Related papers: Coarse-graining strategy for molecular pair intera…

When a colloid is mixed with a depletant such as a non-adsorbing polymer, one observes attractive effective interactions between the colloidal particles. If these particles are anisotropic, analysis of these effective interactions is…

We study photon-mediated interactions between molecular spin qudits in the dispersive regime of operation. We derive from a microscopic model the effective interaction between molecular spins, including their crystal field anisotropy (i.e.,…

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…

We consider pairing in a dilute system of Fermions with a short-range interaction. While the theory is ill-defined for a contact interaction, the BCS equations can be solved in the leading order of low-energy effective field theory. The…

Using one-range addition theorems for noninteger n Slater type orbitals and Coulomb-Yukawa like correlated interaction potentials with noninteger indices obtained by the author with the help of complete orthonormal sets of exponential type…

The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject,…

Current Lagrangian (particle-tracking) algorithms used to simulate diffusion-reaction equations must employ a certain number of particles to properly emulate the system dynamics---particularly for imperfectly-mixed systems. The number of…

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in…

We present new method for studying the equilibrium properties of interacting fluids in an arbitrary external filed. The method is valid in any dimension and it yields an exact results in one dimension. Using this approach, we derive a…

We explore structural correlations of strongly asymmetric mixtures of binary charged colloids within the primitive model of electrolytes considering large charge and size ratios of 10 and higher. Using computer simulations with explicit…

The precise tracking of micron sized colloidal particles - held in the vicinity of each other using optical tweezers - is an elegant way to gain information about the particle-particle pair interaction potential. The accuracy of the method,…

Finding reduced models of spatially-distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy…

An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…

We develop a comprehensive theoretical model for the interaction strength between a pair of exciton-polaritons in microcavity devices. Ab initio numerical calculations for dipolar polaritons in one dimension are used as a starting point to…

The production of molecules from dual species atomic quantum gases has enabled experiments that employ molecules at nanoKelvin temperatures. As a result, every degree of freedom of these molecules is in a well-defined quantum state and…

Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability…

Strongly interacting particles in one dimension subject to external confinement have become a topic of considerable interest due to recent experimental advances and the development of new theoretical methods to attack such systems. In the…

Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…

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…

We have applied the gaussian auxiliary field method introduced by Mazenko to the ordering dynamics of a non-conserved scalar system with attractive long-range interactions. This study provides a test-bed for the approach and shows some of…