Steady-state simulations using weighted ensemble path sampling.

J Chem Phys

Department of Computational Biology, University of Pittsburgh, Pennsylvania 15260, USA.

Published: July 2010

We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing ideas, which accelerates attainment of steady state in complex systems. We apply both WE approaches to several model systems, confirming their correctness and efficiency by comparison with brute-force results. The enhanced version is significantly faster than the brute force and straightforward WE for systems with WE bins that accurately reflect the reaction coordinate(s). The new WE methods can also be applied to equilibrium sampling, since equilibrium is a steady state.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912933PMC
http://dx.doi.org/10.1063/1.3456985DOI Listing

Publication Analysis

Top Keywords

steady state
12
weighted ensemble
8
ensemble path
8
path sampling
8
steady-state simulations
4
simulations weighted
4
sampling
4
sampling extend
4
extend weighted
4
sampling method
4

Similar Publications

: Bempedoic acid (BA) is a novel cholesterol-lowering agent with proven positive effects on cardiovascular endpoints. Because it is an inhibitor of the hepatic transporters OATP1B1 and OATP1B3, two uptake transporters regulating the intrahepatic availability of statins, it increases the systemic exposure of co-administered statins. This interaction could raise the risk of myopathy.

View Article and Find Full Text PDF

The durability of reinforced concrete is associated with several factors that can trigger the corrosion of reinforcement bars. Among these factors, the most significant are chloride-ion attack and carbonation. This study evaluated, through accelerated testing, self-compacting concretes (SCCs) with reduced cement content in binary, ternary, and quaternary mixtures using high-early-strength Portland cement, fly ash (FA), metakaolin (MK), and hydrated lime (HL).

View Article and Find Full Text PDF

This work investigated the CrNiMo stainless steel using laser selective melting (SLM) technology and explored the effect of the tempering temperature on the microstructure and properties. After the tempering treatment, the quenched martensite transformed from a metastable to steady state, and residual austenite was formed. The results indicated that the elongation of the transverse specimen showed an upward trend as the tempering temperature increased, while the elongation of the longitudinal specimen first increased and then decreased.

View Article and Find Full Text PDF

Several mutations of the uppermost arginine, R219, in the voltage-sensing sliding helix S4 of cardiac sodium channel Nav1.5 are reported in the ClinVar databases, but the clinical significance of the respective variants is unknown (VUSs). AlphaFold 3 models predicted a significant downshift of S4 in the R219C VUS.

View Article and Find Full Text PDF

Human hematopoietic stem cells (HSCs) have traditionally been viewed as self-renewing, multipotent cells with enormous potential in sustaining essential steady state blood and immune cell production throughout life. Indeed, around 86% (10-10) of new cells generated daily in a healthy young human adult are of hematopoietic origin. Therapeutically, human HSCs have contributed to over 1.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!