Tag: Molecular dynamics
SIDE models realistic biomolecular transition paths
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in ChemistryWhat the study found The study found that SIDE, a Stochastic Integro-Differential Equation approach based on the Langevin bridge formalism, can generate realistic transition paths between different conformations of large biomolecular systems. In the authors' description, it produces smooth, low-energy trajectories and often recovers experimentally supported intermediate states. Why the authors say this matters The…
Criegee intermediates show environment-dependent spectral shifts
What the study found The study found that the dynamics and infrared spectroscopy of two Criegee intermediates, H2COO and CH3CHOO, depend on the surrounding environment. In water droplets, both species can move easily between surface and interior positions, while on amorphous solid water at 50 K there is no observed surface diffusion over multiple nanoseconds.…
Charge sequence shapes nonlinear elasticity in polyampholyte chains
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What the study found A polyampholyte chain, a polymer with both positive and negative charges, can show continuous or sharp force-induced conformational transitions depending on electrostatic strength. The study also found an elastic softening regime in which the elastic modulus decreases exponentially with force. Why the authors say this matters The authors conclude that these…
Thermostat choices affect sampling in molecular dynamics simulations
What the study found Thermostat algorithms in constant-temperature molecular dynamics simulations do not all behave the same way. In this binary Lennard-Jones liquid glass-former model, the Nosé-Hoover chain and Bussi velocity-rescaling thermostats controlled temperature reliably, while the Grønbech-Jensen-Farago Langevin scheme gave the most consistent sampling of both temperature and potential energy. Why the authors say…