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Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
A rich literature has been produced on the quantum states of atoms and molecules confined into infinite potential wells with a specified symmetry. Apart from their interest as basic quantum systems, confined atoms and molecules are useful…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
For microwave-dressed polar molecules, we analytically derive an intermolecular potential composed of an anisotropic van der Waals shielding core and a long-range dipolar interaction. We validate this effective potential by comparing its…
Meshless methods are commonly used to determine numerical solutions to partial differential equations (PDEs) for problems involving free surfaces and/or complex geometries, approximating spatial derivatives at collocation points via local…
Computational modeling is usually applied to aid experimental exploration of advanced materials to better understand the fundamental plasticity mechanisms during mechanical testing. In this work, we perform Molecular dynamics (MD)…
Evaluating multi-center molecular integrals with Cartesian Gaussian-type basis sets has been a long-standing bottleneck in electronic structure theory calculation for solids and molecules. We have developed a vector-coupling and…
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…
We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Excitations of disordered systems such as glasses are of fundamental and practical interest but computationally very expensive to solve. Here we introduce a technique for modeling these excitations in an infinite disordered medium with a…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
A model potential previously developed for the ammonia molecule is treated in a single-center partial-wave approximation in analogy with a self-consistent field method developed by Moccia. The latter was used in a number of collision…
Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called Approximate Non-Conformal (ANC) and generalized…
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…