Related papers: The Mesoscopic Partition Function:A Combined Spati…
Using the probabilistic language of conditional expectations we reformulate the force matching method for coarse-graining of molecular systems as a projection on spaces of coarse observables. A practical outcome of this probabilistic…
Using the orbital-free density functional theory as a model theory, we present an analysis of the field theoretic approach to quasi-continuum method. In particular, by perturbation method and multiple scale analysis, we provide a formal…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables we…
In this thesis we develop methods for many-body open quantum systems and apply them to systems of organic polaritons. The methods employ a mean-field approach to reduce the dimensionality of large-scale problems. Initially assuming the…
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 establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
In classical statistical mechanics, the partition function is defined in phase space. We extend this concept to quantum statistical mechanics using Bohmian trajectories. The quantum partition function in phase space captures the ensemble of…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
We consider the quantum partition function for a system of quantum spinors and then derive an equivalent (or dual) classical partition function for some scalar degrees of freedom. The coupling between scalars is non-trivial (e.g. a model on…
When modeling geostatistical or areal data, spatial structure is commonly accommodated via a covariance function for the former and a neighborhood structure for the latter. In both cases the resulting spatial structure is a consequence of…
We find all factorized duality functions for a class of interacting particle systems. The functions we recover are self-duality functions for interacting particle systems such as zero-range processes, symmetric inclusion and exclusion…
We propose a large-scale scaling viewpoint for deriving mesoscopic dynamics from interacting particle systems and apply it to the Cucker--Smale flocking model. In contrast with the classical mean-field regime leading to the Vlasov-type…
In this study we derive the governing equations for mesoscopic collective activity in the cortex, starting from the generic Hodgkin-Huxley equations for microscopic cell dynamics. For simplicity, and to maintain focus on the essential…
We implement a Becke fuzzy cells type space partitioning scheme for the purposes of exchange-correlation within the GPAW projector augmented-wave method based density functional theory code. Space partitioning is needed in the situation…
Thermodynamic properties can be in principle derived from the partition function, which, in many-atom systems, is hard to evaluate as it involves a sum on the accessible microscopic states. Recently, the partition function has been computed…
Thermodynamic extensivity is commonly introduced as a postulate -- the homogeneity of degree one in thermodynamic potentials. We provide a constructive derivation of this property from microscopic conditions on the pair potential, without…
Starting from a microscopic approach and using the formalism of quantum Brownian motion, partition function of a system composed of two separated pieces of anisotropic matter and a fluctuating medium in finite temperature is obtained…