Related papers: Integrating Molecular Dynamics Simulations and Exp…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in…
Binary droplet collisions are of importance in a variety of practical applications comprising dispersed two-phase flows. The background of our research is the prediction of properties of particulate products formed in spray processes. To…
We propose a new model and estimation framework for spatiotemporal streamflow exceedances above a threshold that flexibly captures asymptotic dependence and independence in the tail of the distribution. We model streamflow using a mixture…
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…
Particle interactions are key elements of many dynamical systems. In the context of systems described by a Boltzmann equation, such interactions may be described by a collision integral, a multidimensional integral over the momentum-phase…
Atomic displacement parameters (ADPs) are crystallographic information that describe the statistical distribution of atoms around an atom site. Anisotropic ADPs by atom were directly derived from classical molecular dynamics (MD)…
Liquid polyamorphism is the intriguing possibility for a single component substance to exist in multiple liquid phases. We propose a minimal model for this phenomenon. Starting with a binary lattice model with critical azeotropy and…
It is found experimentally that the coexistence region of a vapor-liquid system or a binary mixture is substantially narrowed when the fluid is confined in a aerogel with a high degree of porosity (e.g. of the order of 95% to 99%). A…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
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…
We present an algorithm for computing melting points by autonomously learning from coexistence simulations in the NPT ensemble. Given the interatomic interaction model, the method makes decisions regarding the number of atoms and…
The model assumptions of the recently formulated framework of highly-anisotropic and strongly-dissipative hydrodynamics (ADHYDRO) are analyzed. In particular, we study dependence of numerical results on different forms of the entropy source…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
The fundamental measure approach to classical density functional theory has been shown to be a powerful tool to predict various thermodynamic properties of hard-sphere systems. We employ this approach to determine not only one-particle…
We have recently developed a breakthrough methodology for rapidly computing entropy in both solids and liquids by integrating a multiscale entropy approach (known as zentropy theory) with molecular dynamics (MD) simulations. This approach…
Simple data correlation of flashpoint data of binary mixture has been developed on a basic of rational reciprocal function. The new approximation requires has only two coefficients and needs the flashpoint temperature of the pure flammable…
Generating energy functions for heterogeneous systems suitable for quantitative and predictive atomistic simulations is a challenging undertaking. The present work combines a cluster-based approach with electronic structure calculations at…
Entropy estimation plays a crucial role in various fields, such as information theory, statistical data science, and machine learning. However, traditional entropy estimation methods often struggle with complex data distributions.…