Computational Methods for Sparse Solution of Linear Inverse Problems

The goal of the sparse approximation problem is to approximate a target signal using a linear combination of a few elementary signals drawn from a fixed collection. This paper surveys the major practical algorithms for sparse approximation. Specific attention is paid to computational issues, to the circumstances in which individual methods tend to perform well, and to the theoretical guarantees available. Many fundamental questions in electrical engineering, statistics, and applied mathematics can be posed as sparse approximation problems, making these algorithms versatile and relevant to a plethora of applications

Deep learning-based parameter mapping for joint relaxation and diffusion tensor MR Fingerprinting

Magnetic Resonance Fingerprinting (MRF) enables the simultaneous quantification of multiple properties of biological tissues. It relies on a pseudo-random acquisition and the matching of acquired signal evolutions to a precomputed dictionary. However, the dictionary is not scalable to higher-parametric spaces, limiting MRF to the simultaneous mapping of only a small number of parameters (proton density, T1 and T2 in general). Inspired by diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF sequence with embedded diffusion-encoding gradients along all three axes to efficiently encode orientational diffusion and T1 and T2 relaxation. We take advantage of a convolutional neural network (CNN) to reconstruct multiple quantitative maps from this single, highly undersampled acquisition. We bypass expensive dictionary matching by learning the implicit physical relationships between the spatiotemporal MRF data and the T1, T2 and diffusion tensor parameters. The predicted parameter maps and the derived scalar diffusion metrics agree well with state-of-the-art reference protocols. Orientational diffusion information is captured as seen from the estimated primary diffusion directions. In addition to this, the joint acquisition and reconstruction framework proves capable of preserving tissue abnormalities in multiple sclerosis lesions

DNA nano-mechanics: how proteins deform the double helix

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with proteins. We extract the local mean forces and torques acting on each base-pair of bound DNA from high-resolution complex structures. Our method relies on known elastic potentials and a careful choice of coordinates of the well-established rigid base-pair model of DNA. The results are robust with respect to parameter and conformation uncertainty. They reveal the complex nano-mechanical patterns of interaction between proteins and DNA. Being non-trivially and non-locally related to observed DNA conformations, base-pair forces and torques provide a new view on DNA-protein binding that complements structural analysis.Comment: accepted for publication in JCP; some minor changes in response to review 18 pages, 5 figure + supplement: 4 pages, 3 figure

Stochastic Model Predictive Control for Autonomous Mobility on Demand

This paper presents a stochastic, model predictive control (MPC) algorithm that leverages short-term probabilistic forecasts for dispatching and rebalancing Autonomous Mobility-on-Demand systems (AMoD, i.e. fleets of self-driving vehicles). We first present the core stochastic optimization problem in terms of a time-expanded network flow model. Then, to ameliorate its tractability, we present two key relaxations. First, we replace the original stochastic problem with a Sample Average Approximation (SAA), and characterize the performance guarantees. Second, we separate the controller into two separate parts to address the task of assigning vehicles to the outstanding customers separate from that of rebalancing. This enables the problem to be solved as two totally unimodular linear programs, and thus easily scalable to large problem sizes. Finally, we test the proposed algorithm in two scenarios based on real data and show that it outperforms prior state-of-the-art algorithms. In particular, in a simulation using customer data from DiDi Chuxing, the algorithm presented here exhibits a 62.3 percent reduction in customer waiting time compared to state of the art non-stochastic algorithms.Comment: Submitting to the IEEE International Conference on Intelligent Transportation Systems 201

Doping dependent Irreversible Magnetic Properties of Ba(Fe1-xCox)2As2 Single Crystals

We discuss the irreversible magnetic properties of self-flux grown Ba(Fe1-xCox)2As2 single crystals for a wide range of concentrations covering the whole phase diagram from the underdoped to the overdoped regime, x=0.038, 0.047, 0.058, 0.071, 0.074, 0.10, 0.106 and 0.118. Samples were characterized by a magneto-optical method and show excellent spatial uniformity of the superconducting state. The overall behavior closely follows classical Bean model of the critical state. The field-dependent magnetization exhibits second peak at a temperature and doping - dependent magnetic field, Hp. The evolution of this fishtail feature with doping is discussed. Magnetic relaxation is time-logarithmic and unusually fast. Similar to cuprates, there is an apparent crossover from collective elastic to plastic flux creep above Hp. At high fields, the field dependence of the relaxation rate becomes doping independent. We discuss our results in the framework of the weak collective pinning and show that vortex physics in iron-based pnictide crystals is much closer to high-Tc cuprates than to conventional s-wave (including MgB2) superconductors.Comment: for the special issue of Physica C on iron-based pnictide superconductor

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics