Related papers: Efficient ab initio schemes for finding thermodyna…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
A computational approach by an implementation of the Principle Component Analysis (PCA) with K-means and Gaussian Mixture (GM) clustering methods from Machine Learning (ML) algorithms to identify structural and dynamical heterogeneities of…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
The underlying structural order that transcends the liquid, glass and crystalline states is identified using an efficient genetic algorithm (GA). GA identifies the most common energetically favorable packing motif in crystalline structures…
The paper proposes a method to obtain the optimal basis set for solving the self consistent field (SCF) equations for large atomic systems in order to calculate the energy barriers in tunneling structures, with higher accuracy and speed.…
First-principles based crystal structure prediction (CSP) methods have revealed an essential tool for the discovery of new materials. However, in solids close to displacive phase transitions, which are common in ferroelectrics,…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We present an ab-initio study of boron nitride as well as carbon allotropes. Their relative thermodynamic stabilities and structural phase transitions from low- to high-density phases are investigated. Pressure-temperature phase diagrams…
Estimation of the failure probability of offshore structures exposed to extreme ocean environments is critical to their safe design and operation. The conditional density of the environment (CDE) quantifies regions of the space of long term…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address…
We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an…
The correct calculation of formation enthalpy is one of the enablers of ab-initio computational materials design. For several classes of systems (e.g. oxides) standard density functional theory produces incorrect values. Here we propose the…
The optimization problems defining meta-stable or stationary equilibrium are explored. The Gibbs scheme is modified aiming to describe the statistical properties of a class of non-equilibrium and metastable states. The system is assumed to…
An analytical method to compute thermodynamic properties of a given Hamiltonian system is proposed. This method combines ideas of both dynamical systems and ensemble approaches to thermodynamics, providing de facto a possible alternative to…
We elaborate on a general method that we recently introduced for characterizing the "natural" structures in complex physical systems via a multiscale network based approach for the data mining of such structures. The approach is based on…
The control and manipulation of quantum systems without excitation is challenging, due to the complexities in fully modeling such systems accurately and the difficulties in controlling these inherently fragile systems experimentally. For…
We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
A general method is presented for modeling high entropy alloys as ensembles of randomly sampled, ordered configurations on a given lattice. Statistical mechanics is applied post hoc to derive the ensemble properties as a function of…