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Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics.
We propose an approximate method for calculating Kubo-transformed real-time correlation functions involving position-dependent operators, based on path integral (Parrinello-Rahman) molecular… Expand
A refined ring polymer molecular dynamics theory of chemical reaction rates.
We further develop the ring polymer molecular dynamics (RPMD) method for calculating chemical reaction rates [I. R. Craig and D. E. Manolopoulos, J. Chem. Phys. 122, 084106 (2005)]. We begin by… Expand
Chemical reaction rates from ring polymer molecular dynamics.
We show how the ring-polymer molecular dynamics method can be adapted to calculate approximate Kubo-transformed flux-side correlation functions, and hence rate coefficients for condensed phase… Expand
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
This paper provides quantitative evidence that in some cases docking into a crystallographically derived conformational ensemble does indeed yield better enrichment than docking into any of the individual members of the ensemble. Expand
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins
- I. R. Craig, Christopher Pfleger, H. Gohlke, J. Essex, K. Spiegel
- Computer Science, Medicine
- J. Chem. Inf. Model.
- 30 September 2011
We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm to identify novel binding-site conformations that are yet to be observed crystallographically. Expand
Visual accomodation problems with head-up and helmet-mounted displays?
Virtual-image displays are likely to become more prominent in the aircraft cockpit, the most common examples being the head-up display (HUD) and, more recently, the helmet-mounted display (HMD).… Expand
A Novel Single-Site Mutation in the Catalytic Domain of Protoporphyrinogen Oxidase IX (PPO) Confers Resistance to PPO-Inhibiting Herbicides
- G. Rangani, Reiofeli A. Salas-Perez, +7 authors N. Roma-Burgos
- Chemistry, Medicine
- Front. Plant Sci.
- 15 May 2019
Protoporphyrinogen oxidase (PPO)-inhibiting herbicides are used to control weeds in a variety of crops. These herbicides inhibit heme and photosynthesis in plants. PPO-inhibiting herbicides are used… Expand
Proton transfer in a polar solvent from ring polymer reaction rate theory.
- Rosana Collepardo-Guevara, I. R. Craig, D. Manolopoulos
- Chemistry, Medicine
- The Journal of chemical physics
- 9 April 2008
We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H… Expand
Proton transfer reactions in model condensed-phase environments: Accurate quantum dynamics using the multilayer multiconfiguration time-dependent Hartree approach.
The recently proposed multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) approach to evaluating reactive quantum dynamics is applied to two model condensed-phase proton transfer… Expand
Inelastic neutron scattering from liquid para-hydrogen by ring polymer molecular dynamics
Abstract We investigate the use of the ring polymer molecular dynamics (RPMD) method to calculate the incoherent dynamic structure factor of liquid para -hydrogen at a temperature of 14 K. Two… Expand