Estimation of Free Energy Systematic Errors in Molecular Simulations of Globular Proteins Surrounded by Finite Water Clusters. One Center Multipole Expansion of Reaction Field Differences

1991 ◽  
Vol 6 (1-3) ◽  
pp. 175-184
Author(s):  
Tomasz A. Wesołowski
Keyword(s):  
Free Energy ◽  
Water Clusters ◽  
Molecular Simulations ◽  
Systematic Errors ◽  
Multipole Expansion ◽  
Globular Proteins ◽  
Reaction Field ◽  
Energy Systematic

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

scholarly journals Molecular-dynamics simulations of urea nucleation from aqueous solution

2014 ◽  
Vol 112 (1) ◽  
pp. E6-E14 ◽  
Author(s):  
Matteo Salvalaglio ◽  
Claudio Perego ◽  
Federico Giberti ◽  
Marco Mazzotti ◽  
Michele Parrinello
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Molecular Simulations ◽  
Finite Size ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Science And Engineering ◽  
Finite Size Effects ◽  
Dynamics Simulations ◽  
Insight Into

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Oxygen Reduction Reaction of PEMFC Cathode by Molecular Simulations

2010 ◽  
Vol 105-106 ◽  
pp. 698-700
Author(s):  
Chuang Liu ◽  
Yu Hou Wu ◽  
Hong Sun ◽  
Yu Lan Tang
Keyword(s):  
Free Energy ◽  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Molecular Simulations ◽  
Control Process ◽  
Catalyst Layer ◽  
Reduction Reaction ◽  
Cathode Catalyst ◽  
Cathode Catalyst Layer ◽  
Fourth Step

Cathode catalyst layer plays an important role in PEMFC. Electrochemical reaction in cathode catalyst layer is a control process for the performance in PEMFC. In this paper, oxygen reduction reaction (ORR) is studied by molecular simulations based on a series pathway which consist of four steps. We calculated the free energy of four steps respectively by molecular simulations. Comparing free energy of our steps, we found that the fourth step can release more energy than the other steps. At the same time, we found that the energy released in ORR is decreased with the increase of temperature. The process of the first step in the series pathway release less energy than that of other steps. The results are very helpful for optimization of construction in the cathode and improving performance of PEM fuel cell.

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