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Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
In soft matter systems the local displacement field can be accessed directly by video microscopy enabling one to compute local strain fields and hence the elastic moduli using a coarse-graining procedure. We study this process for a simple…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
We investigate how various coarse-graining methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the…
Reporting extensions of a recently developed approach to density functional theory with correct long-range be-havior (Phys. Rev. Lett. 94, 043002 (2005)). The central quantities are a splitting functional gamma[n] and a complementary…
We use an "equation-free", coarse-grained computational approach to accelerate molecular dynamics-based computations of demixing (segregation) of dissimilar particles subject to an upward gas flow (gas-fluidized beds). We explore the…
Coarse-grained (CG) modeling enables molecular simulations to reach time and length scales inaccessible to fully atomistic methods. For classical CG models, the choice of mapping, that is, how atoms are grouped into CG sites, is a major…
We show that for two classical brownian particles there exists an analog of continuous-variable quantum entanglement: The common probability distribution of the two coordinates and the corresponding coarse-grained velocities cannot be…
We study a classical model of isosceles triatomic "A-B-A" molecules. The atoms, considered mass points, interact mutually via a generic repulsive-attractive binary potential. First we show that the steady states, or relative equilibria…
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…
We investigate the steady state properties of an active fluid modeled as an assembly of soft repulsive spheres subjected to Gaussian colored noise. Such a noise captures one of the salient aspects of active particles, namely the persistence…
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…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
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…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
A microscopic theory for coarse graining diblock copolymers into dumbbells of interacting soft colloidal particles has been developed, based on the solution of liquid-state integral equations. The Ornstein-Zernike equation is solved to…