Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 9 of 9 for “"Biomolecular simulations"”.
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Biomolecular Simulations with Machine Learning Potentials
… crystals, is tested on out-of- distribution biomolecular systems, demonstrating qualitatively accurate predictions. We further demonstrate that these predictions can be improved by finetuning the foundation model on the system of interest.
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Fast Polarizable Force Field Computation in Biomolecular Simulations
… in the next-generation force fields used in biomolecular simulations. The self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense linear system at each timestep in molecular dynamics simulations. Methods are …
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Mapping Ligand Binding Sites in hERG1 Channel with Biomolecular Simulations
The human ether-a-go-go related gene 1 (hERG1) K+ ion channel generates the rapid delayed rectifier potassium current, or IKr, which is essential for the normal repolarization phase in the ventricular action potential. The drug-induced blockade of the channel is a frequent side effect of various …
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Encouraging collaboration through a new data management approach
… in data loss, inaccessibility or repetition of simulations. We propose a framework which promotes collaboration and simplifies data management. In particular we have demonstrated the proposed framework in the scenario of handling large scale data generated from biomolecular simulations in a …
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Modeling larger length and time scales in machine learning force fields
Molecular dynamics simulations describe the collective motion of atoms over time, enabling the study of fundamental processes across physics, chemistry, and biology. This has established molecular dynamics as a cornerstone of modern science and improving its accuracy has a long standing history in …
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Fluctuations and Instantons in Complex Landscapes: From Ligand Unbinding to Proton Transfer
… several techniques are developed to accelerate biomolecular simulations while collaterally lending physical insight. The first segment of this dissertation is concerned with directed simulations of ligand binding in a model system. Using the serum retinol binding protein as a prototype, the …
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Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber
… of electrostatic interactions in the target biomolecular structure. In practical molecular simulations, the electrostatic charge density of molecules is approximated by an arrangement of fractional "point charges" throughout the molecule. While chemically intuitive and straightforward in …
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Multiscale Modelling of Biomolecular Phase Behaviour
… along such wide-ranging spatial scales. Simulations with a minimal coarse-grained model showed how enriching the structural ensemble of proteins in open, expanded conformations can promote their propensity to undergo liquid-liquid phase separation. This is because more expanded …