Related papers: Associative bond swaps in molecular dynamics
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Due to the complexity of the human body and its neuromuscular stabilization, it has been challenging to efficiently and accurately predict human motion and capture posture while being driven. Existing simple models of the seated human body…
When describing the low-energy physics of bosons in a double-well potential with a high barrier between the wells and sufficiently weak atom-atom interactions, one can to a good approximation ignore the high energy states and thereby obtain…
In this Letter, we present a simple model of aqueous interfacial molecular structure and we use this model to isolate the effects of hydrogen bonding on the dielectric properties of the liquid water-vapor interface. By comparing this model…
Simulating large-scale articulated assemblies poses a significant challenge due to the numerical stiffness and geometric complexity of jointed structures. Conventional rigid body solvers struggle with the high nonlinearity induced by…
We propose a coarse-grained model to investigate stress relaxation in star-polymer networks induced by dynamic bond exchange processes. We show how the swapping mechanism, once activated, allows the network to reconfigure, exploring…
A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
In this paper, we present a new multibody physics simulation framework that utilizes the subsystem-based structure and the Alternating Direction Method of Multiplier (ADMM). The major challenge in simulating complex high degree of freedom…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
We propose a new many-body method based on the correlation functions, in which the multiple products of the correlation functions are expanded into the many-body diagrams using the cluster expansion method and every diagram is independently…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD)…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
Non-Hermitian quantum many-body systems are a fascinating subject to be explored. Using the generalized density matrix renormalisation group method and complementary exact diagonalization, we elucidate the many-body ground states and…
A transferable tight-binding potential has been constructed for heteroatomic systems containing carbon and hydrogen. The electronic degree of freedom is treated explicitly in this potential using a small set of transferable parameters which…
Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally…
Active solids such as cell collectives, colloidal clusters, and active metamaterials exhibit diverse collective phenomena, ranging from rigid body motion to shape-changing mechanisms. The nonlinear dynamics of such active materials remains…
Rigid bodies, plastic impact, persistent contact, Coulomb friction, and massless limbs are ubiquitous simplifications introduced to reduce the complexity of mechanics models despite the obvious physical inaccuracies that each incurs…