Related papers: Angle-resolved effective potentials for disk-shape…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
Fully numerical mesh solutions of 2D and 3D quantum equations of Schroedinger and Hartree-Fock type allow us to work with wavefunctions which possess a very flexible geometry. This flexibility is especially important for calculations of…
We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The…
The properties of the electronic ground state of the polar and paramagnetic chromium--closed-shell-atom molecules have been investigated. State-of-the-art \textit{ab initio} techniques have been applied to compute the potential energy…
Unitary Coupled Cluster (UCC) theory is a promising variational method for electronic structure calculations, especially for strongly correlated systems and quantum computers. However, its practical application is limited by the steep…
Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical…
We present a new method for Monte Carlo or Molecular Dynamics numerical simulations of three dimensional polar fluids. The simulation cell is defined to be the surface of the northern hemisphere of a four-dimensional (hyper)sphere. The…
Recent experimental developments in the loading of ultracold KRb molecules into quasi-two-dimensional traps, combined with the ability to tune the ratio between elastic and loss (inelastic/reactive) collisions through application of an…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
For complex molecules, nuclear degrees of freedom can act as an environment for the electronic `system' variables, allowing the theory and concepts of open quantum systems to be applied. However, when molecular system-environment…
The parameters of many-body potentials for Co, Nb and Zr metals, based on the embedded-atom method, have been systematically derived. The analytical potential scheme allows us to reproduce correctly the cohesive energies and structural…
A variety of electrostatic phenomena, including the structure of electric double layers and the aggregation of charged colloids and proteins, are affected by nonuniform electric permittivity. These effects are frequently ignored in…
Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of…
We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where…
This is the second article in which we study the rotating Morse potential model for diatomic molecules using the tridiagonal J-matrix approach. Here, we improve further the accuracy of computing the bound states and resonance energies for…
The electrostatic potential profile of a spherical soft particle is derived by solving the Poisson-Boltzmann equations on a spherical system both numerically and analytically. The soft particle is assumed to consist of an ion-permeable…