Related papers: Computing equilibrium free energies through a none…
We study the energy distribution during the emergence of a quasi-equilibrium (QE) state in the course of relaxation to equipartition in slow-fast Hamiltonian systems. A bead-spring model where beads (masses) are connected by springs is…
Finding optimal solutions to combinatorial optimization problems is pivotal in both scientific and technological domains, within academic research and industrial applications. A considerable amount of effort has been invested in the…
After a quantum quench, the integrable system is expected to relax to a non-thermal equilibrium state (NTES) whose local properties are believed to be governed by a generalized Gibbs ensemble (GGE). Combining quench action and the form…
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…
We present a guide to compute the phase-boundaries of classical systems using a dynamic Clausius-Clapeyron integration (dCCI) method within the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) code. The advantage of the…
In stress field analysis, the finite element analysis is a crucial approach, in which the mesh-density has a significant impact on the results. High mesh density usually contributes authentic to simulation results but costs more computing…
We study spectral properties and the dynamics after a quench of one-dimensional spinless fermions with short-range interactions and long-range random hopping. We show that a sufficiently fast decay of the hopping term promotes localization…
Jamming is a common feature of out of equilibrium systems showing slow relaxation dynamics. Here we review our efforts in understanding jamming in granular materials using experiments and computer simulations. We first obtain an estimation…
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling,…
Data assimilation methods aim at estimating the state of a system by combining observations with a physical model. When sequential data assimilation is considered, the joint distribution of the latent state and the observations is described…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We presented an efficient algorithm, fast adaptive flat-histogram ensemble (FAFE), to estimate the density of states (DOS) and to enhance sampling in large systems. FAFE calculates the means of an arbitrary extensive variable $U$ in…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
We consider the dynamics of an impurity atom immersed in an ideal Fermi gas at zero temperature. We focus on the coherent quantum evolution of the impurity following a quench to strong impurity-fermion interactions, where the interactions…
In computational engineering, ensuring the integrity and safety of structures in fields such as aerospace and civil engineering relies on accurate stress prediction. However, analytical methods are limited to simple test cases, and…
We report on low temperature measurements performed on micro-electro-mechanical systems (MEMS) driven deeply into the non-linear regime. The materials are kept in their elastic domain, while the observed non-linearity is purely of…
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…
A new mathematical model for non-equilibrium evaporation/condensation including boiling effect is proposed. A simplified differential-algebraic system of equations is obtained. A code to solve numerically this differential-algebraic system…