Translational Coupling Research Articles

Magnetic Properties of Self-Assemble Naphthalene Diimide Radical Aggregates.

The concept of creating room-temperature ferromagnets from organic radicals proposed nearly sixty years ago, has recently experienced a resurgence due to advances in organic radical chemistry and materials. However, the lack of definitive design paradigms for achieving stable long-range ferromagnetic coupling between organic radicals presents an uncertain future for this research. Here, an innovative strategy is presented to achieve room-temperature ferromagnets by assembling π-conjugated radicals into π-π stacking aggregates. These aggregates, with ultra-close π-π distances and optimal π-π overlap, provide a platform for strong ferromagnetic (FM) interaction. The planar aromatic naphthalene diimide (NDI) anion radicals form nanorod aggregates with a π-π distance of just 3.26 Å, shorter than typical van der Waals distances. The suppressed electron paramagnetic resonance (EPR) signal and emergent near-infrared (NIR) absorption of the aggregates confirm strong interactions between the radicals. Magnetic measurements of NDI anion radical aggregates demonstrate room-temperature ferromagnetism with a saturated magnetization of 1.1 emug-1, the highest among pure organic ferromagnets. Theoretical calculations reveal that π-stacks of NDI anion radicals with specific interlayer translational slippage favor ferromagnetic coupling over antiferromagnetic coupling.

Cancer cells forgo translating mRNA transcribed from genes of nonspecialized tasks.

The coupling of transcription and translation enables prokaryotes to regulate mRNA stability and reduce nonfunctional transcripts. Eukaryotes evolved other means to perform these functions. Here, we quantify the disparity between gene expression and protein levels and attempt to explain its origins. We collected publicly available simultaneous measurements of gene expression, protein level, division rate, and growth inhibition of breast cancer cells under drug perturbation. We used the cell lines as entities with shared origin, different evolutionary trajectories, and cancer hallmarks to define tasks subject to specializing and trading-off. We observed varying average mRNA and protein correlation across cell lines, and it was consistently higher for the gene products in the cancer hallmarks. The enrichment of hallmark gene products signifies the resources invested in it as a task. Enrichment based on mRNA or protein abundance corresponds to the relative resources dedicated to transcription and translation. The differences in gene- and protein-based enrichment correlated with nominal division rates but not growth inhibition under drug perturbations. Comparing the range of enrichment scores of the hallmarks within each cell signifies the resources dedicated to each. Cells appear to have a wider range of enrichment in protein synthesis relative to gene transcription. The difference and range of enrichment of the hallmark genes and proteins correlated with cell division and inhibition in response to drug treatments. We posit that cancer cells may express the genes coding for seemingly nonspecialized tasks but do not translate them to the corresponding proteins. This trade-off may cost the cells under normal conditions but confer benefits during stress.

Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome

Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that is responsible for major health and economic costs worldwide1. Mtb encounters diverse environments during its life cycle and responds to these changes largely by reprogramming its transcriptional output2. However, the mechanisms of Mtb transcription and how they are regulated remain poorly understood. Here we use a sequencing method that simultaneously determines both termini of individual RNA molecules in bacterial cells3 to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5′ ends aligned at transcription start sites and 3′ ends located 200–500 nucleotides downstream. We show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than being products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription relies on the binding of the σ-factor. Finally, we show that a translating ribosome promotes transcription elongation, revealing a potential role for transcription–translation coupling in controlling Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to environmental changes and could be exploited for TB therapeutics.

Microcanonical treatment of HCl dissociative chemisorption on Au(111): Reactive dampening through inefficient translational energy coupling and an active surface.

Microcanonical unimolecular rate theory is applied to Shirhatti and Wodtke's recent supersonic molecular beam experiments examining the activated dissociative chemisorption of HCl on Au(111). A precursor mediated microcanonical trapping (PMMT) model (where the surface vibrates and HCl rotations, vibration, and translation directed along the surface normal are treated as active degrees of freedom) gave dissociative sticking coefficient predictions that are several orders of magnitude higher than experimental values but in good accord with prior quantum and molecular dynamics simulations. Density functional theory (DFT) electronic structure calculations using the Perdew-Burke-Ernzerhof (PBE) functional served to fix the vibrational frequencies of the reactive transition state and the threshold energy for dissociation, E0 = 72.9 kJ/mol. To explore the possibilities of varying threshold energy, coupling to phonons, and dynamics, a three-parameter [E0, s, ɛn] dynamically biased (d-) PMMT model was fit to the experiments. A dynamical bias was introduced using an efficiency, ɛn, of normal translational energy to contribute to the active exchangeable energy capable of promoting reactivity. To achieve the low sticking probabilities observed in experiment, severe normal translational energy dampening (ɛn → 0.26) was imposed, leading to a large vibrational efficacy of ηv = εv/εn = 3.85. The optimal threshold energy for dissociation was E0 = 30.88 kJ/mol, some 40 kJ/mol below the PBE-DFT prediction, and the optimal number of Au surface oscillators was s = 1. The d-PMMT modeling indicates that HCl/Au(111) reactivity can be consistent with electronically adiabatic passage across a relatively low and late transition state that dynamically disfavors normal translational energy.

Refined secondary Bjerknes force equation for double bubbles with pulsation, translation, and deformation

The secondary Bjerknes force (SBF) is the time-averaged interaction between two bubbles driven in a sound field. We derived a refined formula for the interaction force, incorporating the radial vibration and translational and deformational motions of the bubble. The coupling of pulsation, translation, and deformation enhances the interaction between bubbles but also weakens their stability, making it easier for bubbles to merge or break during motion. The effects of the coupling mode on the magnitude and direction of SBFs coupled with pulsation, translation, and deformation were numerically analyzed and studied. Under certain sound-field conditions, the SBF increased with increasing pressure amplitude, initial radius, and initial velocity, while decreased as the distance increased. In addition, the SBF irregularly increased with increasing frequency.

Microwave Speckle Correlation Modeling Under the Coupling of Illumination Angle Change and Object Translation

Microwave Speckle Correlation Modeling Under the Coupling of Illumination Angle Change and Object Translation

Curvature induces and enhances transport of spinning colloids through narrow channels.

The effect of curvature and how it induces and enhances the transport of colloidal particles driven through narrow channels represent an unexplored research avenue. Here we combine experiments and simulations to investigate the dynamics of magnetically driven colloidal particles confined through a narrow, circular channel. We use an external precessing magnetic field to induce a net torque and spin the particles at a defined angular velocity. Due to the spinning, the particle propulsion emerges from the different hydrodynamic coupling with the inner and outer walls and strongly depends on the curvature. The experimental findings are combined with finite element numerical simulations that predict a positive rotation translation coupling in the mobility matrix. Further, we explore the collective transport of many particles across the curved geometry, making an experimental realization of a driven single file system. With our finding, we elucidate the effect of curvature on the transport of microscopic particles which could be important to understand the complex, yet rich, dynamics of particle systems driven through curved microfluidic channels.

Cycle consistent twin energy-based models for image-to-image translation

Domain shift refers to change of distributional characteristics between the training (source) and the testing (target) datasets of a learning task, leading to performance drop. For tasks involving medical images, domain shift may be caused because of several factors such as change in underlying imaging modalities, measuring devices and staining mechanisms. Recent approaches address this issue via generative models based on the principles of adversarial learning albeit they suffer from issues such as difficulty in training and lack of diversity. Motivated by the aforementioned observations, we adapt an alternative class of deep generative models called the Energy-Based Models (EBMs) for the task of unpaired image-to-image translation of medical images. Specifically, we propose a novel method called the Cycle Consistent Twin EBMs (CCT-EBM) which employs a pair of EBMs in the latent space of an Auto-Encoder trained on the source data. While one of the EBMs translates the source to the target domain the other does vice-versa along with a novel consistency loss, ensuring translation symmetry and coupling between the domains. We theoretically analyze the proposed method and show that our design leads to better translation between the domains with reduced langevin mixing steps. We demonstrate the efficacy of our method through detailed quantitative and qualitative experiments on image segmentation tasks on three different datasets vis-a-vis state-of-the-art methods.

Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.

Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of -4 nt and -1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models for the fate of the post-termination ribosome predict either that overlaps or very short intergenic distances are essential for translational coupling or that the undissociated post-termination ribosome can scan through long intergenic regions, up to hundreds of nucleotides. We aimed to experimentally resolve the contradiction between the two models by analyzing three native gene pairs from the model archaeon Haloferax volcanii and three native pairs from Escherichia coli. A two reporter gene system was used to quantify the reinitiation frequency, and several stop codons in the upstream gene were introduced to increase the intergenic distances. For all six gene pairs from two species, an extremely strong dependence of the reinitiation efficiency on the intergenic distance was unequivocally demonstrated, such that even short intergenic distances of about 20 nt almost completely abolished translational coupling. Bioinformatic analysis of the intergenic distances in all unidirectional gene pairs in the genomes of H. volcanii and E. coli and in 1,695 prokaryotic species representative of 49 phyla showed that intergenic distances of -4 nt or -1 nt (= short gene overlaps of 4 nt or 1 nt) were by far most common in all these groups of archaea and bacteria. A small set of genes in E. coli, but not in H. volcanii, had intergenic distances of around +10 nt. Our experimental and bioinformatic analyses clearly show that translational coupling requires short gene overlaps, whereas scanning of intergenic regions by the post-termination ribosome occurs rarely, if at all. Short overlaps are enriched among genes that encode subunits of heteromeric complexes, and co-translational complex formation requiring precise subunit stoichiometry likely confers an evolutionary advantage that drove the formation and conservation of overlapping gene pairs during evolution.

Description of bandgaps opening in chiral phononic crystals by analogy with Thomson scattering

Chiral phononic crystals (PnCs) provide unique properties not offered by conventional metamaterial based on classic Bragg scattering and local resonance. However, it is insufficient to only consider the inertial amplification effect to describe its bandgap mechanism due to the absence of the bandgap caused by the chirality in some specific chiral structures. Here, we theoretically and experimentally introduce an analogy with Thomson scattering in electromagnetic waves to characterize the bandgap phenomena in chiral PnCs with translation–rotation coupling. Another phononic structures with translation–translation coupling are proposed to illustrate the universality of the analogy. We evidence that the coupling motion in chiral unit cells is similar to the result of Thomson scattering, which quantitatively formulizing as inertial amplification in theory and, twice elastic Thomson scattering allows the waves in the same polarization mode to superpose in antiphase, which is essence of the bandgap formation. This finding sheds a new light on the physics of the elastodynamic wave manipulation in chiral PnCs, thus opening a definite route for the pragmatic exploitation of chiral PnCs as well as other structures with motion coupling in achieving low-frequency and broad bandgaps.

Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.

The half-life of mRNAs, as well as their translation, increases in proportion to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the mRNA stability gain in yeast depends on the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs although they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality-dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.

Analysis of the effect of the translational-rotational coupling on the pseudo-diffusion along the molecular axes of meta-cresol: A molecular dynamics analysis

We investigate the dynamical properties (translation and rotation) of the glass-forming liquid meta-cresol by molecular dynamics simulations. This system is investigated at 9 temperatures between 230 K and 400 K, encompassing the liquid and glassy states of meta-cresol. In order to get insight into the coupling between the translational and rotational motions, the centre of mass velocity autocorrelation function is calculated along the principal axes of meta-cresol. We show that the time behaviour of the velocity and angular velocity is connected to the change in the local structure occurring upon the glass transition. Indeed, the long-time negative region in the velocity autocorrelations is associated with a caging effect while the occurrence of a short time negative region in these functions is considered as a signature of hydrogen bonding interactions. By studying, the centre of mass velocity of meta-cresol in the molecular frame, the translation and rotation coupling was directly evidenced. The time evolution of the translational-rotational coupling is evaluated from the difference ΔαRTC(t) between the velocity autocorrelation function calculated with respect to the molecular frame (where α stands for the three axes of the local cartesian frame fixed to the individual molecule, x, y, and z) of the meta-cresol molecule and that of the same function calculated in the frame of the hypothesis that there is no statistical correlation between the translational and rotational motions. The positive regions of ΔαRTC(t) indicate an occurrence of a cooperative effect, which means that the each of the two motions is realized in the favour of the other. Conversely, negative regions indicate that the rotation and translation motions are anti-cooperative. Our results show that a strong coupling between translation and rotation occurs along the × axis that is perpendicular to the ring of meta-cresol molecule, and also along which the hydrogen bond is established.

Study on the strong earthquake failure mechanism of space grid structure considering rotational ground motion

Space grid structures are increasingly being utilized in public buildings due to their exceptional structural performance. Given that these structures are commonly located in areas with high pedestrian traffic and significant investments, damages incurred during an earthquake could result in significant economic losses and casualties. To explore the rotational seismic response of space grid structures, this study employs the frequency domain method to compute the rotational seismic motion. Using the Lushan Middle School Comprehensive Hall's structural form as a reference, a finite element model of the space grid structure is established. Three types of seismic motions, namely three-way translational, three-way rotational, and six-way translational and rotational, are input into the structural model to investigate strong seismic translation and rotation coupling effects. The impact and features of rotational seismic motion on space grid structures are explored by studying the influence and characteristics of rotational seismic motion. Under varying seismic motion inputs, the failure mechanisms of typical space grid structures' translational and rotational components are also determined.

The Right Spin: Learning Object Motion from Rotation-Compensated Flow Fields

A good understanding of geometrical concepts as well as a broad familiarity with objects lead to excellent human perception of moving objects. The human ability to detect and segment moving objects works in the presence of multiple objects, complex background geometry, motion of the observer and even camouflage. How we perceive moving objects so reliably is a longstanding research question in computer vision and borrows findings from related areas such as psychology, cognitive science and physics. One approach to the problem is to teach a deep network to model all of these effects. This is in contrast with the strategy used by human vision, where cognitive processes and body design are tightly coupled and each is responsible for certain aspects of correctly identifying moving objects. Similarly, from the computer vision perspective there is evidence that classical, geometry-based techniques are better suited to the “motion-based” parts of the problem, while deep networks are more suitable for modeling appearance. In this work, we argue that the coupling of camera rotation and camera translation can create complex motion fields that are difficult for a deep network to untangle directly. We present a novel probabilistic model to estimate the camera’s rotation given the motion field. We then rectify the flow field to obtain a rotation-compensated motion field for subsequent segmentation. This strategy of first estimating camera motion, and then allowing a network to learn the remaining parts of the problem, yields improved results on the widely used DAVIS benchmark as well as the more recent motion segmentation data set MoCA (Moving Camouflaged Animals).

Generalized section–section interaction potentials in the geometrically exact beam theory: Modeling of intermolecular forces, asymptotic limit as strain-energy function, and formulation of rotational constraints

The present contribution proposes a universal framework to formulate generalized section–section interaction potentials (SSIP) within the geometrically exact beam theory. By exploiting the fundamental kinematic assumption of undeformable cross-sections, an objective (i.e., frame-invariant) description of SSIPs via a minimal set of six (translational and rotational) relative coordinates, either in spatial or in material form, is proposed. Based on work-pairing, work-conjugated section–section interaction forces and moments, either in spatial or in material form, are identified that can be consistently derived from a variational principle. Interestingly, it is shown that hyperelastic stored-energy functions relating the deformation measures and stress-resultants of the well-known geometrically exact Simo–Reissner beam theory can also be identified as SSIPs when considering the asymptotic limit of small relative distances and rotations between the interacting cross-sections. Moreover, the proposed variational problem formulation is demonstrated to be of a very general nature, thus allowing for the formulation of translational and rotational constraints between arbitrarily oriented cross-sections based on either a penalty or a Lagrange multiplier potential. Possible applications include fiber-based structures and materials in technical and biological systems, where the proposed approach allows to model short- or long-ranged inter-molecular (e.g., electrostatic, van der Waals or repulsive steric) interactions between fibers in geometrically complex arrangements and to formulate translational and rotational coupling constraints between different fibers (e.g., cross-linked polymer chains) or between fibers and a matrix phase (e.g., fiber-reinforced composites).

Premature termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis

Little is known about the decisions behind transcription elongation versus termination in the human pathogen Mycobacterium tuberculosis (M.TB). By applying Term-seq to M.TB we found that the majority of transcription termination is premature and associated with translated regions, i.e., within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis, upon depletion of termination factor Rho, suggests that Rho-dependent transcription termination dominates all transcription termination sites (TTS), including those associated with regulatory 5' leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novel M.TB cis-regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enable M.TB adaptation to the host environment offering novel potential points of intervention.

Vibration Characteristics and Power Flow Analysis of a Constant Cracked Beam with General Boundary Conditions

The vibration analysis of beams with cracks is an important problem in the structural dynamics community. In this study, a general model for the vibration analysis of a cracked beam with general boundary conditions was developed and investigated, emphasizing its vibration and power flow characteristics. The beam crack was introduced via torsional and translational coupling springs, which separated the beam structure into two segments, and the corresponding vibration characteristics were investigated via an energy-based formulation in conjunction with the Lagrangian procedure. A boundary-smoothed Fourier series was employed to construct the beam displacement field to avoid boundary differential discontinuities. Various crack statuses, including their depths or positions can be easily considered by adjusting the stiffness coefficient of the artificial springs. Several examples were presented to validate the effectiveness and accuracy of the proposed model. The modal characteristics and forced response of a cracked beam were predicted and analyzed, respectively, with a detailed depiction of the power flow around the crack. The results indicate that the presence of a crack has an important effect on the modal characteristics of an elastically restrained beam, as well as on the power flow distribution across the beam structure. This study can provide an effective tool for the dynamic analysis and power flow mechanism of beam structures with various cracks and complex boundary conditions.

Role of ribosome recycling factor in natural termination and translational coupling as a ribosome releasing factor.

The role of ribosome recycling factor (RRF) of E. coli was studied in vivo and in vitro. We used the translational coupling without the Shine-Dalgarno sequence of downstream ORF (d-ORF) as a model system of the RRF action in natural termination of protein synthesis. For the in vivo studies we used the translational coupling by the adjacent coat and lysis genes of RNA phage GA sharing the termination and initiation (UAAUG) and temperature sensitive RRF. The d-ORF translation was measured by the expression of the reporter lacZ gene connected to the 5'-terminal part of the lysis gene. The results showed that more ribosomes which finished upstream ORF (u-ORF) reading were used for downstream reading when RRF was inactivated. The in vitro translational coupling studies with 027mRNA having the junction sequence UAAUG with wild-type RRF were carried out with measuring amino acids incorporation. The results showed that ribosomes released by RRF read downstream from AUG of UAAUG. In the absence of RRF, ribosomes read downstream in frame with UAA. These in vivo and in vitro studies indicate that RRF releases ribosomes from mRNA at the termination codon of u-ORF. Furthermore, the non-dissociable ribosomes read downstream from AUG of UAAUG with RRF in vitro. This suggests that complete ribosomal splitting is not required for ribosome release by RRF in translational coupling. The data are consistent with the interpretation that RRF functions mostly as a ribosome releasing factor rather than ribosome splitting factor. Additionally, the in vivo studies showed that short (less than 5 codons) u-ORF inhibited d-ORF reading by ribosomes finishing u-ORF reading, suggesting that the termination process in short ORF is not similar to that in normal ORF. This means that all the preexisting studies on RRF with short mRNA may not represent what goes on in natural termination step.

DecoupledPoseNet: Cascade Decoupled Pose Learning for Unsupervised Camera Ego-Motion Estimation

Although many impressive works on learning-based camera ego-motion estimation methods have been proposed recently, most of them promote the accuracy of camera pose estimation by various sequential learning with loop closure optimization, while neglecting the improvement of PoseNet itself. In this paper, we focus on the coupling of rotation and translation in ego-motion estimation, and design a cascade decoupling structure to separately learn the rotation and translation of camera relative motion between adjacent frames. Meanwhile, a rigid-aware unsupervised learning framework with iterative pose refinement scheme is proposed for camera ego-motion estimation. It can disambiguate rigid motion and deformations in dynamic scenarios by jointly learning of optical flow, stereo disparity and camera pose. Validated with evaluation experiments on the public available datasets, our method is superior to the state-of-the-art unsupervised methods, and can achieve comparable results with the supervised ones.

Slender body theories for rotating filaments

Slender fibres are ubiquitous in biology, physics and engineering, with prominent examples including bacterial flagella and cytoskeletal fibres. In this setting, slender body theories (SBTs), which give the resistance on the fibre asymptotically in its slenderness $\epsilon$ , are useful tools for both analysis and computations. However, a difficulty arises when accounting for twist and cross-sectional rotation: because the angular velocity of a filament can vary depending on the order of magnitude of the applied torque, asymptotic theories must give accurate results for rotational dynamics over a range of angular velocities. In this paper, we first survey the challenges in applying existing SBTs, which are based on either singularity or full boundary integral representations, to rotating filaments, showing in particular that they fail to consistently treat rotation–translation coupling in curved filaments. We then provide an alternative approach which approximates the three-dimensional dynamics via a one-dimensional line integral of Rotne–Prager–Yamakawa regularized singularities. While unable to accurately resolve the flow field near the filament, this approach gives a grand mobility with symmetric rotation–translation and translation–rotation coupling, making it applicable to a broad range of angular velocities. To restore fidelity to the three-dimensional filament geometry, we use our regularized singularity model to inform a simple empirical equation which relates the mean force and torque along the filament centreline to the translational and rotational velocity of the cross-section. The single unknown coefficient in the model is estimated numerically from three-dimensional boundary integral calculations on a rotating, curved filament.