Related papers: Pseudoatom molecular dynamics
We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
Single-cell organisms and various cell types use a range of motility modes when following a chemical gradient, but it is unclear which mode is best suited for different gradients. Here, we model directional decision-making in chemotactic…
Machine learning has had an enormous impact in many scientific disciplines. Also in the field of low-temperature plasma modeling and simulation it has attracted significant interest within the past years. Whereas its application should be…
A common paradigm used in the construction of equations of state is to decompose the thermodynamics into a superposition of three terms: a static-lattice cold curve, a contribution from the thermal motion of the nuclei, and a contribution…
When supersonic plasma flows collide, many physical processes contribute to the morphology of the resulting shock. One of these processes is the acceleration of non-thermal ions, which will, eventually, reach relativistic speeds and become…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
A recent expansion of cold and ultracold molecule applications has led to renewed focus on molecular species preparation under ultrahigh vacuum conditions. Meanwhile, molecular beams have been used to study gas phase chemical reactions for…
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the…
Non-linear wave-driven processes in plasmas are normally described by either a monochromatic pump wave that couples to other monochromatic waves, or as a random phase wave coupling to other random phase waves. An alternative approach…
Many-body dissipative particle dynamics is constructed to exhibit vapour-liquid coexistence, with a sharp interface, and a vapour phase of vanishingly small density. In this form, the model is an unusual example of a soft-sphere liquid with…
Ultracold molecules confined in optical lattices or tweezer traps can be used to process quantum information and simulate the behaviour of many-body quantum systems. Molecules offer several advantages for these applications. They have a…