Coarse-grained (CG) molecular simulations offer an efficient alternative to atomistic molecular dynamics to study large and complex biological systems. The accuracy of CG simulations has been increased dramatically by the introduction of machine-learned coarse-grained (MLCG) models. However, these models are typically designed to be used at a single thermodynamic point, lack temperature transferability, and can not be used to predict temperature dependent quantities like the heat capacity. Here we introduce a thermodynamically informed, temperature-transferable MLCG framework for proteins that explicitly decomposes the CG potential of mean force (PMF) into its energetic and entropic components. The model architecture enforces an exact thermodynamic relation between the energetic and entropic components of the PMF and guarantees physically consistent extrapolation and interpolation across temperature regimes. We validate this framework on an extensive dataset spanning a total of 250 $μ$s of molecular dynamics simulations across five temperatures between 300 K and 400 K for the Chignolin protein, and demonstrate that it reproduces the temperature dependency of the reference atomistic free energy surfaces, correcting the temperature-unaware baselines. Furthermore, we show that it is possible to apply an inexpensive, post-hoc temperature-dependent correction that does not require retraining the MLCG potential, accurately recovering the atomistic heat capacity at different temperatures. Overall, this work provides a physically grounded pathway toward thermodynamically transferable MLCG simulations of complex biomolecular systems.

Neural Information Processing Systems http://nips.cc/

Large pretrained models can be used as annotators, helping replace or augment crowdworkers and enabling distilling generalist models into smaller specialist models.

Now, let us derive the differential equation that gives a solution to the variational problem. This condition yields the Euler-Lagrange equation, d dt @ L @ q = @ L @q . Here, we derive the Noether's learning dynamics by applying Noether's theorem to the A general form of the Noether's theorem relates the dynamics of Noether By evaluating the right hand side of Eq. 23, we get e Now, we harness the covariant property of the Lagrangian formulation, i.e., it preserves the form Plugging this expression obtained from the steady-state condition of Eq.27 Here, we ignore the inertia term in Eq. 16, assuming that the mass (learning rate) is finite but small All the experiments were run using the PyTorch code base. We used Tiny ImageNet dataset to generate all the empirical figures in this work. The key hyperparameters we used are listed with each figure.

In this work we tested a relatively small number ofPathTracker versions. We mostly focused on small variations to the number of distractors and video length, but in future work we hope to incorporate other variations like speed and velocity manipulations, and generalization across temporalvariations[1]. One potential issue is determining when a visual system should rely on appearance-based vs. appearance-free features for tracking. Our solution is two-pronged and potentially insufficient. The first strategy is for top-down feedback from the TransT into the InT,which we aligns tracks between the two models.

General information: As specified in section3 and 5, we test a single model definition for all experiments in this work, with one layer of dynamic weightsWt. This layer consists in a dense matrix ofsizen Nwith learnt orrandom initialization.

By plugging in Eq. (4), we have X Next, we derive the dynamics of the membrane potential. For the E neurons, we proceed similarly. We cite a theorem from [46]. We apply Thm. 1 to our minimax objective, for the maximization problem with The last two terms are related to nonlinear neural activations. Next we show that the energy function is decreasing.