Related papers: Interactive molecular dynamics
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
Photo-induced processes are fundamental in nature, but accurate simulations are seriously limited by the cost of the underlying quantum chemical calculations, hampering their application for long time scales. Here we introduce a method…
Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in…
Results of quasi-classical molecular dynamics simulations of the quantum electron gas are reported. Quantum effects corresponding to the Pauli and the Heisenberg principle are modeled by an effective momentum-dependent Hamiltonian. The…
The dynamics of internal spin, electronic orbital, and nuclear motion states of atoms and molecules have preoccupied the atomic and molecular physics community for decades. Increasingly, such dynamics are being examined within many-body…
We apply the physics-learning duality to molecular systems by complementing the physical description of interacting particles with a dual learning description, where each particle is modeled as an agent minimizing a loss function. In the…
With the advent of high-level programming languages capable of quickly rendering three-dimensional simulations, the inclusion of computers as a learning tool in the classroom has become more prevalent. Although work has begun to study the…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Particles added to a fluid interface can be used as a surface stabilizer in the food, oil and cosmetic industries. As an alternative to rigid particles, it is promising to consider highly deformable particles that can adapt their…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…
A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats…
The impossibility of experiencing the molecular world with our senses hampers teaching and understanding chemistry because very abstract concepts (such as atoms, chemical bonds, molecular structure, reactivity) are required for this…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
The thermodynamic properties of nuclei are studied in a mean field model using a Skryme interaction. Properties of two component systems are investigated over the complete range of proton fraction from a system of pure neutrons to a system…
The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Consider briefly the equations of fluid dynamics-they describe the enormous wealth of detail in all the interacting physical elements of a fluid flow-whereas in applications we want to deal with a description of just that which is…
We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in…