相关论文: Correction of coarse-graining errors by a two-leve…

We present results for many-body perturbation theory for the one-body Green's function at finite temperatures using the Matsubara formalism. Our method relies on the accurate representation of the single-particle states in standard Gaussian…

In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…

Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…

Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient physical quantities of its AA model,…

The theoretical study of ultracold few-body systems is often done using an idealized 1D model with zero range interactions. Here we study these systems using a more realistic 3D model with finite range interactions. We place…

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…

We formulate an effective-description framework for the dynamics of open quantum systems by extending the time-coarse-graining formalism to open systems. Our coarse-graining procedure efficiently removes high-frequency processes which are…

The macroscopic properties of materials that we observe and exploit in engineering application result from complex interactions between physics at multiple length and time scales: electronic, atomistic, defects, domains etc. Multiscale…

Model order reduction encompasses mathematical techniques aimed at reducing the complexity of mathematical models in simulations while retaining the essential characteristics and behaviors of the original model. This is particularly useful…

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…

This thesis introduces a framework that is able to describe general many-body coarse-grained interactions. We make use of this to describe the free energy surface as a cluster expansion in terms of monomer, dimer, and trimer terms. The…

A numerical model able to simulate the grain breakage with the discrete element method, using the "Non-Smooth Contact Dynamics" is presented. The model reproduces 3D grains having complex shapes and is tested in single grain and in…

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…

Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…

The Ohta-Kawasaki equation models the mesoscopic phase separation of immiscible polymer chains that form diblock copolymers, with applications in directed self-assembly for lithography. We perform a mathematical analysis of this model under…

The automated construction of coarse-grained models represents a pivotal component in computer simulation of physical systems and is a key enabler in various analysis and design tasks related to uncertainty quantification. Pertinent methods…

Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination…

Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for the study of complex systems. This paper examines the use…

Coarse-grained (CG) force field models are extensively utilised in material simulations due to their scalability. Traditionally, these models are parameterized using hybrid strategies that integrate top-down and bottom-up approaches;…