundaries (global SA&F), the more pressing problem of identifying new classes of homologous RNAs in the genome (local SA&F) is intrinsically more difficult and much less understood. Typically, the length of local alignments is strongly overestimated and alignment boundaries are dramatically mispredicted.

Active safety systems for powered two-wheelers: A systematic review.

Active safety systems, of which antilock braking is a prominent example, are going to play an important role to improve powered two-wheeler (PTW) safety. This paper presents a systematic review of the scientific literature on active safety for PTWs. The aim was to list all systems under development, identify knowledge gaps and recognize promising research areas that require further efforts.

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.

Efficient computational tools for the identification of putative target RNAs regulated by prokaryotic sRNAs rely on thermodynamic models of RNA secondary structures. While they typically predict RNA-RNA interaction complexes accurately, they yield many highly-ranked false positives in target screens. One obvious source of this low specificity appears to be the disability of current secondary-structure-based models to reflect steric constraints, which nevertheless govern the kinetic formation of RNA-RNA interactions.

Fixed-parameter tractable sampling for RNA design with multiple target structures.

Background: The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which substantially reduce the need for costly wet-lab experiments.

Results: We devise a novel approach to a central ingredient of most in-silico design methods: the generation of sequences that fold well into multiple target structures.