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Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have…
Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the…
Understanding how protein mutations affect protein structure is essential for advancements in computational biology and bioinformatics. We introduce PRIMRose, a novel approach that predicts energy values for each residue given a mutated…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Given that the physical properties of polymeric liquids extend on a wide range of lengthscales, it is computationally convenient to represent them by coarse-grained (CG) descriptions at various granularities to investigate local and global…
The existence and search for thermodynamic phase transitions is of unfading interest. In this paper, we present numerical evidence of dynamical phase transitions occurring in boundary driven systems with a constrained integrated current. It…
Infrared vibrational spectroscopy in the gas phase has emerged as a powerful tool to determine complex molecular structures with Angstrom accuracy. Among the different approaches IRMPD (InfraRed Multiple Photon Dissociation), which requires…
In this article, we present an improved version of the PULSE method (Partition function Unsupervised Learning Sampling and Evaluation) for estimating the thermodynamic properties of chemically disordered compounds. The aim is to reduce the…
The formation and subsequent growth of structural defects in an irradiated material can strongly influence the material's performance in technological and industrial applications. Predicting how the growth of defects affects material…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
The grand partition function of a model of confined quarks is exactly calculated at arbitrary temperatures and quark chemical potentials. The model is inspired by a softly BRST-broken version of QCD and possesses a quark mass function…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we…
Shape had been intuitively recognized to play a dominant role in determining the global motion patterns of bio-molecular assemblies. However, it is not clear exactly how shape determines the motion patterns. What about the local…
Active matter systems are inherently out of equilibrium and break the detailed balance (DB) at the microscopic scale, exhibiting vital collective phenomena such as motility-induced phase separation (MIPS). Here, we introduce a…
The equilibrium behavior of binary mixtures can be understood through the competition of energy scales, which classifies their corresponding phase diagrams into distinct topological regimes (Types I-IV). However, in many soft-matter…
Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…
Climate models play a critical role in understanding and projecting climate change. Due to their complexity, their horizontal resolution of about 40-100 km remains too coarse to resolve processes such as clouds and convection, which need to…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…