CRM Prediction Accuracy on a Dataset with 208 “Positive” Sequences (CRMs) and 208 “Negative” Sequences (Random Noncoding Genomic Fragments)

<div><p>The <i>y</i>-axis shows the number of negatives included in a given number (<i>x</i>-axis) of top scoring sequences. Green line (diagonal) represents error rate expected by chance.</p><p>(A) Predictions were made based on percentage identity (PID, purple line), Stubb score (blue), Morph LLR1 score (red), and Morph LLR2 score (black).</p><p>(B) Predictions were based on the total number of binding sites predicted by Stubb (blue) and Morph (black).</p></div

A Total of 383 Binding Sites for the Bicoid Transcription Factor Were Predicted Computationally (Using a Threshold) in D. melanogaster CRMs of the BLASTODERM.A-P Dataset

<div><p>(A) The number of sites that were aligned, versus the number of unaligned sites, using different alignments: Diamonds = LAGAN with varying gap penalties; red circle = Morphalign. (Green diamond represents LAGAN with lowest gap penalty.)</p><p>(B) Of the sites aligned by a method, how many were conserved (i.e., PWM match score above threshold) in D. mojavensis. Color code is as in (A).</p></div

Binding Site Prediction Sensitivity (A) and Specificity (B) with Stubb and Morphalign

<p>(A) Sensitivity and (B) specificity with Stubb and Morphalign on experiment sets with simulation parameters μ_I = μ_D = 0.2 are shown.</p

Alignment Sensitivity (A) and Specificity (B) of LAGAN and Morphalign

<p>(A) Sensitivity and (B) specificity of LAGAN and Morphalign on experiment sets with simulation parameters μ_I = μ_D = 0.2 are shown. Diagonal lines represent equal scores.</p

Examples of Difference in Alignments Produced by Morphalign and Its No-Motifs Version, for the hairy stripe 6 enhancer

<div><p>Each panel shows one example, with the Morphalign alignment at the top of that panel and the motif-agnostic alignment at the bottom. D. melanogaster is shown as the top sequence in an alignment. Vertically aligned positions are shown in blue if they are identical, in black otherwise. Red lines indicate aligned positions, with their thickness proportional to confidence (marginal probability) of that positional alignment. Only positional alignments with confidence greater than 0.1 are marked by red lines. (Note that one position may align with multiple positions in the other alignment.) Morphalign additionally shows predicted binding site locations with blue bars (whose height represents confidence level), and the motif names in green characters.</p><p>(A) The red boxes show a predicted Kruppel site that is entirely unaligned by Morphalign, but is poorly and ambiguously aligned by the motif-agnostic alignment. The green box shows a similar situation.</p><p>(B) A very well-aligned block with conserved Kruppel sites is found by Morphalign, but the sites are clearly separated in the motif-agnostic alignment.</p><p>(C) A DStat site is aligned between the two species (by Morphalign). The no-motifs alignment conspicuously separates these potentially orthologous sites.</p></div

Hidden Markov Model Structure of the MORPH Model

<div><p>(A): Transition probabilities among various states. Circular states have emissions, and octagonal states do not.</p><p>(B) Motif emissions from Match, Insert, and Delete states. For each, one of <i>K</i> motif states, or the background motif state is visited. In case of the Match state, two aligned sites are emitted, whereas for the Insert and Delete states, only one unaligned site is emitted.</p></div

Snapshots from Alignments of Three CRMs: eve stripe 2 (Top Left), eve stripe1 (Top Right), and stumps_hbr_early (Bottom)

<p>In the top two panels, the alignment above was produced by Morphalign, and the alignment below it was produced by LAGAN (with gap opening penalty of 300).</p

Morphalign Alignments: Differences from Alternative Alignment Methods

<div><p>(A) For each CRM in the BLASTODERM.A-P set, the fraction of the D. melanogaster sequence that was ambiguously aligned (to two or more positions in D. mojavensis) was computed. The figure shows the histogram of these alignment ambiguity fractions for the set.</p><p>(B) Median of alignment agreement scores between output of Morphalign and output of LAGAN (run separately with a range of gap opening penalties) for CRMs in the BLASTODERM.A-P (blue) and the MESODERM (red) sets.</p><p>(C) Histogram of alignment agreement scores between Morphalign and its no-motifs version, for the BLASTODERM.A-P set of CRMs.</p></div

Mechanochemistry of Physisorbed Molecules at Tribological Interfaces: Molecular Structure Dependence of Tribochemical Polymerization

Physisorbed molecules at a sliding solid interface could be activated by mechanical shear and react with each other to form polymeric products that are often called tribopolymers. The dependence of the tribopolymerization yield on the applied load and adsorbate molecular structure was studied to obtain mechanistic insights into mechanochemical reactions at a tribological interface of stainless steel. Three hydrocarbon precursors containing 10 carbon atomsα-pinene (C₁₀H₁₆), pinane (C₁₀H₁₈), and <i>n</i>-decane (C₁₀H₂₂)were chosen for this study. α-Pinene and pinane are bicyclic compounds with different ring strains. <i>N</i>-Decane was chosen as a reference molecule without any internal strain. By comparing the adsorption isotherm of these molecules and the total volume of tribopolymer products, the reaction yield was found to be proportional to the number of adsorbed molecules. An Arrhenius-type analysis of the applied load dependence of the tribopolymerization yield revealed how the critical activation volume (ΔV*) varies with the structure of adsorbed molecules. The experimentally determined Δ<i>V</i>* values of α-pinene, pinane, and <i>n</i>-decane were 3, 8, and 10% of their molar volumes, respectively. The molecule with the largest ring strain (α-pinene) showed the smallest Δ<i>V</i>*, which implies the critical role of internal molecular strain in the mechanochemical initiation of polymerization reaction. The tribopolymer film synthesized in situ at the sliding interface exhibited an excellent boundary lubrication effect in the absence of any external supply of lubricant molecules

Nonadiabatic Field on Quantum Phase Space: A Century after Ehrenfest

Nonadiabatic transition dynamics lies at the core of many electron/hole transfer, photoactivated, and vacuum field-coupled processes. About a century after Ehrenfest proposed “Phasenraum” and the Ehrenfest theorem, we report a conceptually novel trajectory-based nonadiabatic dynamics approach, nonadiabatic field (NAF), based on a generalized exact coordinate–momentum phase space formulation of quantum mechanics. It does not employ the conventional Born–Oppenheimer or Ehrenfest trajectory in the nonadiabatic coupling region. Instead, in NAF the equations of motion of the independent trajectory involve a nonadiabatic nuclear force term in addition to an adiabatic nuclear force term of a single electronic state. A few benchmark tests for gas phase and condensed phase systems indicate that NAF offers a practical tool to capture the correct correlation of electronic and nuclear dynamics for processes where the states remain coupled all the time as well as for the asymptotic region where the coupling of electronic states vanishes