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Three-body recombination processes are treated numerically for a system of three identical bosons. The two-body model potentials utilized support many bound states, a major leap in complexity that produces an intricate structure of sharp…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Thermodynamics of quantum systems out-of-equilibrium is very important for the progress of quantum technologies, however, the effects of many body interactions and their interplay with temperature, different drives and dynamical regimes is…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…
One has to study multivariable scattering amplitudes to extract properties of the three-body states from the generalizations of the L\"uscher finite-volume formalism. In particular, a three-body amplitude obtained from a Lattice QCD…
We present a mathematically rigorous method suitable for solving three-body bound state and scattering problems when the inter-particle interaction is of a hard-core nature. The proposed method is a variant of the Boundary Condition Model…
Agent-based modelling constitutes a versatile approach to representing and simulating complex systems. Studying large-scale systems is challenging because of the computational time required for the simulation runs: scaling is at least…
We study the dynamics of particles in a multi-component 2d Lennard-Jones (LJ) fluid in the limiting case where {\it all the particles are different} (APD). The equilibrium properties of this APD system were studied in our earlier work…
Conical intersections between electronic potential energy surfaces are paradigmatic for the study of non-adiabatic processes in the excited states of large molecules. However, since the corresponding dynamics occurs on a femtosecond…
This thesis investigates the mechanically controlled break junctions, with a particular emphasis on elucidating the behaviour of molecular currents at room temperature. The core of this experimental investigation involves a detailed…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
In this study we aim for quantifying the role of in-medium 3$\leftrightarrow$3 collisions for systems of fermions which initially are out-off equilibrium. The formulation of the 3-body dynamics is based on the equations of motion method for…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…