Browsing by Author "Lin, L"
Now showing items 117 of 17

A Mathematical Theory of Optimal Milestoning (with a Detour via Exact Milestoning)
Lin, L; Lu, Jianfeng; VandenEijnden, E (20170423)Milestoning is a computational procedure that reduces the dynamics of complex systems to memoryless jumps between intermediates, or milestones, and only retains some information about the probability of these jumps and the ... 
Adaptive local basis set for KohnSham density functional theory in a discontinuous Galerkin framework I: Total energy calculation
Lin, L; Lu, Jianfeng; Ying, L; Weinan, E (Journal of Computational Physics, 20120220)KohnSham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the KohnSham Hamiltonian generally results in a large number ... 
Analysis of time reversible bornoppenheimer molecular dynamics
Lin, L; Lu, Jianfeng; Shao, S (Entropy, 20140101)We analyze the time reversible BornOppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the BornOppenheimer molecular dynamics even with nonconvergent selfconsistent field iteration. ... 
Bayesian analysis of multitype recurrent events and dependent termination with nonparametric covariate functions
Lin, L; Luo, Sheng; Chen, BE; Davis, BR (Statistical Methods in Medical Research, 2015) 
Bayesian regression model for recurrent event data with eventvarying covariate effects and event effect
Lin, L; Luo, Sheng; Davis, BR (Journal of Applied Statistics, 2017) 
Consistency of financial interest disclosures in the biomedical literature: the case of coronary stents.
Califf, Robert M; Lin, L; Schulman, Kevin Alan; Seils, DM; Tzeng, JP; Weinfurt, Kevin Phillip (PLoS One, 20080507)BACKGROUND: Disclosure of authors' financial interests has been proposed as a strategy for protecting the integrity of the biomedical literature. We examined whether authors' financial interests were disclosed consistently ... 
Data augmentation for models based on rejection sampling.
Dunson, David B; Lin, L; Rao, V (Biometrika, 201606)We present a data augmentation scheme to perform Markov chain Monte Carlo inference for models where data generation involves a rejection sampling algorithm. Our idea is a simple scheme to instantiate the rejected proposals ... 
Decay estimates of discretized Green’s functions for Schrödinger type operators
Lin, L; Lu, Jianfeng (Science China Mathematics, 20160801)© 2016, Science China Press and SpringerVerlag Berlin Heidelberg.For a sparse nonsingular matrix A, generally A−1 is a dense matrix. However, for a class of matrices, A−1 can be a matrix with offdiagonal decay properties, ... 
Developing a simplified consent form for biobanking.
Beskow, LM; Friedman, JY; Hardy, NC; Lin, L; Weinfurt, Kevin Phillip (PLoS One, 20101008)BACKGROUND: Consent forms have lengthened over time and become harder for participants to understand. We sought to demonstrate the feasibility of creating a simplified consent form for biobanking that comprises the minimum ... 
ELSI: A Unified Software Interface for KohnSham Electronic Structure Solvers
Blum, Volker; Corsetti, F; Garcia, Ambrosia; Huhn, WP; Jacquelin, M; Jia, W; Lange, B; ... (15 authors) (20170701)Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on KohnSham densityfunctional theory. This problem must be addressed by essentially ... 
Fast construction of hierarchical matrix representation from matrixvector multiplication
Lin, L; Lu, Jianfeng; Ying, L (Journal of Computational Physics, 20110510)We develop a hierarchical matrix construction algorithm using matrixvector multiplications, based on the randomized singular value decomposition of lowrank matrices. The algorithm uses O(logn) applications of the matrix ... 
Multipole representation of the Fermi operator with application to the electronic structure analysis of metallic systems
Car, R; Lin, L; Lu, Jianfeng; Weinan, E (Physical Review B  Condensed Matter and Materials Physics, 20090303)We propose a multipole representation of the FermiDirac function and the Fermi operator and use this representation to develop algorithms for electronic structure analysis of metallic systems. The algorithm is quite simple ... 
Nextgeneration sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations.
Fullwood, Melissa J; Huss, M; Lee, J; Li, G; Lin, L; Ng, P; Shenolikar, Shirish; ... (8 authors) (PLoS One, 2011)DNA fragmentation is a wellrecognized hallmark of apoptosis. However, the precise DNA sequences cleaved during apoptosis triggered by distinct mechanisms remain unclear. We used nextgeneration sequencing of DNA fragments ... 
Novel loci and pathways significantly associated with longevity.
Bae, H; Bolund, L; Cao, H; Chen, H; Chi, LQ; Christensen, Kaare; Christiansen, L; ... (57 authors) (Sci Rep, 20160225)Only two genomewide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health ... 
PEXSI$Σ$: A Green's function embedding method for KohnSham density functional theory
Li, X; Lin, L; Lu, Jianfeng (20170423)In this paper, we propose a new Green's function embedding method called PEXSI$\Sigma$ for describing complex systems within the KohnSham density functional theory (KSDFT) framework, after revisiting the physics literature ... 
Polebased approximation of the Fermidirac function
Lin, L; Lu, Jianfeng; Weinan, E; Ying, L (Chinese Annals of Mathematics. Series B, 20091201)Two approaches for the efficient rational approximation of the FermiDirac function are discussed: one uses the contour integral representation and conformal mapping, and the other is based on a version of the multipole ... 
Rat intersubjective decisions are encoded by frequencyspecific oscillatory contexts.
de Lecea, L; Dunson, David B; Dzirasa, Kafui; Heffner, J; Lin, L; Schaich Borg, Jana; Srivastava, S (Brain Behav, 201706)INTRODUCTION: It is unknown how the brain coordinates decisions to withstand personal costs in order to prevent other individuals' distress. Here we test whether local field potential (LFP) oscillations between brain regions ...