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A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefficients depend on chain configuration is proposed for self-assembly of DBCP/NP composites. Increasing NP…
This work presents new parallelizable numerical schemes for the integration of Dissipative Particle Dynamics with Energy conservation (DPDE). So far, no numerical scheme introduced in the literature is able to correctly preserve the energy…
Diffeomorphic matching (only one of several names for this technique) is a technique for non-rigid registration of curves and surfaces in which the curve or surface is embedded in the flow of a time-series of vector fields. One seeks the…
Solving partial differential equations (PDEs) on fine spatio-temporal scales for high-fidelity solutions is critical for numerous scientific breakthroughs. Yet, this process can be prohibitively expensive, owing to the inherent complexities…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
We propose in this paper a Proper Generalized Decomposition (PGD) solver for reduced-order modeling of linear elastodynamic problems. It primarily focuses on enhancing the computational efficiency of a previously introduced PGD solver based…
We present a mesoscopic approach to granular crystal dynamics, which comprises a three-dimensional finite-element model and a one-dimensional regularized contact model. The approach investigates the role of vibrational-energy trapping…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
We analyze the phase diagram of a quantum particle confined to a finite chain, subject to a dissipative environment described by an Ohmic spectral function. Analytical and numerical techniques are employed to explore both the perturbative…
Herein, we describe new methods to produce colloidal particle chains of three stiffness regimes that can be observed on a single-particle level, that is, on the level of the monomers that make up the chain; the chains can even be observed…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
The mesoscopic modeling of three polysiloxanes in solution is reported in this work, with the purpose of predicting their physicochemical properties as functions of the quality of the solvent, so that a judicious choice of polymer/solvent…
We model a microchannel cooling system and consider the optimization of its shape by means of shape calculus. A three-dimensional model covering all relevant physical effects and three reduced models are introduced. The latter are derived…
We present the Multi-Particle-Collision (MPC) dynamics approach to simulate properties of low-dimensional systems. In particular, we illustrate the method for a simple model: a one-dimensional gas of point particles interacting through…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
We present a microscopic approach to quantum dissipation and sketch the derivation of the kinetic equation describing the evolution of a simple quantum system in interaction with a complex quantum system. A typical quantum complex system is…
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…