Related papers: Coarse-grained protein-protein stiffnesses and dyn…
Fluctuations of the instantaneous local Lagrangian strain $\epsilon_{ij}(\bf{r},t)$, measured with respect to a static ``reference'' lattice, are used to obtain accurate estimates of the elastic constants of model solids from atomistic…
We poorly understand the macroscopic properties of complex fluids and of amorphous bodies in general. This is mainly due to the interplay between phenomena at different levels and length-scales. In particular, it is not necessarily true…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin…
We present a comprehensive study of the discretized modes of an atomic gas in different conditions of confinement. Starting from the equations of hydrodynamics we derive a closed equation for the velocity field, depending on the adiabatic…
We present a new computational framework combining coarse-graining techniques with bootstrap methods to study quantum many-body systems. The method efficiently computes rigorous upper and lower bounds on both zero- and finite-temperature…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Facilitated or kinetically constrained spin models (KCSM) are a class of interacting particle systems reversible w.r.t. to a simple product measure. Each dynamical variable (spin) is re-sampled from its equilibrium distribution only if the…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Many-body systems relaxing to equilibrium can exhibit complex dynamics even if their steady state is trivial. At low temperatures or high densities their evolution is often dominated by steric hindrances affecting particle motion [1,2,3].…
Protein-stabilised emulsions can be seen as mixtures of unadsorbed proteins and of protein-stabilised droplets. To identify the contributions of these two components to the overall viscosity of sodium caseinate o/w emulsions, the…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Static and dynamic analysis of the fracture tests of fiber composites in hydraulically servo-controlled testing machines currently in use shows that their grips are much too soft and light for observing the postpeak softening. Based on…
Stress-strain relations for random packings of entangling chains under triaxial compression can exhibit strain stiffening and sustain stresses several orders-of-magnitude beyond typical granular materials. X-ray tomography reveals the…
3D Computer simulations and experiments are employed to study random packings of compressible spherical grains under external confining stress. Of particular interest is the rigid ball limit, which we describe as a continuous transition in…