Dataset Information

Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

ABSTRACT: The potential of molecular simulations is limited by their computational costs. There is often a need to accelerate simulations using some of the enhanced sampling methods. Metadynamics applies a history-dependent bias potential that disfavors previously visited states. To apply metadynamics, it is necessary to select a few properties of the system─collective variables (CVs) that can be used to define the bias potential. Over the past few years, there have been emerging opportunities for machine learning and, in particular, artificial neural networks within this domain. In this broad context, a specific unsupervised machine learning method was utilized, namely, parametric time-lagged t-distributed stochastic neighbor embedding (ptltSNE) to design CVs. The approach was tested on a Trp-cage trajectory (tryptophan cage) from the literature. The trajectory was used to generate a map of conformations, distinguish fast conformational changes from slow ones, and design CVs. Then, metadynamic simulations were performed. To accelerate the formation of the α-helix, we added the α-RMSD collective variable. This simulation led to one folding event in a 350 ns metadynamics simulation. To accelerate degrees of freedom not addressed by CVs, we performed parallel tempering metadynamics. This simulation led to 10 folding events in a 200 ns simulation with 32 replicas.

SUBMITTER: Hradiska H

PROVIDER: S-EPMC10839826 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

Hradiská Helena H Kurečka Martin M Beránek Jan J Tedeschi Guglielmo G Višňovský Vladimír V Křenek Aleš A Spiwok Vojtěch V

The journal of physical chemistry. B 20240118 4

The potential of molecular simulations is limited by their computational costs. There is often a need to accelerate simulations using some of the enhanced sampling methods. Metadynamics applies a history-dependent bias potential that disfavors previously visited states. To apply metadynamics, it is necessary to select a few properties of the system─collective variables (CVs) that can be used to define the bias potential. Over the past few years, there have been emerging opportunities for machine ...[more]

PMID: 38237064

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Project description:BackgroundLeprosy is an illness persisting for a long time or constantly recurring brought about by Mycobacterium leprae. The collusion of the causing agent with Schwann cells leads to incapable of being changed loss of fringe nerve tissue; followed by incapacity and that is not restricted to actual powerlessness yet additionally makes a negative picture, prompting segregation and social disgrace against the altered people also, their families.MethodsThe analysis of this study comprises 205 samples of patients at All African TB and Leprosy Rehabilitation and Training Centre from January 2015 up to December 2019 G.C who were taking medication for leprosy and who possess all necessary data. Territorial conditions in the region of the patients were utilized as a clustering impact in all frailty models. Acceleration failure time models and parametric shared frailty models with Weibull and log-strategic patterns were utilized to dissect hazard factors related to disability ensued by leprosy. All fitted models were looked at by utilizing AIC.ResultsFrom that of 205, 69(33.7%) experienced at least one kind of disability grade during treatment taking. In light of AIC, log-logistic-gamma shared frailty model was the final best fitting model and also there was considerable variation among patients. The final model showed the age of patients, symptom duration, treatment category of patients, and sensory loss were found to be the most significant determinants of leprosy disability.ConclusionIn this investigation, there is proof of heterogeneity at the group level and disability was related to the age of patients, symptom duration, treatment category of patient, what's more, sensory loss subsequently, uncommon consideration ought to be given to these huge indicators, which eventually diminish the event of disability. To lessen the patient-related postponement, the program should lay more noteworthy accentuation on bringing issues to light in the local area by zeroing in on key messages like indications, inability result of the late discovery, accessibility of free treatment what's more, accessibility of disease care in general wellbeing office.

Dataset Information

Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

Publications

Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics.

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