Real sequence effects on the search dynamics of transcription factors on DNA

Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.Comment: 26 pages, 7 figure

AReS and MaRS - Adversarial and MMD-Minimizing Regression for SDEs

Stochastic differential equations are an important modeling class in many disciplines. Consequently, there exist many methods relying on various discretization and numerical integration schemes. In this paper, we propose a novel, probabilistic model for estimating the drift and diffusion given noisy observations of the underlying stochastic system. Using state-of-the-art adversarial and moment matching inference techniques, we avoid the discretization schemes of classical approaches. This leads to significant improvements in parameter accuracy and robustness given random initial guesses. On four established benchmark systems, we compare the performance of our algorithms to state-of-the-art solutions based on extended Kalman filtering and Gaussian processes.Comment: Published at the Thirty-sixth International Conference on Machine Learning (ICML 2019

The Question of Infrastructure: An Interview with Michael Ralph

Interview with a member of the Occupy Wall Street movement on the infrastructure of the movement during the occupation of Zuccotti Park in New York in 2011

Bypassing the structural bottleneck in the ultrafast melting of electronic order

The emergent properties of quantum materials, such as symmetry-broken phases and associated spectral gaps, can be effectively manipulated by ultrashort photon pulses. Impulsive optical excitation generally results in a complex non-equilibrium electron and lattice dynamics that involves multiple processes on distinct timescales, and a common conception is that for times shorter than about 100 fs the gap in the electronic spectrum is not seriously affected by lattice vibrations. Here, we directly monitor the photo-induced collapse of the spectral gap in a canonical charge-density-wave material, blue bronze Rb0.3MoO3. We find that ultra-fast (about 60 fs) vibrational disordering due to efficient hot-electron energy dissipation quenches the gap significantly faster than the typical structural bottleneck time corresponding to one half-cycle oscillation (about 315 fs) of the coherent charge-density-wave amplitude mode. This result not only demonstrates the importance of incoherent lattice motion in the photo-induced quenching of electronic order, but also resolves the perennial debate about the nature of the spectral gap in a coupled electron-lattice system

Reducing theoretical uncertainties in mb and lambda1

We calculate general moments of the lepton energy spectrum in inclusive semileptonic B -> X_c l \nu decay. Moments which allow the determination of mb^{1S} and lambda1 with theoretical uncertainties Delta(mb^{1S}) ~ 0.04 GeV and Delta(lambda1) ~ 0.05 GeV^2 are presented. The short distance 1S mass is used to extract a mass parameter free of renormalon ambiguities. Moments which are insensitive to mb and lambda1 and therefore test the size of the 1/mb^3 matrix elements and the validity of the OPE are also presented. Finally, we give an expression for the total branching ratio with a lower cut on the lepton energy, which allows one to eliminate a source of model dependence in current determinations of |Vcb| from B -> X_c l \nu decay.Comment: 8 pages, one figur

Polymerisable octahedral rhenium cluster complexes as precursors for photo/electroluminescent polymers

New polymerisable photoluminescent octahedral rhenium cluster complexes trans-[{Re₆Q₈}(TBP)₄VB)₂] (Q = S or Se; TBP – p-tert-butylpyridine; VB – vinyl benzoate) have been synthesised, characterised and used to construct rhe-nium cluster-organic polymer hybrid materials. These novel polymer systems are solution-processable and the rhenium clusters retain their photoluminescent properties within the polymer environment. Notably, when the rhenium cluster complexes are incorporated into the matrix of the electroluminescent polymer poly(N-vinylcarbazole), the resultant cluster polymer hybrid combined properties of both components and was used successfully in the construc-tion of a polymer light emitting diode (PLED). These prototype devices are the first PLEDs to incorporate octahedral rhenium clusters and provide the first direct evidence of the electroluminescent properties of rhenium clusters and indeed, to the best of our knowledge, of any member of the family of 24-electron hexanuclear cluster complexes of molybdenum, tungsten or rhenium

One-Component Order Parameter in URu2_2Si2_2 Uncovered by Resonant Ultrasound Spectroscopy and Machine Learning

The unusual correlated state that emerges in URu$_2$Si$_2$ below T$_{HO}$ = 17.5 K is known as "hidden order" because even basic characteristics of the order parameter, such as its dimensionality (whether it has one component or two), are "hidden". We use resonant ultrasound spectroscopy to measure the symmetry-resolved elastic anomalies across T$_{HO}$. We observe no anomalies in the shear elastic moduli, providing strong thermodynamic evidence for a one-component order parameter. We develop a machine learning framework that reaches this conclusion directly from the raw data, even in a crystal that is too small for traditional resonant ultrasound. Our result rules out a broad class of theories of hidden order based on two-component order parameters, and constrains the nature of the fluctuations from which unconventional superconductivity emerges at lower temperature. Our machine learning framework is a powerful new tool for classifying the ubiquitous competing orders in correlated electron systems

Influence of functional rider and horse asymmetries on saddle force distribution during stance and in sitting trot

Asymmetric forces exerted on the horse's back during riding are assumed to have a negative effect on rider–horse interaction, athletic performance, and health of the horse. Visualized on a saddle pressure mat, they are initially blamed on a nonfitting saddle. The contribution of horse and rider to an asymmetric loading pattern, however, is not well understood. The aim of this study was to investigate the effects of horse and rider asymmetries during stance and in sitting trot on the force distribution on the horse's back using a saddle pressure mat and motion capture analysis simultaneously. Data of 80 horse-rider pairs (HRP) were collected and analyzed using linear (mixed) models to determine the influence of rider and horse variables on asymmetric force distribution. Results showed high variation between HRP. Both rider and horse variables revealed significant relationships to asymmetric saddle force distribution (P < .001). During sitting trot, the collapse of the rider in one hip increased the force on the contralateral side, and the tilt of the rider's upper body to one side led to more force on the same side of the pressure mat. Analyzing different subsets of data revealed that rider posture as well as horse movements and conformation can cause an asymmetric force distribution. Because neither horse nor rider movement can be assessed independently during riding, the interpretation of an asymmetric force distribution on the saddle pressure mat remains challenging, and all contributing factors (horse, rider, saddle) need to be considered

Influence of microphone housing on the directional response of piezoelectric mems microphones inspired by Ormia ochracea

The influence of custom microphone housings on the acoustic directionality and frequency response of a multiband bio-inspired MEMS microphone is presented. The 3.2 mm by 1.7 mm piezoelectric MEMS microphone, fabricated by a cost-effective multi-user process, has four frequency bands of operation below 10 kHz, with a desired first-order directionality for all four bands. 7×7×2.5 mm3 3-D-printed bespoke housings with varying acoustic access to the backside of the microphone membrane are investigated through simulation and experiment with respect to their influence on the directionality and frequency response to sound stimulus. Results show a clear link between directionality and acoustic access to the back cavity of the microphone. Furthermore, there was a change in direction of the first-order directionality with reduced height in this back cavity acoustic access. The required configuration for creating an identical directionality for all four frequency bands is investigated along with the influence of reducing the symmetry of the acoustic back cavity access. This paper highlights the overall requirement of considering housing geometries and their influence on acoustic behavior for bio-inspired directional microphones