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SUMMARY:Accurate Diffusion Estimation From Simulation and the Impacts on T
 emperature Dependent Modelling - Dr Andrew McCluskey (University of Bristo
 l)
DTSTART:20250501T120000Z
DTEND:20250501T130000Z
UID:TALK228970@talks.cam.ac.uk
CONTACT:Anand Srinivasan
DESCRIPTION:Diffusion coefficients are routinely estimated from molecular 
 dynamics simulations by “fitting a straight line” to observe mean-squa
 red displacements (MSDs). Typically\, this fitting is performed without co
 nsidering fundamental concepts of displacements\, such as their heterosced
 asticity and correlation\, leading to a sub-optimal estimation method. The
 se diffusion coefficients are essential in modelling temperature-dependent
  behaviour and determining diffusion’s activation energy and mechanism.\
 n\nI will present a Bayesian scheme for estimating the diffusion coefficie
 nt from a single simulation trajectory with high statistical efficiency an
 d accurately estimating the uncertainty in the predicted value [1]. I will
  then discuss the impact of accurate uncertainty estimation on downstream 
 analysis\, including temperature-dependent behaviour [2\, 3]. Throughout t
 his seminar\, I will introduce kinisi\, a software package developed to im
 prove the analysis of molecular dynamics simulation [4].\n\nYou may enjoy 
 this seminar if you are interested in data analysis\, computational modell
 ing\, or open-source software.\n\n1. A. R. McCluskey\, S. W. Coles and B. 
 J. Morgan\, arXiv:2305.18244v5\, 2024. 2. A. R. McCluskey\, J. Chem. Educ.
 \, 2023\, 100(11)\, 4174–4176. 3. A. R. McCluskey\, S. W. Coles and B. J
 . Morgan\, In Preparation\, 2024. 4. A. R. McCluskey\, A. G. Squires\, J. 
 Dunn\, S. W. Coles and B. J. Morgan\, Journal of Open Source Software\, 20
 24\, 9\, 5984.
LOCATION:MR14\,  Centre for Mathematical Sciences\, Wilberforce Road\, Cam
 bridge
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