The Generalized Langevin Equation (GLE) is an integro-differential equation of motion for a general observable of a many-body system and is rigorously derived using the projection operator formalism. In the standard derivation, a stationary canonical phase space distribution is used for the projection. Here, we derive a novel class of GLEs using a non-stationary projection distribution that constrains the initial ensemble to a hypersurface in phase space on which the observable has a fixed value $A_0$. As a result, all GLE parameters, and in particular the memory friction kernel, depend on $A_0$ and can be extracted from short simulations that do not sample the entire phase space. Applying this non-stationary GLE to protein folding trajectories, we find for villin and an $\alpha$-helical poly-alanine segment that the total friction is higher in the folded state. These results demonstrate that observable-dependent friction effects are non-negligible and can be accounted for using non-stationary GLEs derived by constrained projection schemes.
We investigate the open quantum dynamics of a system of two masses interacting with an environment of linearized gravitational waves. We formulate the analysis in terms of the observable proper distance between the two masses, and show that the canonical variables obtained from the standard Lagrangian, expressed in ter...
O. Angeli, Anirudh Gundhi, Angelo Bassi· 0 citations
We present a general framework for simulating the nonequilibrium vibronic dynamics of molecules interacting with metal surfaces, which utilizes non-Markovian electronic friction and the corresponding generalized Langevin equation. The method employs a Markovian embedding scheme to sample coordinate-dependent quantum co...
S. Rudge, R. Preston, D. Kosov et al.· 0 citations
Establishing a robust and physically interpretable link between static structure and heterogeneous relaxation dynamics remains a fundamental challenge in glass physics. Here, we introduce a weighted pair-entropy descriptor based on the conventional two-body excess entropy. For this, we multiply the integrand used to ca...
Jun Wu, Walter Kob, Yu-Jie Wang et al.· 0 citations
Understanding how collective ion transport emerges from equilibrium fluctuations is central to electrolyte statistical mechanics. Finite-volume fluctuations provide an accessible route to this information, but their interpretation is complicated because they mix wave numbers and collective fields. Here, we extend the f...
An overarching goal of statistical physics is to derive macroscopic irreversible equations starting with microscopic reversible equations of motion. The Mori-Zwanzig Projection Operator Method achieves this by projecting out the motions of irrelevant variables and studying the equations of the relevant variables. Thi...
Pabitra N. Sen· European journal of physics· 0 citations
Large-scale coarse-grained simulations of anisotropic particles require compact interaction models that retain orientation-dependent energetics. We present a symmetry-constrained Fourier--Morse framework in which the radial interaction is described by a Morse potential and its orientational dependence by Fourier expans...
Hadis Ghodrati, S. Gemming, Florian Günther et al.· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
