Related papers: Hierarchical Multiscale Modeling of Macromolecules…
Atomic nuclei exhibit multiple energy scales ranging from hundreds of MeV in binding energies to fractions of an MeV for low-lying collective excitations. As the limits of nuclear binding is approached near the neutron- and proton…
Molecular dynamics simulations are performed to investigate heterogeneous dynamics in amorphous glassy materials under oscillatory shear strain. We consider three-dimensional binary Lennard-Jones mixture well below the glass transition…
We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the…
The macroscopic behaviour of active matter arises from nonequilibrium microscopic processes. In soft materials, active stresses typically drive macroscopic shape changes, which in turn alter the geometry constraining the microscopic…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid…
We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using…
Mathematical models of biological populations commonly use discrete structure classes to capture trait variation among individuals (e.g. age, size, phenotype, intracellular state). Upscaling these discrete models into continuum descriptions…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
Mesoscopic $N-$atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. An efficient method for understanding these systems in the friction dominated regime from the…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
This paper describes a 2D and 3D simulation engine that quantitatively models the statics, dynamics, and non-linear deformation of heterogeneous soft bodies in a computationally efficient manner. There is a large body of work simulating…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…