Related papers: Combining Metadynamics and Integrated Tempering Sa…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Ensemble forecasting is a technique devised to palliate sensitivity to initial conditions in nonlinear dynamical systems. The basic idea to avoid this sensitivity is to run the model many times under several slightly-different initial…
We present a method for modelling star-forming clouds that combines two different models of the thermal evolution of the interstellar medium (ISM). In the combined model, where the densities are low enough that at least some part of the…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system…
We study the sensitivity of thermometric probes that are composed of $N$ spins coupled to a sample prepared at temperature $T$. Our analysis extends beyond the weak-coupling limit into the strong sample-probe coupling regime. In particular,…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
We present here the preliminary results obtained for two experiments on randomly agitated granular assemblies using a novel way of shaking. First we discuss the transport properties of a 2D model system undergoing classical shaking that…
The self-organized Monte Carlo simulations of 2D Ising ferromagnet on the square lattice are performed. The essence of devised simulation method is the artificial dynamics consisting of the single-spin-flip algorithm of Metropolis…
Creating highly spin-squeezed states for quantum metrology surpassing the standard quantum limit is a topic of great interest. Spin squeezing has been achieved by either entangling different atoms in an ensemble, or by controlling the…
We introduce and illustrate a number of performance measures for rare-event sampling methods. These measures are designed to be of use in a variety of expanded ensemble techniques including parallel tempering as well as infinite and partial…
A theoretical treatment of deeply supercooled liquids is difficult because their properties emerge from spatial inhomogeneities that are self-induced, transient, and nanoscopic. I use computer simulations to analyse self-induced static and…
Quantum materials research requires co-design of theory with experiments and involves demanding simulations and the analysis of vast quantities of data, usually including pattern recognition and clustering. Artificial intelligence is a…
We present iterative Monte Carlo algorithm for which the temperature variable is attracted by a critical point. The algorithm combines techniques of single histogram reweighting and linear filtering. The 2d Ising model of ferromagnet is…
We report a weighing metrology experiment of a single silica microsphere optically trapped and immersed in air. Based on fluctuations about thermal equilibrium, three different mass measurements are investigated, each arising from one of…
Current methods to describe the thermodynamic behavior of many-particle systems are often based on perturbation theory with an unperturbed system consisting of free particles. Therefore, only a few methods are able to describe both strongly…
Entanglement plays a crucial role in proposals for quantum metrology, yet demonstrating quantum enhancement in sensing with sustained spin entanglement remains a challenging endeavor. Here, we combine optical pumping and continuous quantum…
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar…
Cloud microphysical parameterizations in atmospheric models describe the formation and evolution of clouds and precipitation, a central weather and climate process. Cloud-associated latent heating is a primary driver of large and…
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…