Related papers: Algebraic and diagrammatic methods for the rule-ba…
Methods for electronic structure based on Gaussian and molecular orbital discretizations offer a well established, compact representation that forms much of the foundation of correlated quantum chemistry calculations on both classical and…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
We introduce a new formulation of the real-spectral-triple formalism in non-commutative geometry (NCG): we explain its mathematical advantages and its success in capturing the structure of the standard model of particle physics. The idea,…
We present a novel method to study the dynamics of bulk fermion systems such as the neutron-star crust. By introducing periodic boundary conditions into Fermionic Molecular Dynamics, it becomes possible to examine the long-range many-body…
A formalism is presented in which quantum particle dynamics can be developed on its own rather than `quantization' of an underlying classical theory. It is proposed that the unification of probability and dynamics should be considered as…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…
Group theoretic method for the systematic study of multi-quark states is developed. The calculation of matrix elements of many body Hamiltonian is simplified by transforming the physical bases (quark cluster bases) to symmetry bases (group…
The approach is developed for the description of isolated Fermi-systems with finite number of particles, such as complex atoms, nuclei, atomic clusters etc. It is based on statistical properties of chaotic excited states which are formed by…
Validity of fluid models breaks down for non-thermal or weakly collisional plasmas which often occur e.g. in the solar wind. In these regimes one has to resort to modelling through the first-principle Vlasov-Maxwell system, but its…
We present a method that captures the fluctuations beyond mean field in chemical reactions in the regime of small copy numbers and hence large fluctuations, using self-consistently determined memory: by integrating information from the past…
The suggested operator manifold formalism enables to develop an approach to the unification of the geometry and the field theory. We also elaborate the formalism of operator multimanifold yielding the multiworld geometry involving the…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Many-mode interacting Bose gases (1D,2D,3D) are simulated from first principles. The model uses a second-quantized Hamiltonian with two-particle interactions (possibly ranged), external potential, and interactions with an environment, with…
This is a self-contained and hopefully readable account on the method of creation and annihilation operators (also known as the Fock space representation or the "second quantization" formalism) for non-relativistic quantum mechanics of many…
Using the scheme of mesoscopic nonequilibrium thermodynamics, we construct the one- and two- particle Fokker-Planck equations for a system of interacting Brownian particles. By means of these equations we derive the corresponding balance…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The methods for studying the epoch of cosmic reionization vary from full radiative transfer simulations to purely analytical models. While numerical approaches are computationally expensive and are not suitable for generating many mock…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…