Related papers: Coupling different levels of resolution in molecul…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
In this work we introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble. In particular, we consider the equations arising from the so-called density dynamics algorithm with any…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
To faithfully simulate ITER and other modern fusion devices, one must resolve electron and ion fluctuation scales in a five-dimensional phase space and time. Simultaneously, one must account for the interaction of this turbulence with the…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
It has been built a strict mathematical model of the thermodynamic equilibrium's establishment in the originally nonequilibrium cosmological ultrarelativistic plasma for the arbitrary accelerated Universe under the assumption that scaling…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
One of the difficulties in 3D reconstruction of molecules from images in single particle Cryo-Electron Microscopy (Cryo-EM), in addition to high levels of noise and unknown image orientations, is heterogeneity in samples: in many cases, the…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
The vast separation dividing the characteristic times of energy confinement and turbulence in the core of toroidal plasmas makes first-principles prediction on long timescales extremely challenging. Here we report the demonstration of a…
Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating…
A model for the thermodynamics of a quantum heat bath is introduced. Under the assumption that the bath molecules have finitely many degrees of freedom and are weakly interacting, we present a general derivation of the equation of state of…
The study of open quantum systems often relies on approximate master equations derived under the assumptions of weak coupling to the environment. However when the system is made of several interacting subsystems such a derivation is in many…
We are interested in simulating blood flow in arteries with variable elasticity with a one dimensional model. We present a well-balanced finite volume scheme based on the recent developments in shallow water equations context. We thus get a…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Computational study of molecules and materials from first principles is a cornerstone of physics, chemistry, and materials science, but limited by the cost of accurate and precise simulations. In settings involving many simulations, machine…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…