Related papers: Mass-scaling replica-exchange molecular dynamics o…
Mixtures of linear dynamical systems (MoLDS) provide a path to model time-series data that exhibit diverse temporal dynamics across trajectories. However, its application remains challenging in complex and noisy settings, limiting its…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function $E_0$ by adding any physical quantity $V$ of interest as a new…
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Inference-time control of diffusion models aims to steer model outputs to satisfy new constraints without retraining. Previous approaches have mostly relied on heuristic guidance or have been coupled with Sequential Monte Carlo (SMC) for…
We propose a new method for the determination of the weight factor for the simulated tempering method. In this method a short replica-exchange simulation is performed and the simulated tempering weight factor is obtained by the…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…