Now showing items 1-20 of 84

• An incremental constraint-based framework for task and motion planning ﻿

(2018)
We present a new constraint-based framework for task and motion planning (TMP). Our approach is extensible, probabilistically complete, and offers improved performance and generality compared with a similar, state-of-the-art ...
• Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods ﻿

(2018)
The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational ...
• Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells ﻿

(2018)
Interrupting the interplay between cancer cells and extracellular matrix (ECM) is a strategy to halt tumor progression and stromal invasion. Perlecan/heparan sulfate proteoglycan 2 (HSPG2) is an extracellular proteoglycan ...
• Bayesian inference of phylogenetic networks from bi-allelic genetic markers ﻿

(2018)
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence ...
• Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data ﻿

(2018)
Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein structure. However, experimentally observing and computationally ...
• Quantitative comparison of adaptive sampling methods for protein dynamics ﻿

(2018)
Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. ...
• Inference of species phylogenies from bi-allelic markers using pseudo-likelihood ﻿

(2018)
MOTIVATION: Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses ...
• Syzygies for translational surfaces ﻿

(2018)
A translational surface is a rational tensor product surface generated from two rational space curves by translating one curve along the other curve. Translational surfaces are invariant under rigid motions: translating ...
• A Polynomial Blossom for the Askey–Wilson Operator ﻿

(2018)
We introduce a blossoming procedure for polynomials related to the Askey–Wilson operator. This new blossom is symmetric, multiaffine, and reduces to the complex representation of the polynomial on a certain diagonal. This ...
• q-Blossoming for analytic functions ﻿

(2018)
We construct aﾠq-analog of the blossom for analytic functions, the analyticﾠq-blossom. Thisﾠq-analog also extends the notion ofﾠq-blossoming from polynomials to analytic functions. We then apply this analyticﾠq-blossom to ...
• General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept ﻿

(2018)
The class I major histocompatibility complex (MHC) is capable of binding peptides derived from intracellular proteins and displaying them at the cell surface. The recognition of these peptide-MHC (pMHC) complexes by T-cells ...
• Efficacy of Novel Carbon Nanoparticle Antioxidant Therapy in a Severe Model of Reversible Middle Cerebral Artery Stroke in Acutely Hyperglycemic Rats ﻿

(2018)
INTRODUCTION: While oxidative stress can be measured during transient cerebral ischemia, antioxidant therapies for ischemic stroke have been clinically unsuccessful. Many antioxidants are limited in their range and/or ...
• Platform-Independent Benchmarks for Task and Motion Planning ﻿

(2018)
We present the first platform-independent evaluation method for task and motion planning (TAMP). Previously point, various problems have been used to test individual planners for specific aspects of TAMP. However, no common ...
• SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models ﻿

(2017-09-19)
Abstract Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under ...
• A review of parameters and heuristics for guiding metabolic pathfinding ﻿

(2017-09-15)
Abstract Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, ...
• Strong $\mu$-Bases for Rational Tensor Product Surfaces and Extraneous Factors Associated to Bad Base Points and Anomalies at Infinity ﻿

(2017)
We investigate conditions under which the resultant of a $\mu$-basis for a rational tensor product surface is the implicit equation of the surface without any extraneous factors. In this case, we also derive a formula for ...
• An Automated System for Interactively Learning Software Testing ﻿

(2017)
Testing is an important, time-consuming, and often difficult part of the software development process. It is therefore critical to introduce testing early in the computer science curriculum, and to provide students with ...
• Continuous checkpointing of HTM transactions in NVM ﻿

(2017)
This paper addresses the challenges of coupling byte addressable non-volatile memory (NVM) and hardware transaction memory (HTM) in high-performance transaction processing. We first show that HTM transactions can be ordered ...
• Reconstructing rooms using photon echoes: A plane based model and reconstruction algorithm for looking around the corner ﻿

(2017)
Can we reconstruct the entire internal shape of a room if all we can directly observe is a small portion of one internal wall, presumably through a window in the room? While conventional wisdom may indicate that this is ...
• Present but Unreachable: Reducing Persistentlatent Secrets in HotSpot JVM ﻿

(2017)
Applications that manage sensitive secrets, including cryptographic keys, are typically engineered to overwrite the secrets in memory once they’re no longer necessary, offering an important defense against forensic attacks ...