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Complex systems often involve higher-order interactions which require us to go beyond their description in terms of pairwise networks. Triadic interactions are a fundamental type of higher-order interaction that occurs when one node…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
General formulas for calculating the several leading long-range interactions among three identical atoms where two atoms are in identical $S$ states and the other atom is in a $P$ state are obtained using perturbation theory for the…
Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…
In this paper, we present a method to project co-authorship networks, that accounts in detail for the geometrical structure of scientists collaborations. By restricting the scope to 3-body interactions, we focus on the number of triangles…
We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson-Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
By constructing a Landau-like energy functional, we investigate the molecular organization of a three-component mixture in cell membranes. In the strongly interacting limit, we model the interaction between molecules using pseudospin…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble…
A multi-component formalism is developed to describe three-body systems with nonstatic pairwise interactions and non-nucleonic degrees of freedom. The dressed-bag model for $NN$ interaction based on the formation of an intermediate…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Network interactions that are nonlinear in the state of more than two nodes - also known as higher-order interactions - can have a profound impact on the collective network dynamics. Here we develop a coupled cell hypernetwork formalism to…
The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…
We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…