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Understanding the mechanisms of proton energy deposition in matter and subsequent damage formation is fundamental to radiation science. Here we exploit the picosecond (10^-12 s) resolution of laser-driven accelerators to track ultra-fast…
Our knowledge about the "cold" Universe often relies on molecular spectra. A general property of such spectra is that the energy level populations are rarely at local thermodynamic equilibrium. Solving the radiative transfer thus requires…
We present a method to determine the equilibrium geometry of large atomistic systems with linear scaling. It is based on a separate treatment of long and short wavelength components of the forces. While the rapidly varying part is handled…
We present an improved formalism for quantum Monte Carlo calculations of energy derivatives and properties (e.g. the interatomic forces), with a multideterminant Jastrow-Slater function. As a function of the number $N_e$ of Slater…
The accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
The scaling form of the critical equation of state is computed for $O(N)$-symmetric models. We employ a method based on an exact flow equation for a coarse grained free energy. A suitable truncation is solved numerically.
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
A theoretical analysis is given of the equation of motion method, due to Alben et al., to compute the eigenvalue distribution (density of states) of very large matrices. The salient feature of this method is that for matrices of the kind…
Living organisms are inherently out-of-equilibrium systems. We employ new developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model…
The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
First-principles calculations are a cornerstone of modern surface science and heterogeneous catalysis. However, accurate reaction energies and barrier heights are frequently inaccessible due to the approximations demanded by the large…
We calculate one-loop quantum energies in a renormalizable self-interacting theory in one spatial dimension by summing the zero-point energies of small oscillations around a classical field configuration, which need not be a solution of the…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
We calculate a new equation of state for baryons at sub-nuclear densities meant for the use in core-collapse simulations of massive stars. The abundance of various nuclei is obtained together with the thermodynamic quantities. The…
In order to find the equilibrium geometries of molecules and solids and to perform ab initio molecular dynamics, it is necessary to calculate the forces on the nuclei. We present a correlated sampling method to efficiently calculate…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem…
Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…