Related papers: Metashooting: A Novel Tool for Free Energy Reconst…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
The crossing of a transition state in a multidimensional reactive system is mediated by invariant geometric objects in phase space: An invariant hyper-sphere that represents the transition state itself and invariant hyper-cylinders that…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations. Such methods can efficiently sample…
We study the 1D ferromagnetic Ising (spin-1/2) model with the Dzyaloshinskii-Moriya (DM) interaction. We analyze the low energy excitation spectrum and the ground state magnetic phase diagram using the Lanczos method. The DM…
The paper presents a novel concept of a 3D structural metasurface with mechanically morphing capability that can be used as a transmit- or reflect-array to manipulate electromagnetic beams for applications in RF sensing and communications…
Metasurfaces have become a promising means for manipulating optical wavefronts in flat and high-performance optical devices. Conventional metasurface device design relies on trial-and-error methods to obtain target electromagnetic (EM)…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
We present a novel technique for assessing the dynamics of multiphase fluid flow in the oil reservoir. We demonstrate an efficient workflow for handling the 3D reservoir simulation data in a way which is orders of magnitude faster than the…
The presence of multiple stable states and associated nonlinear phenomena, such as hysteresis, in multistable mechanical metamaterials enables frequency-independent energy harvesting and shock absorption. This study focuses on shock…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
In a recent publication we established an analogy between the free energy of a hard sphere system and the energy of an elastic network [1]. This result enables one to study the free energy landscape of hard spheres, in particular to define…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
The question on the dominant driving mechanism (displacive or order-disorder) at each structural phase transition of KNbO3 is investigated by means of molecular dynamics simulations. To this purpose, we first develop a shell model by…
Transition state theory formally provides a simplifying approach for determining chemical reaction rates and pathways. Given an underlying potential energy surface for a reactive system, one can determine the dividing surface in phase space…
Investigations of the phase diagram of biaxial liquid crystal systems through analyses of general Hamiltonian models within the simplifications of mean-field theory (MFT), as well as by computer simulations based on microscopic models, are…
We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was…
Beam manipulation is of paramount importance in wave engineering, enabling diverse beam shapes like pencil beams, flat-top beams, and isoflux beams to cater to various application missions. Among the beams, shaping flat-top and isoflux…