Koen Visscher
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View article: Miniature microscopes for manipulating and recording <i>in vivo</i> brain activity
Miniature microscopes for manipulating and recording <i>in vivo</i> brain activity Open
Here we describe the development and application of miniature integrated microscopes (miniscopes) paired with microendoscopes that allow for the visualization and manipulation of neural circuits in superficial and subcortical brain regions…
View article: Calibration of next generation first-principle derived polarizable force fields
Calibration of next generation first-principle derived polarizable force fields Open
Driven by the constant increase in computational resources and power, modeling of biomolecular systems is now more accessible than ever. As simulation time and system size barriers are continuously pushed, the proper treatment of the under…
View article: Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration
Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration Open
Force field parametrization involves a complex set of linked optimization problems, with the goal of describing complex molecular interactions by using simple classical potential-energy functions that model Coulomb interactions, dispersion…
View article: Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model
Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model Open
In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategie…
View article: A QM/MM Derived Polarizable Water Model for Molecular Simulation
A QM/MM Derived Polarizable Water Model for Molecular Simulation Open
In this work, we propose an improved QM/MM-based strategy to determine condensed-phase polarizabilities and we use this approach to optimize a new and simple polarizable four-site water model for classical molecular simulation. For the det…
View article: Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors
Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors Open
View article: A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols
A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols Open
In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes o…
View article: −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process
−1 Programmed Ribosomal Frameshifting as a Force-Dependent Process Open