Transition path theory for Markov jump processes

P Metzner, C Schütte, E Vanden-Eijnden - Multiscale Modeling & Simulation, 2009 - SIAM
The framework of transition path theory (TPT) is developed in the context of continuous-time
Markov chains on discrete state-spaces. Under assumption of ergodicity, TPT singles out …

Sodium binding sites and permeation mechanism in the NaChBac channel: A molecular dynamics study

C Guardiani, PM Rodger, OA Fedorenko… - Journal of Chemical …, 2017 - ACS Publications
NaChBac was the first discovered bacterial sodium voltage-dependent channel, yet
computational studies are still limited due to the lack of a crystal structure. In this work, a …

Increasing application performance in virtual environments through run-time inference and adaptation

AI Sundararaj, A Gupta… - HPDC-14. Proceedings …, 2005 - ieeexplore.ieee.org
Virtual machine distributed computing greatly simplifies the use of widespread computing
resources by lowering the level of abstraction, benefiting both resource providers and users …

Evaluation of network topology inference in opaque compute clouds through end-to-end measurements

D Battré, N Frejnik, S Goel, O Kao… - 2011 IEEE 4th …, 2011 - ieeexplore.ieee.org
Modern Infrastructure-as-a-Service (IaaS) clouds offer an unprecedented flexibility and
elasticity in terms of resource provisioning through the use of hardware virtualization …

Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems

L Meng, FK Sheong, X Zeng, L Zhu… - The Journal of Chemical …, 2017 - pubs.aip.org
Constructing Markov state models from large-scale molecular dynamics simulation
trajectories is a promising approach to dissect the kinetic mechanisms of complex chemical …

[PDF][PDF] Transition path theory for Markov processes

P Metzner - 2008 - core.ac.uk
Transition events in complex systems between long lived states are a key feature of many
systems arising in physics, chemistry, biology, etc. It was early recognized that transition …

Automatic dynamic run-time optical network reservations

JR Lange, AI Sundararaj… - HPDC-14. Proceedings …, 2005 - ieeexplore.ieee.org
Optical networking may dramatically change high performance distributed computing. One
reason is that optical networks can support provisioning dynamically configurable lightpaths …

An optimization problem in adaptive virtual environments

AI Sundararaj, M Sanghi, JR Lange… - ACM SIGMETRICS …, 2005 - dl.acm.org
A virtual execution environment consisting of virtual machines (VMs) interconnected with
virtual networks provides opportunities to dynamically optimize, at run-time, the performance …

Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

X Zeng, ZW Li, X Zheng, L Zhu, ZY Sun… - Physical Chemistry …, 2018 - pubs.rsc.org
Hollow polyhedral cages hold great potential for application in nanotechnological and
biomedical fields. Understanding the formation mechanism of these self-assembled …

Shoal: A network level moving target defense engine with software defined networking

L Wang - EAI Endorsed Transactions on Security and Safety, 2020 - publications.eai.eu
Abstract Moving Target Defense (MTD) was proposed as a promising defense paradigm to
introduce various uncertainties into computer systems, which can greatly raise the bar for the …