Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special cas...

A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a m...

Based on the protonation/deprotonation of poly(β-amino ester) (PAE), mixed-shell micelles (MSMs) with adaptive surfaces could rapidly and reversibly change surface properties to prolong circulation time in blood (pH 7.4) and enhance cellular uptake at tumor sites (pH 6.5).

The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been o...

Abstract Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics fluid mechanics. In the physical sciences, structures such as metastable coherent sets, slow relaxation processes, collective variables, dominant transition pathways or manifolds channels probability flow can be great importance for understanding characterizing kinetic, thermodyna...

P<P Published online July 18, 2013 in advance of the print journal. Preprint Accepted likely to differ from the final, published version. Peer-reviewed and accepted for publication but not copyedited or typeset; preprint is License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as ). After six m...

The identification of phosphocholine and phosphoethanolamine lipids by MALDI TOF/TOF, including characterisation of the headgroup and delineation of the acyl chain at each position of the glycerol backbone, has been explored using lipids representative of each type. The relative intensities of fragments involving the neutral loss of one or other of the acyl chains from ion adducts of 1-palmitoy...