Related papers: Force field optimization by imposing kinetic const…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when…
We investigate the maximum caliber variational principle as an inference algorithm used to predict dynamical properties of complex nonequilibrium, stationary, statistical systems in the presence of incomplete information. Specifically, we…
This article proposes an improved trajectory optimization approach for stochastic optimal control of dynamical systems affected by measurement noise by combining optimal control with maximum likelihood techniques to improve the reduction of…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
Foundational Machine Learning Potentials can resolve the accuracy and transferability limitations of classical force fields. They enable microscopic insights into material behavior through Molecular Dynamics simulations, which can crucially…
Atomic-scale modeling has advanced rapidly through integration of machine learning, yet a key bottleneck remains. Even with an accurate potential energy surface and a clear target material, we still lack a practical atomistic dynamics…
Dynamical reweighting of path measures is a powerful approach for accurately evaluating slow molecular processes using modified potential energy surfaces used in enhanced sampling methods. Integrating this reweighting framework into the…
A new approach for generating stress-constrained topological designs in continua is presented. The main novelty is in the use of elasto-plastic modeling and in optimizing the design such that it will exhibit a linear-elastic response. This…
Simulations with an explicit description of intermolecular forces using electronic structure methods are still not feasible for many systems of interest. As a result, empirical methods such as force fields (FF) have become an established…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Reactive force fields for molecular dynamics have enabled a wide range of studies in numerous material classes. These force fields are computationally inexpensive as compared to electronic structure calculations and allow for simulations of…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent,…
We propose a protocol optimization technique that is applicable to both weighted or unweighted graphs. Our aim is to explore by how much a small variation around the Shortest Path or Optimal Path protocols can enhance protocol performance.…
Equations governing the nonlinear dynamics of complex systems are usually unknown and indirect methods are used to reconstruct their manifolds. In turn, they depend on embedding parameters requiring other methods and long temporal sequences…
The accuracy of molecular simulations is fundamentally limited by the interatomic potentials that govern atomic interactions. Traditional potential development, which relies heavily on ab initio calculations, frequently struggles to…
Computationally intractable tasks are often encountered in physics and optimization. Such tasks often comprise a cost function to be optimized over a so-called feasible set, which is specified by a set of constraints. This may yield, in…